OBO-Edit 2.3.1
15:04:2021 22:57
PSI-MI
1.2
pporras
CVversion: 2.5.5
Each of the top level terms in this file is the root term of an independent controlled vocabulary
Notes:
The PSI MI schema defines short labels for controlled vocabulary terms
The correct use of these vocabularies in the PSI Molecular Interaction XML schema is
The last accession number used in this file is stored in a separate file,
The maintenance of this file is ensured by Luana Licata luana.licata@uniroma2.it and Sandra Orchard orchard@ebi.ac.uk
coverage: This file collect controlled vocabularies describing different aspects of molecular interactions.
formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml.
mapping an element of the PSI Molecular Interaction XML schema.
psi-mi.lastac. It MUST be updated when this file is updated.
publisher: This file is published by the PSI MI working group see http://psidev.info/MI
short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.
definition
Label from MS DeltaMass
Drugable Genome Project
Alternate label curated by PSI-MI
Unique short label curated by PSI-MI
Subset of PSI-MI
Alternate label curated by PSI-MOD
Unique short label curated by PSI-MOD
subset of protein modifications
Agreed label from MS community
Alternate name from RESID
Misnomer label from RESID
Name from RESID
Systematic name from RESID
Alternate name from UniMod
Description (full_name) from UniMod
Interim label from UniMod
Label (title) from UniMod
Protein feature description from UniProtKB
subset_property
synonym_type_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
mi
PSI-MI
MI:0000
molecular interaction
Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
PMID:14755292
mi
Method to determine the interaction.
interaction detect
PSI-MI
MI:0001
interaction detection method
Method to determine the interaction.
PMID:14755292
interaction detect
Method to determine the molecules involved in the interaction.
participant detection
participant ident
PSI-MI
MI:0002
participant identification method
Method to determine the molecules involved in the interaction.
PMID:14755292
participant detection
participant ident
Method to determine the features of the proteins involved in the interaction.
feature detection
PSI-MI
MI:0003
feature detection method
Method to determine the features of the proteins involved in the interaction.
PMID:14755292
feature detection
This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
Affinity purification
affinity chrom
PSI-MI
MI:0004
affinity chromatography technology
This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
PMID:7708014
Affinity purification
affinity chrom
This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
PSI-MI
MI:0005
alanine scanning
This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
PMID:14755292
A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
anti bait coip
PSI-MI
MI:0006
anti bait coimmunoprecipitation
A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
PMID:7708014
anti bait coip
A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
anti tag coip
PSI-MI
MI:0007
anti tag coimmunoprecipitation
A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
PMID:7708014
anti tag coip
In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
PSI-MI
MI:0008
array technology
In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
PMID:14755292
The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
PSI-MI
MI:0009
bacterial display
The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
PMID:10436088
PMID:8248129
Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
beta galactosidase
PSI-MI
MI:0010
beta galactosidase complementation
Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
PMID:12042868
PMID:9237989
beta galactosidase
This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
beta lactamase
PSI-MI
MI:0011
beta lactamase complementation
This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
PMID:12042868
beta lactamase
In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
BRET
LRET
bret
PSI-MI
MI:0012
bioluminescence resonance energy transfer
In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
PMID:10725388
PMID:9874787
BRET
LRET
bret
The application of physical principles and methods to biological experiments.
PSI-MI
MI:0013
biophysical
The application of physical principles and methods to biological experiments.
PMID:14755292
Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
adenylate cyclase
bacterial two-hybrid
PSI-MI
MI:0014
adenylate cyclase complementation
Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
PMID:9576956
adenylate cyclase
bacterial two-hybrid
Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
CD
cd
PSI-MI
MI:0016
circular dichroism
Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
PMID:11578931
CD
cd
Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
fluorescence spectr
PSI-MI
MI:0017
classical fluorescence spectroscopy
Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
PMID:7708014
fluorescence spectr
The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
2 hybrid
2-hybrid
2H
2h
Gal4 transcription regeneration
Y2H
classical two hybrid
two-hybrid
yeast two hybrid
PSI-MI
Y-2H
MI:0018
two hybrid
The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
PMID:10967325
PMID:12634794
PMID:1946372
2 hybrid
2-hybrid
2H
2h
Gal4 transcription regeneration
classical two hybrid
two-hybrid
yeast two hybrid
In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
Co-IP
CoIp
co-immunoprecipitation
coip
immunoprecipitation
PSI-MI
MI:0019
coimmunoprecipitation
In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
PMID:7708014
Co-IP
CoIp
co-immunoprecipitation
coip
immunoprecipitation
Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
tem
PSI-MI
MI:0020
transmission electron microscopy
Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
PMID:14755292
tem
Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.
OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
coloc fluoresc probe
PSI-MI
MI:0021
colocalization by fluorescent probes cloning
true
Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.
OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
PMID:14755292
coloc fluoresc probe
The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.
OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
Immunofluorescence Staining
Immunostaining
coloc immunostaining
PSI-MI
MI:0022
colocalization by immunostaining
true
The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.
OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
PMID:14755292
Immunofluorescence Staining
Immunostaining
coloc immunostaining
Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.
OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
coloc visual technol
PSI-MI
MI:0023
colocalization/visualisation technologies
true
Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.
OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
PMID:14755292
coloc visual technol
Text mining is used to support interactions which have been determined by other methods.
conformational tm
PSI-MI
MI:0024
confirmational text mining
Text mining is used to support interactions which have been determined by other methods.
PMID:14755292
conformational tm
Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.
OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
PSI-MI
MI:0025
copurification
true
Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.
OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
PMID:14755292
Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
PSI-MI
MI:0026
correlated mutations
Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
PMID:11933068
Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
PSI-MI
MI:0027
cosedimentation
Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
PMID:14755292
The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
solution sedimentati
PSI-MI
MI:0028
cosedimentation in solution
The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
PMID:10410796
solution sedimentati
Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
density sedimentation
PSI-MI
MI:0029
cosedimentation through density gradient
Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
PMID:10410796
density sedimentation
Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
crosslink
PSI-MI
MI:0030
cross-linking study
Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
PMID:14755292
crosslink
Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
Label transfer techniques
Photoaffinity labelling
bifunctional agent crosslink
PSI-MI
MI:0031
protein cross-linking with a bifunctional reagent
Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
PMID:10679368
PMID:7708014
Label transfer techniques
Photoaffinity labelling
bifunctional agent crosslink
The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
de novo protein sequence
PSI-MI
MS/MS
MI:0032
de novo protein sequencing by mass spectrometry
The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
PMID:10984529
de novo protein sequence
In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
PSI-MI
MI:0033
deletion analysis
In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
PMID:14755292
All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
PSI-MI
MI:0034
display technology
All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
PMID:14755292
Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
PSI-MI
MI:0035
docking
Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
PMID:11478868
PMID:9631301
The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
Rosetta Stone
PSI-MI
MI:0036
domain fusion
The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
PMID:10573422
Rosetta Stone
This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
PSI-MI
MI:0037
domain profile pairs
This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
PMID:11473021
In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
dls
PSI-MI
MI:0038
dynamic light scattering
In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
PMID:9013660
dls
In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
PSI-MI
MI:0039
edman degradation
In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
PMID:14755292
Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
Electron cryomicroscopy
Electron crystallography
PSI-MI
MI:0040
electron microscopy
Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
PMID:11785754
Electron cryomicroscopy
Electron crystallography
A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
ENDOR
endor
PSI-MI
MI:0041
electron nuclear double resonance
A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
PMID:11817959
PMID:11988476
PMID:12186859
ENDOR
endor
EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
EPR
ESR
epr
PSI-MI
MI:0042
electron paramagnetic resonance
EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
PMID:11817959
EPR
ESR
epr
A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
PSI-MI
MI:0043
electron resonance
A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
PMID:14755292
Methods based on laboratory experiments to determine an interaction.
experimental interac
PSI-MI
MI:0045
experimental interaction detection
experimental interac
Methods based on laboratory experiments to determine an interaction.
PMID:14755292
Predictive algorithms that rely on the information obtained by experimental results.
experimental info
PSI-MI
MI:0046
experimental knowledge based
Predictive algorithms that rely on the information obtained by experimental results.
PMID:14755292
experimental info
Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
Affinity blotting
PSI-MI
MI:0047
far western blotting
Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
PMID:7708014
Affinity blotting
Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
filamentous phage
PSI-MI
MI:0048
filamentous phage display
Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
PMID:7682645
filamentous phage
A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
Filter overlay assay
PSI-MI
dot blot
MI:0049
filter binding
A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
PMID:7708014
Filter overlay assay
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
flag tag coip
PSI-MI
MI:0050
flag tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
flag tag coip
Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
fluorescence
PSI-MI
MI:0051
fluorescence technology
Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
PMID:14755292
fluorescence
FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
FCS
fcs
PSI-MI
fluctuation correlation specctrometry
MI:0052
fluorescence correlation spectroscopy
FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
PMID:10733953
FCS
fcs
Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
FPS
Fluorescence anisotropy
fps
PSI-MI
MI:0053
fluorescence polarization spectroscopy
Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
PMID:12805227
PMID:7708014
FPS
Fluorescence anisotropy
fps
Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
FACS
Flow cytometry
facs
PSI-MI
MI:0054
fluorescence-activated cell sorting
Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
PMID:11988464
FACS
Flow cytometry
facs
FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
FRET
FRET analysis
RET
fret
PSI-MI
MI:0055
fluorescent resonance energy transfer
FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
PMID:11558993
FRET
FRET analysis
RET
fret
Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
full dna sequence
PSI-MI
MI:0056
full identification by DNA sequencing
Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
PMID:14755292
full dna sequence
Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
PSI-MI
MI:0057
gene neighbourhood
Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
PMID:9787636
Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
genome prediction
PSI-MI
MI:0058
genome based prediction
Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
PMID:14755292
genome prediction
The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.
OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
PSI-MI
MI:0059
gst pull down
true
The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.
OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
PMID:14755292
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.
OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
ha tag coip
PSI-MI
MI:0060
ha tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.
OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
ha tag coip
The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.
OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
PSI-MI
MI:0061
his pull down
true
The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.
OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
PMID:14755292
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
his tag coip
PSI-MI
MI:0062
his tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
his tag coip
Computational methods to predict an interaction.
in silico methods
predicted interac
PSI-MI
MI:0063
interaction prediction
Computational methods to predict an interaction.
PMID:14755292
in silico methods
predicted interac
Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
Homology based interaction prediction
PSI-MI
MI:0064
interologs mapping
Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
PMID:11731503
Homology based interaction prediction
Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
ITC
itc
PSI-MI
MI:0065
isothermal titration calorimetry
Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
PMID:11785756
ITC
itc
Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
lambda phage
PSI-MI
MI:0066
lambda phage display
Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
PMID:7682645
lambda phage
Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
PSI-MI
MI:0067
light scattering
Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
PMID:9013660
Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
modified residue ms
PSI-MI
MI:0068
mass detection of residue modification
Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
PMID:11395414
PMID:11875433
modified residue ms
Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
ms of complexes
PSI-MI
MI:0069
mass spectrometry studies of complexes
Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
PMID:12057199
PMID:12504676
ms of complexes
Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
PSI-MI
MI:0070
mobility shift
Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
PMID:14755292
In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
Gel Filtration
Size Exclusion Chromatography
Sizing column
PSI-MI
MI:0071
molecular sieving
In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
PMID:7708014
Gel Filtration
Size Exclusion Chromatography
Sizing column
Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
monoclonal western
PSI-MI
MI:0072
monoclonal antibody western blot
Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
PMID:14755292
monoclonal western
This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
PSI-MI
MI:0073
mrna display
This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
PMID:11551470
Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
PSI-MI
MI:0074
mutation analysis
Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
PMID:14755292
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
myc tag coip
PSI-MI
MI:0075
myc tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
myc tag coip
Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
interface predictor
PSI-MI
MI:0076
neural network on interface properties
Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
PMID:11455607
PMID:11874449
interface predictor
Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
NMR
nmr
PSI-MI
MI:0077
nuclear magnetic resonance
Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
PMID:12062432
PMID:12120505
NMR
nmr
Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
nucleotide sequence
sequence cloning
PSI-MI
MI:0078
nucleotide sequence identification
Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
PMID:14755292
nucleotide sequence
sequence cloning
Experimental methods that could not be assigned to the other large group of technologies.
OBSOLETE use biochemical (MI:0401) instead.
other biochemic tech
PSI-MI
MI:0079
other biochemical technologies
true
Experimental methods that could not be assigned to the other large group of technologies.
OBSOLETE use biochemical (MI:0401) instead.
PMID:14755292
other biochemic tech
Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
partial dna sequence hybrid
PSI-MI
MI:0080
partial DNA sequence identification by hybridization
Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
PMID:14755292
partial dna sequence hybrid
The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
PSI-MI
MI:0081
peptide array
The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
PMID:11167074
This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
fingerprinting
PSI-MI
MI:0082
peptide massfingerprinting
This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
PMID:10967324
PMID:11752590
PMID:11805826
fingerprinting
When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
PSI-MI
MI:0083
peptide synthesis
When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
PMID:14755292
Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
PSI-MI
MI:0084
phage display
Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
PMID:10975452
PMID:7708014
The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
PSI-MI
MI:0085
phylogenetic profile
The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
PMID:10200254
Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
polyclonal western
PSI-MI
MI:0086
polyclonal antibody western blot
Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
PMID:14755292
polyclonal western
Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
predictive tm
PSI-MI
MI:0087
predictive text mining
Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
PMID:11791231
predictive tm
Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
PSI-MI
MI:0088
primer specific pcr
Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
PMID:14755292
The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
PSI-MI
MI:0089
protein array
The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
PMID:10976071
PMID:12067604
In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
PCA
complementation
PSI-MI
MI:0090
protein complementation assay
In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
PMID:11495741
PCA
complementation
Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
chromatography
column chromatography
PSI-MI
MI:0091
chromatography technology
Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
PMID:14755292
chromatography
column chromatography
Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
PISA
pisa
PSI-MI
MI:0092
protein in situ array
Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
PMID:11470888
PISA
pisa
Single amino acid identification along a protein sequence.
protein sequence
PSI-MI
MI:0093
protein sequence identification
Single amino acid identification along a protein sequence.
PMID:14755292
protein sequence
A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
PSI-MI
MI:0094
protein staining
A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
PMID:12015990
ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
SELDI ProteinChip
seldi chip
PSI-MI
MI:0095
proteinchip(r) on a surface-enhanced laser desorption/ionization
ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
PMID:11827829
SELDI ProteinChip
seldi chip
A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
PSI-MI
affinity capture
pulldown
MI:0096
pull down
A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
PMID:14755292
In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
reverse RRS
reverse rrs
PSI-MI
MI:0097
reverse ras recruitment system
In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
PMID:11160938
reverse RRS
reverse rrs
This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
PSI-MI
MI:0098
ribosome display
This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
PMID:11551470
PMID:12167034
SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
RIA Radio Immuno Assay
SPA
spa
PSI-MI
MI:0099
scintillation proximity assay
SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
PMID:3866247
RIA Radio Immuno Assay
SPA
spa
Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
sequence phylogeny
PSI-MI
MI:0100
sequence based phylogenetic profile
Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
PMID:11707606
sequence phylogeny
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
predict from sequenc
PSI-MI
MI:0101
sequence based prediction
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
PMID:14755292
predict from sequenc
This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
sequence tag
PSI-MI
MS/MS
MI:0102
sequence tag identification
This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
PMID:10967324
PMID:11752590
PMID:11805837
sequence tag
A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
PSI-MI
MI:0103
southern blot
A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
PMID:14755292
In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
sls
PSI-MI
MI:0104
static light scattering
In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
PMID:9013660
sls
Methods based on 3D structure information.
predict from struct
PSI-MI
MI:0105
structure based prediction
Methods based on 3D structure information.
PMID:14755292
predict from struct
Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
PSI-MI
MI:0106
surface patches
Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
PMID:9299343
This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
BIAcore(r)
Optical biosensor
spr
PSI-MI
MI:0107
surface plasmon resonance
This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
PMID:11896282
PMID:12120258
PMID:16338355
BIAcore(r)
Optical biosensor
spr
T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
t7 phage
PSI-MI
MI:0108
Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1.
t7 phage display
T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
PMID:14755292
t7 phage
The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).
OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
tap tag coip
PSI-MI
MI:0109
tap tag coimmunoprecipitation
true
The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).
OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
PMID:10504710
tap tag coip
Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
PSI-MI
MI:0110
text mining
Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
PMID:14755292
The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
dhfr reconstruction
PSI-MI
MI:0111
dihydrofolate reductase reconstruction
The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
PMID:10318894
dhfr reconstruction
The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
ub reconstruction
PSI-MI
membrane yeast two-hybrid
myth
split-ubiquitin
MI:0112
ubiquitin reconstruction
The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
PMID:9560251
ub reconstruction
Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
Immuno blot
PSI-MI
MI:0113
western blot
Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
PMID:14755292
Immuno blot
Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
X-ray
x-ray diffraction
PSI-MI
co-crystallization
co-crystallography
MI:0114
x-ray crystallography
Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
PMID:14755292
X-ray
x-ray diffraction
The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
PSI-MI
MI:0115
yeast display
The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
PMID:9181578
Property of a subsequence that may interfere with the binding of a molecule.
PSI-MI
MI:0116
feature type
Property of a subsequence that may interfere with the binding of a molecule.
PMID:14755292
A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
binding site
binding region
PSI-MI
binding component
MI:0117
binding-associated region
A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
PMID:14755292
binding region
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
PSI-MI
MI:0118
mutation
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
PMID:14755292
Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
hotspot
mutation decreasing
PSI-MI
MI:0119
mutation decreasing interaction
Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
PMID:14755292
hotspot
mutation decreasing
Residue covalent modifications occurring in the specific protein form involved in an interaction.
OBSOLETE remap to MOD:00000.
ptm
PSI-MI
MI:0120
post translation modification
true
Residue covalent modifications occurring in the specific protein form involved in an interaction.
OBSOLETE remap to MOD:00000.
PMID:14755292
ptm
Residue modification.
OBSOLETE remap to MOD:00394.
PSI-MI
MI:0121
acetylated residue
true
Residue modification.
OBSOLETE remap to MOD:00394.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00050.
(S)-2-(acetylamino)propanoic acid
AAC
N-acetyl-L-alanine
[A:ac]
acetylalanine
PSI-MI
MI:0122
n-acetyl-alanine
true
Residue modification.
OBSOLETE remap to MOD:00050.
PMID:11125103
RESID:AA0041
(S)-2-(acetylamino)propanoic acid
AAC
N-acetyl-L-alanine
[A:ac]
acetylalanine
acetylalanine
Residue modification.
OBSOLETE remap to MOD:00359.
N2-acetyl-L-arginine
RAC
[R:ac]
acetylarginine
alpha-acetylamino-delta-guanidinovaleric acid
PSI-MI
MI:0123
n2-acetyl-arginine
true
Residue modification.
OBSOLETE remap to MOD:00359.
PMID:11125103
RESID:AA0354
N2-acetyl-L-arginine
RAC
[R:ac]
acetylarginine
acetylarginine
alpha-acetylamino-delta-guanidinovaleric acid
Residue modification.
OBSOLETE remap to MOD:00780.
N-acetyl-L-asparagine
NAC
[N:ac]
acetylasparagine
PSI-MI
MI:0124
n-acetyl-asparagine
true
Residue modification.
OBSOLETE remap to MOD:00780.
PMID:11125103
N-acetyl-L-asparagine
NAC
[N:ac]
acetylasparagine
Residue modification.
OBSOLETE remap to MOD:00051.
(S)-2-(acetylamino)butanedioic acid
DAC
N-acetyl-L-aspartic acid
[D:ac]
acetylaspartate
acetylaspartic acid
PSI-MI
MI:0125
n-acetyl-aspartic acid
true
Residue modification.
OBSOLETE remap to MOD:00051.
PMID:11125103
RESID:AA0042
(S)-2-(acetylamino)butanedioic acid
DAC
N-acetyl-L-aspartic acid
[D:ac]
acetylaspartate
acetylaspartic acid
Residue modification.
OBSOLETE remap to MOD:00052.
(R)-2-acetylamino-3-sulfanylpropanoic acid
2-acetylamino-3-mercaptopropanoic acid
CAC
N-acetyl-L-cysteine
N-acetylcysteine
[C:ac]
acetylcysteine
PSI-MI
MI:0126
n-acetyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00052.
PMID:11125103
RESID:AA0043
(R)-2-acetylamino-3-sulfanylpropanoic acid
2-acetylamino-3-mercaptopropanoic acid
CAC
N-acetyl-L-cysteine
N-acetylcysteine
[C:ac]
acetylcysteine
Residue modification.
OBSOLETE remap to MOD:00054.
(S)-2-acetylamino-5-pentanediamic acid
N-acetyl-L-glutamine
QAC
[Q:ac]
acetylglutamine
PSI-MI
MI:0127
n-acetyl-glutamine
true
Residue modification.
OBSOLETE remap to MOD:00054.
PMID:11125103
RESID:AA0045
(S)-2-acetylamino-5-pentanediamic acid
N-acetyl-L-glutamine
QAC
[Q:ac]
acetylglutamine
acetylglutamine
Residue modification.
OBSOLETE remap to MOD:00053.
(S)-2-(acetylamino)pentanedioic acid
EAC
N-acetyl-L-glutamic acid
[E:ac]
acetylglutamate
acetylglutamic acid
PSI-MI
MI:0128
n-acetyl-glutamic acid
true
Residue modification.
OBSOLETE remap to MOD:00053.
PMID:11125103
RESID:AA0044
(S)-2-(acetylamino)pentanedioic acid
EAC
N-acetyl-L-glutamic acid
[E:ac]
acetylglutamate
acetylglutamic acid
Residue modification.
OBSOLETE remap to MOD:00055.
2-(acetylamino)ethanoic acid
GAC
N-acetylglycine
[G:ac]
aceturic acid
acetylglycine
PSI-MI
MI:0129
n-acetylglycine
true
Residue modification.
OBSOLETE remap to MOD:00055.
PMID:11125103
RESID:AA0046
2-(acetylamino)ethanoic acid
GAC
N-acetylglycine
[G:ac]
aceturic acid
acetylglycine
Residue modification.
OBSOLETE remap to MOD:00781.
HAC
N-acetyl-L-histidine
[H:ac]
acetylhistidine
PSI-MI
MI:0130
n-acetyl-histidine
true
Residue modification.
OBSOLETE remap to MOD:00781.
PMID:11125103
HAC
N-acetyl-L-histidine
[H:ac]
acetylhistidine
Residue modification.
OBSOLETE remap to MOD:00056.
(2S,3S)-2-acetylamino-3-methylpentanoic acid
IAC
N-acetyl-L-isoleucine
[I:ac]
acetylisoleucine
PSI-MI
MI:0131
n-acetyl-isoleucine
true
Residue modification.
OBSOLETE remap to MOD:00056.
PMID:11125103
RESID:AA0047
(2S,3S)-2-acetylamino-3-methylpentanoic acid
IAC
N-acetyl-L-isoleucine
[I:ac]
acetylisoleucine
acetylisoleucine
Residue modification.
OBSOLETE remap to MOD:00782.
LAC
N-acetyl-L-leucine
[L:ac]
acetylleucine
PSI-MI
MI:0132
n-acetyl-leucine
true
Residue modification.
OBSOLETE remap to MOD:00782.
PMID:11125103
LAC
N-acetyl-L-leucine
[L:ac]
acetylleucine
Residue modification.
OBSOLETE remap to MOD:00057.
(S)-2-acetylamino-6-aminohexanoic acid
KAC
N2-acetyl-L-lysine
N2-acetyllysine
[K:ac]
n2-acetyllysine
PSI-MI
MI:0133
n2-acetyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00057.
PMID:11125103
RESID:AA0048
(S)-2-acetylamino-6-aminohexanoic acid
KAC
N2-acetyl-L-lysine
N2-acetyllysine
[K:ac]
n2-acetyllysine
Residue modification.
OBSOLETE remap to MOD:00064.
(S)-2-amino-6-(acetylamino)hexanoic acid
KA6
N(zeta)-acetyllysine
N6-acetyl-L-lysine
[K:N6ac]
epsilon-acetyllysine
n6-acetyllysine
PSI-MI
MI:0134
n6-acetyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00064.
PMID:11125103
RESID:AA0055
(S)-2-amino-6-(acetylamino)hexanoic acid
KA6
N(zeta)-acetyllysine
N6-acetyl-L-lysine
[K:N6ac]
epsilon-acetyllysine
n6-acetyllysine
Residue modification.
OBSOLETE remap to MOD:00058.
(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
2-acetylamino-4-(methylthio)butanoic acid
MAC
N-acetyl-L-methionine
[M:ac]
acetylmethionine
methionamine
PSI-MI
MI:0135
n-acetyl-methionine
true
Residue modification.
OBSOLETE remap to MOD:00058.
PMID:11125103
RESID:AA0049
(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
2-acetylamino-4-(methylthio)butanoic acid
MAC
N-acetyl-L-methionine
[M:ac]
acetylmethionine
acetylmethionine
methionamine
Residue modification.
OBSOLETE remap to MOD:00784.
FAC
N-acetyl-L-phenylalanine
[F:ac]
acetylphenylalanine
PSI-MI
MI:0136
n-acetyl-phenylalanine
true
Residue modification.
OBSOLETE remap to MOD:00784.
PMID:11125103
FAC
N-acetyl-L-phenylalanine
[F:ac]
acetylphenylalanine
Residue modification.
OBSOLETE remap to MOD:00059.
(2S)-1-acetyl-2-pyrrolidinecarboxylic acid
N-acetyl-L-proline
PAC
[P:ac]
acetylproline
PSI-MI
MI:0137
n-acetyl-proline
true
Residue modification.
OBSOLETE remap to MOD:00059.
PMID:11125103
RESID:AA0050
(2S)-1-acetyl-2-pyrrolidinecarboxylic acid
N-acetyl-L-proline
PAC
[P:ac]
acetylproline
acetylproline
Residue modification.
OBSOLETE remap to MOD:00060.
(S)-2-acetylamino-3-hydroxypropanoic acid
N-acetyl-L-serine
N-acetylserine
SAC
[S:ac]
acetylserine
PSI-MI
MI:0138
n-acetyl-serine
true
Residue modification.
OBSOLETE remap to MOD:00060.
PMID:11125103
RESID:AA0051
(S)-2-acetylamino-3-hydroxypropanoic acid
N-acetyl-L-serine
N-acetylserine
SAC
[S:ac]
acetylserine
Residue modification.
OBSOLETE remap to MOD:00061.
(2S,3R)-2-acetylamino-3-hydroxybutanoic acid
N-acetyl-L-threonine
N-acetylthreonine
TAC
[T:ac]
acetylthreonine
PSI-MI
MI:0139
n-acetyl-threonine
true
Residue modification.
OBSOLETE remap to MOD:00061.
PMID:11125103
RESID:AA0052
(2S,3R)-2-acetylamino-3-hydroxybutanoic acid
N-acetyl-L-threonine
N-acetylthreonine
TAC
[T:ac]
acetylthreonine
Residue modification.
OBSOLETE remap to MOD:00785.
N-acetyl-L-tryptophan
WAC
[W:ac]
acetyltryptophan
PSI-MI
MI:0140
n-acetyl-tryptophan
true
Residue modification.
OBSOLETE remap to MOD:00785.
PMID:11125103
N-acetyl-L-tryptophan
WAC
[W:ac]
acetyltryptophan
Residue modification.
OBSOLETE remap to MOD:00062.
(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
N-acetyl-L-tyrosine
N-acetyltyrosine
YAC
[Y:ac]
acetyltyrosine
PSI-MI
MI:0141
n-acetyl-tyrosine
true
Residue modification.
OBSOLETE remap to MOD:00062.
PMID:11125103
RESID:AA0053
(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
N-acetyl-L-tyrosine
N-acetyltyrosine
YAC
[Y:ac]
acetyltyrosine
Residue modification.
OBSOLETE remap to MOD:00063.
(S)-2-acetylamino-3-methylbutanoic acid
N-acetyl-L-valine
N-acetylvaline
VAC
[V:ac]
acetylvaline
PSI-MI
MI:0142
n-acetyl-valine
true
Residue modification.
OBSOLETE remap to MOD:00063.
PMID:11125103
RESID:AA0054
(S)-2-acetylamino-3-methylbutanoic acid
N-acetyl-L-valine
N-acetylvaline
VAC
[V:ac]
acetylvaline
Residue modification.
OBSOLETE remap to MOD:00674.
PSI-MI
MI:0143
amidated residue
true
Residue modification.
OBSOLETE remap to MOD:00674.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00091.
(S)-2-amino-5-guanidinopentanamide
L-arginine amide
RAM
[R:am]
argininamide
arginineamide
PSI-MI
MI:0145
arginine amide
true
Residue modification.
OBSOLETE remap to MOD:00091.
PMID:11125103
RESID:AA0082
(S)-2-amino-5-guanidinopentanamide
L-arginine amide
RAM
[R:am]
argininamide
arginineamide
Residue modification.
OBSOLETE remap to MOD:00493.
PSI-MI
MI:0146
formylated residue
true
Residue modification.
OBSOLETE remap to MOD:00493.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00030.
(S)-2-formylamino-4-(methylsulfanyl)butanoic acid
2-formylamino-4-(methylthio)butanoic acid
MFM
N-formyl-L-methionine
[M:form]
formylmethionine
PSI-MI
MI:0147
n-formyl-methionine
true
Residue modification.
OBSOLETE remap to MOD:00030.
PMID:11125103
RESID:AA0021
(S)-2-formylamino-4-(methylsulfanyl)butanoic acid
2-formylamino-4-(methylthio)butanoic acid
MFM
N-formyl-L-methionine
[M:form]
formylmethionine
Residue modification.
OBSOLETE remap to MOD:00428.
PSI-MI
MI:0148
hydroxylated residue
true
Residue modification.
OBSOLETE remap to MOD:00428.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:01155.
PSI-MI
MI:0150
lipid modification
true
Residue modification.
OBSOLETE remap to MOD:01155.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00111.
(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
CFN
S-farnesyl-L-cysteine
[C:farn]
farnesylcysteine
PSI-MI
MI:0151
s-farnesyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00111.
PMID:11125103
RESID:AA0102
(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
CFN
S-farnesyl-L-cysteine
[C:farn]
farnesylcysteine
Residue modification.
OBSOLETE remap to MOD:00113.
(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
CGR
S-geranylgeranyl-L-cysteine
[C:ger]
geranylgeranylcys
PSI-MI
MI:0152
s-geranylgeranyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00113.
PMID:11125103
RESID:AA0104
(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
CGR
S-geranylgeranyl-L-cysteine
[C:ger]
geranylgeranylcys
Residue modification.
OBSOLETE remap to MOD:00069.
(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
2-hexadecanoylamino-3-mercaptopropanoic acid
CPN
N-(1-oxahexadecyl)-L-cysteine
N-palmitoyl-L-cysteine
[C:palm_n]
n-palmitoylcysteine
PSI-MI
MI:0153
n-palmitoyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00069.
PMID:11125103
RESID:AA0060
(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
2-hexadecanoylamino-3-mercaptopropanoic acid
CPN
N-(1-oxahexadecyl)-L-cysteine
N-palmitoyl-L-cysteine
[C:palm_n]
n-palmitoylcysteine
Residue modification.
OBSOLETE remap to MOD:00115.
(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
2-amino-3-(hexadecanoylthio)propanoic acid
CPS
S-palmitoyl-L-cysteine
[C:palm_s]
cysteine hexadecanoate thioester
cysteine palmitate thioester
s-palmitoylcysteine
PSI-MI
MI:0154
s-palmitoyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00115.
PMID:11125103
RESID:AA0106
(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
2-amino-3-(hexadecanoylthio)propanoic acid
CPS
S-palmitoyl-L-cysteine
[C:palm_s]
cysteine hexadecanoate thioester
cysteine palmitate thioester
s-palmitoylcysteine
Residue modification.
OBSOLETE remap to MOD:00068.
GMY
N-myristoyl-glycine
[G:myr]
myristoylglycine
PSI-MI
MI:0155
n-myristoyl-glycine
true
Residue modification.
OBSOLETE remap to MOD:00068.
PMID:11125103
RESID:AA0059
GMY
N-myristoyl-glycine
[G:myr]
myristoylglycine
Residue modification.
OBSOLETE remap to MOD:00087.
(S)-2-amino-6-(tetradecanoylamino)hexanoic acid
KMY
N(zeta)-myristoyllysine
N6-(1-oxotetradecyl)-L-lysine
N6-myristoyl-L-lysine
[K:myr]
epsilon-myristoyllysine
myristoyllysine
PSI-MI
MI:0156
n6-myristoyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00087.
PMID:11125103
RESID:AA0078
(S)-2-amino-6-(tetradecanoylamino)hexanoic acid
KMY
N(zeta)-myristoyllysine
N6-(1-oxotetradecyl)-L-lysine
N6-myristoyl-L-lysine
[K:myr]
epsilon-myristoyllysine
myristoyllysine
Residue modification.
OBSOLETE remap to MOD:00427.
PSI-MI
MI:0157
methylated residue
true
Residue modification.
OBSOLETE remap to MOD:00427.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00070.
(S)-2-methylaminopropanoic acid
AMT
N-methyl-L-alanine
N-methylalanine
[A:meth_n]
methylalanine
PSI-MI
MI:0158
n-methyl-alanine
true
Residue modification.
OBSOLETE remap to MOD:00070.
PMID:11125103
RESID:AA0061
(S)-2-methylaminopropanoic acid
AMT
N-methyl-L-alanine
N-methylalanine
[A:meth_n]
methylalanine
Residue modification.
OBSOLETE remap to MOD:00071.
(S)-1-carboxy-N,N,N-trimethylethanaminium
(S)-2-(trimethylammonio)propanoic acid
AM3
N,N,N-trimethyl-L-alanine
[A:meth_n3]
trimethylalanine
PSI-MI
MI:0159
n,n,n-trimethyl-alanine
true
Residue modification.
OBSOLETE remap to MOD:00071.
PMID:11125103
RESID:AA0062
(S)-1-carboxy-N,N,N-trimethylethanaminium
(S)-2-(trimethylammonio)propanoic acid
AM3
N,N,N-trimethyl-L-alanine
[A:meth_n3]
trimethylalanine
Residue modification.
OBSOLETE remap to MOD:00077.
(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
NG,NG-dimethylarginine
RM2
[R:meth_n7]
asymmetric dimethylarginine
dimethylarginine
omega-N,omega-N-dimethyl-L-arginine
PSI-MI
MI:0160
omega-n,omega-n-dimethyl-arginine
true
Residue modification.
OBSOLETE remap to MOD:00077.
PMID:11125103
RESID:AA0068
(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
NG,NG-dimethylarginine
RM2
[R:meth_n7]
asymmetric dimethylarginine
dimethylarginine
omega-N,omega-N-dimethyl-L-arginine
Residue modification.
OBSOLETE remap to MOD:00237.
(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
3-carboxy-S-methyl-cysteine
3-methylthio-aspartic acid
DM2
L-beta-methylthioaspartic acid
[D:meth_b]
beta-methylthio-aspartic acid
methylthioaspartate
PSI-MI
MI:0161
beta-methylthioaspartic acid
true
Residue modification.
OBSOLETE remap to MOD:00237.
PMID:11125103
RESID:AA0232
(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
3-carboxy-S-methyl-cysteine
3-methylthio-aspartic acid
DM2
L-beta-methylthioaspartic acid
[D:meth_b]
beta-methylthio-aspartic acid
methylthioaspartate
Residue modification.
OBSOLETE remap to MOD:00080.
(S)-2-amino-N5-methylpentanediamic acid
N(delta)-methylglutamine
N-methylglutamine
N5-methyl-L-glutamine
QM5
[Q:meth_n5]
gamma-methylglutamine
methylglutamine
PSI-MI
MI:0162
n5-methyl-glutamine
true
Residue modification.
OBSOLETE remap to MOD:00080.
PMID:11125103
RESID:AA0071
(S)-2-amino-N5-methylpentanediamic acid
N(delta)-methylglutamine
N-methylglutamine
N5-methyl-L-glutamine
QM5
[Q:meth_n5]
gamma-methylglutamine
methylglutamine
Residue modification.
OBSOLETE remap to MOD:00081.
(S)-2-aminopentanedioic acid 5-methyl ester
5-methyl-L-glutamate
EM5
L-glutamic acid 5-methyl ester
[E:meth_o5]
glutamatemethylester
glutamic acid gamma-methyl ester
PSI-MI
MI:0163
glutamic acid 5-methyl ester
true
Residue modification.
OBSOLETE remap to MOD:00081.
PMID:11125103
RESID:AA0072
(S)-2-aminopentanedioic acid 5-methyl ester
5-methyl-L-glutamate
EM5
L-glutamic acid 5-methyl ester
[E:meth_o5]
glutamatemethylester
glutamic acid gamma-methyl ester
Residue modification.
OBSOLETE remap to MOD:00085.
(S)-2-amino-6-methylaminohexanoic acid
MLZ
N(zeta)-methyllysine
N6-methyl-L-lysine
[K:meth_1]
epsilon-methyllysine
methyllysine
PSI-MI
MI:0165
n6-methyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00085.
PMID:11125103
(S)-2-amino-6-methylaminohexanoic acid
MLZ
N(zeta)-methyllysine
N6-methyl-L-lysine
[K:meth_1]
epsilon-methyllysine
methyllysine
Residue modification.
OBSOLETE remap to MOD:00084.
(S)-2-amino-6-dimethylaminohexanoic acid
MLY
N(zeta)-dimethyllysine
N6,N6-dimethyl-L-lysine
[K:meth_2]
dimethyllysine
epsilon-dimethyllysine
lysine derivative Lys(y)
PSI-MI
MI:0166
n6,n6-dimethyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00084.
PMID:11125103
RESID:AA0075
(S)-2-amino-6-dimethylaminohexanoic acid
MLY
N(zeta)-dimethyllysine
N6,N6-dimethyl-L-lysine
[K:meth_2]
dimethyllysine
epsilon-dimethyllysine
lysine derivative Lys(y)
Residue modification.
OBSOLETE remap to MOD:00083.
(S)-2-amino-6-(trimethylammonio)hexanoic acid
(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium
M3L
N(zeta)-trimethyllysine
N6,N6,N6-trimethyl-L-lysine
[K:meth_3]
epsilon-trimethyllysine
trimethyllysine
PSI-MI
MI:0167
n6,n6,n6-trimethyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00083.
PMID:11125103
RESID:AA0074
(S)-2-amino-6-(trimethylammonio)hexanoic acid
(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium
M3L
N(zeta)-trimethyllysine
N6,N6,N6-trimethyl-L-lysine
[K:meth_3]
epsilon-trimethyllysine
trimethyllysine
Residue modification.
OBSOLETE remap to MOD:00073.
(S)-2-methylamino-4-(methylsulfanyl)butanoic acid
2-methylamino-4-(methylthio)butanoic acid
MMT
N-methyl-L-methionine
N-methylmethionine
[M:meth]
methylmethionine
PSI-MI
MI:0168
n-methyl-methionine
true
Residue modification.
OBSOLETE remap to MOD:00073.
PMID:11125103
RESID:AA0064
(S)-2-methylamino-4-(methylsulfanyl)butanoic acid
2-methylamino-4-(methylthio)butanoic acid
MMT
N-methyl-L-methionine
N-methylmethionine
[M:meth]
methylmethionine
Residue modification.
OBSOLETE remap to MOD:00074.
(S)-2-methylamino-3-phenylpropanoic acid
FMT
N-methyl-L-phenylalanine
N-methylphenylalanine
[F:meth]
methylphenylalanine
PSI-MI
MI:0169
n-methyl-phenylalanine
true
Residue modification.
OBSOLETE remap to MOD:00074.
PMID:14755292
(S)-2-methylamino-3-phenylpropanoic acid
FMT
N-methyl-L-phenylalanine
N-methylphenylalanine
[F:meth]
methylphenylalanine
Residue modification.
OBSOLETE remap to MOD:00696.
phosphorylated
PSI-MI
MI:0170
phosphorylated residue
true
Residue modification.
OBSOLETE remap to MOD:00696.
PMID:11125103
phosphorylated
Residue modification.
OBSOLETE remap to MOD:00227.
(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
N5-[imino(phosphonoamino)methyl]-L-ornithine
RPO
[R:po]
alpha-amino-delta-phosphonoguanidinovaleric acid
omega-N-phospho-L-arginine
phosphoarginine
PSI-MI
MI:0171
omega-n-phospho-arginine
true
Residue modification.
OBSOLETE remap to MOD:00227.
PMID:11125103
RESID:AA0222
(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
N5-[imino(phosphonoamino)methyl]-L-ornithine
RPO
[R:po]
alpha-amino-delta-phosphonoguanidinovaleric acid
omega-N-phospho-L-arginine
phosphoarginine
Residue modification.
OBSOLETE remap to MOD:00042.
(S)-2-aminobutanedioic 4-phosphoric anhydride
DPO
L-aspartic 4-phosphoric anhydride
[D:po]
beta-aspartyl phosphate
phosphoaspartic acid
PSI-MI
MI:0172
aspartic 4-phosphoric anhydride
true
Residue modification.
OBSOLETE remap to MOD:00042.
PMID:11125103
RESID:AA0033
(S)-2-aminobutanedioic 4-phosphoric anhydride
DPO
L-aspartic 4-phosphoric anhydride
[D:po]
beta-aspartyl phosphate
phosphoaspartic acid
phosphoaspartic acid
Residue modification.
OBSOLETE remap to MOD:00043.
(R)-2-amino-3-(phosphonosulfanyl)propanoic acid
CPO
S-phospho-L-cysteine
S-phosphonocysteine
S3-phosphocysteine
[C:po]
cysteine phosphate thioester
phosphocysteine
PSI-MI
MI:0173
s-phospho-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00043.
PMID:11125103
RESID:AA0034
(R)-2-amino-3-(phosphonosulfanyl)propanoic acid
CPO
S-phospho-L-cysteine
S-phosphonocysteine
S3-phosphocysteine
[C:po]
cysteine phosphate thioester
phosphocysteine
Residue modification.
OBSOLETE remap to MOD:00046.
(S)-2-amino-3-(phosphonooxy)propanoic acid
2-amino-3-hydroxypropanoic acid 3-phosphate
2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
O-phospho-L-serine
O-phosphonoserine
O3-phosphoserine
SPO
[S:po]
phosphoserine
serine phosphate ester
PSI-MI
MI:0176
o-phospho-serine
true
Residue modification.
OBSOLETE remap to MOD:00046.
PMID:11125103
RESID:AA0037
(S)-2-amino-3-(phosphonooxy)propanoic acid
2-amino-3-hydroxypropanoic acid 3-phosphate
2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
O-phospho-L-serine
O-phosphonoserine
O3-phosphoserine
SPO
[S:po]
phosphoserine
serine phosphate ester
Residue modification.
OBSOLETE remap to MOD:00047.
(2S,3R)-2-amino-3-phosphonooxybutanoic acid
2-amino-3-hydroxybutanoic acid 3-phosphate
O-phospho-L-threonine
O3-phosphothreonine
TPO
[T:po]
phosphothreonine
threonine phosphate ester
PSI-MI
MI:0177
o-phospho-threonine
true
Residue modification.
OBSOLETE remap to MOD:00047.
PMID:11125103
RESID:AA0038
(2S,3R)-2-amino-3-phosphonooxybutanoic acid
2-amino-3-hydroxybutanoic acid 3-phosphate
O-phospho-L-threonine
O3-phosphothreonine
TPO
[T:po]
phosphothreonine
threonine phosphate ester
Residue modification.
OBSOLETE remap to MOD:00048.
(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
O4'-phospho-L-tyrosine
O4-phosphotyrosine
YPO
[Y:po]
phosphotyrosine
tyrosine phosphate
PSI-MI
MI:0178
o4'-phospho-tyrosine
true
Residue modification.
OBSOLETE remap to MOD:00048.
PMID:11125103
RESID:AA0039
(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
O4'-phospho-L-tyrosine
O4-phosphotyrosine
YPO
[Y:po]
phosphotyrosine
tyrosine phosphate
Residue modification.
OBSOLETE remap to MOD:00032.
PSI-MI
MI:0179
other modification
true
Residue modification.
OBSOLETE remap to MOD:00032.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00031.
3-selenylalanine
CSE
L-selenocysteine
[C:sel]
selenium cysteine
PSI-MI
MI:0180
selenocysteine
true
Residue modification.
OBSOLETE remap to MOD:00031.
PMID:11125103
RESID:AA0022
3-selenylalanine
CSE
L-selenocysteine
[C:sel]
selenium cysteine
Residue modification.
OBSOLETE remap to MOD:00530.
L-selenomethionine
MSE
[M:sel]
PSI-MI
MI:0181
selenomethionine
true
Residue modification.
OBSOLETE remap to MOD:00530.
PMID:11125103
L-selenomethionine
MSE
[M:sel]
Residue modification.
OBSOLETE remap to MOD:01169.
(S)-2-amino-3-oxopropanoic acid
2-amino-3-oxopropionic acid
L-3-oxoalanine
L-alpha-formylglycine
L-amino-malonic acid semialdehyde
L-aminomalonaldehydic acid
L-serinesemialdehyde [misnomer]
SOX
[S:oxal]
oxoalanine
PSI-MI
MI:0182
3-oxoalanine
true
Residue modification.
OBSOLETE remap to MOD:01169.
PMID:11125103
RESID:AA0185
(S)-2-amino-3-oxopropanoic acid
2-amino-3-oxopropionic acid
L-3-oxoalanine
L-alpha-formylglycine
L-amino-malonic acid semialdehyde
L-aminomalonaldehydic acid
L-serinesemialdehyde [misnomer]
SOX
[S:oxal]
oxoalanine
Residue modification.
OBSOLETE remap to MOD:00179.
(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
EGE
L-glutamyl 5-glycerophosphoethanolamine
L-glutamyl 5-glycerophosphorylethanolamine
L-glutamyl 5-glycerylphosphorylethanolamine
[E:gpe]
glycerylpo4etohamine
PSI-MI
MI:0184
glutamyl 5-glycerylphosphorylethanolamine
true
Residue modification.
OBSOLETE remap to MOD:00179.
PMID:11125103
RESID:AA0170
(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
EGE
L-glutamyl 5-glycerophosphoethanolamine
L-glutamyl 5-glycerophosphorylethanolamine
L-glutamyl 5-glycerylphosphorylethanolamine
[E:gpe]
glycerylpo4etohamine
Residue modification.
OBSOLETE remap to MOD:00126.
(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
KBT
N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
N6-biotinyl-L-lysine
N6-biotinyllysine
[K:biotin]
biocytin
biotinyllysine
epsilon-N-biotinyllysine
PSI-MI
MI:0186
n6-biotinyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00126.
PMID:11125103
RESID:AA0117
(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
KBT
N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
N6-biotinyl-L-lysine
N6-biotinyllysine
[K:biotin]
biocytin
biotinyllysine
epsilon-N-biotinyllysine
Residue modification.
OBSOLETE remap to MOD:00125.
(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
KHY
N6-(4-amino-2-hydroxybutyl)-L-lysine
[K:hypu]
hypusine
PSI-MI
MI:0187
n6-(4-amino-2-hydroxybutyl)-lysine
true
Residue modification.
OBSOLETE remap to MOD:00125.
PMID:11125103
RESID:AA0116
(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
KHY
N6-(4-amino-2-hydroxybutyl)-L-lysine
[K:hypu]
hypusine
hypusine
Residue modification.
OBSOLETE remap to MOD:00129.
(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
KRT
N6-retinal-L-lysine
N6-retinyl-lysine
N6-retinylidene-L-lysine
[K:retin]
retinallysine
PSI-MI
MI:0188
n6-retinal-lysine
true
Residue modification.
OBSOLETE remap to MOD:00129.
PMID:11125103
RESID:AA0120
(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
KRT
N6-retinal-L-lysine
N6-retinyl-lysine
N6-retinylidene-L-lysine
[K:retin]
retinallysine
Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.
OBSOLETE remap to MOD:00134.
KUB
N6-glycyl-L-lysine
N6-glycyllysine
[K:ub]
PSI-MI
MI:0189
ubiquitinated lysine
true
Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.
OBSOLETE remap to MOD:00134.
PMID:11125103
RESID:AA0125
KUB
N6-glycyl-L-lysine
N6-glycyllysine
[K:ub]
Connection between molecule.
PSI-MI
MI:0190
interaction type
Connection between molecule.
PMID:14755292
Physical association among molecules.
OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
PSI-MI
MI:0191
aggregation
true
Physical association among molecules.
OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
PMID:14755292
Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
acetylation
PSI-MI
MI:0192
acetylation reaction
Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
GO:0006473
PMID:14755292
RESID:AA0041
RESID:AA0042
RESID:AA0043
RESID:AA0044
RESID:AA0045
RESID:AA0046
RESID:AA0047
RESID:AA0048
RESID:AA0049
RESID:AA0050
RESID:AA0051
RESID:AA0052
RESID:AA0053
RESID:AA0054
RESID:AA0055
RESID:AA0056
acetylation
Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
amidation
PSI-MI
MI:0193
amidation reaction
Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
GO:0001519
PMID:14755292
RESID:AA0081
RESID:AA0082
RESID:AA0083
RESID:AA0084
RESID:AA0085
RESID:AA0086
RESID:AA0087
RESID:AA0088
RESID:AA0089
RESID:AA0090
RESID:AA0091
RESID:AA0092
RESID:AA0093
RESID:AA0094
RESID:AA0095
RESID:AA0096
RESID:AA0097
RESID:AA0098
RESID:AA0099
RESID:AA0100
amidation
Covalent bond breakage in a molecule leading to the formation of smaller molecules.
cleavage
PSI-MI
MI:0194
cleavage reaction
Covalent bond breakage in a molecule leading to the formation of smaller molecules.
PMID:14755292
cleavage
Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
PSI-MI
MI:0195
covalent binding
Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
PMID:14755292
Physical interaction mediated by covalent bond rearrangement.
OBSOLETE use covalent binding (MI:0195) instead.
PSI-MI
MI:0196
covalent interaction
true
Physical interaction mediated by covalent bond rearrangement.
OBSOLETE use covalent binding (MI:0195) instead.
PMID:14755292
N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
deacetylation
PSI-MI
MI:0197
deacetylation reaction
N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
GO:0006476
PMID:14755292
RESID:AA0055
RESID:AA0056
deacetylation
S-farnesyl-L-cysteined is cleaved and returns a C residue.
defarnesylation
PSI-MI
MI:0198
defarnesylation reaction
S-farnesyl-L-cysteined is cleaved and returns a C residue.
PMID:14755292
RESID:AA0102
defarnesylation
N6-formyl-L-lysine is cleaved and returns a K residue.
deformylation
PSI-MI
MI:0199
deformylation reaction
N6-formyl-L-lysine is cleaved and returns a K residue.
PMID:14755292
RESID:AA0211
deformylation
S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
degeranylation
PSI-MI
MI:0200
degeranylation reaction
S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
PMID:14755292
RESID:AA0104
degeranylation
N6-myristoyl-L-lysine is cleaved and returns a K residue.
demyristoylation
PSI-MI
MI:0201
demyristoylation reaction
N6-myristoyl-L-lysine is cleaved and returns a K residue.
PMID:14755292
RESID:AA0078
demyristoylation
S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
depalmitoylation
PSI-MI
MI:0202
depalmitoylation reaction
S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
PMID:14755292
RESID:AA0060
RESID:AA0077
RESID:AA0106
depalmitoylation
Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
dephosphorylation
PSI-MI
MI:0203
dephosphorylation reaction
Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
GO:0016311
PMID:14755292
RESID:AA0033
RESID:AA0034
RESID:AA0035
RESID:AA0036
RESID:AA0037
RESID:AA0038
RESID:AA0039
RESID:AA0222
dephosphorylation
Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
deubiquitination
PSI-MI
MI:0204
deubiquitination reaction
Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
GO:0016579
PMID:11583613
RESID:AA0125
deubiquitination
Dissociation of partners interacting via non-covalent bond.
OBSOLETE because considered misleading.
PSI-MI
MI:0205
disaggregation
true
Dissociation of partners interacting via non-covalent bond.
OBSOLETE because considered misleading.
PMID:14755292
Reversible reaction that can affect C residue.
farnesylation
PSI-MI
MI:0206
farnesylation reaction
Reversible reaction that can affect C residue.
GO:0018347
PMID:14755292
RESID:AA0102
farnesylation
Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
formylation
PSI-MI
MI:0207
formylation reaction
Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
GO:0018256
PMID:14755292
RESID:AA0057
RESID:AA0211
formylation
An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E
A genetic interaction refers to an unexpected phenotype not easily explained by combining the effects of individual genetic variants (7).
A quantitative genetic interaction definition has two components: a quantitative phenotypic measure and a neutrality function that predicts the phenotype of an organism carrying two noninteracting mutations. Interaction is then defined by deviation of a double-mutant organism's phenotype from the expected neutral phenotype.
More generally, a genetic interaction can be defined as the difference between an experimentally measured double-mutant phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the mutations act independently.
Two genes A and B 'genetically interact' when the phenotype generated as the result of mutations in both genes (double mutant ab) is unexpectedly not just a combination of the phenotypes of the two single mutants a and b.
Fisher epistasis
PSI-MI
MI:0208
genetic interaction (sensu unexpected)
An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E
PMID:16527956
Fisher epistasis
PMID:17510664
https://doi.org/10.1017/S0080456800012163
Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
geranylgeranylation
PSI-MI
MI:0209
geranylgeranylation reaction
Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
GO:0018348
PMID:14755292
RESID:AA0104
geranylgeranylation
Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
hydroxylation
PSI-MI
MI:0210
hydroxylation reaction
Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
GO:0018126
PMID:14755292
RESID:AA0028
RESID:AA0029
RESID:AA0030
RESID:AA0146
RESID:AA0215
hydroxylation
Covalent or non covalent binding of lipid group on a protein residue.
PSI-MI
MI:0211
lipid addition
Covalent or non covalent binding of lipid group on a protein residue.
GO:0006497
PMID:14755292
Cleavage of a lipid group covalently bound to a protein residue.
lipid cleavage
PSI-MI
MI:0212
lipoprotein cleavage reaction
Cleavage of a lipid group covalently bound to a protein residue.
PMID:14755292
lipid cleavage
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
methylation
PSI-MI
MI:0213
methylation reaction
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
GO:0043414
PMID:14755292
RESID:AA0061
RESID:AA0062
RESID:AA0063
RESID:AA0064
RESID:AA0065
RESID:AA0066
RESID:AA0067
RESID:AA0068
RESID:AA0069
RESID:AA0070
RESID:AA0071
RESID:AA0072
RESID:AA0073
RESID:AA0074
RESID:AA0075
RESID:AA0076
RESID:AA0234
RESID:AA0272
methylation
Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
myristoylation
PSI-MI
MI:0214
myristoylation reaction
Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
GO:0018319
PMID:14755292
RESID:AA0059
RESID:AA0078
myristoylation
Interaction mediated by non-covalent, weak forces rearrangement.
OBSOLETE use physical interaction (MI:0218) instead.
non covalent inter
PSI-MI
MI:0215
non covalent interaction
true
Interaction mediated by non-covalent, weak forces rearrangement.
OBSOLETE use physical interaction (MI:0218) instead.
PMID:14755292
non covalent inter
Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
palmitoylation
PSI-MI
MI:0216
palmitoylation reaction
Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
GO:0018318
PMID:14755292
RESID:AA0060
RESID:AA0077
RESID:AA0079
RESID:AA0080
RESID:AA0106
palmitoylation
Reversible reaction that can affect D,C,H,S,T,Y,R residues.
phosphorylation
PSI-MI
MI:0217
phosphorylation reaction
Reversible reaction that can affect D,C,H,S,T,Y,R residues.
GO:0016310
PMID:14755292
RESID:AA0033
RESID:AA0034
RESID:AA0035
RESID:AA0036
RESID:AA0037
RESID:AA0038
RESID:AA0039
RESID:AA0222
phosphorylation
Interaction among molecules that can be direct or indirect.
OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
PSI-MI
MI:0218
physical interaction
true
Interaction among molecules that can be direct or indirect.
OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
PMID:14755292
Death phenotype observed on cells carrying combination of two independently silent mutations.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
PSI-MI
MI:0219
synthetic lethal
true
Death phenotype observed on cells carrying combination of two independently silent mutations.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
PMID:15608217
Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
ubiquitination
PSI-MI
MI:0220
ubiquitination reaction
Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
GO:0016567
PMID:11583613
RESID:AA0125
ubiquitination
Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
PSI-MI
MI:0221
expression level
Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
PMID:14755292
A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
endogenous
endogenous level
PSI-MI
MI:0222
physiological level
A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
PMID:14755292
endogenous
endogenous level
A molecule is estimated to be expressed at lower levels than in physiological condition.
under-expressed
PSI-MI
MI:0223
under expressed level
A molecule is estimated to be expressed at lower levels than in physiological condition.
PMID:14755292
under-expressed
The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
chip-chip
PSI-MI
MI:0225
chromatin immunoprecipitation array
The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
PMID:11125145
PMID:11206552
chip-chip
Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
IEC
ion exchange chrom
PSI-MI
MI:0226
ion exchange chromatography
Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
PMID:14755292
IEC
ion exchange chrom
Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
reverse phase chrom
PSI-MI
MI:0227
reverse phase chromatography
Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
PMID:14755292
reverse phase chrom
Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
cytoplasmic compl
PSI-MI
MI:0228
cytoplasmic complementation assay
true
Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
PMID:14755292
cytoplasmic compl
true
OBSOLETE remap to MI:0090 protein complementation assay.
membrane compl
PSI-MI
MI:0230
membrane bound complementation assay
true
OBSOLETE remap to MI:0090 protein complementation assay.
PMID:14755292
membrane compl
The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
mappit
PSI-MI
MI:0231
mammalian protein protein interaction trap
The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
PMID:12853652
mappit
Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
transcription compl
PSI-MI
MI:0232
transcriptional complementation assay
Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
PMID:14755292
transcription compl
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
PSI-MI
MI:0233
protein dna complex
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
PMID:14755292
Molecule labelled with 131 radio isotope of iodine atoms.
131I
I131
PSI-MI
MI:0234
131i radiolabel
Molecule labelled with 131 radio isotope of iodine atoms.
PMID:14755292
131I
I131
Molecule labelled with the radio isotope 14 of carbon atoms.
14C
C14
PSI-MI
MI:0235
14c radiolabel
Molecule labelled with the radio isotope 14 of carbon atoms.
PMID:14755292
14C
C14
Molecule labelled with the radio isotope 32 of phosphorus atoms.
32P
P32
PSI-MI
MI:0236
32p radiolabel
Molecule labelled with the radio isotope 32 of phosphorus atoms.
PMID:14755292
32P
P32
Molecule labelled with the radio isotope 33 of phosphorus atoms.
33P
P33
PSI-MI
MI:0237
33p radiolabel
Molecule labelled with the radio isotope 33 of phosphorus atoms.
PMID:14755292
33P
P33
Molecules labelled with isotope 3 of hydrogen atoms.
3H
H3
tritium
PSI-MI
MI:0238
3h radiolabel
Molecules labelled with isotope 3 of hydrogen atoms.
PMID:14755292
3H
H3
tritium
Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
PSI-MI
MI:0239
biotin tag
Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
PMID:14755292
The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
PSI-MI
MI:0240
fusion protein
The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
PMID:14755292
Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
hrp tag
PSI-MI
MI:0241
horseradish peroxidase tag
Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
PMID:14755292
hrp tag
This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
go-definition-ref
PSI-MI
MI:0242
gene ontology definition reference
This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
PMID:14755292
go-definition-ref
Reference to the master sequence from which this isoform has been derived.
isoform-parent
PSI-MI
MI:0243
isoform parent sequence reference
Reference to the master sequence from which this isoform has been derived.
PMID:14755292
isoform-parent
Collection of functional complexes within Reactome - a knowledgebase of biological processes.
http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
id-validation-regexp:
search-url:
PSI-MI
MI:0244
reactome complex
true
Collection of functional complexes within Reactome - a knowledgebase of biological processes.
http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
PMID:21067998
id-validation-regexp:
REACT_[0-9]{1,5}\.[0-9]{1,3}|[0-9]+
search-url:
http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac}
Collection of protein within the Reactome database - a knowledgebase of biological processes.
http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
id-validation-regexp:
search-url:
PSI-MI
MI:0245
reactome protein
true
Collection of protein within the Reactome database - a knowledgebase of biological processes.
http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
PMID:21067998
id-validation-regexp:
REACT_[0-9]{1,4}\.[0-9]{1,3}|[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10}
search-url:
http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=${ac}
CABRI cell lines catalogue available at.
http://www.cabri.org/
id-validation-regexp:
search-url:
PSI-MI
MI:0246
cabri
CABRI cell lines catalogue available at.
http://www.cabri.org/
PMID:14755292
id-validation-regexp:
[0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\:ACC\s[0-9]+
search-url:
http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]
New EBI Web Taxonomy.
http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
id-validation-regexp:
search-url:
PSI-MI
MI:0247
newt
true
New EBI Web Taxonomy.
http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://www.ebi.ac.uk/newt/display?search=${ac}
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
http://www.ebi.ac.uk/RESID/index.html
id-validation-regexp:
search-url:
PSI-MI
MI:0248
resid
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
http://www.ebi.ac.uk/RESID/index.html
PMID:14755292
id-validation-regexp:
AA[0-9]{4}
search-url:
http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e
A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.
http://www.kazusa.or.jp/huge/
id-validation-regexp:
search-url:
PSI-MI
MI:0249
huge
A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.
http://www.kazusa.or.jp/huge/
PMID:14755292
id-validation-regexp:
KIAA[0-9]{4}[A-Z]{0,1}
search-url:
http://www.kazusa.or.jp/huge/gfpage/${ac}
A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
PSI-MI
MI:0250
gene
A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
PMID:14755292
SO:0000704
Reference of a protein object pointing to its genomic or nucleic acid sequence.
PSI-MI
MI:0251
gene product
Reference of a protein object pointing to its genomic or nucleic acid sequence.
PMID:14755292
Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
PSI-MI
MI:0252
biological feature
Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
PMID:14755292
One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
PSI-MI
MI:0253
isotope label
One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
PMID:14755292
This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
PSI-MI
MI:0254
genetic interference
This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
PMID:14755292
This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
expression interfer
PSI-MI
MI:0255
post transcriptional interference
This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
PMID:14755292
expression interfer
RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
rnai
PSI-MI
MI:0256
rna interference
RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
PMID:12110901
PMID:12408823
rnai
This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
PSI-MI
MI:0257
antisense rna
This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
PMID:1340158
Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PSI-MI
MI:0258
inhibitor antibodies
true
Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PMID:10189716
This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
perturbagens pep
PSI-MI
MI:0259
perturbagens peptides
true
This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PMID:11731788
PMID:8606778
perturbagens pep
Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
inhibitor small mol
PSI-MI
MI:0260
inhibitor small molecules
true
Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PMID:10542155
PMID:10780927
inhibitor small mol
A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
PSI-MI
MI:0261
obsolete suppression
true
A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
PMID:15608217
A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
PSI-MI
MI:0262
suppression mutation
true
A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
PMID:15608217
Knocked out gene is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
suppress knockout
PSI-MI
MI:0263
suppression knockout
true
Knocked out gene is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
PMID:15608217
suppress knockout
A mutation is the partial suppressor of a mutant phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
suppression partial
PSI-MI
MI:0264
suppression partial alteration
true
A mutation is the partial suppressor of a mutant phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
PMID:15608217
suppression partial
An altered expression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
suppress expression
PSI-MI
MI:0265
suppression expression alteration
true
An altered expression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
PMID:15608217
suppress expression
Overexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
suppress overexpress
PSI-MI
MI:0266
suppression overexpression
true
Overexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
PMID:15608217
suppress overexpress
Level of over/underexpression scales the 'extend' of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
PSI-MI
MI:0267
suppression scalable
true
Level of over/underexpression scales the 'extend' of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
PMID:15608217
Underexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
suppress underexpres
PSI-MI
MI:0268
suppression underexpression
true
Underexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
PMID:15608217
suppress underexpres
Two silent mutations show an altered phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
PSI-MI
MI:0269
synthetic phenotype
true
Two silent mutations show an altered phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
PMID:15608217
Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
cond syntetic lethal
PSI-MI
MI:0270
conditional synthetic lethal
true
Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
PMID:15608217
cond syntetic lethal
Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
temprtr synt lethal
PSI-MI
MI:0271
conditional synthetic lethal temperature-sensitivity
true
Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
PMID:15608217
temprtr synt lethal
Two silent mutations show altered growth effect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
synt growth effect
PSI-MI
MI:0273
synthetic growth effect
true
Two silent mutations show altered growth effect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
PMID:15608217
synt growth effect
Two silent mutations show growth defect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
synt growth defect
PSI-MI
MI:0274
synthetic growth defect
true
Two silent mutations show growth defect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
PMID:15608217
synt growth defect
Two silent mutations show growth increase when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
synt growth increase
PSI-MI
MI:0275
synthetic growth increase
true
Two silent mutations show growth increase when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
PMID:15608217
synt growth increase
Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
bn-page
PSI-MI
MI:0276
blue native page
Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
PMID:14665681
bn-page
Descriptor of type of nomenclature used to describe interactor.
CvAliasType
PSI-MI
MI:0300
alias type
Descriptor of type of nomenclature used to describe interactor.
PMID:14755292
CvAliasType
Gene name.
gene
PSI-MI
MI:0301
gene name
Gene name.
PMID:14755292
gene
Gene name synonym.
PSI-MI
MI:0302
gene name synonym
Gene name synonym.
PMID:14755292
Synonym as used in Gene Ontology.
go synonym
PSI-MI
MI:0303
gene ontology synonym
Synonym as used in Gene Ontology.
PMID:14755292
go synonym
Isoform synonym.
PSI-MI
MI:0304
isoform synonym
Isoform synonym.
PMID:14755292
A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
CDS number
ONL
ORF number
Ordered locus name
locus name
systematic gene number
PSI-MI
MI:0305
For instance HI0934, Rv3245c, At5g34500, YER456W.
ordered locus name
A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
PMID:14755292
CDS number
ONL
ORF number
Ordered locus name
locus name
systematic gene number
A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
orf name
PSI-MI
MI:0306
For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames.
open reading frame name
A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
PMID:14755292
orf name
Method by which molecule is delivered or engineered into a cell.
PSI-MI
MI:0307
delivery method
Method by which molecule is delivered or engineered into a cell.
PMID:14755292
Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
PSI-MI
MI:0308
electroporation
Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
PMID:6329708
A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.
OBSOLETE redundant term. Map to feature type : tag (MI:0507).
genetic tag insertion
PSI-MI
MI:0309
genomic tagging
true
A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.
OBSOLETE redundant term. Map to feature type : tag (MI:0507).
PMID:14755292
genetic tag insertion
Molecule introduced into a cell via an external organism, usually a virus or bacteria.
PSI-MI
MI:0310
infection
Molecule introduced into a cell via an external organism, usually a virus or bacteria.
PMID:14755292
The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
micro-injection
PSI-MI
MI:0311
microinjection
The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
PMID:3016916
micro-injection
Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
nucl transfection
PSI-MI
MI:0312
nucleic acid transfection
Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
PMID:14755292
nucl transfection
Molecular species involved in the interaction.
participant type
PSI-MI
MI:0313
interactor type
Molecular species involved in the interaction.
PMID:14755292
participant type
Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
PSI-MI
MI:0314
complex
Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
PMID:14755292
A stable set of interacting proteins that can be copurified and operate as a functional unit.
PSI-MI
MI:0315
protein complex
A stable set of interacting proteins that can be copurified and operate as a functional unit.
PMID:14755292
A macromolecular complex containing both protein and RNA molecules.
protein rna complex
ribonucleoprot compl
PSI-MI
MI:0316
ribonucleoprotein complex
A macromolecular complex containing both protein and RNA molecules.
GO:0030529
PMID:14755292
protein rna complex
ribonucleoprot compl
Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
PSI-MI
MI:0317
interaction
Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
PMID:14755292
Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
PSI-MI
MI:0318
nucleic acid
Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
PMID:14755292
SO:0000348
Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
DNA
deoxyribonucleic acid
dna
PSI-MI
MI:0319
deoxyribonucleic acid
Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
PMID:14755292
SO:0000352
DNA
deoxyribonucleic acid
dna
Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
RNA
rna
PSI-MI
MI:0320
ribonucleic acid
Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
PMID:14755292
SO:0000356
RNA
rna
Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
catalytic RNA
catalytic ribonucleic acid
crna
PSI-MI
MI:0321
catalytic rna
Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
PMID:14755292
catalytic RNA
catalytic ribonucleic acid
crna
Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
grna
guide RNA
PSI-MI
MI:0322
guide rna
Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
PMID:14755292
grna
guide RNA
A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
heterogeneous nuclear RNA
heterogeneous nuclear ribonucleic acid
hnrna
PSI-MI
MI:0323
heterogeneous nuclear rna
A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
PMID:14755292
heterogeneous nuclear RNA
heterogeneous nuclear ribonucleic acid
hnrna
Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
mRNA
mrna
PSI-MI
MI:0324
messenger rna
Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
PMID:14755292
mRNA
mrna
The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
tRNA
transfer RNA
transfer ribonucleic acid
trna
PSI-MI
MI:0325
transfer rna
The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
PMID:14755292
tRNA
transfer RNA
transfer ribonucleic acid
trna
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
PSI-MI
MI:0326
protein
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
PMID:14755292
SO:0000358
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
oligopeptide
polypeptide
PSI-MI
MI:0327
peptide
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
PMID:14755292
oligopeptide
polypeptide
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
PSI-MI
MI:0328
small molecule
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
PMID:14755292
Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
PSI-MI
MI:0329
unknown participant
Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
PMID:14755292
Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
PSI-MI
MI:0330
molecular source
Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
PMID:14755272
Molecule has been added into system from an external source or altered within the cell.
PSI-MI
MI:0331
engineered
Molecule has been added into system from an external source or altered within the cell.
PMID:14755292
Unaltered endogenous molecule in its naturally occurring state.
endogenous
PSI-MI
MI:0332
naturally occurring
Unaltered endogenous molecule in its naturally occurring state.
PMID:14755292
endogenous
Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
CvFuzzyType
endStatus
startStatus
PSI-MI
MI:0333
feature range status
Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
PMID:14755292
CvFuzzyType
endStatus
startStatus
Term describing the last amino acid of a peptide chain.
c-term
c-terminal
c-terminus
carboxy-terminus
PSI-MI
MI:0334
Displayed as 'c'.
c-terminal position
Term describing the last amino acid of a peptide chain.
PMID:14755292
c-term
c-terminal
c-terminus
carboxy-terminus
Position within the sequence clearly defined.
certain
PSI-MI
MI:0335
certain sequence position
Position within the sequence clearly defined.
PMID:14755292
certain
Partially determined sequence position known to be in a location higher than a given position.
PSI-MI
MI:0336
Displayed as '>'.
greater-than
Partially determined sequence position known to be in a location higher than a given position.
PMID:14755292
Partially determined sequence position known to be in a position lower than a given position.
PSI-MI
MI:0337
Displayed as '<'.
less-than
Partially determined sequence position known to be in a position lower than a given position.
PMID:14755292
Describes a sequence position known to be in a certain range, where the exact position is unclear.
PSI-MI
MI:0338
For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'.
range
Describes a sequence position known to be in a certain range, where the exact position is unclear.
PMID:14755292
Term describing a completely unknown or unspecified sequence position.
undetermined
PSI-MI
MI:0339
Displayed as '?'.
undetermined sequence position
Term describing a completely unknown or unspecified sequence position.
PMID:14755292
undetermined
Term describing the first amino acid of a peptide chain.
amino-terminus
n-term
n-terminal
n-terminus
PSI-MI
MI:0340
Displayed as 'n'.
n-terminal position
Term describing the first amino acid of a peptide chain.
PMID:14755292
amino-terminus
n-term
n-terminal
n-terminus
Mixture of protein forms where N-terminus has been progressively truncated.
PSI-MI
MI:0341
ragged n-terminus
Mixture of protein forms where N-terminus has been progressively truncated.
PMID:14755292
Indicates the sample context in which each interacting molecule is presented to its partner.
PSI-MI
MI:0342
sample process
Indicates the sample context in which each interacting molecule is presented to its partner.
PMID:14755292
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
PSI-MI
MI:0343
cdna library
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
PMID:6110205
Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
PSI-MI
MI:0344
cell lysate
Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
PMID:14755292
Name assigned to a molecule by the authors within a paper that may differ from the reference database.
PSI-MI
MI:0345
author assigned name
Name assigned to a molecule by the authors within a paper that may differ from the reference database.
PMID:14755292
Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
experimental prep
PSI-MI
MI:0346
experimental preparation
Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
PMID:14755292
experimental prep
Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
PSI-MI
MI:0348
fixed cell
Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
PMID:14755292
Molecule is observed within in a living cell.
PSI-MI
MI:0349
living cell
Molecule is observed within in a living cell.
PMID:14755292
Molecule has undergone one or more purification steps to isolate it from the cellular environment.
PSI-MI
MI:0350
purified
Molecule has undergone one or more purification steps to isolate it from the cellular environment.
PMID:14755292
The author states a molecule is completely pure, i.e. no other molecular species are present.
pure
PSI-MI
MI:0351
homogeneous
The author states a molecule is completely pure, i.e. no other molecular species are present.
PMID:14755292
pure
The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
PSI-MI
MI:0352
partially purified
The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
PMID:14755292
Qualifier to describe the type of information a cross-reference is pointing to.
CvXrefQualifier
refType
xref type
PSI-MI
MI:0353
cross-reference type
Qualifier to describe the type of information a cross-reference is pointing to.
PMID:14755292
CvXrefQualifier
refType
xref type
Cross reference pointing to a Gene Ontology -'cellular component' term.
search-url:
component
go component term
PSI-MI
MI:0354
cellular component
Cross reference pointing to a Gene Ontology -'cellular component' term.
PMID:14681407
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
component
go component term
Cross reference pointing to a Gene Ontology -'molecular function' term.
search-url:
function
go function term
PSI-MI
MI:0355
molecular function
Cross reference pointing to a Gene Ontology -'molecular function' term.
PMID:14681407
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
function
go function term
Reference to the corresponding object in another database. Correspondence may be complete or partial.
identity
PSI-MI
MI:0356
For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database.
identical object in an external resource
Reference to the corresponding object in another database. Correspondence may be complete or partial.
PMID:14755292
identity
Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
PSI-MI
MI:0357
method reference
Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
PMID:14755292
Used to indicate the PMID from which the experimental data is extracted.
PSI-MI
MI:0358
primary-reference
Used to indicate the PMID from which the experimental data is extracted.
PMID:14755292
Cross reference pointing to a Gene Ontology -'cellular process' term.
search-url:
go process term
process
PSI-MI
MI:0359
biological process
Cross reference pointing to a Gene Ontology -'cellular process' term.
PMID:14681407
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
go process term
process
Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
secondary-ac
PSI-MI
MI:0360
secondary accession number
Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
PMID:14755292
secondary-ac
Related object within the same database or pointing to an external database.
see-also
PSI-MI
MI:0361
additional information
Related object within the same database or pointing to an external database.
PMID:14755292
see-also
Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
modeled
modelled
PSI-MI
MI:0362
inference
Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
PMID:14755292
modeled
modelled
Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
modeled by author
modelled by author
PSI-MI
MI:0363
inferred by author
Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
PMID:14755292
modeled by author
modelled by author
Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
modeled by curator
modelled by curator
PSI-MI
MI:0364
inferred by curator
Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
PMID:14755292
modeled by curator
modelled by curator
Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
PSI-MI
MI:0365
enzyme tag
Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
PMID:10935637
Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
alk phosphatase tag
PSI-MI
MI:0366
alkaline phosphatase tag
Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
PMID:10935637
alk phosphatase tag
The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
GFP
gfp tag
green fluorescent protein
PSI-MI
MI:0367
green fluorescent protein tag
The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:7491768
GFP
gfp tag
green fluorescent protein
Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
YFP
yellow fluorescent protein
yfp tag
PSI-MI
MI:0368
yellow fluorescent protein tag
Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:10929120
YFP
yellow fluorescent protein
yfp tag
The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
gallex
PSI-MI
MI:0369
lex-a dimerization assay
The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
PMID:12446730
gallex
gallex
This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
toxcat
PSI-MI
MI:0370
tox-r dimerization assay
This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
PMID:9927659
toxcat
toxcat
Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
35S
S35
s35 radiolabelled
PSI-MI
MI:0371
35s radiolabel
Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
PMID:14755292
35S
S35
s35 radiolabelled
Cell lysates are partially fractionated to isolate a specific subcellular fraction.
subcellular prep
PSI-MI
MI:0372
subcellular preparation
Cell lysates are partially fractionated to isolate a specific subcellular fraction.
PMID:14755292
subcellular prep
Dye coupled to a molecule allowing its identification isolation and monitoring.
dye labelled
PSI-MI
MI:0373
dye label
Dye coupled to a molecule allowing its identification isolation and monitoring.
PMID:14577292
dye labelled
The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
PSI-MI
MI:0374
cyanine label
The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
PMID:14577292
The organic cyanine Cy3 emits maximally at 570 nm.
PSI-MI
MI:0375
cy3 label
The organic cyanine Cy3 emits maximally at 570 nm.
PMID:14577292
The organic cyanine Cy5 emits maximally at 670 nm.
PSI-MI
MI:0376
cy5 label
The organic cyanine Cy5 emits maximally at 670 nm.
PMID:14577292
Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
FITC labelled
fitc labelled
fluorescein isothiocyanate labbeled
PSI-MI
MI:0377
fluorescein isothiocyanate label
Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
PMID:14577292
FITC labelled
fitc labelled
fluorescein isothiocyanate labbeled
Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
rare isotope label
PSI-MI
MI:0378
rare isotope label
Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
PMID:14577292
rare isotope label
Molecules labelled with isotope 13 of carbon atoms.
13C
C13
PSI-MI
MI:0379
13c label
Molecules labelled with isotope 13 of carbon atoms.
PMID:14577292
13C
C13
Molecules labelled with isotope 15 of nytrogen atoms.
15N
N15
PSI-MI
MI:0380
15n label
Molecules labelled with isotope 15 of nytrogen atoms.
PMID:14577292
15N
N15
Molecules labelled with isotope 2 of hydrogen atoms.
2H2
D2
deuterium
PSI-MI
MI:0381
2h label
Molecules labelled with isotope 2 of hydrogen atoms.
PMID:14577292
2H2
D2
deuterium
Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
mutation increasing
PSI-MI
MI:0382
mutation increasing interaction
Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
PMID:14577292
mutation increasing
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
PSI-MI
MI:0383
biopolymer
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
PMID:14577292
All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
PSI-MI
MI:0384
alexa label
All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
PMID:10449539
Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
PSI-MI
MI:0385
alexa 350 label
Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
PMID:10449539
Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
PSI-MI
MI:0386
alexa 430 label
Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
PMID:10449539
Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
PSI-MI
MI:0387
alexa 488 label
Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
PMID:10449539
Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
PSI-MI
MI:0388
alexa 532 label
Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
PMID:10449539
Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
PSI-MI
MI:0389
alexa 546 label
Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
PMID:10449539
Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
PSI-MI
MI:0390
alexa 568 label
Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
PMID:10449539
Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
PSI-MI
MI:0391
alexa 594 label
Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
PMID:10449539
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
predetermined
PSI-MI
MI:0396
predetermined participant
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
PMID:14755292
predetermined
Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
PSI-MI
MI:0397
two hybrid array
Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
PMID:10688190
PMID:11827624
In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
two hybrid pooling
PSI-MI
MI:0398
two hybrid pooling approach
In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
PMID:11283351
PMID:20946815
two hybrid pooling
Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
2h fragment pooling
PSI-MI
MI:0399
two hybrid fragment pooling approach
Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
PMID:12634794
2h fragment pooling
Techniques which depend upon the strength of the interaction between two entities.
affinity techniques
PSI-MI
MI:0400
affinity technology
Techniques which depend upon the strength of the interaction between two entities.
PMID:14755292
affinity techniques
The application of chemical principles and methods to biological experiments to demonstrate an interaction.
PSI-MI
MI:0401
biochemical
The application of chemical principles and methods to biological experiments to demonstrate an interaction.
PMID:14755292
Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
ch-ip
PSI-MI
MI:0402
chromatin immunoprecipitation assay
Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
PMID:12054902
ch-ip
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
PSI-MI
MI:0403
colocalization
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
PMID:14755292
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
comig non denat gel
PSI-MI
MI:0404
comigration in non denaturing gel electrophoresis
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
PMID:14755292
comig non denat gel
Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
PSI-MI
MI:0405
competition binding
Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
PMID:14755292
Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
PSI-MI
MI:0406
deacetylase assay
Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
PMID:14755292
Interaction between molecules that are in direct contact with each other.
PSI-MI
MI:0407
direct interaction
Interaction between molecules that are in direct contact with each other.
PMID:14755292
Covalent bond mediated by 2 sulfur atoms.
SS-bond
disulfide bridge
PSI-MI
MI:0408
disulfide bond
Covalent bond mediated by 2 sulfur atoms.
PMID:14755292
SS-bond
disulfide bridge
Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.
OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA'
replace by:MI:0417
PSI-MI
MI:0409
dna footprinting
true
Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.
OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA'
replace by:MI:0417
PMID:14755292
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
3D-EM
electron tomog
PSI-MI
MI:0410
3D electron microscopy
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
PMID:12160704
3D-EM
electron tomog
Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
ELISA
elisa
PSI-MI
MI:0411
enzyme linked immunosorbent assay
Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
PMID:11906746
ELISA
elisa
The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
emsa supershift
PSI-MI
MI:0412
electrophoretic mobility supershift assay
The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
PMID:12169687
emsa supershift
This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
Gel retardation assay
band shift
emsa
PSI-MI
MI:0413
electrophoretic mobility shift assay
This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
PMID:12169687
Gel retardation assay
band shift
emsa
terms aiming to represent biochemical reactions referring to their resulting product modifications.
Biochemical reaction
PSI-MI
MI:0414
enzymatic reaction
terms aiming to represent biochemical reactions referring to their resulting product modifications.
PMID:14755292
Biochemical reaction
Participants are enzyme or substrate in a biochemical reaction.
PSI-MI
MI:0415
enzymatic study
Participants are enzyme or substrate in a biochemical reaction.
PMID:14755292
Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
fluorescence imaging
PSI-MI
MI:0416
fluorescence microscopy
Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
PMID:14755292
fluorescence imaging
Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
PSI-MI
MI:0417
footprinting
Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
PMID:14755292
methods supporting genetic interactions.
OBSOLETE as too unspecific use Genetic interference instead MI:0254.
PSI-MI
MI:0418
genetic
true
methods supporting genetic interactions.
OBSOLETE as too unspecific use Genetic interference instead MI:0254.
PMID:14755292
Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
GTPase
gtp hydrolisis
PSI-MI
MI:0419
gtpase assay
Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
PMID:14755292
GTPase
gtp hydrolisis
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
homogeneous time-resolved fluorescence
kinase HTRF
kinase htrf
PSI-MI
MI:0420
kinase homogeneous time resolved fluorescence
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
PMID:14987100
homogeneous time-resolved fluorescence
kinase HTRF
kinase htrf
Antibody mediated participant identification.
antibody detection
PSI-MI
MI:0421
identification by antibody
Antibody mediated participant identification.
PMID:14755292
antibody detection
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PSI-MI
MI:0422
immunostaining
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PMID:14755292
Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
in gel kinase assay
PSI-MI
MI:0423
in-gel kinase assay
Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
PMID:14755292
in gel kinase assay
Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
PSI-MI
MI:0424
protein kinase assay
Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
PMID:14755292
Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
kinase spa
PSI-MI
MI:0425
kinase scintillation proximity assay
Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
PMID:14755292
kinase spa
Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
PSI-MI
MI:0426
light microscopy
Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
PMID:14755292
identification by mass spectrometry.
ms participant
PSI-MI
MI:0427
Identification by mass spectrometry
identification by mass spectrometry.
PMID:14755292
ms participant
Methods that provide images of molecules at various resolution depending on the technology used.
microscopy
PSI-MI
MI:0428
imaging technique
Methods that provide images of molecules at various resolution depending on the technology used.
PMID:14755292
microscopy
A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
deletion disrupting interaction
necessary binding site
required to bind
PSI-MI
MI:0429
necessary binding region
A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
PMID:14755292
required to bind
Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
nucl ac uv crosslink
PSI-MI
MI:0430
nucleic acid uv cross-linking assay
Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
PMID:14755292
nucl ac uv crosslink
Deprecated terms.
OBSOLETE term replaced by the default OBO class 'Obsolete'.
PSI-MI
MI:0431
obsolete
true
Deprecated terms.
OBSOLETE term replaced by the default OBO class 'Obsolete'.
PMID:14755292
Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
1 hybrid
one-hybrid
yeast one hybrid
yeast one-hybrid
PSI-MI
MI:0432
one hybrid
Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
PMID:10589421
1 hybrid
one-hybrid
yeast one hybrid
yeast one-hybrid
partial protein sequence identification.
partial id prot seq
PSI-MI
MI:0433
partial identification of protein sequence
partial protein sequence identification.
PMID:14755292
partial id prot seq
Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
PSI-MI
MI:0434
phosphatase assay
Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
PMID:14755292
Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
PSI-MI
MI:0435
protease assay
Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
PMID:14755292
Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
PSI-MI
MI:0436
protein footprinting
Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
PMID:14600024
PMID:14967031
PMID:14987073
Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
bridge assay
protein 3-hybrid
protein tri hybrid
trihybrid
PSI-MI
MI:0437
protein three hybrid
Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
PMID:12052864
PMID:12761205
PMID:12935900
bridge assay
protein 3-hybrid
protein tri hybrid
trihybrid
In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
Three hybrid system
rna 3-hybrid
rna tri hybrid
rna-three hybrid
PSI-MI
MI:0438
rna three hybrid
In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
PMID:12162957
PMID:8972875
Three hybrid system
rna 3-hybrid
rna tri hybrid
rna-three hybrid
A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
RSA
random-spore analysis
rsa
spore germination
PSI-MI
MI:0439
random spore analysis
A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
PMID:14755292
RSA
random-spore analysis
rsa
spore germination
Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
PSI-MI
MI:0440
saturation binding
Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
PMID:14755292
Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
SGA
sga
PSI-MI
MI:0441
synthetic genetic analysis
Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
PMID:14755292
SGA
sga
Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
sufficient binding site
sufficient to bind
PSI-MI
MI:0442
sufficient binding region
Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
PMID:14755292
sufficient to bind
Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.
OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
PSI-MI
MI:0443
ubiquitin binding
true
Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.
OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
PMID:14755292
Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
PSI-MI
MI:0444
database citation
Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
PMID:14755292
Databases acting as a source of literature information.
literature xref
publication xref
PSI-MI
MI:0445
literature database
Databases acting as a source of literature information.
PMID:14755292
literature xref
publication xref
PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central.
http://www.ncbi.nlm.nih.gov/pubmed
http://europepmc.org
id-validation-regexp:
search-url:
PSI-MI
MI:0446
pubmed
PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central.
http://www.ncbi.nlm.nih.gov/pubmed
http://europepmc.org
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://europepmc.org/abstract/MED/${ac}
A database describing a feature on a molecule.
feature xref
PSI-MI
MI:0447
feature database
A database describing a feature on a molecule.
PMID:14755292
feature xref
The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
http://www.ebi.ac.uk/GO
id-validation-regexp:
search-url:
go
PSI-MI
MI:0448
gene ontology
The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
http://www.ebi.ac.uk/GO
PMID:14755292
id-validation-regexp:
GO:[0-9]{7}
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
go
InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.
https://www.ebi.ac.uk/interpro/
id-validation-regexp:
search-url:
InterPro
PSI-MI
MI:0449
interpro
InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.
https://www.ebi.ac.uk/interpro/
PMID:1252001
id-validation-regexp:
IPR[0-9]{6}
search-url:
https://www.ebi.ac.uk/interpro/entry/InterPro/${ac}
InterPro
The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
id-validation-regexp:
CDD
PSI-MI
MI:0450
cdd
The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
PMID:14755292
id-validation-regexp:
[0-9]+
CDD
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
http://www.sanger.ac.uk/Software/Pfam
id-validation-regexp:
Pfam
PSI-MI
MI:0451
pfam
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
http://www.sanger.ac.uk/Software/Pfam
PMID:14755292
id-validation-regexp:
PF[0-9]{5}
Pfam
PIRSF is a classification system based on evolutionary relationship of whole proteins.
http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
id-validation-regexp:
PIRSF
PSI-MI
MI:0452
pirsf
PIRSF is a classification system based on evolutionary relationship of whole proteins.
http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
PMID:14755292
id-validation-regexp:
PIRSF[0-9]{5}
PIRSF
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
id-validation-regexp:
PRINTS
PSI-MI
MI:0453
prints
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
PMID:14755292
id-validation-regexp:
PR[0-9]{6}
PRINTS
The ProDom protein domain database consists of an automatic compilation of homologous domains.
http://protein.toulouse.inra.fr/prodom.html
id-validation-regexp:
ProDom
PSI-MI
MI:0454
prodom
The ProDom protein domain database consists of an automatic compilation of homologous domains.
http://protein.toulouse.inra.fr/prodom.html
PMID:14755292
id-validation-regexp:
PD[0-9]{6}
ProDom
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.
http://us.expasy.org/prosite/
id-validation-regexp:
Prosite
PSI-MI
MI:0455
prosite
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.
http://us.expasy.org/prosite/
PMID:14755292
id-validation-regexp:
PS[0-9]{5}
Prosite
SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
id-validation-regexp:
SCOP superfamily
PSI-MI
MI:0456
scop superfamily
SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
PMID:14755292
id-validation-regexp:
[0-9]+
SCOP superfamily
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.
http://smart.embl-heidelberg.de/
id-validation-regexp:
SMART
PSI-MI
MI:0457
smart
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.
http://smart.embl-heidelberg.de/
PMID:14755292
id-validation-regexp:
SM[0-9]{5}
SMART
TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.
http://www.tigr.org/TIGRFAMs
id-validation-regexp:
TIGRFAMs
PSI-MI
MI:0458
tigrfams
TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.
http://www.tigr.org/TIGRFAMs
PMID:14755292
id-validation-regexp:
TIGR[0-9]+
TIGRFAMs
MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.
http://www.ncbi.nlm.nih.gov/Structure
id-validation-regexp:
MMDB
PSI-MI
MI:0459
mmdb
MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.
http://www.ncbi.nlm.nih.gov/Structure
PMID:14755292
id-validation-regexp:
[0-9]+
MMDB
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
http://www.pdb.org/
id-validation-regexp:
search-url:
PDB
PSI-MI
MI:0460
rcsb pdb
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
http://www.pdb.org/
PMID:14634627
id-validation-regexp:
[0-9][a-zA-Z0-9]{3}
search-url:
http://www.pdb.org/pdb/explore/explore.do?structureId=${ac}
PDB
Databases that contain experimental or predictive molecular interaction data.
interaction xref
PSI-MI
MI:0461
interaction database
Databases that contain experimental or predictive molecular interaction data.
PMID:14755292
interaction xref
The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.
http://www.blueprint.org/bind
id-validation-regexp:
BIND
PSI-MI
MI:0462
bind
The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.
http://www.blueprint.org/bind
PMID:14755292
id-validation-regexp:
[0-9]+
BIND
The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.
http://thebiogrid.org
BioGRID
PSI-MI
MI:0463
biogrid
The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.
http://thebiogrid.org
PMID:21071413
BioGRID
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
http://mips.gsf.de/proj/yeast/CYGD.
http://mips.gsf.de/genre/proj/mpact
id-validation-regexp:
CYGD
CYGD (MIPS)
MIPS
MPact
PSI-MI
MI:0464
cygd
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
http://mips.gsf.de/proj/yeast/CYGD.
http://mips.gsf.de/genre/proj/mpact
PMID:14755292
id-validation-regexp:
[0-9]+|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]
CYGD
CYGD (MIPS)
MIPS
MPact
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.doe-mbi.ucla.edu/
id-validation-regexp:
search-url:
DIP
PSI-MI
MI:0465
dip
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.doe-mbi.ucla.edu/
PMID:14755292
id-validation-regexp:
DIP[:-]?[0-9]+[NE]
search-url:
http://identifiers.org/dip/${ac}
DIP
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.
http://ecocyc.org/
EcoCyc
PSI-MI
MI:0466
ecocyc
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.
http://ecocyc.org/
PMID:14755292
EcoCyc
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.
http://www.reactome.org/
id-validation-regexp:
search-url:
GKB
Genome Knowledge Base
Reactome
PSI-MI
MI:0467
reactome
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.
http://www.reactome.org/
PMID:21067998
id-validation-regexp:
((R-[A-Z]{3}-\d+)|(REACT_\d+))(\.\d+)?$
search-url:
http://www.reactome.org/content/detail/${ac}
GKB
Genome Knowledge Base
Reactome
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
HPRD
PSI-MI
MI:0468
hprd
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
PMID:14755292
HPRD
INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions.
http://www.ebi.ac.uk/intact
id-validation-regexp:
search-url:
IntAct
intact
PSI-MI
MI:0469
intact
INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions.
http://www.ebi.ac.uk/intact
PMID:14681455
PMID:19850723
PMID:22121220
id-validation-regexp:
EBI-[0-9]+|IA:[0-9]+
search-url:
http://www.ebi.ac.uk/intact/query/${ac}
IntAct
intact
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.
http://www.genome.ad.jp/kegg/
id-validation-regexp:
KEGG
PSI-MI
MI:0470
kegg
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.
http://www.genome.ad.jp/kegg/
PMID:14755292
id-validation-regexp:
[a-zA-Z]+:[a-zA-Z]+[0-9]+
KEGG
The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.
http://mint.bio.uniroma2.it
id-validation-regexp:
search-url:
MINT
PSI-MI
MI:0471
mint
The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.
http://mint.bio.uniroma2.it
PMID:14755292
id-validation-regexp:
MINT-[0-9]+
search-url:
https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac}
MINT
The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
http://www.ebi.ac.uk/pdbe/
id-validation-regexp:
search-url:
PQS
e-MSD
PSI-MI
MSD
MI:0472
pdbe
The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
http://www.ebi.ac.uk/pdbe/
PMID:16381867
id-validation-regexp:
[0-9][a-zA-Z0-9]{3}
search-url:
http://www.ebi.ac.uk/pdbe/entry/pdb/${ac}
PQS
Database of molecules participating in molecular interactions.
participant xref
PSI-MI
MI:0473
participant database
Database of molecules participating in molecular interactions.
PMID:14755292
participant xref
A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).
http://www.ebi.ac.uk/chebi/
id-validation-regexp:
search-url:
ChEBI
PSI-MI
MI:0474
chebi
A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).
http://www.ebi.ac.uk/chebi/
PMID:14755292
id-validation-regexp:
CHEBI:[0-9]+
search-url:
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=${ac}
ChEBI
DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.
http://www.ebi.ac.uk/embl/Contact/collaboration
id-validation-regexp:
search-url:
DDBJ
DDBJ/EMBL/GenBank
EMBL
GenBank
PSI-MI
MI:0475
ddbj/embl/genbank
DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.
http://www.ebi.ac.uk/embl/Contact/collaboration
PMID:14755292
id-validation-regexp:
[A-Z][0-9]{5}|[A-Z][0-9]{5}\.[0-9]+|[A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.[0-9]+|[A-Z]{4}[0-9]{8}|[A-Z]{4}[0-9]{8}\.[0-9]+
search-url:
http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac}
DDBJ
DDBJ/EMBL/GenBank
EMBL
GenBank
Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.
http://www.ensembl.org
id-validation-regexp:
search-url:
Ensembl
PSI-MI
MI:0476
ensembl
Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.
http://www.ensembl.org
PMID:15078858
id-validation-regexp:
ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]
search-url:
http://www.ensembl.org/Multi/Search/Results?q=${ac}
Ensembl
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
http://www.ncbi.nlm.nih.gov/LocusLink/
id-validation-regexp:
Entrez gene/locuslink
entrezgene/locuslink
PSI-MI
MI:0477
entrez gene/locuslink
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
http://www.ncbi.nlm.nih.gov/LocusLink/
PMID:14755292
id-validation-regexp:
[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+
Entrez gene/locuslink
entrezgene/locuslink
FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.
http://flybase.org
id-validation-regexp:
search-url:
FlyBase
PSI-MI
MI:0478
flybase
FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.
http://flybase.org
PMID:14755292
id-validation-regexp:
FB[a-z]{2}[0-9]{7}
search-url:
http://flybase.org/reports/${ac}
FlyBase
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
http://www.informatics.jax.org/
id-validation-regexp:
MGD/MGI
PSI-MI
MI:0479
mgd/mgi
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
http://www.informatics.jax.org/
PMID:14755292
id-validation-regexp:
MGI:[0-9]+
MGD/MGI
Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
id-validation-regexp:
search-url:
OMIM
PSI-MI
MI:0480
omim
Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://www.omim.org/entry/${ac}
OMIM
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.
http://www.ncbi.nlm.nih.gov/RefSeq/
id-validation-regexp:
Refseq
PSI-MI
MI:0481
refseq
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.
http://www.ncbi.nlm.nih.gov/RefSeq/
PMID:14755292
id-validation-regexp:
[XNZ][A-Z]_[0-9]+|[0-9]+|[XNZ][A-Z]_[0-9]+\.[0-9]+
Refseq
Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/
id-validation-regexp:
rfam
PSI-MI
MI:0482
rfam
Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/
PMID:14755292
id-validation-regexp:
RF[0-9]{5}
rfam
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.
http://rgd.mcw.edu/
id-validation-regexp:
RGD
PSI-MI
MI:0483
rgd
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.
http://rgd.mcw.edu/
PMID:14755292
id-validation-regexp:
[0-9]+
RGD
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
http://www.yeastgenome.org/
id-validation-regexp:
search-url:
SGD
Saccharomyces Genome Database
PSI-MI
MI:0484
sgd
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
http://www.yeastgenome.org/
PMID:14755292
id-validation-regexp:
S[0-9]{9}
search-url:
http://www.yeastgenome.org/locus/${ac}/overview
SGD
Saccharomyces Genome Database
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.
http://www.ebi.ac.uk/uniparc/
id-validation-regexp:
search-url:
UniParc
PSI-MI
MI:0485
uniparc
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.
http://www.ebi.ac.uk/uniparc/
PMID:14681372
id-validation-regexp:
UPI[A-F0-9]{10}
search-url:
https://www.uniprot.org/uniparc/${ac}/entry
UniParc
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
http://www.uniprot.org
id-validation-regexp:
search-url:
UniProtKB
uniprotkb
PSI-MI
MI:0486
uniprot knowledge base
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
http://www.uniprot.org
PMID:14681372
id-validation-regexp:
(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
search-url:
https://www.uniprot.org/uniprotkb/${ac}/entry
UniProtKB
uniprotkb
WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.
http://www.wormbase.org/
id-validation-regexp:
WormBase
PSI-MI
MI:0487
wormbase
WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.
http://www.wormbase.org/
PMID:14755292
id-validation-regexp:
WBGene[0-9]{8}
WormBase
PSI-MI.
id-validation-regexp:
search-url:
PSI-MI
PSI-MI
MI:0488
psi-mi
PSI-MI.
PMID:14755292
id-validation-regexp:
MI:[0-9]{4}
search-url:
http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=${ac}
PSI-MI
Database that originally provided the interaction record for exchange purposes.
PSI-MI
MI:0489
source database
Database that originally provided the interaction record for exchange purposes.
PMID:14755292
Describes the location of the experiment.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0490
experiment condition
true
Describes the location of the experiment.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Results generated by predictive bioinformatics approaches rather than experimental data.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Predictive
PSI-MI
MI:0491
in silico
true
Results generated by predictive bioinformatics approaches rather than experimental data.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Predictive
Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0492
in vitro
true
Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0493
in vivo
true
Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Literally, in place i.e. the protein is in its natural environment during the experiment.
OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0494
in situ
true
Literally, in place i.e. the protein is in its natural environment during the experiment.
OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Role played by the participant within the experiment.
PSI-MI
MI:0495
experimental role
Role played by the participant within the experiment.
PMID:14755292
Molecule experimentally treated to capture its interacting partners.
PSI-MI
MI:0496
bait
Molecule experimentally treated to capture its interacting partners.
PMID:14755292
Molecule role in an experimental setting that does not have an embedded asymmetry.
PSI-MI
MI:0497
neutral component
Molecule role in an experimental setting that does not have an embedded asymmetry.
PMID:14755292
Molecule experimentally identified as being captured by a given bait.
PSI-MI
MI:0498
prey
Molecule experimentally identified as being captured by a given bait.
PMID:14755292
Role not specified or not applicable to the data.
PSI-MI
MI:0499
unspecified role
Role not specified or not applicable to the data.
PMID:14755292
Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
PSI-MI
MI:0500
biological role
Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
PMID:14755292
Molecule catalyzing a modification on its interacting partner.
PSI-MI
MI:0501
enzyme
Molecule catalyzing a modification on its interacting partner.
PMID:14755292
Molecule that is the target of its binding partner catalytic activity.
substrate
PSI-MI
MI:0502
enzyme target
Molecule that is the target of its binding partner catalytic activity.
PMID:14755292
substrate
Molecule that makes intramolecular interactions.
PSI-MI
MI:0503
self
Molecule that makes intramolecular interactions.
PMID:14755292
The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
PSI-MI
MI:0505
experimental feature
The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
PMID:14755292
A molecule is estimated to be expressed at higher levels than in physiological condition.
over-expressed
PSI-MI
MI:0506
over expressed level
A molecule is estimated to be expressed at higher levels than in physiological condition.
PMID:14755292
over-expressed
Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
PSI-MI
MI:0507
tag
Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
PMID:14755292
Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
radiolabeled acetate
PSI-MI
MI:0508
deacetylase radiometric assay
Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
PMID:14755292
radiolabeled acetate
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase.
homogeneous time-resolved fluorescence
phosphatase HTRF
phosphatase htrf
PSI-MI
MI:0509
phosphatase homogeneous time resolved fluorescence
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase.
PMID:14987100
homogeneous time-resolved fluorescence
phosphatase HTRF
phosphatase htrf
Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates.
homogeneous time-resolved fluorescence
htrf
PSI-MI
MI:0510
homogeneous time resolved fluorescence
Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates.
PMID:14987100
homogeneous time-resolved fluorescence
htrf
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease.
Protease HTRF
protease htrf
PSI-MI
MI:0511
protease homogeneous time resolved fluorescence
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease.
PMID:14987100
Protease HTRF
protease htrf
Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity.
PSI-MI
MI:0512
zymography
Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity.
PMID:2071592
Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen.
PSI-MI
MI:0513
collagen film assay
Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen.
PMID:6247938
Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography.
in gel phosphatase
PSI-MI
MI:0514
in gel phosphatase assay
Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography.
PMID:14755292
in gel phosphatase
Measures the catalysis of the transfer of a methyl group to an acceptor molecule.
methyltransferase as
PSI-MI
MI:0515
methyltransferase assay
Measures the catalysis of the transfer of a methyl group to an acceptor molecule.
PMID:14755292
methyltransferase as
Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor.
radiolabeled methyl
PSI-MI
MI:0516
methyltransferase radiometric assay
Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor.
PMID:14755292
radiolabeled methyl
A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
radiolabeled
radiolabelled
PSI-MI
MI:0517
radiolabel
A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
PMID:14755292
radiolabeled
radiolabelled
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
DYKDDDDKV epitope tag
FLAG
FLAG-tagged
PSI-MI
MI:0518
flag tag
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
PMID:14755292
DYKDDDDKV epitope tag
FLAG
FLAG-tagged
The protein is expressed and purified as a fusion to the glutathione S-tranferase protein.
glutathione S-tranferase tag
gst tag
PSI-MI
MI:0519
glutathione s tranferase tag
The protein is expressed and purified as a fusion to the glutathione S-tranferase protein.
PMID:14755292
glutathione S-tranferase tag
gst tag
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available.
YPYDVPDYA epitope tag
PSI-MI
MI:0520
ha tag
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available.
PMID:14755292
YPYDVPDYA epitope tag
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
6-His-tag
Hexa-His-tag
Histidine-tag
PSI-MI
MI:0521
his tag
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
PMID:14755292
6-His-tag
Hexa-His-tag
Histidine-tag
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
EUKLISEED epitope tag
PSI-MI
MI:0522
myc tag
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
PMID:14755292
EUKLISEED epitope tag
The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available.
MASMTGGQQMG epitope tag
PSI-MI
MI:0523
t7 tag
The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available.
PMID:14755292
MASMTGGQQMG epitope tag
Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein.
CBP-ProtA tagged
tap tagged
PSI-MI
MI:0524
calmodulin binding peptide plus protein a tag
Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein.
PMID:14755292
CBP-ProtA tagged
tap tagged
The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available.
GKPIPNPLLGLDST epitope tag
PSI-MI
MI:0525
v5 tag
The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available.
PMID:14755292
GKPIPNPLLGLDST epitope tag
Residue modification.
OBSOLETE remap to MOD:00723.
acetyllysine
PSI-MI
MI:0526
n-acetyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00723.
PMID:14755292
RESID:AA0048
RESID:AA0055
acetyllysine
Residue modification.
OBSOLETE remap to MOD:00752.
adp-ribosylated
PSI-MI
MI:0527
adp ribosylated residue
true
Residue modification.
OBSOLETE remap to MOD:00752.
PMID:14755292
adp-ribosylated
Residue modification.
OBSOLETE remap to MOD:00177.
(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid
N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine
N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adp-ribosylarginine
omega-N-(ADP-ribosyl)-L-arginine
PSI-MI
MI:0528
omega-n-(adp-ribosyl)-arginine
true
Residue modification.
OBSOLETE remap to MOD:00177.
PMID:14755292
RESID:AA0168
(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid
N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine
N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adp-ribosylarginine
omega-N-(ADP-ribosyl)-L-arginine
Residue modification.
OBSOLETE remap to MOD:00178.
(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid
S-(ADP-ribosyl)-L-cysteine
S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adp-ribosylcysteine
PSI-MI
MI:0529
s-(adp-ribosyl)-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00178.
PMID:14755292
RESID:AA0169
(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid
S-(ADP-ribosyl)-L-cysteine
S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adp-ribosylcysteine
Residue modification.
OBSOLETE remap to MOD:00300.
(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid
L-glutamyl-5-poly(ADP-ribose)
L-isoglutamyl-poly(ADP-ribose)
adp-ribosylglutamate
PSI-MI
MI:0530
glutamyl-5-poly(adp-ribose)
true
Residue modification.
OBSOLETE remap to MOD:00300.
PMID:14755292
RESID:AA0295
(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid
L-glutamyl-5-poly(ADP-ribose)
L-isoglutamyl-poly(ADP-ribose)
adp-ribosylglutamate
Residue modification.
OBSOLETE remap to MOD:00242.
(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula
O-(ADP-ribosyl)-L-serine
O3-(ADP-ribosyl)-L-serine
O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine
O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adp-ribosylserine
PSI-MI
MI:0531
o-(adp-ribosyl)-serine
true
Residue modification.
OBSOLETE remap to MOD:00242.
PMID:14755292
RESID:AA0237
(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula
O-(ADP-ribosyl)-L-serine
O3-(ADP-ribosyl)-L-serine
O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine
O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adp-ribosylserine
Residue modification.
OBSOLETE remap to MOD:00236.
(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid
N4-(ADP-ribosyl)-L-asparagine
N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine
N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adpribosylasparagine
PSI-MI
MI:0532
n4-(adp-ribosyl)-asparagine
true
Residue modification.
OBSOLETE remap to MOD:00236.
PMID:14755292
RESID:AA0231
(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid
N4-(ADP-ribosyl)-L-asparagine
N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine
N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
adpribosylasparagine
Residue modification.
OBSOLETE remap to MOD:00693.
PSI-MI
MI:0533
glycosylated residue
true
Residue modification.
OBSOLETE remap to MOD:00693.
PMID:14755292
Residue modification.
OBSOLETE remap to MOD:00131.
S-glycosyl-L-cysteine
PSI-MI
MI:0534
glycosyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00131.
PMID:14755292
RESID:AA0122
S-glycosyl-L-cysteine
Residue modification.
OBSOLETE remap to MOD:00163.
O-glycosyl-L-serine
O3-glycosyl-L-serine
PSI-MI
MI:0535
glycosyl-serine
true
Residue modification.
OBSOLETE remap to MOD:00163.
PMID:14755292
RESID:AA0154
O-glycosyl-L-serine
O3-glycosyl-L-serine
Residue modification.
OBSOLETE remap to MOD:00164.
O-glycosyl-L-threonine
O3-glycosyl-L-threonine
PSI-MI
MI:0536
glycosyl-threonine
true
Residue modification.
OBSOLETE remap to MOD:00164.
PMID:14755292
RESID:AA0155
O-glycosyl-L-threonine
O3-glycosyl-L-threonine
Residue modification.
OBSOLETE remap to MOD:00332.
glycosylarginine
omega-N-glycosyl-L-arginine
PSI-MI
MI:0537
omega-n-glycosyl-arginine
true
Residue modification.
OBSOLETE remap to MOD:00332.
PMID:14755292
RESID:AA0327
glycosylarginine
omega-N-glycosyl-L-arginine
Residue modification.
OBSOLETE remap to MOD:00160.
N4-glycosyl-L-asparagine
glycosylasparagine
PSI-MI
MI:0538
n4-glycosyl-asparagine
true
Residue modification.
OBSOLETE remap to MOD:00160.
PMID:14755292
RESID:AA0151
N4-glycosyl-L-asparagine
glycosylasparagine
Residue modification.
OBSOLETE remap to MOD:00818.
PSI-MI
MI:0539
gpi anchor residue
true
Residue modification.
OBSOLETE remap to MOD:00818.
PMID:14755292
Residue modification.
OBSOLETE remap to MOD:00172.
N-alanyl-glycosylphosphatidylinositolethanolamine
gpi-alanine
PSI-MI
MI:0540
gpi-anchor amidated alanine
true
Residue modification.
OBSOLETE remap to MOD:00172.
PMID:14755292
RESID:AA0163
N-alanyl-glycosylphosphatidylinositolethanolamine
gpi-alanine
Residue modification.
OBSOLETE remap to MOD:00167.
N-asparaginyl-glycosylphosphatidylinositolethanolamine
gpi-asparagine
PSI-MI
MI:0541
gpi-anchor amidated asparagine
true
Residue modification.
OBSOLETE remap to MOD:00167.
PMID:14755292
RESID:AA0158
N-asparaginyl-glycosylphosphatidylinositolethanolamine
gpi-asparagine
Residue modification.
OBSOLETE remap to MOD:00168.
N-aspartyl-glycosylphosphatidylinositolethanolamine
gpi-aspartate
PSI-MI
MI:0542
gpi-anchor amidated aspartate
true
Residue modification.
OBSOLETE remap to MOD:00168.
PMID:14755292
RESID:AA0159
N-aspartyl-glycosylphosphatidylinositolethanolamine
gpi-aspartate
Residue modification.
OBSOLETE remap to MOD:00169.
N-cysteinyl-glycosylphosphatidylinositolethanolamine
gpi-cysteine
PSI-MI
MI:0543
gpi-anchor amidated cysteine
true
Residue modification.
OBSOLETE remap to MOD:00169.
PMID:14755292
RESID:AA0160
N-cysteinyl-glycosylphosphatidylinositolethanolamine
gpi-cysteine
Residue modification.
OBSOLETE remap to MOD:00170.
N-glycyl-glycosylphosphatidylinositolethanolamine
gpi-glycine
PSI-MI
MI:0544
gpi-anchor amidated glycine
true
Residue modification.
OBSOLETE remap to MOD:00170.
PMID:14755292
RESID:AA0161
N-glycyl-glycosylphosphatidylinositolethanolamine
gpi-glycine
Residue modification.
OBSOLETE remap to MOD:00171.
N-seryl-glycosylphosphatidylinositolethanolamine
gpi-serine
PSI-MI
MI:0545
gpi-anchor amidated serine
true
Residue modification.
OBSOLETE remap to MOD:00171.
PMID:14755292
RESID:AA0162
N-seryl-glycosylphosphatidylinositolethanolamine
gpi-serine
Residue modification.
OBSOLETE remap to MOD:00173.
N-threonyl-glycosylphosphatidylinositolethanolamine
gpi-threonine
PSI-MI
MI:0546
gpi-anchor amidated threonine
true
Residue modification.
OBSOLETE remap to MOD:00173.
PMID:14755292
RESID:AA0164
N-threonyl-glycosylphosphatidylinositolethanolamine
gpi-threonine
Residue modification.
OBSOLETE remap to MOD:01110.
prenylcysteine
PSI-MI
MI:0547
s-prenyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:01110.
PMID:14755292
prenylcysteine
Residue modification.
OBSOLETE remap to MOD:00663.
methylatedlysine
PSI-MI
MI:0548
methylated-lysine
true
Residue modification.
OBSOLETE remap to MOD:00663.
PMID:14755292
RESID:AA0074
RESID:AA0075
RESID:AA0076
methylatedlysine
Artificial residue modification enabling studies of cysteine binding status.
OBSOLETE remap to MOD:00660.
PSI-MI
MI:0549
alkylated cysteine
true
Artificial residue modification enabling studies of cysteine binding status.
OBSOLETE remap to MOD:00660.
PMID:15325307
Residue modification.
OBSOLETE remap to MOD:00041.
(S)-3-amino-1,1,3-propanetricarboxylic acid
1-carboxyglutamic acid [misnomer]
4-carboxyglutamic acid
L-gamma-carboxyglutamic acid
carboxyglutamic acid
PSI-MI
MI:0550
gamma-carboxyglutamic acid
true
Residue modification.
OBSOLETE remap to MOD:00041.
PMID:14755292
RESID:AA0032
(S)-3-amino-1,1,3-propanetricarboxylic acid
1-carboxyglutamic acid [misnomer]
4-carboxyglutamic acid
L-gamma-carboxyglutamic acid
carboxyglutamic acid
Residue modification.
OBSOLETE remap to MOD:00461.
nitrated tyrosine
PSI-MI
MI:0551
nitro-tyrosine
true
Residue modification.
OBSOLETE remap to MOD:00461.
PMID:15657065
PMID:9636206
nitrated tyrosine
Residue modification.
OBSOLETE remap to MOD:00235.
(R)-2-amino-3-nitrososulfanyl-propanoic acid
L-cysteine nitrite ester
S-nitrosocysteine
S-nitrosyl-L-cysteine
nitrosylcysteine
PSI-MI
MI:0552
s-nitrosyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00235.
PMID:14755292
RESID:AA0230
(R)-2-amino-3-nitrososulfanyl-propanoic acid
L-cysteine nitrite ester
S-nitrosocysteine
S-nitrosyl-L-cysteine
nitrosylcysteine
Residue modification.
OBSOLETE remap to MOD:00181.
(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate
O4'-sulfo-L-tyrosine
O4-sulfotyrosine
sulfotyrosine
tyrosine sulfate
PSI-MI
MI:0553
o4'-sulfo-tyrosine
true
Residue modification.
OBSOLETE remap to MOD:00181.
PMID:14755292
RESID:AA0172
(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate
O4'-sulfo-L-tyrosine
O4-sulfotyrosine
sulfotyrosine
tyrosine sulfate
Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein.
OBSOLETE remap to MOD:01149.
(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid
N6-glycyl-L-lysine
N6-glycyllysine
PSI-MI
MI:0554
sumoylated lysine
true
Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein.
OBSOLETE remap to MOD:01149.
PMID:12612601
RESID:AA0125
(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid
N6-glycyl-L-lysine
N6-glycyllysine
Residue modification.
OBSOLETE remap to MOD:00890.
phosphoshistidine
PSI-MI
MI:0555
phospho-histidine
true
Residue modification.
OBSOLETE remap to MOD:00890.
PMID:14755292
RESID:AA0035
RESID:AA0036
phosphoshistidine
Gln-Lys cross-link catalyzed by a transglutaminase.
transglutamination
PSI-MI
MI:0556
transglutamination reaction
Gln-Lys cross-link catalyzed by a transglutaminase.
PMID:14755292
RESID:AA0124
transglutamination
Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
adp ribosylation
PSI-MI
MI:0557
adp ribosylation reaction
Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
GO:0006471
PMID:14755292
RESID:AA0168
RESID:AA0169
RESID:AA0231
RESID:AA0237
RESID:AA0295
adp ribosylation
Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
deglycosylation
PSI-MI
MI:0558
deglycosylation reaction
Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
GO:0006517
PMID:15670854
deglycosylation
The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
glycosylation
PSI-MI
MI:0559
glycosylation reaction
The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
GO:0043413
PMID:14755292
RESID:AA0122
RESID:AA0151
RESID:AA0154
RESID:AA0155
RESID:AA0327
glycosylation
Residue modification.
OBSOLETE remap to MOD:00438.
myristoylated aa
PSI-MI
MI:0560
myristoylated residue
true
Residue modification.
OBSOLETE remap to MOD:00438.
PMID:14755292
myristoylated aa
Residue modification.
OBSOLETE remap to MOD:00440.
palmitoylated aa
PSI-MI
MI:0561
palmitoylated residue
true
Residue modification.
OBSOLETE remap to MOD:00440.
PMID:14755292
palmitoylated aa
Residue modification.
OBSOLETE remap to MOD:00665.
PSI-MI
MI:0562
methylated alanine
true
Residue modification.
OBSOLETE remap to MOD:00665.
PMID:14755292
RESID:AA0061
RESID:AA0062
Residue modification.
OBSOLETE remap to MOD:00658.
PSI-MI
MI:0563
methylated arginine
true
Residue modification.
OBSOLETE remap to MOD:00658.
PMID:14755292
RESID:AA0068
RESID:AA0069
Residue modification.
OBSOLETE remap to MOD:00078.
(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid
NG-methylarginine;
methylarginine
omega-N-methyl-L-arginine
PSI-MI
MI:0564
omega-n-methyl-arginine
true
Residue modification.
OBSOLETE remap to MOD:00078.
PMID:14755292
RESID:AA0069
(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid
NG-methylarginine;
methylarginine
omega-N-methyl-L-arginine
Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family.
OBSOLETE remap to MOD:01150.
PSI-MI
MI:0565
neddylated lysine
true
Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family.
OBSOLETE remap to MOD:01150.
PMID:111
Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
sumoylation
PSI-MI
MI:0566
sumoylation reaction
Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
GO:0016925
PMID:15985640
sumoylation
Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
neddylation
PSI-MI
MI:0567
neddylation reaction
Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
GO:0045116
PMID:16127432
neddylation
Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
desumoylation
PSI-MI
MI:0568
desumoylation reaction
Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
GO:0016926
PMID:15985640
desumoylation
Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
deneddylation
PSI-MI
MI:0569
deneddylation reaction
Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
GO:0000338
PMID:16127432
deneddylation
Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
PSI-MI
MI:0570
protein cleavage
Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
PMID:14744292
Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
PSI-MI
MI:0571
mrna cleavage
Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
GO:0006379
PMID:14681407
Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
PSI-MI
MI:0572
dna cleavage
Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
PMID:14755292
Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction)..
mutation disrupting
PSI-MI
MI:0573
mutation disrupting interaction
Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction)..
PMID:14755292
mutation disrupting
Identifier of a publication prior to pubmed indexing.
id-validation-regexp:
search-url:
doi
PSI-MI
MI:0574
digital object identifier
Identifier of a publication prior to pubmed indexing.
PMID:14755292
id-validation-regexp:
\d+.\d+/[a-zA-Z0-9\.\:]+
search-url:
http://dx.doi.org/${ac}
doi
Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all.
http://www.signaling-gateway.org
id-validation-regexp:
search-url:
AfCS
afcs
PSI-MI
MI:0575
alliance for cellular signaling
Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all.
http://www.signaling-gateway.org
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac}
AfCS
afcs
Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact.
PSI-MI
MI:0576
structural proximity
Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact.
PMID:15353450
Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules.
feature struct pred
PSI-MI
MI:0577
feature prediction from structure
Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules.
PMID:14755292
feature struct pred
The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin.
maltose binding protein tag
mbp tag
PSI-MI
MI:0578
maltose binding protein tag
The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin.
PMID:14755292
maltose binding protein tag
mbp tag
Any molecule that is able to transfer an electron to another chemical species.
PSI-MI
MI:0579
electron donor
Any molecule that is able to transfer an electron to another chemical species.
PMID:14755292
Molecule to which an electron may be transferred from an electron donor.
PSI-MI
MI:0580
electron acceptor
Molecule to which an electron may be transferred from an electron donor.
PMID:14755292
A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation.
suppressor
PSI-MI
MI:0581
suppressor gene
A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation.
PMID:14755292
suppressor
A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation.
suppressed
PSI-MI
MI:0582
suppressed gene
A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation.
PMID:14755292
suppressed
Fluorophore which emits electromagnetic radiation of given wavelength.
PSI-MI
MI:0583
fluorescence donor
Fluorophore which emits electromagnetic radiation of given wavelength.
PMID:14755292
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence.
fluorescence accept
PSI-MI
MI:0584
fluorescence acceptor
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence.
PMID:14755292
fluorescence accept
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at.
http://www.ebi.ac.uk/intenz
id-validation-regexp:
search-url:
PSI-MI
MI:0585
intenz
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at.
http://www.ebi.ac.uk/intenz
PMID:14681451
id-validation-regexp:
[0-6]{1}\.(\d+|-)\.(\d+|-)\.(\d+|-)
search-url:
http://www.ebi.ac.uk/intenz/query?cmd=Search&q=${ac}&t=exact&fields=ec
Molecule inhibiting an interaction by interacting with one or more of its participants.
PSI-MI
MI:0586
inhibitor
Molecule inhibiting an interaction by interacting with one or more of its participants.
PMID:14755292
Molecule being identified as target of an inhibitor.
OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role.
PSI-MI
MI:0587
inhibited
true
Molecule being identified as target of an inhibitor.
OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role.
PMID:14755292
Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey.
3 hybrid
3-hybrid
tri hybrid
tri-hybrid assay
PSI-MI
MI:0588
three hybrid
Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey.
PMID:14755292
3 hybrid
3-hybrid
tri hybrid
tri-hybrid assay
Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery.
in vitro translated
PSI-MI
MI:0589
in vitro translated protein
Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery.
PMID:14755292
in vitro translated
Collection of topics describing the free text stored as an attribute value.
CvTopic
PSI-MI
MI:0590
attribute name
Collection of topics describing the free text stored as an attribute value.
PMID:14755292
CvTopic
The experimental condition text description, should contain information about the organisms hosting the interaction.
experiment descripti
PSI-MI
MI:0591
experiment description
The experimental condition text description, should contain information about the organisms hosting the interaction.
PMID:14755292
experiment descripti
Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at.
http://www.sanger.ac.uk/Software/Pfam/iPfam/
PSI-MI
MI:0592
ipfam
Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at.
http://www.sanger.ac.uk/Software/Pfam/iPfam/
PMID:15353450
Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'.
PSI-MI
MI:0593
translocation
Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'.
PMID:14681407
Xref pointing to a GO compartment term describing the start location of a migrating molecule.
PSI-MI
MI:0594
translocation start
Xref pointing to a GO compartment term describing the start location of a migrating molecule.
PMID:14681407
Xref pointing to a GO compartment term describing the end location of a migrating molecule.
PSI-MI
MI:0595
translocation end
Xref pointing to a GO compartment term describing the end location of a migrating molecule.
PMID:14755292
Free text description of all the tags and artificial process undergone by a molecule during an experiment.
experimental form de
PSI-MI
MI:0596
experimental form description
Free text description of all the tags and artificial process undergone by a molecule during an experiment.
PMID:14755292
experimental form de
The feature text description may include information about the feature detection method.
PSI-MI
MI:0597
feature description
The feature text description may include information about the feature detection method.
PMID:14755292
The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction).
PSI-MI
MI:0598
feature constraint
The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction).
PMID:14755292
Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found.
PSI-MI
MI:0599
figure legend
Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found.
PMID:14755292
Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description.
nutrition synt letal
PSI-MI
MI:0600
conditional synthetic lethal nutrition-sensitivity
true
Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description.
PMID:15608217
nutrition synt letal
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data.
id-validation-regexp:
so
PSI-MI
MI:0601
sequence ontology
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data.
PMID:15892872
id-validation-regexp:
SO:[0-9]{7}
so
Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
chemical footprint
PSI-MI
MI:0602
chemical footprinting
Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
PMID:8238889
chemical footprint
Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction.
dms footprinting
PSI-MI
MI:0603
dimethylsulphate footprinting
Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction.
PMID:8238889
dms footprinting
Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control.
k-mn-04 footprinting
PSI-MI
MI:0604
potassium permanganate footprinting
Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control.
PMID:8238889
k-mn-04 footprinting
Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
enzymatic footprint
PSI-MI
MI:0605
enzymatic footprinting
Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
PMID:8238889
enzymatic footprint
Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA.
dnase 1 footprinting
PSI-MI
DNase I protection
MI:0606
DNase I footprinting
Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA.
PMID:8238889
dnase 1 footprinting
These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome.
snRNA
snrna
PSI-MI
MI:0607
small nuclear rna
These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome.
PMID:14755292
snRNA
snrna
RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes.
rRNA
rrna
PSI-MI
MI:0608
ribosomal rna
RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes.
PMID:14755292
rRNA
rrna
The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA.
snoRNA
snorna
PSI-MI
MI:0609
small nucleolar rna
The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA.
PMID:14755292
snoRNA
snorna
Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression.
dicer RNA
micro RNA
siRNA
sirna
PSI-MI
MI:0610
small interfering rna
Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression.
PMID:10542148
dicer RNA
micro RNA
siRNA
sirna
Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
srpRNA
srprna
PSI-MI
MI:0611
signal recognition particle rna
Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
PMID:14755292
srpRNA
srprna
Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant.
PSI-MI
MI:0612
comment
Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant.
PMID:14755292
Biological function of a participant or of an interaction.
PSI-MI
MI:0613
function
Biological function of a participant or of an interaction.
PMID:14755292
URL/Web address describing an experiment, an interaction, a Cv term or an organism.
PSI-MI
MI:0614
url
URL/Web address describing an experiment, an interaction, a Cv term or an organism.
PMID:14755292
Search engine URL associated to Cv Database terms.
PSI-MI
MI:0615
search-url
Search engine URL associated to Cv Database terms.
PMID:14755292
Example generally associated to Cv terms. Test.
PSI-MI
MI:0616
example
Example generally associated to Cv terms. Test.
PMID:14755292
The interaction has a known or demonstrated disease association.
PSI-MI
MI:0617
disease
The interaction has a known or demonstrated disease association.
PMID:14755292
Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant.
PSI-MI
MI:0618
caution
Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant.
PMID:14755292
Refers to the metabolic or signalling pathway involving an interaction or a complex.
PSI-MI
MI:0619
pathway
Refers to the metabolic or signalling pathway involving an interaction or a complex.
PMID:14755292
Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms.
PSI-MI
MI:0620
search-url-ascii
Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms.
PMID:14755292
Confidence classification assigned by the author of the publication to a specific interaction.
PSI-MI
MI:0621
author-confidence
Confidence classification assigned by the author of the publication to a specific interaction.
PMID:14755292
Description of confidence assessment method generally associated to the experiment.
PSI-MI
MI:0622
confidence-mapping
Description of confidence assessment method generally associated to the experiment.
PMID:14755292
The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors.
PSI-MI
MI:0623
inhibition
The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors.
PMID:14755292
Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule.
PSI-MI
MI:0624
stimulant
Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule.
PMID:14755292
Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors.
PSI-MI
MI:0625
agonist
Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors.
PMID:14755292
Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors.
PSI-MI
MI:0626
antagonist
Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors.
PMID:14755292
Modifications of the standard experimental method described in the CV.
exp-modification
PSI-MI
MI:0627
experiment modification
Modifications of the standard experimental method described in the CV.
PMID:14755292
exp-modification
Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database.
id-validation-regexp
PSI-MI
MI:0628
validation regular expression
Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database.
PMID:14755292
id-validation-regexp
Information on the complex being annotated. Attribute generally associated to an interaction.
PSI-MI
MI:0629
complex-properties
Information on the complex being annotated. Attribute generally associated to an interaction.
PMID:14755292
Comments on the 3D structure. This attribute is generally associated to an interaction.
PSI-MI
MI:0630
3d-structure
Comments on the 3D structure. This attribute is generally associated to an interaction.
PMID:14755292
Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction.
PSI-MI
MI:0631
3d-r-factors
Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction.
PMID:14755292
Resolution of the 3D structure. This attribute is generally associated to an interaction.
PSI-MI
MI:0632
3d-resolution
Resolution of the 3D structure. This attribute is generally associated to an interaction.
PMID:14755292
Information about how the data was processed. This attribute is used mainly for large scale experiment.
PSI-MI
MI:0633
data-processing
Information about how the data was processed. This attribute is used mainly for large scale experiment.
PMID:14755292
E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment.
PSI-MI
MI:0634
contact-email
E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment.
PMID:14755292
Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment.
PSI-MI
MI:0635
contact-comment
Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment.
PMID:14755292
List of authors associated to a publication. This attribute is generally associated to an experiment.
PSI-MI
MI:0636
author-list
List of authors associated to a publication. This attribute is generally associated to an experiment.
PMID:14755292
Participant isoform's comment. This attribute can be attached to interactions or participants.
PSI-MI
MI:0637
isoform-comment
Participant isoform's comment. This attribute can be attached to interactions or participants.
PMID:14755292
Post translational modification required for an interaction to occur.
prerequisite ptm
prerequisite-ptm
required ptm
required-ptm
PSI-MI
MI:0638
prerequisite-ptm
Post translational modification required for an interaction to occur.
PMID:14755292
prerequisite ptm
prerequisite-ptm
required ptm
required-ptm
Post translational modification occurs subsequently to an interaction.
resulting ptm
resulting-ptm
PSI-MI
MI:0639
resulting-ptm
Post translational modification occurs subsequently to an interaction.
PMID:14755292
resulting ptm
resulting-ptm
Parameter for enzymatic or binding kinetic studies.
PSI-MI
MI:0640
parameter type
Parameter for enzymatic or binding kinetic studies.
PMID:14755292
Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
IC50
PSI-MI
MI:0641
ic50
Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
PMID:14755292
IC50
Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
EC50
PSI-MI
MI:0642
ec50
Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
PMID:14755292
EC50
Equilibrium constant for dissociation of an inhibitor. Unit Molar.
Ki
PSI-MI
MI:0643
ki
Equilibrium constant for dissociation of an inhibitor. Unit Molar.
PMID:14755292
Ki
Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar.
Km
PSI-MI
MI:0644
km
Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar.
PMID:14755292
Km
The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1.
turnover number
PSI-MI
MI:0645
kcat
The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1.
PMID:14755292
turnover number
The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1).
Kd
PSI-MI
MI:0646
Kd
The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1).
PMID:14755292
Kd
Controlled vocabulary for kinetic constant units.
PSI-MI
MI:0647
parameter unit
Controlled vocabulary for kinetic constant units.
PMID:14755292
Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles).
M
PSI-MI
MI:0648
molar
Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles).
PMID:14755292
M
The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant.
s
sec
PSI-MI
MI:0649
second
The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant.
PMID:14755292
s
sec
10E-3 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
mM
PSI-MI
MI:0650
millimolar
true
10E-3 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
PMID:14755292
mM
10E-6 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
uM
PSI-MI
MI:0651
micromolar
true
10E-6 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
PMID:14755292
uM
10E-9 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
nM
PSI-MI
MI:0652
nanomolar
true
10E-9 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
PMID:14755292
nM
10E-12 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
pM
PSI-MI
MI:0653
picomolar
true
10E-12 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
PMID:14755292
pM
10E-15 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
fM
PSI-MI
MI:0654
fentomolar
true
10E-15 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.
PMID:14755292
fM
A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization.
BacterioMatch
lambda two hybrid
PSI-MI
MI:0655
lambda repressor two hybrid
A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization.
PMID:15792953
BacterioMatch
lambda two hybrid
Peptide whose sequence is experimentally identified and can lead to a full protein identification.
PSI-MI
MI:0656
identified peptide
Peptide whose sequence is experimentally identified and can lead to a full protein identification.
PMID:14755292
RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing.
in vitro evolution of nucleic acids
selex
PSI-MI
MI:0657
systematic evolution of ligands by exponential enrichment
RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing.
PMID:11539574
in vitro evolution of nucleic acids
selex
MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified.
mudpit
PSI-MI
MI:0658
multidimensional protein identification technology
MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified.
PMID:11231557
mudpit
Experimental method by which a feature is detected or identified.
exp feature detect
PSI-MI
MI:0659
experimental feature detection
Experimental method by which a feature is detected or identified.
PMID:14755292
exp feature detect
Feature detection based on computational analysis.
PSI-MI
MI:0660
feature prediction
Feature detection based on computational analysis.
PMID:14755292
experimental participant identification.
experimental particp
PSI-MI
MI:0661
experimental participant identification
experimental participant identification.
PMID:14755292
experimental particp
IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner.
http://imex.sourceforge.net/
PSI-MI
MI:0662
imex-primary
IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner.
http://imex.sourceforge.net/
PMID:14755292
A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen.
PSI-MI
MI:0663
confocal microscopy
A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen.
PMID:14755292
Attribute name of annotation associated to an interaction element.
interaction att name
PSI-MI
MI:0664
interaction attribute name
Attribute name of annotation associated to an interaction element.
PMID:14755292
interaction att name
Attribute name of annotation associated to an experiment element.
experiment att name
PSI-MI
MI:0665
experiment attribute name
Attribute name of annotation associated to an experiment element.
PMID:14755292
experiment att name
Attribute name of annotation associated to a participant element.
participant att name
PSI-MI
MI:0666
participant attribute name
Attribute name of annotation associated to a participant element.
PMID:14755292
participant att name
Attribute name of annotation associated to a CV term.
cv att name
PSI-MI
MI:0667
controlled vocabulary attribute name
Attribute name of annotation associated to a CV term.
PMID:14755292
cv att name
Attribute name of annotation associated to a feature element.
feature att name
PSI-MI
MI:0668
feature attribute name
Attribute name of annotation associated to a feature element.
PMID:14755292
feature att name
Attribute name of annotation associated to an organism element.
organism att name
PSI-MI
MI:0669
organism attribute name
Attribute name of annotation associated to an organism element.
PMID:14755292
organism att name
International Molecular Interaction Exchange.
search-url:
IMEx
PSI-MI
MI:0670
imex
International Molecular Interaction Exchange.
PMID:22453911
search-url:
http://www.ebi.ac.uk/intact/imex/main.xhtml?query=${ac}
IMEx
This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used.
PSI-MI
MI:0671
antibodies
This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used.
PMID:14755292
This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library.
PSI-MI
MI:0672
library-used
This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library.
PMID:14755292
Alternative names to describe a complex.
complex-synonym
PSI-MI
MI:0673
complex synonym
Alternative names to describe a complex.
PMID:14755292
Describe a cross reference pointing to a peptide parent sequence.
peptide-parent
PSI-MI
MI:0674
peptide parent sequence reference
Describe a cross reference pointing to a peptide parent sequence.
PMID:14755292
peptide-parent
IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources.
id-validation-regexp:
ipi
PSI-MI
MI:0675
international protein index
IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources.
PMID:15221759
id-validation-regexp:
IPI[0-9]+.[0-9]+|IPI[0-9]+
ipi
Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification.
TAP
tap
PSI-MI
MI:0676
tandem affinity purification
Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification.
PMID:11403571
TAP
tap
A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features.
PSI-MI
MI:0677
tandem tag
A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features.
PMID:14755292
A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others).
antigen capture assay
sandwich immunoassay
PSI-MI
MI:0678
antibody array
A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others).
PMID:12454649
antigen capture assay
sandwich immunoassay
A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule.
poly A
poly a
PSI-MI
MI:0679
poly adenine
A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule.
PMID:14755292
poly A
poly a
DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form.
ss DNA
ss dna
PSI-MI
MI:0680
single stranded deoxyribonucleic acid
DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form.
PMID:14755292
ss DNA
ss dna
DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
ds DNA
ds dna
PSI-MI
MI:0681
double stranded deoxyribonucleic acid
DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
PMID:14755292
ds DNA
ds dna
A cofactor is a small molecule required for the catalysis of an enzyme.
coenzyme
PSI-MI
MI:0682
cofactor
A cofactor is a small molecule required for the catalysis of an enzyme.
PMID:14755292
coenzyme
Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing.
PSI-MI
MI:0683
sequence database
Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing.
PMID:14755292
Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc).
PSI-MI
MI:0684
ancillary
Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc).
PMID:14755292
Publication or document describing the originating resource where an interaction, or other curated information, was first described.
PSI-MI
MI:0685
source reference
Publication or document describing the originating resource where an interaction, or other curated information, was first described.
PMID:14755292
Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation.
PSI-MI
MI:0686
unspecified method
Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation.
PMID:14755292
Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification.
fluorescent prot tag
PSI-MI
MI:0687
fluorescent protein tag
Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification.
PMID:14755292
fluorescent prot tag
Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag.
dna binding domain
PSI-MI
MI:0688
dna binding domain tag
Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag.
PMID:14755292
dna binding domain
Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag.
activation domain
PSI-MI
MI:0689
activation domain tag
Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag.
PMID:14755292
activation domain
Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation.
gal4 ad
PSI-MI
MI:0690
gal4 activation domain
Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation.
PMID:14755292
gal4 ad
Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor.
vp16 ad
PSI-MI
MI:0691
vp16 activation domain
Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor.
PMID:14755292
vp16 ad
B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection.
b42 ad
PSI-MI
MI:0692
b42 activation domain
B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection.
PMID:14613974
b42 ad
Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.
gal4 dna bd
PSI-MI
MI:0693
gal4 dna binding domain
Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.
PMID:14755292
gal4 dna bd
Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences.
lexa dna bd
PSI-MI
MI:0694
lexa dna binding domain
Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences.
PMID:14755292
lexa dna bd
Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin.
PSI-MI
MI:0695
sandwich immunoassay
Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin.
PMID:12454649
Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain.
nucleotidyltransferase assay
PSI-MI
MI:0696
polymerase assay
Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain.
PMID:14755292
nucleotidyltransferase assay
Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer.
dna dna pol assay
PSI-MI
MI:0697
dna directed dna polymerase assay
Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer.
PMID:14755292
dna dna pol assay
Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
dna rna pol assay
PSI-MI
MI:0698
dna directed rna polymerase assay
Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
PMID:14755292
dna rna pol assay
Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
rna dna pol assay
PSI-MI
MI:0699
rna directed dna polymerase assay
Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
PMID:14755292
rna dna pol assay
Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
rna rna pol assay
PSI-MI
MI:0700
rna directed rna polymerase assay
Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
PMID:14755292
rna rna pol assay
The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
DNA replication elongation
dna elongation
PSI-MI
MI:0701
dna strand elongation
The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
GO:0006271
PMID:14755292
DNA replication elongation
dna elongation
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
www.pantherdb.org/
PANTHER
PSI-MI
MI:0702
panther
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
www.pantherdb.org/
PMID:14755292
PANTHER
The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species.
http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
Gene3D
PSI-MI
MI:0703
gene3d
The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species.
http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
PMID:14755292
Gene3D
Method by which nucleic acids are delivered or engineered into a cell.
nucl delivery
PSI-MI
MI:0704
nucleic acid delivery
Method by which nucleic acids are delivered or engineered into a cell.
PMID:14755292
nucl delivery
Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal.
anti tag western
PSI-MI
MI:0705
anti tag western blot
Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal.
PMID:14755292
anti tag western
Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA).
nucl transformation
PSI-MI
MI:0706
nucleic acid transformation
Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA).
PMID:14755292
nucl transformation
Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal.
anti tag immunost
PSI-MI
MI:0707
anti tag immunostaining
Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal.
PMID:14755292
anti tag immunost
A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample.
monoclonal immunost
PSI-MI
MI:0708
monoclonal antibody immunostaining
A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample.
PMID:14755292
monoclonal immunost
Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample.
polyclonal immunost
PSI-MI
MI:0709
polyclonal antibody immunostaining
Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample.
PMID:14755292
polyclonal immunost
Stable introduction and expression of nucleic acid carried out by treatment with divalent cation.
n transformat cation
PSI-MI
MI:0710
nucleic acid transformation by treatment with divalent cation
Stable introduction and expression of nucleic acid carried out by treatment with divalent cation.
PMID:14755292
n transformat cation
Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA.
nucl electroporation
PSI-MI
MI:0711
nucleic acid electroporation
Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA.
PMID:14755292
nucl electroporation
Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids.
nucl microinjection
PSI-MI
MI:0712
nucleic acid microinjection
Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids.
PMID:14755292
nucl microinjection
Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes.
nucl passive uptake
PSI-MI
MI:0713
nucleic acid passive uptake
Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes.
PMID:14755292
nucl passive uptake
Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus.
nucl transduction
PSI-MI
MI:0714
nucleic acid transduction
Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus.
PMID:14755292
nucl transduction
Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient
nucl conjugation
PSI-MI
MI:0715
nucleic acid conjugation
Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient
PMID:14755292
nucl conjugation
Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes.
PSI-MI
MI:0716
passive uptake
Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes.
PMID:14755292
Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer.
nucl lipotransfect
PSI-MI
MI:0717
nucleic acid transfection with liposome
Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer.
PMID:14755292
nucl lipotransfect
Transient introduction and expression of nucleic acid carried out by treatment with chemicals.
n transfection treat
PSI-MI
MI:0718
nucleic acid transfection by treatment
Transient introduction and expression of nucleic acid carried out by treatment with chemicals.
PMID:14755292
n transfection treat
Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate.
ca po nuc transfect
PSI-MI
MI:0719
calcium phosphate nucleic acid transfection
Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate.
PMID:14755292
ca po nuc transfect
Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria..
nucl infection
PSI-MI
MI:0720
nucleic acid delivery by infection
Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria..
PMID:14755292
nucl infection
Method by which proteins are delivered into a cell.
PSI-MI
MI:0721
protein delivery
Method by which proteins are delivered into a cell.
PMID:14755292
Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein.
prot electroporation
PSI-MI
MI:0722
protein electroporation
Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein.
PMID:14755292
prot electroporation
Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins.
prot microinjection
PSI-MI
MI:0723
protein microinjection
Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins.
PMID:14755292
prot microinjection
Proteins are delivered into cells by treatment with cationic lipids.
prot cationic lipid
PSI-MI
MI:0724
protein delivery by cationic lipid treatment
Proteins are delivered into cells by treatment with cationic lipids.
PMID:14755292
prot cationic lipid
Protein introduced into a cell via an external organism, usually a virus or bacteria.
prot infection
PSI-MI
MI:0725
protein delivery by infection
Protein introduced into a cell via an external organism, usually a virus or bacteria.
PMID:14755292
prot infection
Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site.
PSI-MI
MI:0726
reverse two hybrid
Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site.
PMID:8816797
Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements.
LexA B52 transcription complementation
lexa b52 complement
PSI-MI
MI:0727
lexa b52 complementation
Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements.
PMID:14613974
LexA B52 transcription complementation
lexa b52 complement
A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated.
KISS
gal4 vp16 complement
karyoplasmic interaction ion strategy
mammalian two hybrid
PSI-MI
MI:0728
gal4 vp16 complementation
A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated.
PMID:1387709
KISS
gal4 vp16 complement
karyoplasmic interaction ion strategy
mammalian two hybrid
This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates.
lumier
PSI-MI
MI:0729
luminescence based mammalian interactome mapping
This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates.
PMID:15761153
lumier
PubChem provides information on the biological activities of small molecules.
http://pubchem.ncbi.nlm.nih.gov/
PubChem
PSI-MI
MI:0730
pubchem
PubChem provides information on the biological activities of small molecules.
http://pubchem.ncbi.nlm.nih.gov/
PMID:16381840
PubChem
The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository.
3D Repertoire
PSI-MI
MI:0731
3d repertoire
The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository.
PMID:14755292
3D Repertoire
The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
RFP
red fluorescent protein
rfp tag
PSI-MI
MI:0732
red fluorescent protein tag
The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:14755292
RFP
red fluorescent protein
rfp tag
The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
CFP
cfp tag
cyan fluorescent protein
PSI-MI
MI:0733
cyan fluorescent protein tag
The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:14755292
CFP
cfp tag
cyan fluorescent protein
Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
EGFP
egfp tag
enhanced green fluorescent protein
PSI-MI
MI:0734
enhanced green fluorescent protein tag
Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:14755292
EGFP
egfp tag
enhanced green fluorescent protein
Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells.
Tat tag
tat tag
PSI-MI
MI:0735
transactivating tag
Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells.
PMID:8290579
Tat tag
tat tag
Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes.
prot passive uptake
PSI-MI
MI:0736
protein passive uptake
Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes.
PMID:14755292
prot passive uptake
database storing sequences detected by peptide identification methods.
pep seq db
PSI-MI
MI:0737
peptide sequence database
database storing sequences detected by peptide identification methods.
PMID:14755292
pep seq db
PRIDE is a public repository of protein and peptide identifications for the proteomics community.
http://www.ebi.ac.uk/pride/
search-url:
PSI-MI
MI:0738
pride
PRIDE is a public repository of protein and peptide identifications for the proteomics community.
http://www.ebi.ac.uk/pride/
PMID:16381953
search-url:
http://www.ebi.ac.uk/pride/archive/projects/${ac}
Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK
PSI-MI
MI:0739
penetrating tag
Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK
PMID:16574060
The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus.
CPPs
MTS
PTDs
Trojan peptides
cell penetrating pep
cell-penetrating peptides
membrane translocating sequences
protein transduction domains
PSI-MI
MI:0740
cell penetrating peptide tag
The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus.
PMID:16574060
CPPs
MTS
PTDs
Trojan peptides
cell penetrating pep
cell-penetrating peptides
membrane translocating sequences
protein transduction domains
PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms.
http://www.peptideatlas.org/
PeptideAtlas
PSI-MI
MI:0741
peptide atlas
PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms.
http://www.peptideatlas.org/
PMID:15642101
PMID:16381952
PeptideAtlas
Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.
http://www.thegpm.org
Global Proteome Machine
PSI-MI
MI:0742
gpm
Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.
http://www.thegpm.org
PMID:15595733
Global Proteome Machine
Descriptor of an experimental form involved in a genetic interaction
genetic exp form
PSI-MI
MI:0787
genetic experimental form
Descriptor of an experimental form involved in a genetic interaction
PMID:14755292
genetic exp form
The gene has been completely removed e.g. by genetic engineering
knock-out
PSI-MI
MI:0788
knock out
The gene has been completely removed e.g. by genetic engineering
PMID:14755292
knock-out
The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference.
knock-down
PSI-MI
MI:0789
knock down
The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference.
PMID:14755292
knock-down
The gene function has been partially improved compared to wild-type by altering its sequence.
PSI-MI
MI:0790
hypermorph
The gene function has been partially improved compared to wild-type by altering its sequence.
PMID:14755292
The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant.
PSI-MI
MI:0791
hypomorph
The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant.
PMID:14755292
The gene function has been antagonized by a mutation in another copy of the gene.
PSI-MI
MI:0792
antimorph
The gene function has been antagonized by a mutation in another copy of the gene.
PMID:14755292
The gene function has been abolished by mutation, though the type of mutation is not known.
PSI-MI
MI:0793
amorph
The gene function has been abolished by mutation, though the type of mutation is not known.
PMID:14755292
An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations.
wt = a = b = E (not=) ab
aphenotypic diverging genetic interaction
synthetic genetic interaction (sensu inequality)
synthetic genetic interaction defined by inequality
PSI-MI
MI:0794
synthetic genetic interaction
An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations.
wt = a = b = E (not=) ab
PMID:15833125
An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a = b = ab != wt
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
A, B, and the AB combination all have the same effect on the WT background (2 inequalities).
Another subtype of alleviating interaction, 'coequal' interaction, is defined by single- and double-mutant strains that exhibit fitness values that are indistinguishable from one another (19).
Lastly, we observed ten gene pairs for which the MMS sensitivity of the single- and double-deletion strains was statistically indistinguishable (Sxy = Sx = Sy). These interactions, which we call ‘coequal’, are related to‘complementary gene action’, ‘complementary epistasis’ or ‘asynthetic’ relationship types that have been previously described18,30,31.
asynthetic
asynthetic genetic interaction (sensu inequality)
coequal genetic interaction
isophenotypic masking genetic interaction
PSI-MI
MI:0795
asynthetic genetic interaction
An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a = b = ab != wt
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
asynthetic
asynthetic genetic interaction (sensu inequality)
coequal genetic interaction
PMID:18305163
An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab <= wt [E = a*]
OR
wt <= ab < a* [E = a*]
where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
suppression
suppressive genetic interaction (sensu inequality)
PSI-MI
Alleviating interaction
MI:0796
genetic suppression (sensu unexpected)
An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab <= wt [E = a*]
OR
wt <= ab < a* [E = a*]
where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
suppression
suppressive genetic interaction (sensu inequality)
An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
masking genetic interaction
Bateson genetic epistasis
epistatic
epistatic genetic interaction (sensu inequality)
PSI-MI
MI:0797
genetic epistasis (sensu Bateson)
An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
PMID:15833125
Bateson genetic epistasis
PMID:17510664
https://archive.org/details/mendelsprinciple00bate/page/n8
epistatic
epistatic genetic interaction (sensu inequality)
The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
conditional
conditional genetic interaction (sensu inequality)
PSI-MI
MI:0798
conditional genetic interaction defined by inequality
true
The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
PMID:15833125
conditional
conditional genetic interaction (sensu inequality)
Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
additive
additive genetic interaction (sensu inequality)
PSI-MI
MI:0799
additive genetic interaction defined by inequality
true
Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
PMID:15833125
additive
additive genetic interaction (sensu inequality)
The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b.
single nonmonotonic
single nonmonotonic genetic interaction (sensu inequality)
PSI-MI
MI:0800
single nonmonotonic genetic interaction defined by inequality
true
The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b.
PMID:15833125
single nonmonotonic
single nonmonotonic genetic interaction (sensu inequality)
The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b
double nonmonotonic
double nonmonotonic genetic interaction (sensu inequality)
PSI-MI
MI:0801
double nonmonotonic genetic interaction defined by inequality
true
The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b
PMID:15833125
double nonmonotonic
double nonmonotonic genetic interaction (sensu inequality)
The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme.
OBSOLETE: remap to MI:0933 'negative genetic interaction'
enhancement
PSI-MI
MI:0802
enhancement interaction
true
The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme.
OBSOLETE: remap to MI:0933 'negative genetic interaction'
PMID:15833125
enhancement
Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell.
expression modif
PSI-MI
MI:0803
expression level alteration
Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell.
PMID:14755292
expression modif
The gene is mutated in some unknown manner
PSI-MI
MI:0804
mutated gene
The gene is mutated in some unknown manner
PMID:14755292
The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.
http://www.wwpdb.org/
id-validation-regexp:
search-url:
wwPDB
PSI-MI
MI:0805
wwpdb
The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.
http://www.wwpdb.org/
PMID:14634627
id-validation-regexp:
[0-9][a-zA-Z0-9]{3}
search-url:
http://www.pdbe.org/${ac}
wwPDB
PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites.
http://www.pdbj.org/
id-validation-regexp:
search-url:
PDBj
PSI-MI
MI:0806
pdbj
PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites.
http://www.pdbj.org/
PMID:12099029
id-validation-regexp:
[0-9][a-zA-Z0-9]{3}
search-url:
http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary
PDBj
The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel.
comigration in gel
PSI-MI
MI:0807
comigration in gel electrophoresis
The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel.
PMID:14755292
comigration in gel
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel.
comigration in sds
PSI-MI
MI:0808
comigration in sds page
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel.
PMID:14755292
PMID:16732283
comigration in sds
The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy.
MI:0229
bifc
gfp complementation
green fluorescence protein complementation assay
PSI-MI
MI:0809
bimolecular fluorescence complementation
The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy.
PMID:11983170
bifc
In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction.
substitut analysis
PSI-MI
MI:0810
substitution analysis
In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction.
PMID:14755292
substitut analysis
In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction.
PSI-MI
MI:0811
insertion analysis
In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction.
PMID:14755292
The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin.
cam tag
PSI-MI
MI:0812
calmodulin binding protein tag
The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin.
PMID:14755292
cam tag
Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides.
PLA
p elisa
pELISA
PSI-MI
in situ proximity ligation assay
pLISA
proximity ligation
MI:0813
proximity ligation assay
Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides.
PMID:15155907
PMID::17072308
PLA
pELISA
In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis).
pal
protease access
PSI-MI
MI:0814
protease accessibility laddering
In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis).
PMID:16615907
pal
protease access
Molecule whose sequence identity is derived from their molecular weight
weight identificat
PSI-MI
MI:0815
confirmation by molecular weight
Molecule whose sequence identity is derived from their molecular weight
PMID:14755292
weight identificat
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker.
weight by staining
PSI-MI
MI:0816
molecular weight estimation by staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker.
PMID:14755292
weight by staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver.
weight silver stain
PSI-MI
MI:0817
molecular weight estimation by silver staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver.
PMID:14755292
weight silver stain
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye.
weight by comassie
PSI-MI
MI:0818
molecular weight estimation by coomasie staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye.
PMID:14755292
weight by comassie
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes.
weight by bromide
PSI-MI
MI:0819
molecular weight estimation by bromide staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes.
PMID:14755292
weight by bromide
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes.
safe DNA gel stain
weight by sybr
PSI-MI
MI:0820
molecular weight estimation by sybr staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes.
PMID:14755292
safe DNA gel stain
weight by sybr
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography.
weight autoradiogra
PSI-MI
MI:0821
molecular weight estimation by autoradiography
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography.
PMID:14755292
weight autoradiogra
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes.
weight by hoechst
PSI-MI
MI:0822
molecular weight estimation by hoechst staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes.
PMID:14755292
weight by hoechst
Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s).
predetermined featur
PSI-MI
MI:0823
predetermined feature
Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s).
PMID:14755292
predetermined featur
Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals.
X-ray
x-ray powder diffrac
PSI-MI
MI:0824
x-ray powder diffraction
Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals.
PMID:14755292
X-ray
x-ray powder diffrac
Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray.
X-ray
x-ray fiber diffrac
PSI-MI
MI:0825
x-ray fiber diffraction
Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray.
PMID:14755292
X-ray
x-ray fiber diffrac
Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles.
saxs
PSI-MI
MI:0826
x ray scattering
Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles.
PMID:14755292
saxs
X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells.
PSI-MI
MI:0827
x-ray tomography
X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells.
PMID:14755292
Subpart of a polyprotein that is naturally cleaved in vivo.
polyprotein frag
PSI-MI
chain
MI:0828
polyprotein fragment
Subpart of a polyprotein that is naturally cleaved in vivo.
PMID:14577292
polyprotein frag
This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules.
multiple parent
PSI-MI
MI:0829
multiple parent reference
This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules.
PMID:14755292
multiple parent
List of tissue used as topic in UniProt RC line.
http://www.expasy.org/cgi-bin/lists?tisslist.txt
PSI-MI
MI:0830
tissue list
List of tissue used as topic in UniProt RC line.
http://www.expasy.org/cgi-bin/lists?tisslist.txt
PMID:14755292
Ontology of cell types.
http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
PSI-MI
MI:0831
cell ontology
Ontology of cell types.
http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
PMID:16381901
A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed
Half of a disulfide bridge
PSI-MI
MI:0832
half cystine
true
A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed
MOD:00798
RESID:AA0025
Half of a disulfide bridge
Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film.
PSI-MI
MI:0833
autoradiography
Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film.
PMID:14755292
Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)
kon
PSI-MI
MI:0834
ka
Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)
PMID:14755292
kon
Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)
koff
PSI-MI
Kd
MI:0835
koff
Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)
PMID:14755292
koff
Temperature at which interaction was determined. Unit KELVIN (K)
T interaction
Tint
temp interaction
PSI-MI
MI:0836
temperature of interaction
Temperature at which interaction was determined. Unit KELVIN (K)
PMID:14755292
T interaction
Tint
temp interaction
pH at which interaction was determined.
pHint
PSI-MI
MI:0837
pH of interaction
pH at which interaction was determined.
PMID:14755292
pHint
The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F.
K
PSI-MI
MI:0838
kelvin
The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F.
PMID:14755292
K
Per mole per second, unit for association rate constant.
M-1s-1
PSI-MI
MI:0839
per mole per second
Per mole per second, unit for association rate constant.
PMID:14755292
M-1s-1
Molecule stimulating an interaction by interacting with one or more of the participants.
PSI-MI
MI:0840
stimulator
Molecule stimulating an interaction by interacting with one or more of the participants.
PMID:14755292
Measures the rate of a phosphate transfer between two molecules.
phosphotransferase
PSI-MI
phosphotransfer assay
MI:0841
phosphotransferase assay
Measures the rate of a phosphate transfer between two molecules.
PMID:14755292
phosphotransferase
Any molecule that is able to transfer a phosphate group to another chemical species.
PSI-MI
MI:0842
phosphate donor
Any molecule that is able to transfer a phosphate group to another chemical species.
PMID:14755292
Molecule to which a phosphate group may be transferred from a phosphate donor.
PSI-MI
MI:0843
phosphate acceptor
Molecule to which a phosphate group may be transferred from a phosphate donor.
PMID:14755292
Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
phosphotransfer
PSI-MI
MI:0844
phosphotransfer reaction
Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
PMID:14755292
PMID:16712436
phosphotransfer
Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest.
PSI-MI
MI:0845
spin label
Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest.
PMID:10966640
Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline-
3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide
side chain designated R1.
PSI-MI
MI:0846
r1 spin label
Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline-
3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide
side chain designated R1.
PMID:10966640
Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups.
5-dimethylaminonaphthalene-1-sulfonyl tag
dansyl tag
PSI-MI
MI:0847
dansyl label
Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups.
PMID:14755292
5-dimethylaminonaphthalene-1-sulfonyl tag
dansyl tag
Molecule labelled with 125 radio isotope of iodine atoms.
125I
I125
PSI-MI
MI:0848
125i radiolabel
Molecule labelled with 125 radio isotope of iodine atoms.
PMID:14755292
125I
I125
The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available.
http://www.ncbi.nlm.nih.gov/Taxonomy/
id-validation-regexp:
search-url:
PSI-MI
MI:0849
ncbi taxonomy
The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available.
http://www.ncbi.nlm.nih.gov/Taxonomy/
PMID:10592169
id-validation-regexp:
[0-9]+
search-url:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock
ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.
http://www.genome.gov/10005107
ENCODE
Encyclopedia Of DNA Elements
PSI-MI
MI:0850
encode
ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.
http://www.genome.gov/10005107
PMID:17372197
ENCODE
Encyclopedia Of DNA Elements
GenBank Identifier or GI numbers for proteins.
id-validation-regexp:
search-url:
GenBank Protein GI
genbank protein gi
genbank_protein_gi
genpept id
PSI-MI
MI:0851
protein genbank identifier
GenBank Identifier or GI numbers for proteins.
PMID:17170002
id-validation-regexp:
[0-9]+
search-url:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=${ac}
GenBank Protein GI
genbank protein gi
genbank_protein_gi
GenBank Identifier or GI numbers for nucleotide.
id-validation-regexp:
search-url:
GenBank Nucleotide
genbank nucleotide
genbank_nucl_gi
PSI-MI
MI:0852
nucleotide genbank identifier
GenBank Identifier or GI numbers for nucleotide.
PMID:17170002
id-validation-regexp:
[0-9]+
search-url:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Retrieve&dopt=Graphics&list_uids=$
GenBank Nucleotide
genbank nucleotide
genbank_nucl_gi
An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase
cohessive ends
sticky ends
PSI-MI
MI:0853
dna overhang
An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase
PMID:14755292
cohessive ends
sticky ends
An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule.
3 prime sticky end
PSI-MI
MI:0854
3 prime overhang
An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule.
PMID:14755292
3 prime sticky end
An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule.
5 prime sticky end
PSI-MI
MI:0855
5 prime overhang
An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule.
PMID:14755292
5 prime sticky end
A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore.
PSI-MI
MI:0856
fluorophore
A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore.
PMID:14755292
Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength.
fluorescent dye
PSI-MI
MI:0857
fluorescent dye label
Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength.
PMID:14755292
fluorescent dye
Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex.
immunodepleted coip
immunodepletion
PSI-MI
MI:0858
immunodepleted coimmunoprecipitation
Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex.
PMID:17081976
immunodepleted coip
immunodepletion
A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force.
intermolecular force
PSI-MI
force measurement
molecular force measurement
single molecule force measurement
surface adhesion force measurement
MI:0859
force spectroscopy
A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force.
PMID:18511917
intermolecular force
edit
id-validation-regexp:
PSI-MI
MI:0860
genbank identifier
edit
PMID:15078858
id-validation-regexp:
ENS[A-Z]+[0-9]{11}
The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis.
protein A
PSI-MI
MI:0861
protein a tag
The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis.
PMID:14755292
protein A
The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain.
ZZ tag
PSI-MI
MI:0862
zz tag
The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain.
PMID:11694505
ZZ tag
Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA.
Tb3+-DTPA-cs124-EMCH
thiol lanthanide
PSI-MI
MI:0863
thiol reactive lanthanide label
Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA.
PMID:10077482
Tb3+-DTPA-cs124-EMCH
thiol lanthanide
A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
http://www.brenda-enzymes.info
PSI-MI
MI:0864
brenda
A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
http://www.brenda-enzymes.info
PMID:14755292
Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes.
fret pair
PSI-MI
MI:0865
fluorescence acceptor donor pair
Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes.
PMID:14755292
fret pair
Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag.
PSI-MI
MI:0866
tag visualisation
Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag.
PMID:14755292
The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction.
tag fluorescence
PSI-MI
MI:0867
tag visualisation by fluorescence
The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction.
PMID:14755292
tag fluorescence
Author published identifier.
PSI-MI
MI:0868
author identifier
Author published identifier.
PMID:14755292
Identifier assigned when the record was created by a source database.
original identifier
PSI-MI
MI:0869
originally assigned identifier
Identifier assigned when the record was created by a source database.
PMID:14755292
original identifier
Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule.
PSI-MI
MI:0870
demethylase assay
Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule.
PMID:14755292
The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
demethylation
PSI-MI
MI:0871
demethylation reaction
The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
GO:0006482
PMID:17277772
demethylation
The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler.
http://en.wikipedia.org/wiki/Atomic_force_microscope
AFM
atomic force microsc
PSI-MI
MI:0872
atomic force microscopy
The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler.
http://en.wikipedia.org/wiki/Atomic_force_microscope
PMID:17502105
AFM
atomic force microsc
Annotation of a published paper which has been externally requested.
PSI-MI
MI:0873
curation request
Annotation of a published paper which has been externally requested.
PMID:14755292
Targeted curation dataset grouping experiments by topic or dataset origin.
PSI-MI
MI:0875
dataset
Targeted curation dataset grouping experiments by topic or dataset origin.
PMID:14755292
Data directly submitted by the authors to a database prior to publication.
PSI-MI
MI:0878
author submitted
Data directly submitted by the authors to a database prior to publication.
PMID:14755292
Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
triphosphatase ass
PSI-MI
MI:0879
nucleoside triphosphatase assay
Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
PMID:14755292
triphosphatase ass
Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate.
PSI-MI
MI:0880
atpase assay
Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate.
PMID:14755292
Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
triphosphatase react
PSI-MI
MI:0881
nucleoside triphosphatase reaction
Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
GO:0017111
PMID:14755292
triphosphatase react
Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
PSI-MI
MI:0882
atpase reaction
Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
GO:0016887
PMID:14755292
Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
PSI-MI
MI:0883
gtpase reaction
Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
GO:0003924
PMID:14755292
Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available.
vesicular stomatitis virus tag
PSI-MI
MI:0884
vsv tag
Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available.
PMID:14755292
vesicular stomatitis virus tag
Name and details of a journal from which paper has been taken.
PSI-MI
MI:0885
journal
Name and details of a journal from which paper has been taken.
PMID:14755292
Year of publication of a paper.
PSI-MI
MI:0886
publication year
Year of publication of a paper.
PMID:14755292
In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt)
HAt
hat
PSI-MI
histone acetylation
MI:0887
histone acetylase assay
In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt)
PMID:14755292
HAt
hat
During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample.
SANS
sans
PSI-MI
MI:0888
small angle neutron scattering
During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample.
PMID:11578931
SANS
sans
Measures the catalysis of the addition of an acetyl group to a target molecule.
PSI-MI
acetylation
MI:0889
acetylase assay
Measures the catalysis of the addition of an acetyl group to a target molecule.
PMID:14755292
Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications.
PSI-MI
MI:0890
qdot
Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications.
PMID:17569782
Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam.
neutron fiber diff
PSI-MI
MI:0891
neutron fiber diffraction
Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam.
PMID:10771422
PMID:15272083
PMID:15546977
PMID:15914673
PMID:16041074
PMID:16707576
neutron fiber diff
Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution.
PSI-MI
MI:0892
solid phase assay
Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution.
PMID:14755292
Analysis of diffraction pattern using neutron beam
PSI-MI
MI:0893
neutron diffraction
Analysis of diffraction pattern using neutron beam
PMID:10771422
PMID:15272083
PMID:15546977
PMID:15914673
PMID:16041074
PMID:16707576
Analysis of diffraction pattern using electron beam.
PSI-MI
MI:0894
electron diffraction
Analysis of diffraction pattern using electron beam.
PMID:10949309
PMID:11034202
PMID:11171962
PMID:11532455
PMID:11700061
PMID:15141214
PMID:16325200
This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA.
pka complementation
PSI-MI
MI:0895
protein kinase A complementation
This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA.
PMID:17942691
pka complementation
Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm.
renilla luciferase
PSI-MI
MI:0896
renilla luciferase protein tag
Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm.
PMID:14755292
renilla luciferase
Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue.
id-validation-regexp:
psi-mod
PSI-MI
MI:0897
protein modification ontology
Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue.
PMID:14755292
id-validation-regexp:
MOD:[0-9]{5}
psi-mod
Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer).
PSI-MI
MI:0898
putative self
Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer).
PMID:14755292
pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display.
low valency display
p3 filamentous phage
PSI-MI
MI:0899
p3 filamentous phage display
pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display.
PMID:1696028
low valency display
p3 filamentous phage
pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display.
high valency display
p8 filamentous phage
PSI-MI
MI:0900
p8 filamentous phage display
pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display.
PMID:1720463
high valency display
p8 filamentous phage
Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange.
isotope footprinting
PSI-MI
MI:0901
isotope label footprinting
Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange.
PMID:18184591
isotope footprinting
Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
PSI-MI
MI:0902
rna cleavage
Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
GO:0006396
PMID:14681407
The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact).
MPDIB
PSI-MI
MI:0903
mpidb
The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact).
PMID:14755292
MPDIB
A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
PSI-MI
MI:0904
polysaccharide
A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
PMID:14755292
AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3).
AlphaScreen
alpha-screen
PSI-MI
MI:0905
amplified luminescent proximity homogeneous assay
AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3).
PMID:17092917
AlphaScreen
alpha-screen
The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available.
DTYRYI epitope tag
PSI-MI
MI:0906
au1 tag
The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available.
PMID:18216269
DTYRYI epitope tag
Statement about the native/denatured conformation of the protein.
conformation
PSI-MI
MI:0907
conformational status
Statement about the native/denatured conformation of the protein.
PMID:14755292
conformation
Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein.
PSI-MI
MI:0908
denatured
Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein.
PMID:14755292
State of the protein without interference i.e. the natural form.
PSI-MI
MI:0909
native
State of the protein without interference i.e. the natural form.
PMID:14755292
Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
ncl acid cleavage
PSI-MI
MI:0910
nucleic acid cleavage
Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
PMID:14755292
ncl acid cleavage
A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed.
crosslinker
PSI-MI
MI:0911
cross linker
A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed.
PMID:14755292
crosslinker
N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable
and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester
that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond.
N -Succinimidyl 3-(2-pyridyldithio)-propionate
PSI-MI
MI:0912
spdp cross linker
N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable
and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester
that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond.
PMID:17360572
N -Succinimidyl 3-(2-pyridyldithio)-propionate
Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable
and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester
that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm.
Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate
PSI-MI
MI:0913
lc-spdp cross linker
Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable
and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester
that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm.
PMID:17360572
Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate
Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
PSI-MI
MI:0914
association
Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
PMID:14755292
Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
PSI-MI
MI:0915
physical association
Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
PMID:14755292
Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream.
LexA VP16 transcription complementation
lexa vp16 complement
PSI-MI
MI:0916
lexa vp16 complementation
Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream.
PMID:9371806
LexA VP16 transcription complementation
lexa vp16 complement
Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions.
search-url:
MatrixDB
PSI-MI
MI:0917
matrixdb
Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions.
PMID:19147664
search-url:
http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=${ac}
MatrixDB
Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule.
PSI-MI
MI:0918
donor
Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule.
PMID:14755292
Molecule able to receive active chemical groups, electrons or ions from a donor molecule.
PSI-MI
MI:0919
acceptor
Molecule able to receive active chemical groups, electrons or ions from a donor molecule.
PMID:14755292
Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
PSI-MI
MI:0920
ribonuclease assay
Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
PMID:14755292
This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot.
Biacore Flexchip(r)
SPRImager
SPRi-Plex
spr array
PSI-MI
MI:0921
surface plasmon resonance array
This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot.
PMID:16510109
PMID:16837183
PMID:17889820
Biacore Flexchip(r)
SPRImager
SPRi-Plex
spr array
Experimental evidence supporting an interaction curated and released under the IMEx agreement.
PSI-MI
MI:0922
imex evidence
Experimental evidence supporting an interaction curated and released under the IMEx agreement.
PMID:14755292
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
http://irefindex.uio.no/
iRefIndex
PSI-MI
MI:0923
irefindex
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
http://irefindex.uio.no/
PMID:18823568
iRefIndex
Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.
http://www.sanger.ac.uk/Projects/C_jejuni/
PSI-MI
MI:0924
camjedb
Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.
http://www.sanger.ac.uk/Projects/C_jejuni/
PMID:106882042
Post translational modification observed on a protein in the context of an interaction.
observed ptm
observed-ptm
PSI-MI
MI:0925
observed-ptm
Post translational modification observed on a protein in the context of an interaction.
PMID:14755292
observed ptm
observed-ptm
This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties.
4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein
FIAsH label
PSI-MI
MI:0926
fiash label
This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties.
PMID:9657724
4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein
FIAsH label
IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups.
(5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid)
1,5-IAEDANS
IAEDANS
PSI-MI
MI:0927
iaedans label
IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups.
PMID:11052891
(5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid)
1,5-IAEDANS
IAEDANS
Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified.
Filter retention assay
filter binding
PSI-MI
filter retardation assay
membrane filtration
MI:0928
filter trap assay
Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified.
PMID:10859365
Filter retention assay
A standard procedure to identify RNA fragments containing specific
sequences. In this procedure RNA fragments are separated by
electrophoresis, the fragments are transferred to a membrane and the
membrane is incubated with a radio labelled probe that hybridises any
complementary subsequence.
northen
PSI-MI
MI:0929
northern blot
A standard procedure to identify RNA fragments containing specific
sequences. In this procedure RNA fragments are separated by
electrophoresis, the fragments are transferred to a membrane and the
membrane is incubated with a radio labelled probe that hybridises any
complementary subsequence.
PMID:414220
northen
An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
epistatic genetic interaction
PSI-MI
MI:0930
epistatis
true
An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
PMID:11988766
Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship.
genetic inequality
PSI-MI
MI:0931
genetic interaction defined by inequality
true
Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship.
PMID:14755292
genetic inequality
The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
expected multigenic phenotypic result
neutral genetic interaction
noninteractive
noninteractive genetic interaction (sensu inequality)
noninteractive genetic interaction defined by inequality
PSI-MI
MI:0932
neutral multigenic phenotype result
The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
PMID:15833125
noninteractive genetic interaction (sensu inequality)
An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E <= wt
OR
wt <= E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PSI-MI
MI:0933
diverging genetic interaction
An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E <= wt
OR
wt <= E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:14755292
OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b [ab != E]
OR
With respect to two qualitatively different phenotypes, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.
neutral gent int
PSI-MI
MI:0934
obsolete neutral genetic interaction
true
OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b [ab != E]
OR
With respect to two qualitatively different phenotypes, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.
PMID:14755292
neutral gent int
An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E < ab <= wt
OR
wt <= ab < E
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PSI-MI
MI:0935
converging genetic interaction
An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E < ab <= wt
OR
wt <= ab < E
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:14755292
The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files.
https://www.ebi.ac.uk/emdb
search-url:
Electron Microscopy Data Bank
eMDB
PSI-MI
MI:0936
emdb
The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files.
https://www.ebi.ac.uk/emdb
PMID:14643225
search-url:
https://www.ebi.ac.uk/emdb/${ac}
Electron Microscopy Data Bank
eMDB
This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide.
glu tag
PSI-MI
MI:0937
glu tag
This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide.
PMID:8077219
glu tag
Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules.
rheology
PSI-MI
MI:0938
rheology measurement
Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules.
PMID:18445655
rheology
Fluorescence label used to monitor the presence of a protein.
fluorescein
PSI-MI
MI:0939
fluorescein label
Fluorescence label used to monitor the presence of a protein.
PMID:14755292
fluorescein
Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions.
fluor-5-maleimide
PSI-MI
MI:0940
fluorescein-5-maleimide label
Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions.
PMID:18066077
fluor-5-maleimide
Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site.
competitor
PSI-MI
MI:0941
competitor
Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site.
PMID:14755292
competitor
Based on NCBO Taxonomy but adapted for UniProt
http://www.uniprot.org/taxonomy/
id-validation-regexp:
search-url:
uniprot taxon
PSI-MI
MI:0942
uniprot taxonomy
Based on NCBO Taxonomy but adapted for UniProt
http://www.uniprot.org/taxonomy/
PMID:18836194
id-validation-regexp:
[0-9]+
search-url:
http://www.uniprot.org/taxonomy/${ac}
uniprot taxon
'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer.
ms interact detect
PSI-MI
MI:0943
detection by mass spectrometry
'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer.
PMID:14755292
ms interact detect
Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange.
h1-h2 ms
PSI-MI
MI:0944
mass spectrometry study of hydrogen/deuterium exchange
Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange.
PMID:18948593
h1-h2 ms
An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
redox reaction
PSI-MI
MI:0945
oxidoreductase activity electron transfer reaction
An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:GO:0016491
PMID:14755292
redox reaction
Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs.
protein interaction network generator
MITOMI
mIP
ping
PSI-MI
MI:0946
miniaturized immunoprecipitation
Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs.
PMID:19098921
MITOMI
mIP
Binding of proteins bound to beads leads to a measurable aggregation of the beads.
bead aggregation
PSI-MI
MI:0947
bead aggregation assay
Binding of proteins bound to beads leads to a measurable aggregation of the beads.
PMID:19114658
bead aggregation
A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed.
kinetic_conditions
PSI-MI
MI:0948
kinetic conditions
A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed.
PMID:14755292
kinetic_conditions
Experiments monitoring
interactions of GTP-GDP exchange factors with their cognate GTPases.
gdp_gtp exchange
gtp/gdp exchange
guanine nucleotide exchange assay
PSI-MI
MI:0949
gdp/gtp exchange assay
Experiments monitoring
interactions of GTP-GDP exchange factors with their cognate GTPases.
PMID:17925023
gdp_gtp exchange
gtp/gdp exchange
guanine nucleotide exchange assay
Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate.
trap-mutant
PSI-MI
MI:0950
trapping mutant
Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate.
PMID:9050838
trap-mutant
Reference to the master sequence from which this chain has been derived.
chain-parent
PSI-MI
MI:0951
chain parent sequence reference
Reference to the master sequence from which this chain has been derived.
PMID:17925023
chain-parent
Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier.
PSI-MI
MI:0952
imex secondary
Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier.
PMID:17925023
Interaction inferred by monitoring polymerization/depolymerization of an interactor
polymerization
PSI-MI
MI:0953
polymerization
Interaction inferred by monitoring polymerization/depolymerization of an interactor
PMID:19081060
An assessment of the depth and extent to which a paper has been curated
PSI-MI
MI:0954
curation quality
An assessment of the depth and extent to which a paper has been curated
PMID:17893861
Assessment of the depth to which a paper has been curated
PSI-MI
MI:0955
curation depth
Assessment of the depth to which a paper has been curated
PMID:17893861
Assessment to the extent of interactions captured in this paper
PSI-MI
MI:0956
curation coverage
Assessment to the extent of interactions captured in this paper
PMID:17893861
All interactions which can be ascribed to an unambiguous identified in this paper have been captured.
PSI-MI
MI:0957
full coverage
All interactions which can be ascribed to an unambiguous identified in this paper have been captured.
PMID:17893861
Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured.
PSI-MI
MI:0958
partial coverage
Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured.
PMID:17893861
Paper has been curated to full IMEx specifications
PSI-MI
MI:0959
imex curation
Paper has been curated to full IMEx specifications
PMID:17893861
Paper has been curated to meet MIMIx specifications
PSI-MI
MI:0960
mimix curation
Paper has been curated to meet MIMIx specifications
PMID:17687370
Minimal interaction data has been extracted from the paper
PSI-MI
MI:0961
rapid curation
Minimal interaction data has been extracted from the paper
PMID:17687370
The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK).
Strep (II)
Strep II
PSI-MI
MI:0962
strep ii tag
The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK).
PMID:17571060
Strep (II)
Strep II
A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press).
orchard
2009-05-14T10:56:21Z
ipac
PSI-MI
MI:0963
interactome parallel affinity capture
A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press).
PMID:14681455
ipac
Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum.
orchard
2009-10-28T10:55:01Z
ir spectrometry
PSI-MI
MI:0964
infrared spectroscopy
Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum.
PMID:15212548
ir spectrometry
Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles.
orchard
2009-10-28T11:05:01Z
2d-ir
PSI-MI
MI:0965
2d-infrared spectrometry
Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles.
PMID:17502604
2d-ir
Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges.
orchard
2009-10-28T11:12:27Z
UV/Vis
ultraviolet-visible spectrophotometry
uv-vis
PSI-MI
MI:0966
ultraviolet-visible spectroscopy
Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges.
PMID:18799738
uv-vis
ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
orchard
2009-10-28T11:20:55Z
id-validation-regexp:
search-url:
chembl
PSI-MI
MI:0967
chembl compound
ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
PMID:19194660
PMID:24214965
id-validation-regexp:
[0-9]+
search-url:
http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/${ac}
A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component
orchard
2009-10-28T11:44:32Z
PSI-MI
MI:0968
biosensor
A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component
PMID:10872504
BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer
orchard
2009-10-28T11:48:40Z
bli
PSI-MI
MI:0969
bio-layer interferometry
BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer
PMID:19561609
bli
InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character
orchard
2009-10-28T01:13:25Z
inchi key
PSI-MI
MI:0970
inchi key
InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character
PMID:15889163
inchi key
The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
orchard
2009-10-28T01:20:40Z
p_patetheinylation
PSI-MI
MI:0971
phosphopantetheinylation
The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
PMID:19679086
p_patetheinylation
Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
orchard
2009-10-28T01:23:19Z
p_pantethinyl assay
PSI-MI
phosphopantetheinylation
MI:0972
phosphopantetheinylase assay
Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
PMID:19346479
p_pantethinyl assay
Databases that contain curated experimental interaction data and exchanging it with other IMEx databases.
orchard
2009-12-18T10:24:37Z
PSI-MI
MI:0973
imex source
Databases that contain curated experimental interaction data and exchanging it with other IMEx databases.
PMID:17893861
Human and mouse experimentally verified interactions and pathways involved in innate immunity.
orchard
2010-04-09T03:11:54Z
InnateDB
PSI-MI
MI:0974
innatedb
Human and mouse experimentally verified interactions and pathways involved in innate immunity.
PMID:18766178
InnateDB
A fusion protein tag consisting of a portion of the constant region of IgG.
orchard
2010-04-21T02:18:04Z
PSI-MI
MI:0975
fc-igg tag
A fusion protein tag consisting of a portion of the constant region of IgG.
PMID:11757069
Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface.
orchard
2010-04-21T02:30:46Z
tirfs
PSI-MI
MI:0976
total internal reflection fluorescence spectroscopy
Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface.
PMID:9013655
tirfs
Prevents export of experiment and associated interactions to IMEx
orchard
2010-04-21T02:49:48Z
PSI-MI
MI:0977
no-imex-export
Prevents export of experiment and associated interactions to IMEx
PMID:17893861
Author given name for a participant, not commonly found in source databases.
orchard
2010-04-21T02:55:39Z
PSI-MI
MI:0978
author-name
Author given name for a participant, not commonly found in source databases.
PMID:14755292
Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor.
orchard
2010-04-21T03:04:54Z
oxidoreduct assay
PSI-MI
MI:0979
oxidoreductase assay
Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor.
PMID:14755292
oxidoreduct assay
The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction.
orchard
2010-04-21T03:18:09Z
tag enzyme assay
PSI-MI
MI:0980
tag visualisation by enzyme assay
The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction.
PMID:14755292
tag enzyme assay
The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction.
orchard
2010-04-21T03:34:14Z
tag perox activity
PSI-MI
MI:0981
tag visualisation by peroxidase activity
The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction.
PMID:14755292
tag perox activity
Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field.
orchard
2010-04-26T10:30:36Z
electrophoresis
PSI-MI
MI:0982
electrophoretic mobility-based method
Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field.
PMID:19517512
electrophoresis
GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted
into the gas phase by a charged reduced electrospray process. The generated particles, each
containing one protein molecule with a +1 charge, are separated according to size in a differential
mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry,
this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass.
orchard
2010-04-26T10:36:41Z
PSI-MI
MI:0983
gemma
GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted
into the gas phase by a charged reduced electrospray process. The generated particles, each
containing one protein molecule with a +1 charge, are separated according to size in a differential
mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry,
this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass.
PMID:16861739
The measurement of the removal of an amine group from a molecule.
orchard
2010-04-26T10:45:01Z
aminase assay
deamination
PSI-MI
MI:0984
deamination assay
The measurement of the removal of an amine group from a molecule.
PMID:14755292
aminase assay
deamination
The removal of an amine group from a molecule.
orchard
2010-04-26T10:49:06Z
deamination
PSI-MI
MI:0985
deamination reaction
The removal of an amine group from a molecule.
PMID:14760721
deamination
The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
orchard
2010-04-26T10:52:22Z
strand elongation
PSI-MI
MI:0986
nucleic acid strand elongation reaction
The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
PMID:159156
strand elongation
The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
orchard
2010-04-26T11:00:08Z
rna elongation
PSI-MI
MI:0987
rna strand elongation
The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
PMID:14755292
rna elongation
Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK).
orchard
2010-04-26T11:07:37Z
PSI-MI
MI:0988
strep tag
Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK).
PMID:17571060
The measurement of the addition of an amine group to a molecule.
orchard
2010-04-26T11:20:23Z
amidation
PSI-MI
MI:0989
amidase assay
The measurement of the addition of an amine group to a molecule.
PMID:14760721
amidation
The cleavage of a biomolecule either into its component parts or sub-parts.
orchard
2010-04-26T11:27:22Z
cleavage
PSI-MI
MI:0990
cleavage assay
The cleavage of a biomolecule either into its component parts or sub-parts.
PMID:14760721
cleavage
The cleavage of a lipid molecule from a larger biomolecule.
orchard
2010-04-26T11:30:12Z
PSI-MI
MI:0991
lipoprotein cleavage assay
The cleavage of a lipid molecule from a larger biomolecule.
PMID:14760721
Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue.
orchard
2010-04-26T12:27:47Z
defarnesylation assay
PSI-MI
MI:0992
defarnesylase assay
Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue.
PMID:14760721
defarnesylation assay
Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue.
orchard
2010-04-26T12:36:51Z
degeranylation assay
PSI-MI
MI:0993
degeranylase assay
Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue.
PMID:14760721
degeranylation assay
measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue.
orchard
2010-04-26T12:39:30Z
demyristoylation assay
PSI-MI
MI:0994
demyristoylase assay
measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue.
PMID:14760721
demyristoylation assay
Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues.
orchard
2010-04-26T12:42:00Z
depalmitoylation assay
PSI-MI
MI:0995
depalmitoylase assay
Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues.
PMID:14760721
depalmitoylation assay
Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue.
orchard
2010-04-26T12:50:38Z
deformylase reaction
PSI-MI
deformylation
MI:0996
deformylase assay
Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue.
PMID:14760721
deformylase reaction
Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
orchard
2010-04-26T12:54:02Z
ubiquitinase assay
PSI-MI
ubiquitination
MI:0997
ubiquitinase assay
Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
PMID:14760721
ubiquitinase assay
Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
orchard
2010-04-26T12:56:41Z
deubiquitinase assay
PSI-MI
deubiquinase assay
deubiquitination
MI:0998
deubiquitinase assay
Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
PMID:14760721
deubiquitinase assay
Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group.
orchard
2010-04-26T01:01:44Z
PSI-MI
MI:0999
formylase assay
Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group.
PMID:14760721
Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues.
orchard
2010-04-26T01:05:19Z
PSI-MI
MI:1000
hydroxylase assay
Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues.
PMID:14760721
The covalent binding of a lipid group to a peptide chain.
orchard
2010-04-26T01:09:49Z
PSI-MI
lipidation
MI:1001
lipidase assay
The covalent binding of a lipid group to a peptide chain.
PMID:14760721
Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid.
orchard
2010-04-26T01:16:11Z
PSI-MI
myristoylation
MI:1002
myristoylase assay
Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid.
PMID:14707621
Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).
orchard
2010-04-26T01:20:07Z
geranylgeranylase
PSI-MI
geranylgeranylation
MI:1003
geranylgeranylase assay
Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).
PMID:14760721
geranylgeranylase
Measurement of the covalent attachment of palmitic acid to a protein.
orchard
2010-04-26T01:27:50Z
palmitoylase assay
PSI-MI
myristoylation
MI:1004
palmitoylase assay
Measurement of the covalent attachment of palmitic acid to a protein.
PMID:14760721
palmitoylase assay
Measurement of the addition of one or more ADP-ribose moieties to molecules.
orchard
2010-04-26T01:30:24Z
adp ribosylase
PSI-MI
adp ribosylation
MI:1005
adp ribosylase assay
Measurement of the addition of one or more ADP-ribose moieties to molecules.
PMID:14760721
adp ribosylase
Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
orchard
2010-04-26T01:34:07Z
PSI-MI
MI:1006
deglycosylase assay
Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
PMID:14760721
Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
orchard
2010-04-26T01:35:37Z
PSI-MI
glycosylation
MI:1007
glycosylase assay
Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
PMID:14760721
Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
orchard
2010-04-26T01:37:31Z
PSI-MI
sumoylation
MI:1008
sumoylase assay
Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
PMID:14760721
Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
orchard
2010-04-26T01:38:56Z
PSI-MI
desumylation
MI:1009
desumoylase assay
Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
PMID:14760721
Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
orchard
2010-04-26T01:41:40Z
PSI-MI
neddylation
MI:1010
neddylase assay
Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
PMID:14760721
Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
orchard
2010-04-26T01:42:49Z
PSI-MI
deneddylation
MI:1011
deneddylase assay
Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
PMID:14760721
38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide.
orchard
2010-04-29T08:42:26Z
PSI-MI
steptavidin binding peptide
MI:1012
sbp
38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide.
PMID:117222181
Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range.
http://www.ensemblgenomes.org
orchard
2010-05-06T08:09:20Z
search-url:
PSI-MI
MI:1013
ensemblgenomes
Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range.
http://www.ensemblgenomes.org
PMID:19884133
search-url:
http://ensemblgenomes.org/search/eg/${ac}
STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.
orchard
2010-07-15T11:00:57Z
PSI-MI
MI:1014
string
STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.
PMID:18940858
dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome.
orchard
2010-07-29T01:19:40Z
id-validation-regexp:
PSI-MI
MI:1015
dictybase
id-validation-regexp:
DDB_G(0-9){7}
Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction.
orchard
2010-11-11T10:39:37Z
frap
PSI-MI
MI:1016
fluorescence recovery after photobleaching
Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction.
PMID:15695095
PMID:17711354
frap
Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR.
orchard
2010-11-11T10:58:47Z
rna-ip
PSI-MI
rip
MI:1017
rna immunoprecipitation
Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR.
PMID:18265380
rna-ip
A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home
orchard
2010-11-11T11:04:13Z
PSI-MI
MI:1018
deltamass
A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home
PMID:8322616
Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate.
orchard
2010-11-11T11:30:47Z
PSI-MI
MI:1019
protein phosphatase assay
A carbonyl-reactive fluorescent labelling dye.
orchard
2010-11-11T11:35:48Z
hilyte 488
PSI-MI
MI:1020
hilyte fluor 488
A carbonyl-reactive fluorescent labelling dye.
PMID:19795889
hilyte 488
Nonfluorescent dye, act as a quencher in FRET assays.
orchard
2010-11-11T11:40:16Z
PSI-MI
MI:1021
qx 520
A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids.
orchard
2010-11-11T11:55:40Z
PSI-MI
MI:1022
field flow fractionation
A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids.
PMID:959835
A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell.
orchard
2010-11-11T12:10:26Z
PSI-MI
MI:1023
luminogreen
A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell.
PMID:19935683
A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
orchard
2010-11-11T12:17:54Z
sem
PSI-MI
MI:1024
scanning electron microscopy
A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
PMID:20463740
sem
A database of protein modifications for mass spectrometry. www.unimod.org
orchard
2010-11-11T12:24:10Z
PSI-MI
MI:1025
unimod
A database of protein modifications for mass spectrometry. www.unimod.org
PMID:15174123
Measurement of a modification that converts an L-histidine residue to diphthamide.
orchard
2010-11-11T12:33:29Z
diphtamidase
PSI-MI
MI:1026
diphtamidase assay
Measurement of a modification that converts an L-histidine residue to diphthamide.
PMID:14760721
diphtamidase
A modification that converts an L-histidine residue to diphthamide.
orchard
2010-11-11T12:36:51Z
diphthamidation
PSI-MI
MI:1027
diphtamidation reaction
A modification that converts an L-histidine residue to diphthamide.
PMID:14760721
diphthamidation
Chromatin-bound protein networks isolated using magnetic beads coated with antibodies.
orchard
2010-11-11T12:58:52Z
mch-ip
PSI-MI
MI:1028
modified chromatin immunoprecipitation
Chromatin-bound protein networks isolated using magnetic beads coated with antibodies.
PMID:19106085
mch-ip
Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified.
orchard
2010-11-11T01:03:21Z
pich
PSI-MI
MI:1029
proteomics of isolated chromatin segments
Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified.
PMID:19135898
pich
Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule.
orchard
2010-11-11T01:15:19Z
excimer fluoresc
PSI-MI
MI:1030
excimer fluorescence
Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule.
PMID:18480256
excimer fluoresc
A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding.
orchard
2010-11-11T01:24:11Z
protein folding
PSI-MI
MI:1031
protein folding/unfolding
A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding.
PMID:19940245
protein folding
Fluorescent tag - maleimide couples to thiols.
orchard
2010-11-11T01:33:13Z
atto 488 maleimide
PSI-MI
atto488
MI:1032
atto 488
Fluorescent tag - maleimide couples to thiols.
PMID:14760721
Fluorescent tag - maleimide couples to thiols.
orchard
2010-11-11T01:39:43Z
PSI-MI
atto550
MI:1033
atto 550
Fluorescent tag - maleimide couples to thiols.
PMID:14760721
Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids.
orchard
2010-11-11T01:43:11Z
PSI-MI
MI:1034
nuclease assay
Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids.
PMID:14760721
Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA.
orchard
2010-11-11T01:45:29Z
deoxyribonuclease
PSI-MI
MI:1035
deoxyribonuclease assay
Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA.
PMID:14760721
deoxyribonuclease
Experiments monitoring
interactions of nucleotide exchange factors with their cognate nucleotidases.
orchard
2010-11-11T01:54:00Z
nucleotide exchange
PSI-MI
MI:1036
nucleotide exchange assay
Experiments monitoring
interactions of nucleotide exchange factors with their cognate nucleotidases.
PMID:14760721
nucleotide exchange
The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light.
orchard
2010-11-11T02:54:08Z
renilla luciferase
PSI-MI
MI:1037
Split renilla luciferase complementation
The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light.
PMID:12705589
PMID:22070901
renilla luciferase
Measures selective electrical response to molecules binding to the immobilised bait.
orchard
2010-11-11T03:11:33Z
nanowire transistor
PSI-MI
MI:1038
silicon nanowire field-effect transistor
Measures selective electrical response to molecules binding to the immobilised bait.
PMID:20080536
nanowire transistor
The C-terminal region of a sequence, exact coordinates not available.
orchard
2010-11-11T03:20:34Z
c-term range
PSI-MI
MI:1039
c-terminal range
The C-terminal region of a sequence, exact coordinates not available.
PMID:14760721
c-term range
The N-terminal region of a sequence, exact coordinates not available.
orchard
2010-11-11T03:27:57Z
n-term range
PSI-MI
MI:1040
n-terminal range
The N-terminal region of a sequence, exact coordinates not available.
PMID:14760721
n-term range
Alternative name or descriptor for an entity.
orchard
2010-12-02T10:26:35Z
PSI-MI
MI:1041
synonym
Alternative name or descriptor for an entity.
PMID:14681455
PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals.
orchard
2010-12-08T01:20:48Z
search-url:
pmc
PSI-MI
MI:1042
pubmed central
PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals.
PMID:12519941
search-url:
http://europepmc.org/abstract/PMC/${ac}
pmc
A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)
orchard
2011-01-06T01:16:48Z
id-validation-regexp:
PSI-MI
MI:1043
flannotator
A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)
PMID:19126575
id-validation-regexp:
CPTO-[0-9]{6}
NSF funded annotation project.
orchard
2011-02-11T01:33:28Z
PSI-MI
RGAP
MI:1044
rice genome annotation project
NSF funded annotation project.
PMID:17145706
Indicates source, depth and standards by which an entry has been added to a database.
orchard
2011-03-11T01:16:55Z
PSI-MI
MI:1045
curation content
Indicates source, depth and standards by which an entry has been added to a database.
PMID:14755292
Defines an interaction by the type of binary molecule pairs it can generates.
orchard
2011-03-11T01:19:27Z
PSI-MI
MI:1046
interacting molecules
Defines an interaction by the type of binary molecule pairs it can generates.
PMID:14755292
Interaction between a protein or peptide and a corresponding protein or peptide.
orchard
2011-03-11T01:21:28Z
PSI-MI
MI:1047
protein-protein
Interaction between a protein or peptide and a corresponding protein or peptide.
PMID:14755292
Interaction between a small molecule and a corresponding protein or peptide.
orchard
2011-03-11T01:22:36Z
PSI-MI
MI:1048
smallmolecule-protein
Interaction between a small molecule and a corresponding protein or peptide.
PMID:14755292
Interaction between a nucleic acid and a corresponding protein or peptide.
orchard
2011-03-11T01:23:29Z
PSI-MI
MI:1049
nucleicacid-protein
Interaction between a nucleic acid and a corresponding protein or peptide.
PMID:14755292
Provides an indication of the level of post-processing of experimental data relating to specific binary pairs
orchard
2011-03-11T01:25:29Z
PSI-MI
MI:1050
interaction representation
Provides an indication of the level of post-processing of experimental data relating to specific binary pairs
PMID:14755292
Binary pair is defined by a single piece of experimental evidence.
orchard
2011-03-11T01:27:00Z
PSI-MI
MI:1051
evidence
Binary pair is defined by a single piece of experimental evidence.
PMID:14755292
Binary pair is defined by multiple pieces of experimental evidence which have been clustered together.
orchard
2011-03-11T01:28:50Z
PSI-MI
MI:1052
clustered
Binary pair is defined by multiple pieces of experimental evidence which have been clustered together.
PMID:14755292
The source of the data entered into the database.
orchard
2011-03-11T01:32:16Z
PSI-MI
MI:1053
data source
The source of the data entered into the database.
PMID:14755292
Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter.
orchard
2011-03-11T01:33:48Z
PSI-MI
MI:1054
experimentally-observed
Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter.
PMID:14755292
Data has been directly curated into this database from the paper describing the experimental evidence
orchard
2011-03-11T01:35:12Z
PSI-MI
MI:1055
internally-curated
Data has been directly curated into this database from the paper describing the experimental evidence
PMID:14755292
The data has been entered into the database following extraction from the literature by a computational process.
orchard
2011-03-11T01:36:34Z
PSI-MI
MI:1056
text-mining
The data has been entered into the database following extraction from the literature by a computational process.
PMID:14755292
The interaction has been predicted using a specific algorithm.
orchard
2011-03-11T01:37:47Z
PSI-MI
MI:1057
predicted
The interaction has been predicted using a specific algorithm.
PMID:14755292
The data has been imported into the database form an external resource.
orchard
2011-03-11T01:39:23Z
PSI-MI
MI:1058
imported
The data has been imported into the database form an external resource.
PMID:14755292
The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export.
orchard
2011-03-11T01:41:16Z
PSI-MI
MI:1059
complex expansion
The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export.
PMID:14755292
Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait.
orchard
2011-03-11T01:42:35Z
PSI-MI
MI:1060
spoke expansion
Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait.
PMID:14755292
Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other.
orchard
2011-03-11T01:45:52Z
PSI-MI
MI:1061
matrix expansion
Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other.
PMID:14755292
Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity.
orchard
2011-03-11T01:49:08Z
PSI-MI
MI:1062
bipartite expansion
Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity.
PMID:14755292
ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided.
orchard
2011-06-21T02:40:16Z
PSI-MI
MI:1063
consensuspathdb
ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided.
PMID:21071422
A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction.
orchard
2011-07-05T07:13:57Z
confidence
scoring system
PSI-MI
MI:1064
interaction confidence
A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction.
PMID:19420069
confidence
Methods based on counting the number of replicates in which an interaction has been observed.
orchard
2011-07-05T07:22:02Z
replication score
PSI-MI
replication-based scoring system
MI:1065
replication-based confidence
Methods based on counting the number of replicates in which an interaction has been observed.
PMID:19420069
replication score
Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc.
orchard
2011-07-05T07:38:50Z
structure score
structure-based scoring system
PSI-MI
MI:1066
structure-based confidence
Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc.
PMID:15044803
structure score
Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms.
orchard
2011-07-05T07:46:28Z
function score
function-based scoring system
PSI-MI
MI:1067
function-based confidence
Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms.
PMID:21443973
function score
Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues.
orchard
2011-07-05T07:52:36Z
colocation score
location-based scoring system
PSI-MI
MI:1068
location-based confidence
Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues.
PMID:18624398
colocation score
Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison
with genetic interactions.
orchard
2011-07-05T07:59:13Z
network score
network-based scoring system
PSI-MI
MI:1069
network-based confidence
Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison
with genetic interactions.
PMID:19010802
network score
network-based scoring system
Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules.
orchard
2011-07-05T08:09:46Z
standard score
standard-based scoring system
PSI-MI
gold standard
MI:1070
standard-based confidence
Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules.
PMID:16554755
standard score
Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining.
orchard
2011-07-05T08:24:46Z
literature score
literature-based scoring system
PSI-MI
MI:1071
literature-based confidence
Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining.
PMID:18005433
literature score
The confidence of an interaction is assessed on the number of different methods by which it is observed.
orchard
2011-07-05T08:42:47Z
method score
method-based scoring system
PSI-MI
MI:1072
method-based confidence
The confidence of an interaction is assessed on the number of different methods by which it is observed.
PMID:19420069
method score
Confidence in an interaction is based on a measure of the probability of these molecules interacting.
orchard
2011-07-05T08:50:05Z
statistical score
statistical-based scoring system
PSI-MI
MI:1073
statistical-based confidence
Confidence in an interaction is based on a measure of the probability of these molecules interacting.
PMID:19420069
statistical score
The protein of interest is expressed as a fusion to a RGS(His)n tag.
orchard
2011-07-05T09:52:28Z
rgs-his
PSI-MI
MI:1074
rgs-his tag
The protein of interest is expressed as a fusion to a RGS(His)n tag.
PMID:19223579
rgs-his
The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number.
orchard
2011-07-05T10:03:13Z
beilstein
PSI-MI
MI:1075
beilstein
The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number.
PMID:ID:11604014
beilstein
The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets.
orchard
2011-07-05T10:09:35Z
European Inventory of Existing Commercial Chemical Substances
einecs
PSI-MI
MI:1076
einecs
The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets.
PMID:17125194
einecs
Comprehensive information on chemicals, drugs, and biologicals.
orchard
2011-07-05T10:15:56Z
merck index
PSI-MI
MI:1077
merck index
Comprehensive information on chemicals, drugs, and biologicals.
PMID:17832605
merck index
PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
orchard
2011-07-05T10:27:50Z
plantgdb
PSI-MI
MI:1078
plantgdb
PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
PMID:18063570
plantgdb
The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap.
orchard
2011-07-05T10:32:10Z
ratmap
PSI-MI
MI:1079
ratmap
The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap.
PMID:15608244
ratmap
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
orchard
2011-07-05T10:34:26Z
The Arabidopsis Information Resource
tair
PSI-MI
MI:1080
tair
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
PMID:20521243
tair
The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR).
orchard
2011-07-05T10:44:11Z
J. Craig Venter Institute
The Institute for Genomic Research
tigr/jcvi
PSI-MI
MI:1081
tigr/jcvi
The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR).
PMID:18287690
The Institute for Genomic Research
tigr/jcvi
Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools.
orchard
2011-07-05T10:53:21Z
The Zebrafish Model Organism Database
zfin
PSI-MI
MI:1082
zfin
Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools.
PMID:21036866
zfin
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
orchard
2011-07-05T10:59:06Z
Clusters of Orthologous Groups
cogg
PSI-MI
MI:1083
cog
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
PMID:11125040
cogg
Any molecule that is able to transfer a photon to another chemical species.
orchard
2011-07-05T11:03:38Z
photon donor
PSI-MI
MI:1084
photon donor
Any molecule that is able to transfer a photon to another chemical species.
PMID:14755292
photon donor
Molecule to which a photon may be transferred from an photon donor.
orchard
2011-07-05T11:06:47Z
photon acceptor
PSI-MI
MI:1085
photon acceptor
Molecule to which a photon may be transferred from an photon donor.
PMID:14755292
photon acceptor
Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time.
orchard
2011-07-05T11:12:25Z
equilib. dialysis
PSI-MI
MI:1086
equilibrium dialysis
Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time.
PMID:21609686
equilib. dialysis
Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule.
orchard
2011-07-05T11:19:37Z
mab blockade
PSI-MI
MI:1087
monoclonal antibody blockade
Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule.
PMID:14755292
mab blockade
Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor.
orchard
2011-07-05T11:24:37Z
phenotype-based
PSI-MI
MI:1088
phenotype-based detection assay
Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor.
PMID:14755292
phenotype-based
Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules.
orchard
2011-07-05T11:27:16Z
nuclear translocation
PSI-MI
MI:1089
nuclear translocation assay
Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules.
PMID:21684252
nuclear translocation
Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione.
orchard
2011-07-05T12:03:52Z
bimane
PSI-MI
MI:1090
bimane label
Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione.
PMID:7378449
bimane
Title of the publication.
orchard
2011-07-05T12:07:49Z
title
PSI-MI
MI:1091
publication title
Title of the publication.
PMID:14755292
title
Fluorescent dyes - spectral range 500 to 700 nm.
orchard
2011-07-05T12:14:52Z
atto label
PSI-MI
MI:1092
atto label
Fluorescent dyes - spectral range 500 to 700 nm.
PMID:14755292
atto label
Attributes specific to the publication.
orchard
2011-07-05T12:55:21Z
bib attribute
publication attribute
PSI-MI
MI:1093
bibliographic attribute name
Attributes specific to the publication.
PMID:14755292
bib attribute
Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences.
orchard
2011-07-06T07:57:46Z
genome databases
PSI-MI
MI:1094
genome databases
Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences.
PMID:14755292
genome databases
HGNC is the nomenclature committee responsible for the naming of human genes.
orchard
2011-07-06T08:02:03Z
Human Genome Nomenclature Committee
hgnc
PSI-MI
MI:1095
hgnc
HGNC is the nomenclature committee responsible for the naming of human genes.
PMID:20929869
Human Genome Nomenclature Committee
hgnc
Databases dedicated to the collection and annotation of protein sequences.
orchard
2011-07-06T08:10:40Z
protein seq db
PSI-MI
MI:1096
protein sequence databases
Databases dedicated to the collection and annotation of protein sequences.
PMID:21447597
protein seq db
UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation.
orchard
2011-07-06T08:14:40Z
uniprot
PSI-MI
MI:1097
uniprot
UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation.
PMID:21051339
uniprot
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator.
http://www.uniprot.org
orchard
2011-07-06T08:17:34Z
id-validation-regexp:
search-url:
UniProt
swiss-prot
PSI-MI
MI:1098
uniprot/swiss-prot
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator.
http://www.uniprot.org
PMID:14681372
PMID:21447597
id-validation-regexp:
(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
search-url:
https://www.uniprot.org/uniprotkb/${ac}/entry
UniProt
swiss-prot
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification.
http://www.uniprot.org
orchard
2011-07-06T08:20:24Z
id-validation-regexp:
search-url:
UniProt
trembl
PSI-MI
MI:1099
uniprot/trembl
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification.
http://www.uniprot.org
PMID:14681372
PMID:21447597
id-validation-regexp:
(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
search-url:
https://www.uniprot.org/uniprotkb/${ac}/entry
UniProt
trembl
Molecules showing activity in a living system but not encoded by a genomic sequence.
orchard
2011-07-06T08:23:48Z
bioactive entity
PSI-MI
MI:1100
bioactive entity
Molecules showing activity in a living system but not encoded by a genomic sequence.
PMID:14760721
bioactive entity
The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes).
orchard
2014-01-21T10:14:02Z
PSI-MI
MI:1101
standard inchi key
The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes).
PMID:23343401
Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database.
orchard
2011-07-06T09:07:02Z
mapped-identity
PSI-MI
MI:1102
mapped-identity
Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database.
PMID:14760721
mapped-identity
NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp
transitions, due to averaging of anisotropic NMR interactions
by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations.
orchard
2011-07-06T09:16:45Z
solution nmr
solution state nmr
PSI-MI
MI:1103
solution state nmr
NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp
transitions, due to averaging of anisotropic NMR interactions
by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations.
PMID:20951674
solution nmr
Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full
effects of anisotropic or orientation-dependent interactions are observed in the spectrum.
orchard
2011-07-06T09:23:11Z
solid state nmr
ssnmr
PSI-MI
MI:1104
solid state nmr
Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full
effects of anisotropic or orientation-dependent interactions are observed in the spectrum.
PMID:20951674
solid state nmr
BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/).
orchard
2011-07-06T09:43:03Z
biocyc
PSI-MI
MI:1105
biocyc
BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/).
PMID:19850718
biocyc
Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways.
orchard
2011-07-07T02:52:18Z
pathways db
PSI-MI
MI:1106
pathways database
Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways.
PMID:14755292
pathways db
Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/).
orchard
2011-07-07T03:00:27Z
pathways interaction database
pid
PSI-MI
MI:1107
pid
Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/).
PMID:18832364
pid
BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways.
orchard
2011-07-07T03:05:55Z
biocarta
PSI-MI
MI:1108
biocarta
BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways.
PMID:14760721
biocarta
Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes.
orchard
2011-07-08T08:00:33Z
gene dbs
PSI-MI
MI:1109
gene database
Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes.
PMID:14755292
gene dbs
Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
orchard
2011-08-03T11:14:11Z
predicted
PSI-MI
MI:1110
predicted interaction
Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
PMID:14755292
predicted
Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
orchard
2011-09-29T03:19:21Z
PSI-MI
MI:1111
two hybrid bait or prey pooling approach
Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
PMID:11283351
PMID:20946815
Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
orchard
2011-09-29T03:21:01Z
PSI-MI
MI:1112
two hybrid prey pooling approach
Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
PMID:20946815
def
orchard
2011-09-29T03:23:17Z
PSI-MI
MI:1113
two hybrid bait and prey pooling approach
def
PMID:10655498
A database of viral-host interactions.
orchard
2011-10-19T01:28:24Z
PSI-MI
MI:1114
virhostnet
A database of viral-host interactions.
PMID:18984613
SPIKE
orchard
2011-11-09T10:27:04Z
Signalling Pathways Integrated Knowledge Engine
PSI-MI
MI:1115
spike
SPIKE
PMID:21097778
GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity.
orchard
2011-11-09T02:13:28Z
PSI-MI
MI:1116
genemania
GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity.
PMID:20576703
TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided.
orchard
2011-11-16T11:09:25Z
Termini-oriented protein function inferred database
PSI-MI
MI:1117
topfind
TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided.
PMID:21822272
A variation of yellow fluorescent protein derived from eGFP.
orchard
2011-11-24T03:17:33Z
eyfp
PSI-MI
MI:1118
enhanced yellow fluorescent protein tag
A variation of yellow fluorescent protein derived from eGFP.
PMID:10929120
eyfp
n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
orchard
2011-11-24T03:30:18Z
PSI-MI
N-terminal part of YFP
MI:1119
nYFP
n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
PMID:11983170
c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
orchard
2011-11-24T03:43:07Z
PSI-MI
C-terminal part of YFP
MI:1120
cYFP
c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
PMID:11983170
c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
orchard
2011-11-24T03:43:30Z
PSI-MI
C-terminal part of EYFP
MI:1121
ceYFP
c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
PMID:11983170
n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
orchard
2011-11-24T03:44:40Z
PSI-MI
N-terminal part of EYFP
MI:1122
neYFP
n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
PMID:11983170
BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org
orchard
2011-11-28T08:55:26Z
PSI-MI
MI:1123
bindingdb
BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org
PMID:11812264
PMID:11836221
PMID:11987162
PMID:17145705
Allows the user to browse and search pathways across multiple public pathway databases.
http://www.pathwaycommons.org
orchard
2011-11-30T03:04:14Z
Pathway Commons
PSI-MI
MI:1124
pathwaycommons
Allows the user to browse and search pathways across multiple public pathway databases.
http://www.pathwaycommons.org
PMID:21071392
The defined region of protein which makes physical contact with the interacting partner.
orchard
2012-01-03T01:10:25Z
direct binding
PSI-MI
MI:1125
Should normally be used with X-ray crystallography or NMR data.
direct binding region
The defined region of protein which makes physical contact with the interacting partner.
PMID:14755292
direct binding
Intra-molecular interaction between two or more regions of the same molecule.
orchard
2012-01-03T01:19:22Z
PSI-MI
MI:1126
The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.
self interaction
Intra-molecular interaction between two or more regions of the same molecule.
PMID:14755292
Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
orchard
2012-01-03T01:21:58Z
PSI-MI
MI:1127
The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.
putative self interaction
Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
PMID:14755292
Region of a molecule whose mutation or deletion totally disrupts an interaction strength.
orchard
2012-01-03T01:36:37Z
mutation disrupting strength
PSI-MI
MI:1128
mutation disrupting interaction strength
Region of a molecule whose mutation or deletion totally disrupts an interaction strength.
PMID:14755292
mutation disrupting strength
Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction)..
orchard
2012-01-03T01:37:43Z
mutation disrupting rate
PSI-MI
MI:1129
mutation disrupting interaction rate
Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction)..
PMID:14755292
mutation disrupting rate
Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
orchard
2012-01-03T01:38:58Z
mutation decreasing rate
PSI-MI
MI:1130
mutation decreasing interaction rate
Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
PMID:14755292
mutation decreasing rate
Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
orchard
2012-01-03T01:45:09Z
mutation increasing rate
PSI-MI
MI:1131
mutation increasing interaction rate
Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
PMID:14577292
mutation increasing rate
Region of a molecule whose mutation or deletion increases significantly interaction strength.
orchard
2012-01-03T01:45:42Z
mutation increasing strength
PSI-MI
MI:1132
mutation increasing interaction strength
Region of a molecule whose mutation or deletion increases significantly interaction strength.
PMID:14577292
mutation increasing strength
Region of a molecule whose mutation or deletion decreases significantly interaction strength.
orchard
2012-01-03T01:48:40Z
mutation decreasing strength
PSI-MI
MI:1133
mutation decreasing interaction strength
Region of a molecule whose mutation or deletion decreases significantly interaction strength.
PMID:14755292
mutation decreasing strength
mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm.
orchard
2012-01-03T02:53:23Z
mcherry
PSI-MI
MI:1134
mcherry fluorescent protein tag
mcherry
Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively.
orchard
2012-01-03T03:05:01Z
venus
PSI-MI
MI:1135
venus fluorescent protein tag
Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively.
PMID:14755292
venus
Monomeric coral fluorescent reporter protein.
orchard
2012-01-03T03:10:28Z
kusabira-green
PSI-MI
MI:1136
kusabira-green protein tag
Monomeric coral fluorescent reporter protein.
PMID:14755292
kusabira-green
The measurement of a the introduction of a carboxylic acid group into a substrate.
orchard
2012-01-03T03:17:56Z
carboxylation assay
PSI-MI
MI:1137
carboxylation assay
The measurement of a the introduction of a carboxylic acid group into a substrate.
PMID:14755292
carboxylation assay
The measurement of a the introduction of a carboxylic acid group into a substrate.
orchard
2012-01-03T03:22:04Z
decarboxxylation assay
PSI-MI
MI:1138
decarboxylation assay
The measurement of a the introduction of a carboxylic acid group into a substrate.
PMID:14755292
decarboxxylation assay
Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
orchard
2012-01-03T03:24:05Z
carboxylation
PSI-MI
MI:1139
carboxylation reaction
Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
PMID:14755292
carboxylation
Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
orchard
2012-01-03T03:31:42Z
decarboxylation
PSI-MI
MI:1140
decarboxylation reaction
Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
PMID:14755292
decarboxylation
S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser.
orchard
2012-01-03T03:37:51Z
PSI-MI
MI:1141
s tag
S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser.
PMID:14755292
The measurement of the addition of an aminoacyl group to a compound.
orchard
2012-01-03T03:46:46Z
aminoacylation
PSI-MI
MI:1142
aminoacylation assay
The measurement of the addition of an aminoacyl group to a compound.
PMID:14755292
aminoacylation
Aminoacylation is the process of adding an aminoacyl group to a compound.
orchard
2012-01-03T03:49:50Z
aminoacylation
PSI-MI
MI:1143
aminoacylation reaction
Aminoacylation is the process of adding an aminoacyl group to a compound.
PMID:14755292
aminoacylation
Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A.
orchard
2012-01-03T03:54:35Z
protein a visualisation
PSI-MI
MI:1144
protein a tag visualisation
Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A.
PMID:14755292
protein a visualisation
A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
orchard
2012-01-03T04:04:16Z
PSI-MI
MI:1145
phospholipase assay
A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
PMID:14755292
Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
orchard
2012-01-03T04:08:14Z
PSI-MI
MI:1146
phospholipase reaction
Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
PMID:14755292
Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.
orchard
2012-01-03T04:18:27Z
ampylation assay
PSI-MI
MI:1147
ampylation assay
Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.
PMID:14755292
ampylation assay
AMPylation, previously known as adenylylation, is formation of a
phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys
(RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.
orchard
2012-01-03T04:21:12Z
ampylation
PSI-MI
MI:1148
ampylation reaction
AMPylation, previously known as adenylylation, is formation of a
phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys
(RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.
PMID:14755292
ampylation
A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema.
orchard
2012-06-07T12:21:30Z
cooperativity
PSI-MI
MI:1149
cooperative interaction
A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema.
PMID:18641616
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id.
orchard
2012-06-07T12:26:42Z
PSI-MI
MI:1150
affected interaction
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id.
PMID:18641616
Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction.
orchard
2012-06-07T12:30:48Z
PSI-MI
MI:1151
participant-ref
Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction.
PMID:18641616
This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification.
orchard
2012-06-07T12:35:01Z
cooperative coupling
PSI-MI
MI:1152
cooperative effect value
This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification.
PMID:18706817
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished.
orchard
2012-06-07T12:40:41Z
PSI-MI
MI:1153
cooperative effect outcome
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished.
PMID:18706817
This term specifies that an interaction augments a subsequent interaction.
orchard
2012-06-07T12:42:19Z
PSI-MI
MI:1154
positive cooperative effect
This term specifies that an interaction augments a subsequent interaction.
PMID:18706817
This term specifies that an interaction diminishes a subsequent interaction.
orchard
2012-06-07T12:43:48Z
PSI-MI
MI:1155
negative cooperative effect
This term specifies that an interaction diminishes a subsequent interaction.
PMID:18706817
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect.
orchard
2012-06-07T12:46:30Z
PSI-MI
MI:1156
cooperative mechanism
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect.
PMID:18641616
Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event.
orchard
2012-06-07T12:50:20Z
allosteric regulation
PSI-MI
MI:1157
allostery
Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event.
PMID:18641616
PMID:18706817
A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists.
orchard
2012-06-07T12:52:44Z
PSI-MI
MI:1158
pre-assembly
A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists.
PMID:18641616
A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id.
orchard
2012-06-07T12:55:09Z
PSI-MI
MI:1159
allosteric molecule
A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id.
PMID:18706817
A ligand that elicits an allosteric response upon binding to a target molecule.
orchard
2012-06-07T12:57:50Z
PSI-MI
MI:1160
allosteric effector
A ligand that elicits an allosteric response upon binding to a target molecule.
PMID:18706817
This term describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site.
orchard
2012-06-07T01:05:17Z
PSI-MI
MI:1161
allosteric response
An allosteric response in which the affinity of a molecule is altered.
orchard
2012-06-07T01:08:01Z
PSI-MI
MI:1162
allosteric k-type response
An allosteric response in which the affinity of a molecule is altered.
PMID:18706817
An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered.
orchard
2012-06-07T01:09:07Z
PSI-MI
MI:1163
allosteric v-type response
An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered.
PMID:18706817
The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector.
orchard
2012-06-07T01:10:45Z
PSI-MI
MI:1164
allosteric mechanism
The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties.
orchard
2012-06-07T01:16:20Z
PSI-MI
MI:1165
allosteric change in structure
The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties.
PMID:18706817
The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties.
orchard
2012-06-07T01:17:54Z
PSI-MI
MI:1166
allosteric change in dynamics
The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties.
PMID:18706817
This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled.
orchard
2012-06-07T01:19:57Z
PSI-MI
MI:1167
allostery type
This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled.
PMID:18706817
The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical.
orchard
2012-06-07T01:21:25Z
PSI-MI
MI:1168
heterotropic allostery
The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical.
PMID:18706817
The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical.
orchard
2012-06-07T01:22:35Z
PSI-MI
MI:1169
homotropic allostery
The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical.
PMID:18706817
This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components.
orchard
2012-06-07T01:24:42Z
PSI-MI
MI:1170
pre-assembly response
This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components.
PMID:18641616
The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex.
orchard
2012-06-07T01:25:50Z
PSI-MI
MI:1171
composite binding site formation
The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex.
PMID:18641616
The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction.
orchard
2012-06-07T01:26:56Z
PSI-MI
MI:1172
altered physicochemical compatibility
The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction.
PMID:22480932
The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present.
orchard
2012-06-07T01:28:07Z
PSI-MI
MI:1173
binding site hiding
The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present.
PMID:22480932
Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions.
orchard
2012-06-07T01:29:13Z
PSI-MI
MI:1174
configurational pre-organization
Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions.
PMID:18641616
A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id.
orchard
2012-06-07T01:33:16Z
allosteric ptm
PSI-MI
MI:1175
allosteric post-translational modification
A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id.
PMID:18706817
allosteric ptm
Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur.
orchard
2012-06-07T01:40:25Z
PSI-MI
gene regulatory region prediction
sequence based prediction of TG regulatory region binding sites for TF
MI:1176
sequence based prediction of gene regulatory region binding sites
Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur.
PMID:15131651
Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models.
orchard
2012-06-07T01:41:59Z
gene regulatory region phylogeny
PSI-MI
phylogenetic footprinting
MI:1177
phylogenetic profiling of predicted gene regulatory region binding sites
Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models.
PMID:12671656
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor.
orchard
2012-06-07T01:43:57Z
sequence based prediction of binding of TF to TG promoter
transcription factor prediction
PSI-MI
MI:1178
sequence based prediction of binding of transcription factor to transcribed gene regulatory elements
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor.
PMID:16381970
Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s
orchard
2012-06-07T01:47:03Z
partial nucleotide sequence
PSI-MI
MI:1179
partial nucleotide sequence identification
Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s
PMID:14755292
partial nucleotide sequence
Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
orchard
2012-06-07T01:52:27Z
partial dna sequence
PSI-MI
MI:1180
partial DNA sequence identification
Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
PMID:14755292
partial dna sequence
Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA.
orchard
2012-06-07T01:53:38Z
paired end tags
PSI-MI
MI:1181
paired end tags sequence identification
Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA.
PMID:19339662
paired end tags
Sequencing occurs during the course of the experiment. To sequence RNA, the usual method is first to reverse transcribe the sample to generate cDNA fragments.
orchard
2012-06-07T02:02:37Z
PSI-MI
MI:1182
full identification by RNA sequencing
Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified.
orchard
2012-06-07T02:08:36Z
PSI-MI
nuclease protection
MI:1183
nuclease footprinting
Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified.
PMID:7685766
DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site.
orchard
2012-06-07T02:13:03Z
DamID
PSI-MI
MI:1184
dna adenine methyltransferase identification
DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site.
PMID:10748524
DamID
Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization.
orchard
2012-06-07T02:22:19Z
tag DNA methyltransferase
PSI-MI
MI:1185
tag visualisation by dna adenine methyltransferase
Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization.
PMID:10748524
tag DNA methyltransferase
The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites.
orchard
2012-06-07T02:32:02Z
PSI-MI
MI:1186
dna methyltransferase tag
The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites.
PMID:10748524
A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis.
orchard
2012-06-07T02:41:40Z
PSI-MI
MI:1187
damip
A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis.
PMID:21472695
A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA.
orchard
2012-06-07T02:46:08Z
PSI-MI
MI:1188
tag visualisation by mutated dna adenine methyltransferase
In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points".
orchard
2012-06-07T02:54:00Z
methylation interference
PSI-MI
contact point analysis
methylation protection assay
MI:1189
methylation interference assay
In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points".
PMID:21720958
methylation interference
Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected.
orchard
2012-06-07T03:10:48Z
PSI-MI
MI:1190
hydroxy radical footprinting
Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected.
PMID:3090544
Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts.
orchard
2012-06-07T03:13:02Z
PSI-MI
MI:1191
ultraviolet (uv) footprinting
Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts.
PMID:2842760
PMID:6728031
This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
orchard
2012-06-07T03:19:22Z
PSI-MI
MI:1192
antisense oligonucleotides
This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
PMID:14755292
Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment.
orchard
2012-06-07T03:40:14Z
partial rna sequence
PSI-MI
MI:1193
partial RNA sequence identification
Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment.
PMID:14755292
partial rna sequence
Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR.
orchard
2012-06-07T03:47:13Z
RT-PCR
PSI-MI
RPCR
reverse PCR
MI:1194
reverse transcription pcr
Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR.
PMID:12958470
RT-PCR
Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.
orchard
2012-06-07T03:56:38Z
q-pcr
PSI-MI
QRT-PCR
RQ-PCR
RTQ-PCR
MI:1195
quantitative pcr
Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.
PMID:12958470
q-pcr
Technique used to measure the quantity of DNA amplified from RNA.
orchard
2012-06-07T04:04:42Z
QRT-PCR
PSI-MI
RTQ-PCR
MI:1196
quantitative reverse transcription pcr
Technique used to measure the quantity of DNA amplified from RNA.
PMID:12958470
QRT-PCR
To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured.
orchard
2012-06-07T04:13:30Z
RIA
PSI-MI
MI:1197
radioimmunoassay
To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured.
PMID:13846364.
Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
orchard
2012-06-07T04:17:12Z
PSI-MI
MI:1198
immunohistochemistry
Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PMID:16006601
Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
orchard
2012-06-07T04:21:23Z
PSI-MI
MI:1199
anti-tag immunohistochemistry
Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PMID:16006601
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
orchard
2012-06-07T04:22:00Z
PSI-MI
MI:1200
immunocytochemistry
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PMID:14755292
Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
orchard
2012-06-07T04:33:37Z
PSI-MI
MI:1201
anti-tag immunocytochemistry
Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PMID:14755292
Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)
orchard
2012-06-07T04:44:55Z
twin-strep-tag
PSI-MI
MI:1202
one-strep-tag
Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)
PMID:19688738
twin-strep-tag
Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
orchard
2012-06-07T04:56:59Z
PSI-MI
MI:1203
split luciferase complementation
Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
PMID:20734273
Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
orchard
2012-06-07T05:05:36Z
PSI-MI
MI:1204
split firefly luciferase complementation
Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
PMID:20734273
PMID:22070901
Luciferase is a generic term for the class of oxidative enzymes used in bioluminescence and is distinct from a photoprotein. Luciferase catalyzes a bioluminescent reaction which requires the substrate luciferin as well as Mg2+ and ATP, produces green light with a wavelength of 562 nm.
orchard
2012-06-07T05:20:20Z
PSI-MI
MI:1205
luciferase tag
The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
orchard
2012-06-07T05:26:34Z
PSI-MI
N-terminal fragment of renilla luciferase
MI:1206
renilla-n
The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:12705589
The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
orchard
2012-06-07T05:31:32Z
C-terminal fragment of renilla luciferase
PSI-MI
MI:1207
renilla-c
The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:12705589
Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range.
orchard
2012-06-07T05:32:53Z
PSI-MI
MI:1208
firefly luciferase protein tag
Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range.
PMID:22070901
The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
orchard
2012-06-07T05:40:04Z
C-terminal fragment of firefly luciferase
PSI-MI
MI:1209
firefly-c
The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:22070901
The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
orchard
2012-06-07T05:41:30Z
PSI-MI
N-terminal fragment of firefly luciferase
MI:1210
firefly-n
The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:22070901
Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out.
orchard
2012-06-07T05:51:15Z
PSI-MI
liposome centrifugation assay
MI:1211
liposome binding assay
Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out.
PMID:14734570
A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing.
orchard
2012-06-07T05:54:41Z
PSI-MI
hashsum
MI:1212
checksum
A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing.
PMID:14755292
N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
orchard
2012-06-07T06:33:51Z
PSI-MI
MI:1213
n-venus
N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
PMID:22229727
C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
orchard
2012-06-07T06:39:30Z
PSI-MI
MI:1214
c-venus
C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
PMID:22229727
Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured.
orchard
2012-06-07T07:13:53Z
PSI-MI
MI:1215
bifc tag
Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured.
PMID:17406412
c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
orchard
2012-06-07T07:19:55Z
PSI-MI
MI:1216
cGFP
c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
PMID:17406412
n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
orchard
2012-06-07T07:20:57Z
PSI-MI
MI:1217
nGFP
n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
PMID:17406412
Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library.
orchard
2012-06-07T07:25:28Z
chip-3c
PSI-MI
MI:1218
chromosome conformation capture assay
Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library.
PMID:11847345
chip-3c
Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP).
orchard
2012-06-07T07:34:30Z
emars
PSI-MI
MI:1219
enzyme-mediated activation of radical sources
Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP).
PMID:21214558
emars
The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction.
orchard
2012-06-11T11:52:57Z
tag luciferase
PSI-MI
MI:1220
tag visualisation by luciferase assay
The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction.
PMID:20609414
tag luciferase
A score generated by an author, usually only relevant for that particular dataset.
orchard
2012-06-11T11:54:23Z
author score
PSI-MI
MI:1221
author-based confidence
A score generated by an author, usually only relevant for that particular dataset.
PMID:14755292
author score
MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/).
orchard
2012-06-11T12:20:53Z
MBInfo
PSI-MI
MI:1222
mbinfo
MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/).
PMID:14755292
MBInfo
Post translational modification on a protein observed to decrease the strength or rate of an interaction.
orchard
2012-06-11T12:56:47Z
decreasing-ptm
PSI-MI
MI:1223
ptm decreasing an interaction
Post translational modification on a protein observed to decrease the strength or rate of an interaction.
PMID:14744292
decreasing-ptm
Post translational modification on a protein observed to increase the strength or rate of an interaction.
orchard
2012-06-11T12:58:43Z
increasing-ptm
PSI-MI
MI:1224
ptm increasing an interaction
Post translational modification on a protein observed to increase the strength or rate of an interaction.
PMID:14744292
increasing-ptm
Post translational modification on a protein observed to disrupt the strength or rate of an interaction.
orchard
2012-06-11T12:59:28Z
disrupting-ptm
PSI-MI
MI:1225
ptm disrupting an interaction
Post translational modification on a protein observed to disrupt the strength or rate of an interaction.
PMID:14744292
disrupting-ptm
Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids
orchard
2012-06-11T01:06:07Z
PSI-MI
ampylation
MI:1226
ampylation assay
true
Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids
PMID:14755292
Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification.
orchard
2012-06-11T01:16:05Z
lap tag
PSI-MI
location and purification tag
MI:1227
lap tag
Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification.
PMID:15644491
lap tag
A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME).
orchard
2012-08-10T07:28:55Z
PSI-MI
MI:1228
pyo tag
A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME).
PMID:9371754
Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166).
orchard
2012-08-10T07:46:07Z
PSI-MI
MI:1229
uridylation assay
Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166).
PMID:14755292
The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
orchard
2012-08-10T07:50:08Z
uridylation
PSI-MI
umpylation
MI:1230
uridylation reaction
The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
PMID:14755292
uridylation
AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring.
orchard
2012-08-10T07:59:18Z
AMC label
PSI-MI
MI:1231
aminomethylcoumarin label
AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring.
PMID:14755292
AMC label
An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second.
orchard
2012-08-10T08:07:15Z
aggregation
PSI-MI
MI:1232
aggregation assay
An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second.
PMID:22179788
aggregation
The cleavage which results due to the action of a proteolytic enzyme on its substrate.
orchard
2012-08-10T08:14:45Z
PSI-MI
MI:1233
Any feature range given should span the cleavage region e.g. 102-103 if the peptide bond between residues 102 and 103 is cut.
resulting-cleavage
The cleavage which results due to the action of a proteolytic enzyme on its substrate.
PMID:14755292
SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction.
orchard
2012-08-10T08:45:50Z
PSI-MI
MI:1234
silac
SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction.
PMID:17139335
PMID:18369856
Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state.
orchard
2012-08-10T08:52:14Z
thermal shift
PSI-MI
thermshift binding assay
MI:1235
thermal shift binding
Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state.
PMID:22052482
thermal shift
Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly.
orchard
2012-08-10T08:56:38Z
PSI-MI
MI:1236
proline isomerase assay
Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly.
PMID:9344417
The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
orchard
2012-08-10T09:02:28Z
PSI-MI
MI:1237
proline isomerization reaction
The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
PMID:9344417
Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry.
orchard
2012-08-10T09:11:36Z
ms subunit exchange
PSI-MI
MI:1238
mass spectrometry studies of subunit exchange
Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry.
PMID:20351246
ms subunit exchange
A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events.
orchard
2012-08-10T09:20:55Z
PSI-MI
SAP
single amino-acid polymorphism
MI:1239
amino-acid variant
A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events.
PMID:18175334
A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition.
orchard
2012-08-10T09:28:06Z
disease aa variant
PSI-MI
disease sap
disease single amino acid polymorphism
MI:1240
disease causing amino-acid variant
A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition.
PMID:18175334
disease aa variant
A natural change in a sequence or structure in comparison to a reference entity.
orchard
2012-08-10T09:32:29Z
PSI-MI
MI:1241
variant
A fusion protein tag consisting of a portion of the constant region of IgG1.
orchard
2012-08-10T10:10:25Z
PSI-MI
MI:1242
fc-igg1
A fusion protein tag consisting of a portion of the constant region of IgG1.
PMID:11757069
A fusion protein tag consisting of a portion of the constant region of IgG2.
orchard
2012-08-10T10:14:13Z
PSI-MI
MI:1243
fc-igg2
A fusion protein tag consisting of a portion of the constant region of IgG2.
PMID:11757069
Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
orchard
2012-08-10T11:22:13Z
PSI-MI
MI:1244
mkate2
Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
PMID:17721542
Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
orchard
2012-08-10T11:48:12Z
PSI-MI
TagFP635
MI:1245
mkate
Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
PMID:17721542
IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex.
orchard
2012-08-10T11:56:05Z
ion mobility mass spec
PSI-MI
iM-MS
MI:1246
ion mobility mass spectrometry of complexes
IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex.
PMID:18600219
ion mobility mass spec
Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored.
orchard
2012-08-10T12:20:37Z
mst
PSI-MI
MI:1247
microscale thermophoresis
Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored.
PMID:17164337
mst
Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields.
orchard
2012-08-10T12:34:54Z
PSI-MI
4,4-difluoro-4-bora-3a,4a-diaza-s-indacene
boron-dipyrromethene label
MI:1248
bodipy label
Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields.
PMID:19067126
Measurement of the catalysis of the structural rearrangement of isomers.
orchard
2012-08-10T12:45:27Z
PSI-MI
MI:1249
isomerase assay
Measurement of the catalysis of the structural rearrangement of isomers.
PMID:14755292
The catalysis of the structural rearrangement of isomers.
orchard
2012-08-10T12:51:00Z
PSI-MI
MI:1250
isomerase reaction
The catalysis of the structural rearrangement of isomers.
PMID:14755292
The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
orchard
2012-08-10T01:23:35Z
PSI-MI
MI:1251
methylmalonyl-CoA isomerase reaction
The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
PMID:14755292
The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2
orchard
2012-08-10T01:29:23Z
PSI-MI
MI:1252
methylmalonyl-CoA isomerase asf say
The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2
PMID:147292
Fluorescent tag - maleimide couples to thiols.
orchard
2012-08-10T01:49:01Z
atto 532 maleimide
PSI-MI
atto532
MI:1253
atto 532
Fluorescent tag - maleimide couples to thiols.
PMID:14760721
Fluorescent tag - maleimide couples to thiols.
orchard
2012-08-10T01:51:00Z
atto 647 maleimide
PSI-MI
atto647
MI:1254
atto 647
Fluorescent tag - maleimide couples to thiols.
PMID:14760721
1,2-Diphenylethene
orchard
2012-08-10T01:56:28Z
PSI-MI
MI:1255
stilbene label
1,2-Diphenylethene
PMID:16287229
Luminescent dyes such as cyanines,commonly used for DNA labelling.
orchard
2012-08-10T02:18:02Z
PSI-MI
MI:1256
luminscent dye label
Luminescent dyes such as cyanines,commonly used for DNA labelling.
PMID:14755292
Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining.
orchard
2012-08-10T02:39:00Z
PSI-MI
MI:1257
rhodamine label
Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining.
PMID:12622145
Tetramethyl rhodamine - a derivative of rhodamine.
orchard
2012-08-10T02:44:52Z
PSI-MI
MI:1258
tetramethyl rhodamine label
Tetramethyl rhodamine - a derivative of rhodamine.
PMID:12622145
The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding.
orchard
2012-08-10T02:55:26Z
PSI-MI
6-acryloyl-2-dimethylaminonaphthalene
MI:1259
acrylodan label
The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding.
PMID:12622145
Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime.
orchard
2012-08-10T03:09:54Z
PSI-MI
MI:1260
pyrene label
Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime.
PMID:12622145
Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins
orchard
2012-08-10T03:17:05Z
PSI-MI
MI:1261
oregon green label
Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins
PMID:12622145
Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions.
orchard
2012-10-22T02:57:59Z
url:http://iid.ophid.utoronto.ca/iid/
I2D
IID
Interologous Interaction Database
PSI-MI
MI:1262
iid
Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions.
PMID:19850753
I2D
IID
Interologous Interaction Database
Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com
orchard
2012-10-22T03:03:01Z
Molecular Connections
PSI-MI
MolCon
MI:1263
molecular connections
Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com
PMID:22453911
Molecular Connections
Norwegian University of Science and Technology. www.ntnu.no/home.
orchard
2012-10-22T03:15:27Z
NTNU
PSI-MI
MI:1264
ntnu
Norwegian University of Science and Technology. www.ntnu.no/home.
PMID:14755292
NTNU
In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases.
orchard
2012-10-24T11:08:40Z
PSI-MI
MI:1265
ubiquitin reconstruction tag
In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases.
PMID:9560251
A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays.
orchard
2012-10-24T11:10:19Z
PSI-MI
c-terminal ubiquitin tag
MI:1266
cub
A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays.
PMID:9560251
N-terminal ubiquitin moiety (nub, residues 1-34).
orchard
2012-10-24T11:12:47Z
PSI-MI
N-terminal ubiquitin tag
MI:1267
nub
N-terminal ubiquitin moiety (nub, residues 1-34).
PMID:9560251
N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation.
orchard
2012-10-24T11:31:11Z
PSI-MI
Ile13Gly N-terminal ubiquitin tag
MI:1268
nubg
N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation.
PMID:9560251
An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged.
orchard
2012-11-28T03:23:28Z
PSI-MI
MI:1269
duplicated protein
An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged.
PMID:21051339
Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys.
orchard
2013-05-30T08:29:27Z
PSI-MI
MI:1270
xpress tag
Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys.
PMID:14755292
An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E < wt
OR
wt < E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T19:12:17Z
enhancing diverging genetic interaction
PSI-MI
aggravating interaction
MI:1271
genetic enhancement (sensu unexpected)
An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E < wt
OR
wt < E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:05:15Z
PSI-MI
MI:1272
converging genetic epistasis
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab = a* < b < wt
OR
wt < b < a* = ab
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:11:27Z
cisphenotypic masking genetic interaction
PSI-MI
MI:1273
maximal genetic epistasis
An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab = a* < b < wt
OR
wt < b < a* = ab
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab = b < wt
OR
wt < b = ab < a*
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:13:14Z
cisphenotypic semi-suppressing converging genetic interaction
cisphenotypic semi-suppressing genetic interaction
PSI-MI
MI:1274
minimal genetic epistasis
An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab = b < wt
OR
wt < b = ab < a*
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
OR
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.
orchard
2013-06-05T20:22:53Z
PSI-MI
MI:1275
obsolete neutral epistasis
true
OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
OR
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.
PMID:15833125
An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:25:26Z
MI:1285
transphenotypic masking genetic interaction
PSI-MI
MI:1276
opposing genetic epistasis
An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.
orchard
2013-06-05T20:26:38Z
PSI-MI
MI:1277
qualitative genetic epistasis
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.
PMID:15833125
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a* <= b < wt [E = a*]
OR
wt < b <= a* < ab [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:31:30Z
cisphenotypic enhancing diverging genetic interaction
PSI-MI
MI:1278
mutual genetic enhancement (sensu unexpected)
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a* <= b < wt [E = a*]
OR
wt < b <= a* < ab [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a < b = wt [E = a]
OR
wt = b < a < ab [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:33:13Z
monophenotypic enhancing diverging genetic interaction
monophenotypic enhancing genetic interaction
unilateral genetic enhancement
PSI-MI
MI:1279
monophenotypic genetic enhancement
An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a < b = wt [E = a]
OR
wt = b < a < ab [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab <= wt) [E = a*]
OR
(wt < b <= a*) AND (wt <= ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:35:53Z
cisphenotypic suppressing converging genetic interaction
cisphenotypic suppressing genetic interaction
PSI-MI
MI:1280
cisphenotypic genetic suppression
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab <= wt) [E = a*]
OR
(wt < b <= a*) AND (wt <= ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < ab = wt
OR
wt = ab < b <= a*
OR
a < wt = ab < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:37:41Z
PSI-MI
MI:1281
mutual genetic suppression (complete)
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < ab = wt
OR
wt = ab < b <= a*
OR
a < wt = ab < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab < wt) [E = a*]
OR
(wt < b <= a*) AND (wt < ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:39:12Z
cisphenotypic sub-suppressing converging genetic interaction
cisphenotypic sub-suppressing genetic interaction
PSI-MI
MI:1282
cisphenotypic genetic suppression (partial)
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab < wt) [E = a*]
OR
(wt < b <= a*) AND (wt < ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < b < wt [E = a*]
OR
wt < b < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:43:52Z
cisphenotypic inter-suppressing converging genetic interaction
genetic suppression-enhancement
PSI-MI
MI:1283
cisphenotypic inter-suppressing genetic interaction
An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < b < wt [E = a*]
OR
wt < b < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.
orchard
2013-06-05T20:47:35Z
PSI-MI
MI:1284
quantitative genetic epistasis
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.
PMID:15833125
OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T20:51:51Z
PSI-MI
MI:1285
Term replaced by
http://purl.obolibrary.org/obo/MI_1276
obsolete opposing epistasis
true
OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < wt < E
OR
E < wt < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:04:18Z
PSI-MI
MI:1286
surpassing genetic interaction
An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < wt < E
OR
E < wt < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < wt < ab [E = a*]
OR
ab < wt < b <= a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:06:09Z
cisphenotypic super-suppressing genetic interaction
PSI-MI
MI:1287
mutual genetic over-suppression
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < wt < ab [E = a*]
OR
ab < wt < b <= a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b < ab
OR
ab < a < wt < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:11:03Z
genetic over-suppression-enhancement
PSI-MI
MI:1288
transphenotypic enhancing genetic interaction
An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b < ab
OR
ab < a < wt < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (a < ab < b) AND (ab != wt)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:15:34Z
PSI-MI
MI:1289
obsolete phenotype bias
true
OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (a < ab < b) AND (ab != wt)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
wt = ab != a = E
where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:34:57Z
all-suppressing genetic interaction
PSI-MI
MI:1290
genetic suppression (complete)
An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
wt = ab != a = E
where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < wt [E = a*]
OR
wt < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:36:07Z
sub-suppressing genetic interaction
PSI-MI
MI:1291
genetic suppression (partial)
An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < wt [E = a*]
OR
wt < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab <= b = wt [E = a]
OR
wt = b <= ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:37:28Z
monophenotypic suppressing converging genetic interaction
monophenotypic suppressing genetic interaction
unilateral genetic suppression
PSI-MI
MI:1292
monophenotypic genetic suppression
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab <= b = wt [E = a]
OR
wt = b <= ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab = b = wt [E = a]
OR
wt = b = ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:38:36Z
monophenotypic all-suppressing converging genetic interaction
monophenotypic all-suppressing genetic interaction
unilateral genetic suppression (complete)
PSI-MI
MI:1293
monophenotypic genetic suppression (complete)
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab = b = wt [E = a]
OR
wt = b = ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab < b = wt [E = a]
OR
wt = b < ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:39:32Z
monophenotypic sub-suppressing converging genetic interaction
monophenotypic sub-suppressing genetic interaction
unilateral genetic suppression (partial)
PSI-MI
MI:1294
monophenotypic genetic suppression (partial)
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab < b = wt [E = a]
OR
wt = b < ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E = a < b = wt < ab
OR
ab < wt = b < a = E
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
orchard
2013-06-05T21:54:08Z
monophenotypic super-suppressing genetic interaction
unilateral genetic over-suppression
PSI-MI
MI:1295
monophenotypic genetic over-suppression
An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E = a < b = wt < ab
OR
ab < wt = b < a = E
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PMID:15833125
The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
orchard
2013-06-06T07:49:49Z
PSI-MI
MI:1296
amino acid analysis
The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
PMID:19072539
The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
orchard
2013-06-06T07:55:30Z
PSI-MI
MI:1297
phosphoamino acid analysis
The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
PMID:19072539
A classification of the structural characteristics of a macromolecular complex.
orchard
2013-06-06T08:52:34Z
PSI-MI
MI:1298
complex type
A classification of the structural characteristics of a macromolecular complex.
PMID:12853463
A description of the molecule types of which a macromolecular complex is composed.
orchard
2013-06-06T08:55:37Z
PSI-MI
MI:1299
complex composition
A description of the molecule types of which a macromolecular complex is composed.
PMID:12853464
The protein chains present in the complex are not found as independent stable structures in vivo.
orchard
2013-06-06T08:57:32Z
PSI-MI
MI:1300
obligate complex
The protein chains present in the complex are not found as independent stable structures in vivo.
PMID:12853463
Protein chains present in the complex may also be found as independent stable proteins in vivo.
orchard
2013-06-06T09:02:52Z
PSI-MI
MI:1301
non-obligate complex
Protein chains present in the complex may also be found as independent stable proteins in vivo.
PMID:12853463
A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo.
orchard
2013-06-06T09:05:59Z
PSI-MI
MI:1302
stable complex
A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo.
PMID:12853464
A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium.
orchard
2013-06-06T09:09:01Z
PSI-MI
MI:1303
transient complex
A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium.
PMID:12853463
A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods.
orchard
2013-06-06T09:20:00Z
PSI-MI
MI:1304
molecule set
A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods.
PMID:14755292
A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so.
orchard
2013-06-06T10:09:09Z
PSI-MI
MI:1305
candidate set
A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so.
PMID:14755292
A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid.
orchard
2013-06-06T10:19:10Z
PSI-MI
MI:1306
open set
A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid.
PMID:14755292
Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP).
orchard
2013-06-06T10:22:53Z
PSI-MI
MI:1307
defined set
Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP).
PMID:14755292
Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description
provided in the feature name.
orchard
2013-06-06T10:26:19Z
PSI-MI
MI:1308
resulting sequence
Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description
provided in the feature name.
PMID:14755292
Hydrolytic reactions that release ADP-ribose.
orchard
2013-06-06T10:31:58Z
mono-ADP-ribosylhydrolase
PSI-MI
MI:1309
de-ADP-ribosylation assay
Hydrolytic reactions that release ADP-ribose.
PMID:23474712
PMID:23474714
Measure of hydrolytic reactions that release ADP-ribose.
orchard
2013-06-06T10:34:18Z
PSI-MI
mono-ADP-ribosylhydrolase reaction
MI:1310
de-ADP-ribosylation reaction
Measure of hydrolytic reactions that release ADP-ribose.
PMID:23474712
PMID:23474714
Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants.
orchard
2013-06-06T10:39:30Z
dsc
PSI-MI
MI:1311
differential scanning calorimetry
Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants.
PMID:10398392
dsc
Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent.
orchard
2013-06-06T10:43:24Z
PSI-MI
acetic acid/urea/triton PAGE
MI:1312
aut-page
Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent.
PMID:12875839
Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification.
orchard
2013-06-06T11:20:43Z
PSI-MI
MI:1313
proximity labelling technology
Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification.
PMID:22412018
A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification.
orchard
2013-06-06T11:23:53Z
PSI-MI
BioID
MI:1314
proximity-dependent biotin identification
A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification.
PMID:22412018
The most accepted name in the literature for this complex.
orchard
2013-10-14T15:00:37Z
PSI-MI
MI:1315
complex recommended name
The most accepted name in the literature for this complex.
PMID:14755292
A name for a complex built of the component parts of that complex.
orchard
2013-10-14T15:04:57Z
PSI-MI
MI:1316
complex systematic name
The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/
orchard
2013-10-22T09:49:10Z
id-validation-regexp:
search-url:
elm
PSI-MI
MI:1317
eukaryotic linear motif resource
The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/
PMID:22110040
id-validation-regexp:
[A-Za-z_0-9]+$
search-url:
http://elm.eu.org/elms/elmPages/${ac}.html
elm
Any molecule that is able to transfer a sulphate group to another chemical species.
orchard
2014-01-08T07:51:29Z
PSI-MI
sulphate donor
MI:1318
sulfate donor
Any molecule that is able to transfer a sulphate group to another chemical species.
PMID:14755292
Molecule to which a sulphate group may be transferred from a sulphate donor.
orchard
2014-01-08T07:52:46Z
PSI-MI
sulphate acceptor
MI:1319
sulfate acceptor
Molecule to which a sulphate group may be transferred from a sulphate donor.
PMID:14755292
Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
orchard
2014-01-08T10:14:46Z
MYTH
PSI-MI
MI:1320
membrane yeast two hybrid
Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
PMID:2261051
Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum.
orchard
2014-01-08T10:17:38Z
PSI-MI
ER-MYTH
endoplasmic reticulum membrane yeast-two hybrid
MI:1321
ire1 reconstruction
Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum.
PMID:22665516
Fluorescent tag - maleimide couples to thiols.
orchard
2014-01-08T10:27:34Z
atto 465 maleimide
atto465
PSI-MI
MI:1322
atto 465
Fluorescent tag - maleimide couples to thiols.
PMID:14755292
The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction.
orchard
2014-01-08T11:00:36Z
tag alk phosphatase activity
PSI-MI
MI:1323
tag visualisation by alkaline phosphatase activity
The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction.
PMID:14755292
tag alk phosphatase activity
Molecule present in media harvested from cultured cells.
orchard
2014-01-08T11:07:44Z
PSI-MI
MI:1324
conditioned medium
Molecule present in media harvested from cultured cells.
PMID:14755292
Measures the rate of a sulphate molecule transfer between two molecules.
orchard
2014-01-08T11:13:39Z
sulfertransferase
PSI-MI
sulfurtransfer assay
sulphurtransferase assay
MI:1325
sulfurtransferase assay
Measures the rate of a sulphate molecule transfer between two molecules.
PMID:14755292
sulfertransferase
Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
orchard
2014-01-08T11:15:51Z
phosphotransfer
PSI-MI
MI:1326
CLONE OF phosphotransfer reaction
true
Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
PMID:14755292
PMID:16712436
phosphotransfer
Reaction where a sulfate group is transferred between two proteins
orchard
2014-01-08T11:16:12Z
sulfurtransfer
sulphurtransfer reaction
PSI-MI
MI:1327
sulfurtransfer reaction
Reaction where a sulfate group is transferred between two proteins
GO:GO:0016783
PMID:14755292
sulfurtransfer
A class of labels derived from the benzopyrone coumarin.
orchard
2014-01-08T11:25:00Z
PSI-MI
MI:1328
coumarin label
A class of labels derived from the benzopyrone coumarin.
PMID:14755292
The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm.
orchard
2014-01-08T11:36:48Z
7-diethylamino-3-(4' maleimidylphenyl)-4-methylcoumarin
PSI-MI
MI:1329
cpm
The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm.
PMID:14755292
Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria.
orchard
2014-01-08T12:01:24Z
2, 4-DNP
2,4-Dinitrophenol
dinitrophenol
PSI-MI
MI:1330
dnp
Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria.
PMID:14755292
The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means.
orchard
2014-01-08T12:48:33Z
id-validation-regexp:
search-url:
PSI-MI
ECO
MI:1331
evidence ontology
The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means.
PMID:14755292
id-validation-regexp:
ECO:\d{7}$
search-url:
http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=${ac}
The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium.
orchard
2014-01-08T12:56:27Z
BHF-UCL
PSI-MI
Cardiovascular Gene Annotation Initiative
MI:1332
bhf-ucl
The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium.
PMID:21419760
BHF-UCL
SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value):
+/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order.
orchard
2014-01-09T11:17:18Z
PSI-MI
MI:1333
rogid
SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value):
+/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order.
PMID:18823568
A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding.
orchard
2014-01-09T11:17:32Z
PSI-MI
MI:1334
rigid
A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding.
PMID:18823568
Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface.
http://www.agbase.msstate.edu/hpi/main.html
orchard
2014-03-03T11:43:31Z
HPIDB
Host Pathogen Interaction database
PSI-MI
MI:1335
hpidb
Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface.
http://www.agbase.msstate.edu/hpi/main.html
PMID:20946599
HPIDB
Host Pathogen Interaction database
Databases that contain information used to add additional information to experiments (meta-data).
orchard
2014-01-20T11:56:03Z
experiment xref
PSI-MI
MI:1336
experiment database
Databases that contain information used to add additional information to experiments (meta-data).
PMID:14755292
experiment xref
The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms.
orchard
2014-01-20T11:58:47Z
id-validation-regexp:
search-url:
Experimental facto ontology
PSI-MI
MI:1337
efo
The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms.
pmid:20200009
id-validation-regexp:
([A-Z]+:)?\d{7}$
search-url:
http://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=${ac}
Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2
orchard
2014-01-20T12:13:30Z
PSI-MI
Glu-Glu-Phe epitope tag
MI:1338
eef tag
Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2
PMID:6204858
Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation.
orchard
2014-01-20T13:13:03Z
PSI-MI
stGFP
MI:1339
supercharged green fluorescent protein
Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation.
PMID:17665911
A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants.
orchard
2014-04-08T16:15:19Z
search-url:
PSI-MI
MI:1340
human orfeome collection
A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants.
PMID:14755292
search-url:
http://horfdb.dfci.harvard.edu/
Indicates that this protein is a member of a set of proteins with similar sequence and/or function.
orchard
2014-04-25T09:19:21Z
PSI-MI
MI:1341
set member
Indicates that this protein is a member of a set of proteins with similar sequence and/or function.
PMID:14755292
The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions.
orchard
2014-07-17T08:26:51Z
QCM-D
Quartz Crystal Microbalance with Dissipation monitoring
PSI-MI
MI:1342
qcmd
The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions.
PMID:19137101
PMID:22158962
PMID:23504432
Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits.
orchard
2014-07-17T08:43:17Z
enzyme complex regulatory subunit
PSI-MI
MI:1343
enzyme regulator
Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits.
PMID:14755292
Fluoresceine-derived label.
orchard
2014-07-17T08:47:44Z
ErIA
erythrosin-5-iodoacetamide
PSI-MI
MI:1344
erythrosin iodoacetamide label
Fluoresceine-derived label.
PMID:14755292
A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope.
orchard
2014-09-19T14:24:43Z
1D4 tag
rho1D4 tag
PSI-MI
MI:1345
rho tag
A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope.
PMID:12110672
PMID:24943310
1D4 tag
rho1D4 tag
Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US.
orchard
2014-09-19T14:42:33Z
PSI-MI
BioMagResBank
Biological Magnetic Resonance Data Bank
MI:1346
bmrb
Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US.
PMID:18288446
PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes.
orchard
2014-09-26T14:06:25Z
id-validation-regexp:
search-url:
PSI-MI
PRO
MI:1347
protein ontology
PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes.
PMID:24270789
id-validation-regexp:
[0-9]{9}|[A-Z][0-9][A-Z0-9]{3}[0-9]|[A-Z][0-9][A-Z0-9]{3}[0-9]-[1-9]+
search-url:
http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=${ac}
ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
orchard
2014-10-16T10:10:03Z
regexp:
search-url:
PSI-MI
MI:1348
chembl target
regexp:
CHEMBL:[0-9]+
search-url:
http://www.ebi.ac.uk/chembldb/index.php/target/inspect/${ac}
ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
orchard
2014-10-16T10:16:54Z
PSI-MI
MI:1349
chembl
ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
PMID:24214965
Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
orchard
2014-10-16T10:27:01Z
id-validation-regexp:
search-url:
PSI-MI
MI:1350
orphanet
Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
PMID:19058507
id-validation-regexp:
^\d+$
search-url:
http://www.ebi.ac.uk/ols/ontologies/ordo/terms?obo_id=${ac}
Refers to the original experimentally verified object from which the described object has been derived.
orchard
2014-10-16T10:39:21Z
PSI-MI
MI:1351
inferred-from
Refers to the original experimentally verified object from which the described object has been derived.
PMID:25313161
In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points".
orchard
2015-01-28T10:12:25Z
PSI-MI
MI:1352
uracil interference assay
In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points".
PMID:18265086
Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK.
orchard
2015-01-28T10:23:06Z
PSI-MI
MI:1353
au5 tag
Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK.
PMID:9765280
Cleavage (hydrolysis) of a lipid molecule.
orchard
2015-02-03T13:18:55Z
PSI-MI
MI:1354
lipase assay
Cleavage (hydrolysis) of a lipid molecule.
PMID:14760721
Reaction monitoring the cleavage (hydrolysis) or a lipid molecule.
orchard
2015-02-03T13:25:21Z
PSI-MI
MI:1355
lipid cleavage
Reaction monitoring the cleavage (hydrolysis) or a lipid molecule.
PMID:14760721
The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique.
orchard
2015-02-03T13:36:20Z
PSI-MI
MI:1356
validated two hybrid
The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique.
PMID:25416956
Provides unified access to the ncRNA sequence data supplied by the expert databases.
orchard
2015-02-03T13:37:23Z
id-validation-regexp:
search-url:
PSI-MI
MI:1357
RNAcentral
Provides unified access to the ncRNA sequence data supplied by the expert databases.
PMID:25352543
id-validation-regexp:
/URS[0-9A-F]{10}/i
search-url:
http://rnacentral.org/rna/${ac}
DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins.
PSI-MI
MI:2002
drugbank
DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins.
PMID:14755292
Standard name of drug or any reagent as provided by its manufacturer.
generic name
PSI-MI
MI:2003
commercial name
Standard name of drug or any reagent as provided by its manufacturer.
PMID:14755292
generic name
Alternate names of the drug, brand names from different manufacturers.
PSI-MI
MI:2004
drug brand name
Alternate names of the drug, brand names from different manufacturers.
PMID:14755292
Brand names and composition of mixtures that include the drug described in this DrugCard file.
mix brand name
PSI-MI
MI:2005
drug mixture brand name
Brand names and composition of mixtures that include the drug described in this DrugCard file.
PMID:14755292
mix brand name
Description of the drug (for biotech drugs) describing its composition and/or preparation.
biotech prep
PSI-MI
MI:2006
biotech product preparation
Description of the drug (for biotech drugs) describing its composition and/or preparation.
PMID:14755292
biotech prep
IUPAC or standard chemical name for a drug, or a chemical.
PSI-MI
MI:2007
iupac name
IUPAC or standard chemical name for a drug, or a chemical.
PMID:14755292
Chemical formula describing atomic or elemental composition
PSI-MI
MI:2008
chemical formula
Chemical formula describing atomic or elemental composition
PMID:14755292
Image of the drug structure (if small molecule) or its sequence (if biotech drug)
PSI-MI
MI:2009
chemical structure
Image of the drug structure (if small molecule) or its sequence (if biotech drug)
PMID:14755292
IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.
standard inchi
PSI-MI
inchi id
MI:2010
standard inchi
IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.
PMID:14755292
standard inchi
Chemical Abstract Service identification number
PSI-MI
MI:2011
cas registry number
Chemical Abstract Service identification number
PMID:14755292
Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)
KEGG Compound ID
PSI-MI
MI:2012
kegg compound
Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)
PMID:14755292
KEGG Compound ID
NCBI's PubChem database identification number (if molecule is in PubChem).
OBSOLETE as redudant with MI:0730
PubChem ID
PSI-MI
MI:2013
pubchem
true
NCBI's PubChem database identification number (if molecule is in PubChem).
OBSOLETE as redudant with MI:0730
PMID:14755292
PubChem ID
Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)
PSI-MI
MI:2015
pharmgkb
Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)
PMID:14755292
BIND database Small Molecule Identification number (if molecule is in BIND)
PSI-MI
MI:2016
May not be publicly available any more since now owned by Thompson Scientific.
bind smid
BIND database Small Molecule Identification number (if molecule is in BIND)
PMID:14755292
The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for
which coordinates are supplied. Groups are considered HET if they are:
- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A,
+T, +U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to
indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.
het
PSI-MI
MI:2017
heterogen
The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for
which coordinates are supplied. Groups are considered HET if they are:
- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A,
+T, +U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to
indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.
PMID:14755292
het
Drug Identification Number (Canadian Drug ID system)
din
PSI-MI
MI:2020
canadian drug identification number
Drug Identification Number (Canadian Drug ID system)
PMID:14755292
din
Hyperlink to RxList entry for the given drug (if it exists)
PSI-MI
MI:2021
rxlist link
Hyperlink to RxList entry for the given drug (if it exists)
PMID:14755292
Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs.
MSDS Material Safety Sheet
msds
PSI-MI
MI:2023
material safety data sheet
Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs.
PMID:14755292
MSDS Material Safety Sheet
msds
number of the patent describing a drug's synthesis or use.
PSI-MI
MI:2024
patent number
number of the patent describing a drug's synthesis or use.
PMID:14755292
Molecular weight in g/mol, determined from molecular formula or sequence.
PSI-MI
MI:2025
molecular weight
Molecular weight in g/mol, determined from molecular formula or sequence.
PMID:14755292
The melting point of a solid is the temperature range at which it changes state from solid to liquid.
PSI-MI
MI:2026
melting point
The melting point of a solid is the temperature range at which it changes state from solid to liquid.
PMID:14755292
Water solubility in mg/mL or g/L
logSw
PSI-MI
MI:2027
water solubility
Water solubility in mg/mL or g/L
PMID:14755292
logSw
Water/octanol partition coefficient of a small molecule.
PSI-MI
MI:2029
logp
Water/octanol partition coefficient of a small molecule.
PMID:14755292
The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule.
PSI-MI
MI:2030
isoelectric point
The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule.
PMID:14755292
Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score.
PSI-MI
MI:2033
hydrophobicity
Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score.
PMID:14755292
The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure.
PSI-MI
MI:2036
boiling point
The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure.
PMID:14755292
SMILES string corresponding to drug structure
PSI-MI
MI:2039
smiles string
SMILES string corresponding to drug structure
PMID:14755292
Type of drug (approved, experimental, biotech, nutraceutical)
PSI-MI
MI:2040
drug type
Type of drug (approved, experimental, biotech, nutraceutical)
PMID:14755292
Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.).
PSI-MI
MI:2041
drug category
Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.).
PMID:14755292
Description or common names of diseases that the drug is used to treat.
PSI-MI
MI:2042
Source of further terms could be MeSH term or SNOWMAN.
disease indication
Description or common names of diseases that the drug is used to treat.
PMID:14755292
Text description of how the drug works at a clinical or physiological level.
PSI-MI
MI:2043
pharmacology
Text description of how the drug works at a clinical or physiological level.
PMID:14755292
Description of how the drug works or what it binds to at a molecular level.
PSI-MI
MI:2044
mechanism of action
Description of how the drug works or what it binds to at a molecular level.
PMID:14755292
Determination of how quickly and how much of a drug reaches its intended target (site) of action.
PSI-MI
MI:2045
drug absorption
Determination of how quickly and how much of a drug reaches its intended target (site) of action.
PMID:14755292
The LD50 is the dose that kills half (50%) of the animals tested
ld50
lethal dose 50 %
PSI-MI
MI:2046
lethal dose 50
The LD50 is the dose that kills half (50%) of the animals tested
PMID:14755292
ld50
lethal dose 50 %
Percentage of the drug that is bound in plasma proteins
plasma prot binding
protein binding %
PSI-MI
MI:2047
percentage of plasma protein binding
Percentage of the drug that is bound in plasma proteins
PMID:14755292
plasma prot binding
protein binding %
The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media.
drug metabolism
PSI-MI
MI:2048
drug biotransformation
The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media.
PMID:14755292
drug metabolism
Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%.
distribution halflife
elimin half life
t1/2
PSI-MI
MI:2049
elimination half life
Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%.
PMID:14755292
distribution halflife
elimin half life
t1/2
How the drug is dispensed (tablets, capsules, solutions), packing material.
PSI-MI
MI:2050
dosage form
How the drug is dispensed (tablets, capsules, solutions), packing material.
PMID:14755292
Information on the disease indications and treatment regime for the drug. May also include contra-indications.
PSI-MI
MI:2051
patient information
Information on the disease indications and treatment regime for the drug. May also include contra-indications.
PMID:14755292
Cautions or conditions indicating why or when the drug should not be taken or prescribed.
PSI-MI
MI:2053
contraindications
Cautions or conditions indicating why or when the drug should not be taken or prescribed.
PMID:14755292
General on-line reference to other details about a drug or other bioactive entity.
bioactive entity ref
PSI-MI
MI:2054
bioactive entity reference
General on-line reference to other details about a drug or other bioactive entity.
PMID:14755292
bioactive entity ref
chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent.
thermodynamic stability
PSI-MI
MI:2055
chemical stability
chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent.
PMID:14755292
thermodynamic stability
Potential ability of a substance to dissolve in a liquid.
dt theoretical pi
PSI-MI
MI:2064
solubility
Potential ability of a substance to dissolve in a liquid.
PMID:14755292
dt theoretical pi
Names of organisms which are affected, positively or negatively, by the drug.
PSI-MI
MI:2084
organisms affected
Names of organisms which are affected, positively or negatively, by the drug.
PMID:14755292
Chemical and physical properties of a molecule.
physicochemical att
PSI-MI
MI:2086
physicochemical attribute name
Chemical and physical properties of a molecule.
PMID:14755292
physicochemical att
Properties of a chemical tested or used as a drug, herbicide, insecticide etc.
bioactive entity att
PSI-MI
MI:2089
bioactive entity attribute name
Properties of a chemical tested or used as a drug, herbicide, insecticide etc.
PMID:14755292
bioactive entity att
Human artefact to describe and report the structure of a molecule.
struc representation
PSI-MI
MI:2091
structure representation attribute name
Human artefact to describe and report the structure of a molecule.
PMID:14755292
struc representation
Therapeutic category or general category of drug -anti-convulsant
PSI-MI
MI:2097
anti-convulsant
Therapeutic category or general category of drug -anti-convulsant
PMID:14755292
Therapeutic category or general category of drug -anti-bacterial
PSI-MI
MI:2098
anti-bacterial
Therapeutic category or general category of drug -anti-bacterial
PMID:14755292
A drug licensed for sale in the USA by the FDA.
PSI-MI
MI:2099
fda approved drug
A drug licensed for sale in the USA by the FDA.
PMID:14755292
A drug which has yet to be formally approved for the indication which it is currently being used to treat.
PSI-MI
MI:2100
experimental drug
A drug which has yet to be formally approved for the indication which it is currently being used to treat.
PMID:14755292
A natural product, such as a protein or peptide, which is produced used biotechnology as a drug.
PSI-MI
MI:2101
biotech drug
A natural product, such as a protein or peptide, which is produced used biotechnology as a drug.
PMID:14755292
A drug which may also be regarded as a foodstuff.
PSI-MI
MI:2102
nutraceutical drug
A drug which may also be regarded as a foodstuff.
PMID:14755292
Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid.
PSI-MI
MI:2105
Quantitative prediction of this parameter is possible.
pka
Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid.
PMID:14755292
The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4
ionisation ph 7.4
PSI-MI
MI:2106
Quantitative prediction of this parameter is possible.
degree of ionisation ph 7.4
The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4
PMID:14755292
ionisation ph 7.4
The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4
PSI-MI
MI:2107
Quantitative prediction of this parameter is possible.
logd
The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4
PMID:14755292
Solubility pH 7.4
PSI-MI
MI:2108
Quantitative prediction of this parameter is possible.
solubility ph 7.4
Solubility pH 7.4
PMID:14755292
Solubility in DMSO
PSI-MI
MI:2109
solubility in dmso
Solubility in DMSO
PMID:14755292
Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s.
diffusion coeff
PSI-MI
MI:2111
Quantitative prediction of this parameter is possible.
diffusion coefficient
Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s.
PMID:14755292
diffusion coeff
Chemical stability at pH 2
chem stab ph 2
PSI-MI
MI:2112
Qualitative prediction of this parameter is possible.
chemical stability at pH 2
Chemical stability at pH 2
PMID:14755292
chem stab ph 2
The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations.
PSI-MI
MI:2113
The prediction of the value for this paramter is currently not possible.
dissolution profile
The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations.
PMID:14755292
Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug.
PSI-MI
MI:2115
pharmacokinetics attribute name
Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug.
PMID:14755292
The permitting or activating of the passage of substances into, out of, or through cells.
PSI-MI
MI:2116
Quantitative prediction of this parameter is possible.
cell permeability
The permitting or activating of the passage of substances into, out of, or through cells.
PMID:14755292
The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd.
distribution volume
vd
vol of distribution
PSI-MI
MI:2118
Quantitative prediction of this parameter is possible.
volume of distribution
The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd.
PMID:14755292
distribution volume
vd
vol of distribution
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
PSI-MI
MI:2120
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
tissue distribution
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
PMID:14755292
Substrate of a carrier system allowing the intake of an agent into an organ or part of body.
PSI-MI
MI:2121
The prediction of the value for this parameter is currently not possible.
transporter binding
Substrate of a carrier system allowing the intake of an agent into an organ or part of body.
PMID:14755292
The ratio of excretion is or measure of the speed at which a constituent is lost from the body.
PSI-MI
MI:2122
clearance
The ratio of excretion is or measure of the speed at which a constituent is lost from the body.
PMID:14755292
The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine.
PSI-MI
MI:2123
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
renal clearance
The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine.
PMID:14755292
The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
cl
clearance
PSI-MI
MI:2124
The prediction of the value for this paramter is currently not possible.
total clearance
The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
PMID:14755292
cl
clearance
The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier.
mad
PSI-MI
MI:2125
Quantitative prediction of this parameter is possible.
maximum absorbable dose
The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier.
PMID:8987073
mad
Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion.
paracellular absorp
PSI-MI
MI:2126
Quantitative prediction of this parameter is possible.
paracellular absorption
Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion.
PMID:14755292
paracellular absorp
Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself.
PSI-MI
MI:2127
The prediction of the value for this paramter is currently not possible.
tmax/cmax
Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself.
PMID:14755292
Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile.
abcb1 substrate
pgp(mdr1) substrate
PSI-MI
MI:2128
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
ABCB1 transporter substrate
Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile.
PMID:14755292
abcb1 substrate
pgp(mdr1) substrate
Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
bile trans substrate
PSI-MI
MI:2129
The prediction of the value for this paramater is currently not possible.
bile transporter substrate
Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
PMID:14755292
bile trans substrate
Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds.
Cytochrome P450 inhibition
cyp-450 inhibition
PSI-MI
MI:2130
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
cyp-450 inhibition
Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds.
PMID:14755292
Cytochrome P450 inhibition
cyp-450 inhibition
Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body
metabolite identific
PSI-MI
MI:2131
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
metabolite identification
Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body
PMID:14755292
metabolite identific
Derivative molecule which has formed from a reaction with glutathione.
PSI-MI
MI:2132
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
gsh adducts
Derivative molecule which has formed from a reaction with glutathione.
PMID:14755292
Neutralization of a compound occuring via its glucuronidation or sulfatation.
neutraliz gluc/sulf
PSI-MI
MI:2133
Quantitative prediction of this parameter is possible.
neutralization by glucuronidation or sulfatation
Neutralization of a compound occuring via its glucuronidation or sulfatation.
PMID:14755292
neutraliz gluc/sulf
The mechanism by which a substance can harm humans or animals.
PSI-MI
MI:2135
toxicity attribute name
The mechanism by which a substance can harm humans or animals.
PMID:14755292
Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential.
PSI-MI
MI:2136
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
herg binding
Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential.
PMID:14755292
Tendency of a bioactive entity to induce damage at the level of the gene.
PSI-MI
MI:2137
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
genotoxicity
Tendency of a bioactive entity to induce damage at the level of the gene.
PMID:14755292
Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences.
PSI-MI
MI:2138
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
mutagenicity
Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences.
PMID:14755292
Tendency of a bioactive entity to induce a cancer.
cancerogenicity
PSI-MI
MI:2139
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
carcinogenicity
Tendency of a bioactive entity to induce a cancer.
PMID:14755292
cancerogenicity
Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number.
PSI-MI
MI:2140
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
chromosome damage
Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number.
PMID:14755292
Tendency of a bioactive entity to affect liver function.
PSI-MI
MI:2141
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
hepatotoxicity
Tendency of a bioactive entity to affect liver function.
PMID:14755292
Causes excess phospholipids to accumulate within cells.
PSI-MI
MI:2142
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
phospholipidosis
Causes excess phospholipids to accumulate within cells.
PMID:14755292
Solubility pH 6.5.
PSI-MI
MI:2145
Quantitative prediction of this parameter is possible.
solubility ph 6.5
Solubility pH 6.5.
PMID:14755292
Solubility pH 2.0
solubility ph2.0
PSI-MI
MI:2146
Quantitative prediction of this parameter is possible.
solubility ph 2.0
Solubility pH 2.0
PMID:14755292
solubility ph2.0
Chemical stabilityat at pH 7.4
chem stab ph 7.4
PSI-MI
MI:2147
Qualitative prediction of this parameter is possible.
chemical stability at pH 7.4
Chemical stabilityat at pH 7.4
PMID:14755292
chem stab ph 7.4
A drug currently under clinical development.
PSI-MI
MI:2148
Intact.
investigational drug
A drug currently under clinical development.
PMID:14755292
A drug for which the licencing for prescriptive use has been withdrawn.
PSI-MI
MI:2149
Intact.
withdrawn drug
A drug for which the licencing for prescriptive use has been withdrawn.
PMID:14755292
A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription.
PSI-MI
MI:2150
illicit drug
A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription.
PMID:14755292
Effect of additional drug treatments on a given drug action.
drug interaction
PSI-MI
MI:2151
other drug interaction
Effect of additional drug treatments on a given drug action.
PMID:14755292
drug interaction
Effect of food ingestion on a given drug treatment.
PSI-MI
MI:2152
IntAct MeSH term or SNOWMAN.
food interaction
Effect of food ingestion on a given drug treatment.
PMID:14755292
Hyperlink to PDRhealth entry for the given drug (if it exists)
PDRhealth
PSI-MI
MI:2153
pdr health
Hyperlink to PDRhealth entry for the given drug (if it exists)
PMID:14755292
PDRhealth
Hyperlink to wikipedia entry for the given drug (if it exists)
PSI-MI
MI:2154
wikipedia
Hyperlink to wikipedia entry for the given drug (if it exists)
PMID:14755292
Molecular weight in g/mol, determined from molecular formula or sequence.
avrg mol weight
PSI-MI
MI:2155
average molecular weight
Molecular weight in g/mol, determined from molecular formula or sequence.
PMID:14755292
avrg mol weight
Molecular weight in g/mol, determined from molecular formula or sequence.
monoisotopic mol wgt
PSI-MI
MI:2156
monoisotopic molecular weight
Molecular weight in g/mol, determined from molecular formula or sequence.
PMID:14755292
monoisotopic mol wgt
Water solubility in mg/mL or g/L.
exp h2o solubilty
experimental h2o solubility
PSI-MI
MI:2157
experimental water solubility
Water solubility in mg/mL or g/L.
PMID:14755292
exp h2o solubilty
experimental h2o solubility
Water solubility in mg/mL or g/L
predicted h2o solub
predicted h2o solubility
PSI-MI
MI:2158
predicted water solubility
Water solubility in mg/mL or g/L
PMID:14755292
predicted h2o solub
predicted h2o solubility
Solubility of a molecule in a given solvant.
logS
PSI-MI
MI:2160
logs
Solubility of a molecule in a given solvant.
PMID:14755292
logS
Experimental derived value for the solubility of a molecule in a given solvant.
experimental logS
PSI-MI
MI:2161
Quantitative prediction of this parameter is possible.
experimental logs
Experimental derived value for the solubility of a molecule in a given solvant.
PMID:14755292
experimental logS
Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption
caco2 permeability
PSI-MI
MI:2162
Quantitative prediction of this parameter is possible.
experimental CaCO2 permeability
Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption
PMID:14755292
caco2 permeability
Reference assigned to a molecule by sequence homology with another similar sequence.
PSI-MI
MI:2163
by homology
Reference assigned to a molecule by sequence homology with another similar sequence.
PMID:14755292
The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php
orchard
2013-02-26T12:27:35Z
PSI-MI
MI:2164
mind
The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php
PMID:14755292
The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624]
orchard
2013-02-26T12:49:13Z
bar-arabidopsis interactions viewer
PSI-MI
MI:2165
bar
The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624]
PMID:15960624
The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins.
http://interactome.dfci.harvard.edu/A_thaliana/index.php
orchard
2013-02-26T12:54:32Z
AI
PSI-MI
MI:2166
ai
The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins.
http://interactome.dfci.harvard.edu/A_thaliana/index.php
PMID:21798944
In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag.
ppm
2015-04-27T15:51:46Z
kinetic exclusion
kinexa
PSI-MI
MI:2167
kinetic exclusion assay
In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag.
PMID:15674023
kinetic exclusion
kinexa
The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection.
ppm
2015-04-29T10:19:28Z
PSI-MI
active site labelling
MI:2168
conditional site labelling
The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection.
PMID:19416890
Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin.
ppm
2015-04-29T11:50:41Z
PSI-MI
MI:2169
luminiscence technology
Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin.
PMID:24166364
The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection.
ppm
2015-04-29T12:03:27Z
bilc
bioluminescence complementation
bioluminescence complementation assay
luminescence complementation assay
luminiscence complementation
PSI-MI
split-luciferase complementation
split-luciferase complementation assay
MI:2170
bimolecular luminiscence complementation
The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection.
PMID:25859972
bilc
bioluminescence complementation
bioluminescence complementation assay
luminescence complementation assay
luminiscence complementation
This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished.
ppm
2015-04-29T13:25:55Z
bret complementation
bret complementation assay
copa-ret
PSI-MI
MI:2171
complemented donor-acceptor resonance energy transfer
This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished.
PMID:21785426
PMID:25706338
bret complementation
bret complementation assay
copa-ret
AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species.
www.aspergillusgenome.org/
ppm
2015-05-05T14:28:59Z
id-validation-regexp:
search-url:
AspGD
Aspergillus Genome Database
aspgd
PSI-MI
MI:2172
aspgd
AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species.
www.aspergillusgenome.org/
PMID:24194595
id-validation-regexp:
ASPL[0-9]{10}
search-url:
http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=${ac}
AspGD
Aspergillus Genome Database
aspgd
Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health.
www.candidagenome.org/
ppm
2015-05-05T14:41:00Z
id-validation-regexp:
search-url:
CGD
Candida Genome Database
cgd
PSI-MI
MI:2173
cgd
Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health.
www.candidagenome.org/
PMID:22064862
id-validation-regexp:
(CAL|CAF)[0-9]{7}
search-url:
http://www.candidagenome.org/cgi-bin/locus.pl?dbid=${ac}
CGD
Candida Genome Database
cgd
Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about
everything related to non-pathogenic E. coli, its phages, plasmids, and
mobile genetic elements.
http://ecoliwiki.net/colipedia/
ppm
2015-05-05T14:55:06Z
id-validation-regexp:
search-url:
EcoliWiki
ecoliwiki
PSI-MI
MI:2174
ecoliwiki
Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about
everything related to non-pathogenic E. coli, its phages, plasmids, and
mobile genetic elements.
http://ecoliwiki.net/colipedia/
PMID:22064863
id-validation-regexp:
[A-Za-z]{3,4}
search-url:
http://ecoliwiki.net/colipedia/${ac}
EcoliWiki
ecoliwiki
The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are:
-to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group.
-to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.
GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation.
www.genedb.org
ppm
2015-05-05T15:04:16Z
id-validation-regexp:
search-url:
GeneDB
genedb
PSI-MI
MI:2175
genedb
The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are:
-to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group.
-to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.
GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation.
www.genedb.org
PMID:22116062
id-validation-regexp:
((LmjF|LinJ|LmxM)\.[0-9]{2}\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\.[A-Za-z0-9]+\.[0-9]+)|(TcCLB\.[0-9]{6}\.[0-9]+)
search-url:
www.genedb.org/gene/${ac}
GeneDB
genedb
Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations.
http://www.gramene.org
ppm
2015-05-05T15:12:03Z
id-validation-regexp:
search-url:
Gramene
gramene
PSI-MI
MI:2176
gramene
Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations.
http://www.gramene.org
PMID:24217918
id-validation-regexp:
[A-Z][0-9][A-Z0-9]{3}[0-9]
search-url:
http://tools.gramene.org/search?query=${ac}
Gramene
gramene
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
www.pombase.org
ppm
2015-05-05T15:17:42Z
id-validation-regexp:
search-url:
PomBase
pombase
PSI-MI
MI:2177
pombase
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
www.pombase.org
PMID:22039153
id-validation-regexp:
S\w+(\.)?\w+(\.)?
search-url:
www.pombase.org/spombe/result/${ac}
PomBase
pombase
The Arabidopsis Genome Initiative comprises TAIR, TIGR and MIPS.
ppm
2015-05-05T16:12:18Z
id-validation-regexp:
search-url:
AGI_LocusCode
Arabidopsis Genome Initiative
agi_locuscode
PSI-MI
MI:2178
agi_locuscode
id-validation-regexp:
A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})?
search-url:
http://arabidopsis.org/servlets/TairObject?type=locus&name=${ac}
AGI_LocusCode
Arabidopsis Genome Initiative
agi_locuscode
Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).
ppm
2015-05-11T09:59:36Z
part of
subset
PSI-MI
MI:2179
subset
Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).
PMID:14755292
part of
subset
AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation.
http://www.agbase.msstate.edu/
ppm
2015-05-11T10:23:14Z
search-url:
AgBase
agbase
PSI-MI
MI:2180
agbase
AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation.
http://www.agbase.msstate.edu/
PMID:21075795
search-url:
http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=${ac}
AgBase
agbase
The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.
http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
ppm
2015-05-11T10:51:57Z
search-url:
CACAO
Community Assessment of Community Annotation with Ontologies
cacao
PSI-MI
MI:2181
cacao
search-url:
http://gowiki.tamu.edu/wiki/index.php/${ac}
CACAO
Community Assessment of Community Annotation with Ontologies
cacao
Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation.
http://bcb.cs.tufts.edu/dflat/
ppm
2015-05-11T11:01:34Z
DFLAT
Developmental FunctionaL Annotation at Tufts
dflat
PSI-MI
MI:2182
dflat
DFLAT
Developmental FunctionaL Annotation at Tufts
dflat
The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool.
http://www.geneontology.org/GO.refgenome.shtml
ppm
2015-05-11T11:10:30Z
GO central
GO_central
The Reference Genome Annotation Project
go_central
PSI-MI
MI:2183
go_central
The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool.
http://www.geneontology.org/GO.refgenome.shtml
PMID:19578431
GO central
GO_central
The Reference Genome Annotation Project
go_central
Collection and Refinement of Physiological Data on Mycobacterium tuberculosis in the form of GO annitations. MTBBASE data has also been rendered as pathway information in Reactome.
http://www.ark.in-berlin.de/Site/MTBbase.html
http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121237.1
ppm
2015-05-11T11:34:15Z
MTBBASE
mtbbase
PSI-MI
MI:2184
mtbbase
MTBBASE
mtbbase
The Parkinson's UK Gene Ontology Project represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK. This annotation group is a member of the IMEx Consortium.
http://www.ucl.ac.uk/functional-gene-annotation/neurological
ppm
2015-05-11T11:45:34Z
Parkinson-UCL
Parkinsons Disease Gene Ontology Initiative
ParkinsonsUK-UCL
parkinsonsuk-ucl
PSI-MI
MI:2185
parkinsonsuk-ucl
Parkinson-UCL
Parkinsons Disease Gene Ontology Initiative
ParkinsonsUK-UCL
parkinsonsuk-ucl
The Alzheimers-University of Toronto project adds functional annotation to Alzheimer's related gene products using the Gene Ontology.
http://www.ims.utoronto.ca/
ppm
2015-05-11T13:13:02Z
Alzheimers Project at University of Toronto
Alzheimers University of Toronto
Alzheimers_University_of_Toronto
alut
PSI-MI
MI:2186
alut
Alzheimers Project at University of Toronto
Alzheimers University of Toronto
Alzheimers_University_of_Toronto
alut
The Roslin Institute uses the Gene Ontology to add functional annotation to different gene products.
http://www.roslin.ac.uk/
ppm
2015-05-11T13:18:36Z
RI
Roslin Institute
Roslin_Institute
ri
roslin_institute
PSI-MI
MI:2187
ri
RI
Roslin Institute
Roslin_Institute
ri
roslin_institute
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology.
http://en.wikipedia.org/wiki/PAR-CLIP
ppm
2015-05-11T15:13:05Z
PAR-CLIP
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation
par-clip
PSI-MI
MI:2188
par-clip
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology.
http://en.wikipedia.org/wiki/PAR-CLIP
PMID:20371350
PMID:20644507
PAR-CLIP
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation
par-clip
Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates.
ppm
2015-06-01T15:05:13Z
AVidity-based EXtracellular Interaction Screen
avexis
avidity-based extracellular interaction screen
PSI-MI
MI:2189
avexis
Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates.
pmid:22414956
AVidity-based EXtracellular Interaction Screen
avexis
avidity-based extracellular interaction screen
Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far.
ppm
2015-06-02T11:33:27Z
lncRNA
lncrna
long non coding RNA
long non coding ribonucleic acid
long non-coding RNA
PSI-MI
MI:2190
long non-coding ribonucleic acid
Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far.
PMID:23750541
lncRNA
lncrna
long non coding RNA
long non coding ribonucleic acid
long non-coding RNA
Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
https://en.wikipedia.org/wiki/CLIP
ppm
2015-06-15T10:17:34Z
CLIP
clip
cross linking immunoprecipitation
cross-linking immunoprecipitation
PSI-MI
MI:2191
clip
Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
https://en.wikipedia.org/wiki/CLIP
PMID:14615540
CLIP
clip
cross linking immunoprecipitation
cross-linking immunoprecipitation
This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins.
https://en.wikipedia.org/wiki/HITS-CLIP
ppm
2015-06-15T10:44:44Z
CLIP-Seq
HITS-CLIP
UV cross-linking immunoprecipitation combined with high-throughput sequencing
clip-seq
PSI-MI
MI:2192
clip-seq
This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins.
https://en.wikipedia.org/wiki/HITS-CLIP
PMID:18978773
PMID:21633356
CLIP-Seq
HITS-CLIP
UV cross-linking immunoprecipitation combined with high-throughput sequencing
clip-seq
iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution.
https://en.wikipedia.org/wiki/ICLIP
ppm
2015-06-15T11:17:22Z
iCLIP
iclip
individual-nucleotide resolution cross-linking and immunoprecipitation
PSI-MI
MI:2193
iclip
iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution.
https://en.wikipedia.org/wiki/ICLIP
PMID:20601959
iCLIP
iclip
individual-nucleotide resolution cross-linking and immunoprecipitation
Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
ppm
2015-06-15T11:26:33Z
CRAC
crac
cross-linking and analysis of cDNAs
PSI-MI
MI:2194
crac
Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
PMID:19482942
CRAC
crac
cross-linking and analysis of cDNAs
This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs.
ppm
2015-06-15T11:45:38Z
CLASH
clash
cross-linking, ligation, and sequencing of hybrids
PSI-MI
MI:2195
clash
This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs.
PMID:21610164
CLASH
clash
cross-linking, ligation, and sequencing of hybrids
A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator.
ppm
2015-07-07T09:46:51Z
QCM
qcm
PSI-MI
MI:2196
quartz crystal microbalance
A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator.
PMID:23504432
QCM
qcm
An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study.
ppm
2015-07-07T10:11:26Z
probe interaction assay
PSI-MI
MI:2197
probe interaction assay
An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study.
PMID:14755292
probe interaction assay
The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners.
ppm
2015-07-07T10:14:29Z
labelling assay
PSI-MI
MI:2198
labelling assay
The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners.
PMID:14755292
labelling assay
The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label
ppm
2015-07-07T11:51:57Z
site-labelling technology
specific site-labelling technology
PSI-MI
MI:2199
specific site-labelling technology
The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label
PMID:8441405
site-labelling technology
specific site-labelling technology
PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks.
http://primesdb.eu/
ppm
2015-07-13T16:36:21Z
PRIMESDB
primesdb
PSI-MI
MI:2200
primesdb
PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks.
http://primesdb.eu/
PMID:22453911
PRIMESDB
primesdb
Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification.
ppm
2015-08-11T15:37:49Z
DNA chemical modification
DNA epigenetic modification
dna chemical modification
PSI-MI
MI:2201
DNA chemical modification
Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification.
PMID:14755292
DNA chemical modification
DNA epigenetic modification
dna chemical modification
Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation).
ppm
2015-08-11T15:55:40Z
RNA chemical modification
post-transcriptional modification
rna chemical modification
PSI-MI
MI:2202
RNA chemical modification
Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation).
PMID:14755292
RNA chemical modification
post-transcriptional modification
rna chemical modification
Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site.
ppm
2015-08-11T17:22:38Z
primer extension assay
PSI-MI
MI:2203
primer extension assay
Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site.
PMID:23378648
primer extension assay
A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression.
ppm
2016-01-20T16:25:10Z
url:
miRNA
micro RNA
micro-RNA
micro-rna
mirna
PSI-MI
MI:2204
micro rna
A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression.
PMID:14744438
url:
https://en.wikipedia.org/wiki/MicroRNA
miRNA
micro RNA
micro-RNA
micro-rna
mirna
The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records.
Legacy data can be found at
http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
ppm
2016-01-20T16:48:10Z
PIR
Protein Information Resource
pir
PSI-MI
MI:2205
pir
PIR
Protein Information Resource
pir
Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
ppm
2016-01-21T14:50:29Z
observed na chemical modification
observed nucleic acid chemical modification
PSI-MI
MI:2206
observed nucleic acid chemical modification
Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
PMID:14755292
observed na chemical modification
observed nucleic acid chemical modification
Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
ppm
2016-01-21T15:02:23Z
resulting na chemical modification
resulting nucleic acid chemical modification
PSI-MI
MI:2207
resulting nucleic acid chemical modification
Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
PMID:14755292
resulting na chemical modification
resulting nucleic acid chemical modification
Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
ppm
2016-01-21T15:12:35Z
prerequisite-na chemical modification
prerequisite-nucleic acid chemical modification
PSI-MI
MI:2208
prerequisite-nucleic acid chemical modification
Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
PMID:14755292
prerequisite-na chemical modification
prerequisite-nucleic acid chemical modification
Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
ppm
2016-01-21T15:17:08Z
na chemical modification decreasing
nucleic acid chemical modification decreasing an interaction
PSI-MI
MI:2209
nucleic acid chemical modification decreasing an interaction
Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
PMID:14755292
na chemical modification decreasing
nucleic acid chemical modification decreasing an interaction
Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
ppm
2016-01-21T15:18:52Z
na chemical modification disrupting
nucleic acid chemical modification disrupting an interaction
PSI-MI
MI:2210
nucleic acid chemical modification disrupting an interaction
Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
PMID:14755292
na chemical modification disrupting
nucleic acid chemical modification disrupting an interaction
Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
ppm
2016-01-21T15:25:51Z
na chemical modification increasing
nucleic acid chemical modification increasing an interaction
PSI-MI
MI:2211
nucleic acid chemical modification increasing an interaction
Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
PMID:14755292
na chemical modification increasing
nucleic acid chemical modification increasing an interaction
The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE.
http://www.proteomexchange.org
ppm
2016-02-02T13:52:54Z
ProteomExchange
proteomexchange
PSI-MI
MI:2212
proteomexchange
The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE.
http://www.proteomexchange.org
PMID:25047258
ProteomExchange
proteomexchange
Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image.
ppm
2016-02-11T11:10:32Z
super resolution microscopy
super-resolution microscopy
PSI-MI
MI:2213
super-resolution microscopy
Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image.
PMID:14755292
super resolution microscopy
super-resolution microscopy
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
ppm
2016-03-15T15:31:08Z
search-url:
SIGNOR
SIGnaling Network Open Resource
signaling network open resource
signor
PSI-MI
MI:2214
signor
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
PMID:26467481
search-url:
http://signor.uniroma2.it/relation_result.php?id=${ac}
SIGNOR
SIGnaling Network Open Resource
signaling network open resource
signor
This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs.
ppm
2016-05-05T14:33:32Z
BGF-2h
barcode fusion genetics two hybrid
bfg two hybrid
bfg-2h
PSI-MI
MI:2215
barcode fusion genetics two hybrid
This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs.
PMID:27107012
BGF-2h
barcode fusion genetics two hybrid
bfg two hybrid
bfg-2h
Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.
ppm
2016-05-09T09:40:07Z
de-AMPylation assay
de-ampylation assay
deAMPylation assay
deampylation assay
PSI-MI
MI:2216
deampylation assay
Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.
PMID:14755292
de-AMPylation assay
de-ampylation assay
deAMPylation assay
deampylation assay
The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
ppm
2016-05-09T09:45:05Z
luciferase-c
PSI-MI
MI:2217
luciferase-c
The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:22070901
luciferase-c
The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
ppm
2016-05-09T09:45:23Z
luciferase-n
PSI-MI
MI:2218
luciferase-n
The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:22070901
luciferase-n
Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range.
ppm
2016-05-09T10:05:39Z
GLuc tag
gaussia luciferase
gaussia luciferase protein tag
gluc tag
PSI-MI
MI:2219
gaussia luciferase protein tag
Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range.
PMID:26025768
GLuc tag
gaussia luciferase
gaussia luciferase protein tag
gluc tag
The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
ppm
2016-05-09T10:13:06Z
gaussia-c
PSI-MI
MI:2220
gaussia-c
The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:17099704
gaussia-c
The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
ppm
2016-05-09T10:13:23Z
gaussia-n
PSI-MI
MI:2221
gaussia-n
The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
PMID:17099704
gaussia-n
Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set.
ppm
2016-05-13T16:16:06Z
inference by socio-affinity scoring
socio-affinity index inference
socio-affinity inference
socioaffinity index scoring
socioaffinity inference
PSI-MI
MI:2222
inference by socio-affinity scoring
Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set.
PMID:16429126
inference by socio-affinity scoring
socio-affinity index inference
socio-affinity inference
socioaffinity index scoring
socioaffinity inference
This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs.
ppm
2016-05-17T10:36:05Z
inference by quantitative co-purification
quantitative tagless co - purification
PSI-MI
MI:2223
inference by quantitative co-purification
This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs.
PMID:27099342
inference by quantitative co-purification
quantitative tagless co - purification
In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified.
ppm
2016-05-23T13:32:07Z
chemical rna modification plus base pairing prediction
PSI-MI
MI:2224
chemical rna modification plus base pairing prediction
In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified.
PMID:10024243
chemical rna modification plus base pairing prediction
ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology.
http://zinc15.docking.org/
ppm
2016-06-13T15:47:30Z
id-validation-regexp:
search-url:
ZINC
zinc
PSI-MI
MI:2225
zinc
ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology.
http://zinc15.docking.org/
PMID:26479676
id-validation-regexp:
[0-9]*
search-url:
http://zinc15.docking.org/substances/${ac}
ZINC
zinc
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type.
ppm
2016-06-13T15:57:12Z
mutation not affecting interaction
mutation with no effect
PSI-MI
MI:2226
mutation with no effect
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type.
PMID:14577292
mutation not affecting interaction
mutation with no effect
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact.
ppm
2016-06-13T16:25:47Z
mutation causing
mutation causing an interaction
mutation enabling interaction
PSI-MI
MI:2227
mutation causing an interaction
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact.
PMID:14755292
mutation causing
mutation causing an interaction
mutation enabling interaction
Interactions and complexes curated by scientists at the Central European Institute of Technology (CEITEC).
ppm
2016-09-14T10:41:07Z
search-url:
CEITEC
Central European Institute of Technology
ceitec
PSI-MI
MI:2228
ceitec
search-url:
www.ceitec.eu/
CEITEC
Central European Institute of Technology
ceitec
Interaction between a nucleic acid and a gene region.
ppm
2016-09-21T11:39:49Z
PSI-MI
MI:2229
nucleicacid-gene
Interaction between a nucleic acid and a gene region.
PMID:14755292
Interaction between a nucleic acid and a corresponding nucleic acid.
ppm
2016-09-21T11:41:03Z
PSI-MI
MI:2230
nucleicacid-nucleicacid
Interaction between a nucleic acid and a corresponding nucleic acid.
PMID:14755292
This approach infers interacting pairs of proteins looking at expression data coming from transcript expression datasets. Co-expressed pairs of genes are ranked and predicted to be interacting proteins as well.
ppm
2016-10-05T11:48:53Z
co-expression
coexpression
coexpression prediction
PSI-MI
MI:2231
coexpression
co-expression
coexpression
coexpression prediction
A particular way two or more molecules influence one another.
ppm
2016-12-08T15:17:45Z
molecular association
PSI-MI
MI:2232
molecular association
molecular association
Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema.
ppm
2017-01-19T13:17:37Z
causal interaction
PSI-MI
MI:2233
causal interaction
Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema.
DOI:10.1142/S0219525908001465
causal interaction
The effect of modulator entity A on a modulated entity B.
ppm
2017-01-19T13:20:22Z
causal statement
PSI-MI
MI:2234
causal statement
The effect of modulator entity A on a modulated entity B.
PMID:26467481
causal statement
The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B.
ppm
2017-01-19T13:47:54Z
up regulates
up-regulates
activates
PSI-MI
MI:2235
up-regulates
The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B.
PMID:26467481
up regulates
up-regulates
The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
ppm
2017-01-19T13:50:43Z
GO:GO:0044093
activates activity
up-regulates activity
PSI-MI
MI:2236
up-regulates activity
The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
PMID:26467481
activates activity
up-regulates activity
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B.
ppm
2017-01-19T13:53:41Z
increases quantity
up-regulates quantity
PSI-MI
MI:2237
up-regulates quantity
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B.
PMID:26467481
increases quantity
up-regulates quantity
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression.
ppm
2017-01-19T13:56:00Z
increases quantity by expression
up-regulates quantity by expression
PSI-MI
MI:2238
up-regulates quantity by expression
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression.
PMID:26467481
increases quantity by expression
up-regulates quantity by expression
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation.
ppm
2017-01-19T13:58:03Z
increases quantity by stabilization
up-regulates quantity by stabilization
PSI-MI
MI:2239
up-regulates quantity by stabilization
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation.
PMID:26467481
increases quantity by stabilization
up-regulates quantity by stabilization
The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B.
ppm
2017-01-19T14:00:20Z
down regulates
down-regulates
PSI-MI
MI:2240
down-regulates
The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B.
PMID:26467481
down regulates
down-regulates
The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
ppm
2017-01-19T14:13:34Z
GO:GO:0044093
down-regulates activity
inhibits activity
PSI-MI
MI:2241
down-regulates activity
The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
PMID:26467481
down-regulates activity
inhibits activity
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B.
ppm
2017-01-19T14:15:10Z
decreases quantity
down-regulates quantity
PSI-MI
MI:2242
down-regulates quantity
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B.
PMID:26467481
decreases quantity
down-regulates quantity
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression.
ppm
2017-01-19T14:25:28Z
Decrease quantity by repression
down-regulates quantity by repression
PSI-MI
MI:2243
down-regulates quantity by repression
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression.
PMID:26467481
Decrease quantity by repression
down-regulates quantity by repression
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation.
ppm
2017-01-19T14:28:52Z
decrease quantity by destabilization
down-regulates quantity by destabilization
PSI-MI
MI:2244
down-regulates quantity by destabilization
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation.
PMID:26467481
decrease quantity by destabilization
down-regulates quantity by destabilization
Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B.
ppm
2017-01-19T15:44:29Z
causal regulatory mechanism
indirect causal regulation
PSI-MI
MI:2245
causal regulatory mechanism
Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B.
PMID:26467481
causal regulatory mechanism
indirect causal regulation
The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B.
ppm
2017-01-19T15:45:44Z
indirect
indirect causal regulation
PSI-MI
MI:2246
indirect causal regulation
true
The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B.
PMID:15845847
indirect
indirect causal regulation
Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
ppm
2017-01-19T15:47:39Z
transcriptional regulation
PSI-MI
MI:2247
transcriptional regulation
Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
PMID:25428369
transcriptional regulation
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
ppm
2017-01-19T15:48:53Z
translation regulation
translational regulation
PSI-MI
MI:2248
translation regulation
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
PMID:25428369
translation regulation
translational regulation
Any process that control gene expression at the RNA level, between the transcription and the translation of the gene.
ppm
2017-01-19T15:54:32Z
post transcriptional regulation
post-transcriptional regulation
PSI-MI
MI:2249
post transcriptional regulation
Any process that control gene expression at the RNA level, between the transcription and the translation of the gene.
PMID:25428369
post transcriptional regulation
post-transcriptional regulation
The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B.
ppm
2017-01-19T15:56:00Z
direct
direct causal regulation
PSI-MI
MI:2250
direct causal regulation
true
The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B.
PMID:15845847
direct
direct causal regulation
Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
ppm
2017-01-19T15:57:01Z
PSI-MI
MI:2251
transcriptional regulation by direct binding of dbTF to DNA regulatory element
true
Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
PMID:25428369
The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP.
ppm
2017-01-19T16:13:36Z
GEF reaction
PSI-MI
MI:2252
guanine nucleotide exchange factor reaction
The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP.
PMID:23303910
GEF reaction
A family of cellular proteins able to increases the activity of a GTPase.
ppm
2017-01-19T16:16:04Z
GAP reaction
GTPase-Accelerating Protein reaction
RGS protein reaction
PSI-MI
MI:2253
gtpase-activating protein reaction
true
A family of cellular proteins able to increases the activity of a GTPase.
PMID:17173929
GAP reaction
GTPase-Accelerating Protein reaction
RGS protein reaction
The effect of a chemical compound that results in the activation or in an increased activation of a target molecule.
ppm
2017-01-19T16:23:55Z
chemical activation reaction
PSI-MI
MI:2254
chemical activation reaction
true
The effect of a chemical compound that results in the activation or in an increased activation of a target molecule.
PMID:26467481
chemical activation reaction
The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule.
ppm
2017-01-19T16:25:05Z
chemical inhibition reaction
PSI-MI
MI:2255
chemical inhibition reaction
true
The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule.
PMID:26467481
chemical inhibition reaction
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
ppm
2017-01-19T16:26:15Z
relocalization
PSI-MI
MI:2256
relocalization
true
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
PMID:26467481
relocalization
The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules.
ppm
2017-01-19T16:27:34Z
small molecule catalysis reaction
PSI-MI
MI:2257
small molecule catalysis reaction
true
The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules.
PMID:26467481
small molecule catalysis reaction
Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism.
ppm
2017-01-19T16:46:33Z
chemical
drug
xenobiotic
PSI-MI
MI:2258
xenobiotic
Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism.
PMID:14755292
chemical
drug
xenobiotic
Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements.
ppm
2017-01-19T16:51:20Z
causal interactor type
PSI-MI
MI:2259
causal interactor type
Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements.
PMID:26467481
causal interactor type
Any detectable change in the internal or external environment of a cell, tissue, organ, or organism.
ppm
2017-01-19T16:52:44Z
stimulus
PSI-MI
MI:2260
stimulus
Any detectable change in the internal or external environment of a cell, tissue, organ, or organism.
PMID:14755292
stimulus
Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function.
ppm
2017-01-19T16:54:07Z
phenotype
PSI-MI
MI:2261
phenotype
Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function.
PMID:19380745
phenotype
The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity.
ppm
2017-01-19T17:03:04Z
causal regulatory modification
PSI-MI
MI:2262
CAUTION: This is a temporary branch. These terms will be soon added in the PSI-MOD ontology and this branch will became obsolete.
causal regulatory modification
The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity.
PMID:26467481
causal regulatory modification
Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine.
ppm
2017-01-19T17:11:46Z
s-nitrosylation
PSI-MI
MI:2263
s-nitrosylation
Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine.
PMID:15688001
s-nitrosylation
A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin.
ppm
2017-01-23T10:26:40Z
tyrosinated residue
PSI-MI
MI:2264
tyrosinated residue
A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin.
PMID:26467481
tyrosinated residue
A protein modification that effectively remove an acyl group from a protein.
ppm
2017-01-23T10:30:06Z
de-acetylated residue
deacetylated residue
PSI-MI
MI:2265
de-acetylated residue
A protein modification that effectively remove an acyl group from a protein.
PMID:26467481
de-acetylated residue
deacetylated residue
A protein modification that effectively remove a phosphate group from a protein by hydrolysis.
ppm
2017-01-23T10:32:50Z
de-phosphorylated residue
dephosphorylated residue
PSI-MI
MI:2266
de-phosphorylated residue
A protein modification that effectively remove a phosphate group from a protein by hydrolysis.
PMID:26467481
de-phosphorylated residue
dephosphorylated residue
A protein modification that effectively cleaves the G-K bond and releases SUMO proteins.
ppm
2017-01-23T10:46:01Z
de-sumoylated residue
desumoylated residue
PSI-MI
MI:2267
de-sumoylated residue
A protein modification that effectively cleaves the G-K bond and releases SUMO proteins.
PMID:26467481
de-sumoylated residue
desumoylated residue
A protein modification that effectively removes one or more methyl groups from a protein.
ppm
2017-01-23T10:47:33Z
de-methylated residue
demethylated residue
PSI-MI
MI:2268
de-methylated residue
A protein modification that effectively removes one or more methyl groups from a protein.
PMID:26467481
de-methylated residue
demethylated residue
A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins.
ppm
2017-01-23T10:48:53Z
de-ubiquitinylated residue
deubiquitinylated residue
PSI-MI
MI:2269
de-ubiquitinylated residue
A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins.
PMID:26467481
de-ubiquitinylated residue
deubiquitinylated residue
SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks.
http://signalink.org
ppm
2017-01-23T11:41:20Z
url:http://signalink.org
SignaLink
signalink
PSI-MI
MI:2270
signalink
SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks.
http://signalink.org
PMID:23331499
SignaLink
signalink
EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats.
http://edamontology.org/
ppm
2017-01-26T15:09:47Z
url:http://edamontology.org/
EDAM
EMBRACE Data And Methods
edam
PSI-MI
MI:2271
edam
EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats.
http://edamontology.org/
PMID:23479348
EDAM
EMBRACE Data And Methods
edam
Reversible reaction that add a tyrosine residue to an amino-acid.
ppm
2017-01-26T15:21:43Z
GO:GO:0018322
tyrosinylation
PSI-MI
MI:2272
tyrosinylation
tyrosinylation
Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin.
ppm
2017-01-26T15:22:39Z
GO:GO:0018166
tyrosination
PSI-MI
MI:2273
tyrosination
Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin.
PMID:10842328
tyrosination
Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity.
ppm
2017-01-26T15:29:51Z
modulator
regulator
PSI-MI
MI:2274
regulator
Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity.
PMID:14755292
modulator
regulator
Entity whose concentration, frequency, rate or extent are regulated by the regulator entity.
ppm
2017-01-26T15:31:14Z
modulator target
regulator target
PSI-MI
MI:2275
regulator target
Entity whose concentration, frequency, rate or extent are regulated by the regulator entity.
PMID:14755292
modulator target
regulator target
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification.
ppm
2017-03-06T11:04:25Z
carbohydrate chemical modification
PSI-MI
MI:2276
carbohydrate chemical modification
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification.
PMID:14755292
carbohydrate chemical modification
This method uses Cre recombinase as a two-hybrid protein-protein interaction reporter that functions intracellularly to covalently and unidirectionally link interacting bait and prey plasmids via specialized loxP sites that flank the protein-coding sequences. The linked protein-coding sequences serve as interaction-identifying DNA molecules that enable massively multiplexed screening coupled with next-generation DNA sequencing to detect protein-protein interactions.
ppm
2017-06-20T15:57:41Z
Cre recombinase two hybrid
cr-2h
cr-two hybrid
PSI-MI
MI:2277
Cr-two hybrid
Cre recombinase two hybrid
cr-2h
cr-two hybrid
Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers.
ppm
2017-07-05T10:27:19Z
polymer chain length
PSI-MI
MI:2278
polymer chain length
Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers.
PMID:14755292
polymer chain length
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.
ppm
2017-07-28T09:34:45Z
search-url:
Complex Portal
complex portal
PSI-MI
MI:2279
complex portal
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.
PMID:25313161
search-url:
http://www.ebi.ac.uk/complexportal/complex/${ac}
Complex Portal
complex portal
Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline).
ppm
2017-08-08T14:38:29Z
deamidation
PSI-MI
MI:2280
deamidation reaction
Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline).
PMID:2703484
PMID:3440704
deamidation
Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
ppm
2017-08-08T14:49:09Z
amidase assay
deamidation
PSI-MI
MI:2281
deamidation assay
Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
GO:0004040
amidase assay
deamidation
Complex object unique primary identifier that is assigned to a complex in the Complex Portal.
ppm
2017-08-25T13:31:03Z
complex-primary
PSI-MI
MI:2282
complex-primary
Complex object unique primary identifier that is assigned to a complex in the Complex Portal.
PMID:25313161
complex-primary
Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting.
ppm
2017-11-15T15:35:20Z
southwestern blot
southwestern blotting
PSI-MI
MI:2283
southwestern blotting
Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting.
PMID:26404144
southwestern blot
southwestern blotting
Indicates that the cross-referenced molecule is a component of a containing complex.
ppm
2017-12-15T11:08:53Z
complex component
complex-component
PSI-MI
MI:2284
complex component
Indicates that the cross-referenced molecule is a component of a containing complex.
PMID:25313161
complex component
complex-component
The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs.
pporras
2018-05-02T15:22:12Z
miRNA interference luciferase assay
PSI-MI
MI:2285
miRNA interference luciferase reporter assay
The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs.
PMID:14697198
PMID:21431711
miRNA interference luciferase assay
Binary relationship between biological entities when one of them modulates the other in terms of function, expression, degradation or stability of the other and the relationship between the partners cannot be ascertained as direct, so intermediate steps are implicitly present. This relation specifically does not imply a physical interaction between the entities involved.
pporras
2018-06-27T15:24:40Z
functional association
PSI-MI
MI:2286
functional association
functional association
Identity of the participant was established (or confirmed) by
fitting its molecular model to the experimentally determined
electron density.
pporras
2018-06-28T15:00:41Z
identification by structure determination
structure determination
PSI-MI
MI:2287
identification by structure determination
Identity of the participant was established (or confirmed) by
fitting its molecular model to the experimentally determined
electron density.
PMID:7877166
identification by structure determination
structure determination
DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced.
pporras
2018-06-28T16:09:45Z
DNA affinity purification sequencing
dap-seq
PSI-MI
MI:2288
DAP-seq
DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced.
PMID:27203113
DNA affinity purification sequencing
dap-seq
The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots.
pporras
2018-09-13T10:18:19Z
viral particle co-purification
PSI-MI
MI:2289
virotrap
The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots.
PMID:27122307
viral particle co-purification
Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
pporras
2018-09-13T10:39:59Z
PSI-MI
MI:2290
optical tweezers
Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
PMID:17023539
PMID:17081984
Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip.
pporras
2018-09-13T10:49:44Z
afm cantilevers
PSI-MI
MI:2291
atomic force microscopy cantilevers
Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip.
PMID:18511917
afm cantilevers
Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
pporras
2018-09-13T12:04:16Z
electromagnetic tweezers
PSI-MI
MI:2292
magnetic tweezers
Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
PMID:18511917
electromagnetic tweezers
Term describing the upstream end of a nucleotide sequence.
pporras
2018-09-14T09:15:05Z
PSI-MI
MI:2293
5' position
Term describing the upstream end of a nucleotide sequence.
PMID:14755292
Term describing the upstream region of a nucleotide sequence, exact coordinates not available.
pporras
2018-09-14T09:25:33Z
PSI-MI
MI:2294
5' range
Term describing the upstream region of a nucleotide sequence, exact coordinates not available.
PMID:14755292
Term describing the downstream end of a nucleotide sequence.
pporras
2018-09-14T09:26:47Z
PSI-MI
MI:2295
3' position
Term describing the downstream end of a nucleotide sequence.
PMID:14755292
Term describing the downstream region of a nucleotide sequence, exact coordinates not available.
pporras
2018-09-14T09:27:33Z
PSI-MI
MI:2296
3' range
Term describing the downstream region of a nucleotide sequence, exact coordinates not available.
PMID:14755292
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact.
pporras
2018-09-14T09:45:20Z
carbohydrate chemical modification causing
PSI-MI
MI:2297
carbohydrate chemical modification causing an interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact.
PMID:14755292
carbohydrate chemical modification causing
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form.
pporras
2018-09-14T09:49:02Z
carbohydrate chemical modification not affecting interaction
PSI-MI
MI:2298
carbohydrate chemical modification with no effect
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form.
PMID:14755292
carbohydrate chemical modification not affecting interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
pporras
2018-09-14T09:53:05Z
carbohydrate chemical modification decreasing
PSI-MI
MI:2299
carbohydrate chemical modification decreasing interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification decreasing
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
pporras
2018-09-14T09:56:38Z
carbohydrate chemical modification decreasing rate
PSI-MI
MI:2300
carbohydrate chemical modification decreasing interaction rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification decreasing rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate.
pporras
2018-09-14T09:58:21Z
carbohydrate chemical modification decreasing strength
PSI-MI
MI:2301
carbohydrate chemical modification decreasing interaction strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification decreasing strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
pporras
2018-09-14T10:03:25Z
carbohydrate chemical modification disrupting
PSI-MI
MI:2302
carbohydrate chemical modification disrupting interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification disrupting
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate.
pporras
2018-09-14T10:06:44Z
carbohydrate chemical modification disrupting strength
PSI-MI
MI:2303
carbohydrate chemical modification disrupting interaction strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification disrupting strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
pporras
2018-09-14T10:08:37Z
carbohydrate chemical modification disrupting rate
PSI-MI
MI:2304
carbohydrate chemical modification disrupting interaction rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification disrupting rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
pporras
2018-09-14T10:11:37Z
carbohydrate chemical modification increasing
PSI-MI
MI:2305
carbohydrate chemical modification increasing interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification increasing
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate.
pporras
2018-09-14T10:22:03Z
carbohydrate chemical modification increasing strength
PSI-MI
MI:2306
carbohydrate chemical modification increasing interaction strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification increasing strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
pporras
2018-09-14T10:23:21Z
carbohydrate chemical modification increasing rate
PSI-MI
MI:2307
carbohydrate chemical modification increasing interaction rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
PMID:14755292
carbohydrate chemical modification increasing rate
Carbohydrate species chemically attached to proteins, or other organic molecules.
pporras
2018-09-14T10:26:12Z
attached glycan
glycosylation
PSI-MI
MI:2308
Specific carbohydrate species can be represented through the MOD ontology and their representation escapes the scope of this CV.
attached carbohydrate
Carbohydrate species chemically attached to proteins, or other organic molecules.
PMID:14755292
attached glycan
glycosylation
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact.
pporras
2018-09-14T10:37:41Z
attached carbohydrate causing
glycosylation causing interaction
PSI-MI
MI:2309
attached carbohydrate causing an interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact.
PMID:14755292
attached carbohydrate causing
glycosylation causing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact.
pporras
2018-09-14T10:40:12Z
attached carbohydrate not affecting interaction
glycosylation with no effect
PSI-MI
MI:2310
attached carbohydrate with no effect
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact.
PMID:14755292
attached carbohydrate not affecting interaction
glycosylation with no effect
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
pporras
2018-09-14T10:42:27Z
attached carbohydrate decreasing
glycosylation decreasing interaction
PSI-MI
MI:2311
attached carbohydrate decreasing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate decreasing
glycosylation decreasing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
pporras
2018-09-14T10:46:39Z
attached carbohydrate increasing
glycosylation increasing interaction
PSI-MI
MI:2312
attached carbohydrate increasing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate increasing
glycosylation increasing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule.
pporras
2018-09-14T10:47:14Z
attached carbohydrate increasing strength
glycosylation increasing strength
PSI-MI
MI:2313
attached carbohydrate increasing interaction strength
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate increasing strength
glycosylation increasing strength
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
pporras
2018-09-14T10:49:39Z
attached carbohydrate increasing rate
glycosylation increasing rate
PSI-MI
MI:2314
attached carbohydrate increasing interaction rate
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate increasing rate
glycosylation increasing rate
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
pporras
2018-09-14T10:50:23Z
attached carbohydrate disrupting rate
glycosylation disrupting rate
PSI-MI
MI:2315
attached carbohydrate disrupting interaction rate
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate disrupting rate
glycosylation disrupting rate
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule.
pporras
2018-09-14T10:51:06Z
attached carbohydrate disrupting strength
glycosylation disrupting strength
PSI-MI
MI:2316
attached carbohydrate disrupting interaction strength
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate disrupting strength
glycosylation disrupting strength
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
pporras
2018-09-18T09:11:58Z
attached carbohydrate disrupting
glycosylation disrupting interaction
PSI-MI
MI:2317
attached carbohydrate disrupting interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
PMID:14755292
attached carbohydrate disrupting
glycosylation disrupting interaction
A technique that measures forces generated by interactions between molecules.
pporras
2018-10-11T13:41:11Z
intermolecular force
PSI-MI
molecular force measurement
MI:2318
force measurement
A technique that measures forces generated by interactions between molecules.
PMID:14755292
intermolecular force
A technique that measures interaction force between two surfaces as they are brought together and retracted.
pporras
2018-10-11T13:44:53Z
PSI-MI
surface adhesion force measurement
MI:2319
surface force measurement
A technique that measures interaction force between two surfaces as they are brought together and retracted.
doi:10.1038/262774a0
The Alzheimer's Research UK Gene Ontology Project represents a collaboration between University College London, the European Bioinformatics Institute (EBI) and the University of Manchester, funded by Alzheimer's Research UK. This annotation group is a member of the IMEx Consortium.
www.ucl.ac.uk/functional-gene-annotation/neurological
pporras
2018-10-16T09:26:24Z
Alzheimer's Research UK Gene Ontology Project
PSI-MI
MI:2320
aruk-ucl
Alzheimer's Research UK Gene Ontology Project
High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases.
pporras
2018-11-13T14:59:35Z
next-generation sequencing
ngs sequencing
PSI-MI
MI:2321
high-throughput sequencing
High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases.
PMID:19900591
next-generation sequencing
ngs sequencing
This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence.
pporras
2018-11-13T15:23:38Z
illumina sequencing
solexa sequencing
PSI-MI
MI:2322
Illumina dye sequencing
This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence.
PMID:18987734
illumina sequencing
solexa sequencing
KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges.
pporras
2019-04-02T09:58:26Z
KISS
kinase substrate sensor
kiss
PSI-MI
MI:2323
kiss
KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges.
PMID:25154561
PMID:29855964
KISS
kinase substrate sensor
kiss
dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
pporras
2019-04-02T10:52:06Z
search-url:
dbSNP
dbsnp
PSI-MI
MI:2324
dbsnp
dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
PMID:11125122
search-url:
https://www.ncbi.nlm.nih.gov/snp/${ac}
dbSNP
dbsnp
NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris.
pporras
2019-04-11T14:07:06Z
NLuc
NanoLuc
nanoluc luciferase
nluc
PSI-MI
MI:2325
nanoluc luciferase protein tag
NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris.
PMID:22894855
NLuc
NanoLuc
nanoluc luciferase
nluc
The n-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
pporras
2019-04-11T14:14:54Z
N-terminal fragment of nanoluc luciferase
nluc-n
PSI-MI
MI:2326
nanoluc-n
N-terminal fragment of nanoluc luciferase
nluc-n
The c-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
pporras
2019-04-11T14:16:59Z
C-terminal fragment of nanoluc luciferase
nluc-c
PSI-MI
MI:2327
nanoluc-c
C-terminal fragment of nanoluc luciferase
nluc-c
The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives.
pporras
2019-04-23T10:19:29Z
SNAP tag
snap tag
PSI-MI
MI:2328
snap tag
The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives.
PMID:12725859
SNAP tag
snap tag
Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix.
pporras
2019-04-23T13:40:51Z
HIC
hic
PSI-MI
MI:2329
hydrophobic interaction chromatography
Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix.
PMID:27730562
HIC
hic
Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein.
pporras
2019-07-11T15:50:31Z
SUMO tag
sumo tag
PSI-MI
MI:2330
sumo tag
Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein.
PMID:19107426
SUMO tag
sumo tag
A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion.
pporras
2019-07-11T15:54:51Z
PSI-MI
MI:2331
phage library
A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion.
PMID:9661810
Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain.
pporras
2019-07-11T16:04:14Z
Gd3+-4MMDPA tag
g1 spin label
g1-spin label
PSI-MI
MI:2332
g1 spin label
Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain.
PMID:25438671
Gd3+-4MMDPA tag
g1 spin label
g1-spin label
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that has a complex effect over the interaction when compared with the wild-type. A complex effect is such that cannot be described in increasing, decreasing, causing, disrupting or no effect terms.
pporras
2019-07-11T16:17:45Z
PSI-MI
MI:2333
mutation with complex effect
Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength.
pporras
2019-07-11T16:26:29Z
PSI-MI
MI:2334
luminescence donor
Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength.
PMID:14755292
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self.
pporras
2019-07-11T16:26:47Z
luminescence accept
PSI-MI
MI:2335
luminescence acceptor
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self.
PMID:14755292
luminescence accept
Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes.
pporras
2019-07-11T16:27:09Z
luminescence acceptor-donor pair
PSI-MI
MI:2336
luminescence acceptor donor pair
Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes.
PMID:14755292
luminescence acceptor-donor pair
Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process.
pporras
2019-07-11T16:37:54Z
PSI-MI
MI:2337
chemiluminiscence donor
Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process.
PMID:14755292
Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope.
pporras
2019-07-17T13:23:36Z
3D-EM-tomo
PSI-MI
MI:2338
electron tomography
Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope.
PMID:12160704
3D-EM-tomo
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope.
pporras
2019-07-22T13:39:03Z
3D-EM-single
PSI-MI
MI:2339
electron microscopy 3D single particle reconstruction
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope.
PMID:12160704
3D-EM-single
Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope.
pporras
2019-07-22T13:40:56Z
3D-EM-helical
PSI-MI
MI:2340
electron microscopy 3D helical reconstruction
Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope.
PMID:12160704
3D-EM-helical
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself.
pporras
2019-07-22T13:51:08Z
PSI-MI
MI:2341
luminescence transmitter
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself.
PMID:14755292
Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical.
pporras
2019-07-30T15:05:43Z
partial match
similar object in an external resource
PSI-MI
MI:2342
partial identity match
Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical.
PMID:14755292
partial match
similar object in an external resource
Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies.
pporras
2019-07-30T16:06:16Z
genomic coord
PSI-MI
MI:2343
genomic coordinates
Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies.
PMID:14755292
genomic coord
Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB.
pporras
2019-10-28T17:31:37Z
search-url:
Rhea
PSI-MI
MI:2344
rhea
Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB.
PMID:27980062
search-url:
https://www.rhea-db.org/reaction?id=${ac}
Rhea
The protein is fused to a 12-residue peptide segment (GVAMPGAEDDVV) derived from human podoplanin PLAG domain for which antibodies are available.
pporras
2019-10-30T16:29:27Z
PA tag
PSI-MI
MI:2345
pa tag
The protein is fused to a 12-residue peptide segment (GVAMPGAEDDVV) derived from human podoplanin PLAG domain for which antibodies are available.
PMID:24480187
PA tag
Protein is fused to a 21 amino acid residues-long peptide (YPGQYPGQYPGQYPGQYPGQV) derived from human PAR-4 N-terminal peptide. The final sequence of the peptide resulted from optimization involving mutagenesis and repetition of the original reference sequence in order to maximize affinity with the P20.1 antibody.
pporras
2019-10-30T16:41:19Z
TARGET tag
tandemly-arranged recognition motif combined with gentle elution technology tag
PSI-MI
MI:2346
target tag
Protein is fused to a 21 amino acid residues-long peptide (YPGQYPGQYPGQYPGQYPGQV) derived from human PAR-4 N-terminal peptide. The final sequence of the peptide resulted from optimization involving mutagenesis and repetition of the original reference sequence in order to maximize affinity with the P20.1 antibody.
PMID:20566373
TARGET tag
tandemly-arranged recognition motif combined with gentle elution technology tag
bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, operated by Cold Spring Harbor Laboratory. Articles are not peer-reviewed, edited, or typeset before being posted online.
http://biorxiv.org/
pporras
2019-10-30T16:49:12Z
id-validation-regexp:
search-url:
bioRxiv
PSI-MI
MI:2347
biorxiv
id-validation-regexp:
\d+.\d+/[a-zA-Z0-9\.\:]+
search-url:
https://www.biorxiv.org/content/${ac}
bioRxiv
In sequential BRET-FRET (BRET combined with FRET) bioluminiscence generated by a luciferase triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. This technique can identify multimolecular complexes through detection of the resulting fluoresecence.
pporras
2019-10-30T17:07:01Z
SRET
Sequential BRET-FRET
sret
PSI-MI
MI:2348
sequential bret-fret
In sequential BRET-FRET (BRET combined with FRET) bioluminiscence generated by a luciferase triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. This technique can identify multimolecular complexes through detection of the resulting fluoresecence.
PMID:18587404
SRET
Sequential BRET-FRET
sret
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.
https://www.ncbi.nlm.nih.gov/clinvar
pporras
2019-10-30T17:16:41Z
id-validation-regexp:
search-url:
ClinVAR
PSI-MI
MI:2349
clinvar
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.
https://www.ncbi.nlm.nih.gov/clinvar
PMID:29165669
id-validation-regexp:
[0-9]+
search-url:
https://www.ncbi.nlm.nih.gov/clinvar/variation/${ac}
ClinVAR
EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers.
https://www.ebi.ac.uk/empiar
pporras
2019-12-17T09:31:30Z
id-validation-regex:
search-url:
EMPIAR
Electron Microscopy Public Image Archive
empiar
PSI-MI
MI:2350
empiar
EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers.
https://www.ebi.ac.uk/empiar
PMID:27067018
id-validation-regex:
EMPIAR-[0-9]{5}
search-url:
https://www.ebi.ac.uk/empiar/${ac}
EMPIAR
Electron Microscopy Public Image Archive
empiar
A gene whose genetic perturbation enhances the phenotype resulting from a different genetic perturbation.
pporras
2020-02-12T14:19:39Z
enhancer
PSI-MI
MI:2351
enhancer gene
A gene whose genetic perturbation enhances the phenotype resulting from a different genetic perturbation.
PMID:14755292
enhancer
A gene whose genetic perturbation phenotype is enhanced by a different genetic perturbation.
pporras
2020-02-12T14:21:40Z
enhanced
PSI-MI
MI:2352
enhanced gene
A gene whose genetic perturbation phenotype is enhanced by a different genetic perturbation.
PMID:14755292
enhanced
A gene whose genetic perturbation masks the phenotype resulting from a different genetic perturbation.
pporras
2020-02-12T14:22:57Z
epistatic
PSI-MI
MI:2353
epistatic gene
A gene whose genetic perturbation masks the phenotype resulting from a different genetic perturbation.
PMID:14755292
epistatic
A gene whose genetic perturbation phenotype is masked by a different genetic perturbation.
pporras
2020-02-12T14:24:11Z
hypostatic
PSI-MI
MI:2354
hypostatic gene
A gene whose genetic perturbation phenotype is masked by a different genetic perturbation.
PMID:14755292
hypostatic
Measurement of the substraction of one or more ADP-ribose moieties to molecules.
pporras
2020-06-02T17:02:11Z
adp deribosylase
PSI-MI
adp deribosylation
MI:2355
adp deribosylase assay
Measurement of the substraction of one or more ADP-ribose moieties to molecules.
PMID:14760721
adp deribosylase
Involves the substraction of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
pporras
2020-06-02T17:02:30Z
adp de-ribosylation
adp deribosylation
PSI-MI
MI:2356
adp deribosylation reaction
Involves the substraction of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
GO:0051725
PMID:14755292
RESID:AA0168
RESID:AA0169
RESID:AA0231
RESID:AA0237
RESID:AA0295
adp de-ribosylation
adp deribosylation
This parameter represents the rate of the reaction at negligible substrate concentration, indicating how the velocity varies according to how often enzyme and substrate combine.
pporras
2020-06-30T16:04:54Z
catalytic efficiency
kcat/km
specificity constant
PSI-MI
MI:2357
kcat/km
This parameter represents the rate of the reaction at negligible substrate concentration, indicating how the velocity varies according to how often enzyme and substrate combine.
PMID:14755292
catalytic efficiency
kcat/km
specificity constant
A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
Homepage: http://www.mirbase.org/
pporras
2020-06-30T17:05:08Z
search-url:
miRBASE
PSI-MI
MI:2358
mirbase
A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
Homepage: http://www.mirbase.org/
PMID:30423142
search-url:
http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=${ac}
miRBASE
RNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
pporras
2020-07-01T16:15:22Z
double stranded ribonucleic acid
PSI-MI
MI:2359
ds rna
RNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
PMID:14755292
double stranded ribonucleic acid
Protein is fused to beta-galactosidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
pporras
2020-07-01T16:18:26Z
beta gal tag
beta-galactosidase tag
PSI-MI
MI:2360
beta gal tag
Protein is fused to beta-galactosidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
PMID:10459153
beta gal tag
beta-galactosidase tag
Bait protein is fused to a standard protein fusion tag and an intein fragment, prey a with a different protein fusion tag and the complementary intein fragment. The bait and prey are co-expressed in a cell line where the association of bait and prey brings the intein fragments into close proximity, allowing them to reconstitute a fully functional intein, which then catalyzes its own excision and the concurrent ligation of the bait and the prey peptides (as well as the standard protein fusion tags). The resulting spliced protein can be resolved by regular western blot analysis due to its altered mobility, while the presence of the standard protein fusion tags allows visualization or purification of protein using regular biochemical techniques.
pporras
2020-12-02T11:31:51Z
SIMPL
simpl
PSI-MI
MI:2361
Split Intein-Mediated Protein Ligation
Bait protein is fused to a standard protein fusion tag and an intein fragment, prey a with a different protein fusion tag and the complementary intein fragment. The bait and prey are co-expressed in a cell line where the association of bait and prey brings the intein fragments into close proximity, allowing them to reconstitute a fully functional intein, which then catalyzes its own excision and the concurrent ligation of the bait and the prey peptides (as well as the standard protein fusion tags). The resulting spliced protein can be resolved by regular western blot analysis due to its altered mobility, while the presence of the standard protein fusion tags allows visualization or purification of protein using regular biochemical techniques.
PMID:32415080
SIMPL
simpl
Intein C-terminal fragment tag, commonly used in SIMPL and related methods.
pporras
2020-12-02T11:39:05Z
IC tag
intein c-terminal fragment tag
PSI-MI
MI:2362
ic tag
IC tag
intein c-terminal fragment tag
Intein N-terminal fragment tag, commonly used in SIMPL and related methods.
pporras
2020-12-02T11:40:48Z
IN tag
intein n-terminal fragment tag
PSI-MI
MI:2363
in tag
IN tag
intein n-terminal fragment tag
Coincident occurrence of molecules within very close proximity (in the nanometer range), detected through molecule-level resolution methodology, but from which a physical interaction among those molecules cannot be inferred.
pporras
2020-12-02T11:42:19Z
close-contact colocalization
neighbourhood interaction
PSI-MI
MI:2364
proximity
close-contact colocalization
neighbourhood interaction
FluoPPI system (Fluorescent Protein-Protein Interaction-visualization):-FLUOPPI utilises the formation of fluorescence foci whereby the interacting proteins of interest are genetically fused with either a tetramerizing fluorescent protein (FP-tag) or an assembly helper tag (Ash-tag). The incorporation of these tags onto a pair of interacting proteins enables the formation of intensely bright foci when co-expressed in mammalian cells. In these foci the FP-tag induces the fused protein to form a tetramer that can now interact with up to 4 copies of the Ash-tagged partner protein. The cognate interacting protein also forms an oligomer through the Ash tag, which in turn can interact with multiple copies of the FP-fused partner protein. The potential of both constructs to interact with multiple copies of each other enable large foci incorporating the fluorescent protein to form, which can be clearly observed when imaging the cell.
pporras
2020-12-07T17:35:40Z
FluoPPI
fluoppi
PSI-MI
MI:2365
fluorescent protein-protein interaction-visualization
FluoPPI system (Fluorescent Protein-Protein Interaction-visualization):-FLUOPPI utilises the formation of fluorescence foci whereby the interacting proteins of interest are genetically fused with either a tetramerizing fluorescent protein (FP-tag) or an assembly helper tag (Ash-tag). The incorporation of these tags onto a pair of interacting proteins enables the formation of intensely bright foci when co-expressed in mammalian cells. In these foci the FP-tag induces the fused protein to form a tetramer that can now interact with up to 4 copies of the Ash-tagged partner protein. The cognate interacting protein also forms an oligomer through the Ash tag, which in turn can interact with multiple copies of the FP-fused partner protein. The potential of both constructs to interact with multiple copies of each other enable large foci incorporating the fluorescent protein to form, which can be clearly observed when imaging the cell.
PMID:31784573
FluoPPI
fluoppi
The phenotype outcome resulting from two or more genetic perturbations to an organism, individually and in combination.
PSI-MI
MI:2366
multigenic phenotype result
A multigenic phenotype result in which the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations.
PSI-MI
MI:2367
genetic interaction (sensu phenotype modification)
Genetic perturbation of multiple genes in combination that results in a more severe phenotype (except lethality or growth defect) than individual genetic perturbations.
PSI-MI
MI:2368
phenotypic enhancement (sensu BioGRID)
Mutation of multiple genes in combination that results in a more severe growth defect than from individual mutation.
PSI-MI
MI:2369
synthetic growth defect (sensu BioGRID)
Mutation of multiple genes in combination that results in lethality when individual single mutations are viable.
PSI-MI
MI:2370
synthetic lethality (sensu BioGRID)
Genetic perturbation of multiple genes in combination that results in a less severe phenotype than from individual perturbations. This term is reserved for high throughput studies with scores.
PSI-MI
MI:2371
positive genetic interaction (sensu BioGRID)
Genetic perturbations of multiple genes in combination that results in a more severe growth defect than each individual perturbation, when one mutation is hemizygous.
PSI-MI
MI:2372
synthetic haploinsufficiency (sensu BioGRID)
Genetic perturbation of multiple genes in combination that results in a more severe phenotypic defect (or lethality) than from individual viable perturbations. This term is reserved for high throughput studies with scores.
PSI-MI
MI:2373
negative genetic interaction (sensu BioGRID)
Genetic perturbation of one gene suppresses a phenotype (other than lethality or growth defect) associated with perturbation of another gene.
PSI-MI
MI:2374
phenotypic suppression (sensu BioGRID)
Mutation of one gene rescues lethality or a growth defect associated with perturbation of another gene.
PSI-MI
MI:2375
synthetic rescue (sensu BioGRID)
Increased dosage of one gene rescues lethality or a growth defect associated with perturbation of another gene.
PSI-MI
MI:2376
dosage rescue (sensu BioGRID)
Increased dosage of one gene causes lethality in combination with another viable genetic perturbation.
PSI-MI
MI:2377
dosage lethality (sensu BioGRID)
Increased dosage of one gene causes a growth defect in (or enhances an existing growth defect of) a strain with perturbation of another gene.
PSI-MI
MI:2378
dosage growth defect (sensu BioGRID)
A genetic phenotype modification whereby one genetic perturbation suppresses, or alleviates, the phenotype of another genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result.
suppressing genetic interaction
PSI-MI
MI:2379
genetic suppression
A genetic phenotype modification whereby one genetic perturbation enhances, or exacerbates, the phenotype of another genetic perturbation. Note that this may be an expected result.
enhancing genetic interaction
PSI-MI
MI:2380
genetic enhancement
A phenotype result in which each of multiple perturbations results in no (or only a minimal) phenotype for the phenotype in question.
PSI-MI
MI:2381
aphenotypic phenotype result
A phenotype result in which only one of multiple perturbations results in the phenotype in question.
PSI-MI
MI:2382
monophenotypic phenotype result
The expression of a phenotype in an organism or a population of organisms resulting from one or more organismal perturbations, including genetic perturbations and environmental (including chemical/drug exposure) perturbations.
PSI-MI
MI:2383
phenotype result
A phenotype result in which multiple perturbations affect an organism individually and in combination.
PSI-MI
MI:2384
multiple perturbation phenotype result
A phenotype result in which both of two perturbations result in the phenotype in question and do so in the same manner compared to wild type. For example, both perturbations result in an increased quality phenotype, or both perturbations result in a decreased quality phenotype.
PSI-MI
MI:2385
cisphenotypic phenotype result
A cisphenotypic phenotype result in which both of two perturbations result in the same phenotype, both in manner and degree, compared to wild type.
PSI-MI
MI:2386
isophenotypic phenotype result
A phenotype result in which two perturbations result in the opposite phenotype compared to wild type. For example, one perturbation results in an increased quality phenotype and the second perturbation results in a decreased quality phenotype.
PSI-MI
MI:2387
transphenotypic phenotype result
A genetic phenotype modification whereby introduction of one genetic perturbation to another genetic perturbation results in the opposite phenotype compared to the phenotype of the starting individual genetic perturbation. For example, one perturbation results in an increased quality phenotype and introduction of the second perturbation results in a decreased quality phenotype. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result.
super-suppressing genetic interaction
PSI-MI
MI:2388
genetic over-suppression
A genetic phenotype modification whereby each of two genetic perturbations suppress, or alleviate, the phenotype of the other genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result.
PSI-MI
MI:2389
mutual genetic suppression
A genetic mutual suppression in which each genetic perturbation results in opposite phenotypes (for example, one genetic perturbation results in an increased quality phenotype and the second genetic perturbation results in a decreased quality phenotype), and their combination (the double genetic perturbation) results in an intermediate phenotype that is at least closer to wild type than the most severe phenotype of the individual genetic perturbations. Note that the double genetic perturbation phenotype may be expected according to some chosen neutrality function.
transphenotypic suppressing genetic interaction
PSI-MI
MI:2390
transphenotypic genetic suppression
A transphenotypic suppression in which the double genetic perturbation phenotype is equivalent to the wild type (or control) phenotype.
transphenotypic all-suppressing genetic interaction
PSI-MI
MI:2391
transphenotypic genetic suppression (complete)
A genetic enhancement in which the double genetic perturbation phenotype is equivalent to the expected phenotype, according to some chosen neutrality function.
cisphenotypic enhancing neutral genetic interaction
PSI-MI
MI:2392
mutual genetic enhancement (expected)
A transphenotypic suppression in which the double genetic perturbation phenotype is expected, according to some chosen neutrality function.
transphenotypic suppressing neutral genetic interaction
PSI-MI
MI:2393
transphenotypic genetic suppression (expected)
An effect in which two genetic perturbations, when combined, result in a fitness that is less than expected given the fitness resulting from the individual perturbations.
Negative genetic interactions describe double mutants whose phenotype is stronger than expected (66, 77) (Figure 1b).
Negative interactions (also called aggravating or synergistic interactions) describe double mutants exhibiting a more severe phenotype than expected, such as synthetic sickness or synthetic lethality (35, 49) (Figure 2a).
aggravating interaction
synergistic interaction
negative gen int
PSI-MI
MI:2394
negative genetic interaction
aggravating interaction
PMID:19712041
synergistic interaction
PMID:19712041
negative gen int
An effect in which two genetic perturbations, when combined, result in a fitness that is greater than expected given the fitness resulting from the individual perturbations.
Positive genetic interactions define double mutants whose phenotype is less severe than expected based on single-mutant phenotypes (30, 66, 87) (Figure 1c,d).
Positive interactions describe double mutants exhibiting a less severe phenotype than expected from the multiplicative model. Positive interactions have also been referred to as alleviating or epistatic interactions.
alleviating interaction
positive gent int
PSI-MI
MI:2395
positive genetic interaction
alleviating interaction
PMID:19712041
positive gent int
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is equivalent to the wild type phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (ab = wt) [E = a*]
OR
(wt < b <= a*) AND (ab = wt) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic all-suppressing converging genetic interaction
cisphenotypic all-suppressing genetic interaction
PSI-MI
MI:2396
cisphenotypic genetic suppression (complete)
An effect in which individual perturbations of different genes result in the same mutant phenotype but to varying degrees of severity/penetrance and the resulting phenotype of their combination is less severe/penetrant than both of the phenotypes resulting from the individual perturabtions. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < b < ab < wt [E = a*]
OR
wt < ab < b < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PSI-MI
MI:2397
cisphenotypic co-suppressing genetic interaction
A genetic aphenotypic phenotype result (both genetic perturbations result in a wild type (or control) phenotype) in which case the double genetic perturbation also results in the wild type (or control) phenotype, thus resulting in the expected phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
wt = a = b = ab [E = wt]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PSI-MI
MI:2398
aphenotypic neutral multigenic phenotype result
A phenotype modification whereby introduction of a genetic perturbation in an organism with another genetic perturbation results in, or enhances, a phenotype in that organism.
PSI-MI
MI:2399
deleterious multigenic phenotype result
A phenotype result in which only one of two perturbations results in the phenotype in question and the phenotype of the combined perturbations a and b result in the expected phenotype, namely the same phenotype as the single perturbation that exhibits that phenotype. The interpretation is that no interaction was observed between the two genes, for the indicated phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab = a ≠ wt = b [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
PSI-MI
MI:2400
monophenotypic neutral multigenic phenotype result
A phenotype result in which both of two genetic perturbations result in the phenotype in question and do so in the same manner compared to wild type (for example, both genetic perturbations result in an increased quality phenotype, or both genetic perturbations result in a decreased quality phenotype) and the resulting double genetic perturbation results in a phenotype that is more severe than the most severe single genetic perturbation phenotype. Note that this may be an expected result.
cisphenotypic enhancing genetic interaction
PSI-MI
MI:2401
mutual genetic enhancement
A multigenic phenotype result in which (1) the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations AND/OR (2) an effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E
PSI-MI
MI:2402
genetic interaction
E. coli BirA* biotin ligase tag used in BioID experiments. This generally refers to a promiscuous mutant version of the biotin ligase with an R118H mutation.
pporras
2021-03-22T14:27:04Z
BirA* biotin ligase tag
BirA* tag
bira biotin ligase tag
bira tag
PSI-MI
MI:2403
bira tag
E. coli BirA* biotin ligase tag used in BioID experiments. This generally refers to a promiscuous mutant version of the biotin ligase with an R118H mutation.
PMID:22412018
BirA* biotin ligase tag
BirA* tag
bira biotin ligase tag
bira tag
Enzymatic oxido-reductions where only O2 is an acceptor of hydrogen or electrons
Licata
2021-07-05T23:48:40Z
oxidase
PSI-MI
MI:2404
oxidase assay
Enzymatic oxido-reductions where only O2 is an acceptor of hydrogen or electrons
PMID:31273118
oxidase
oxidase
Circular RNAs are stable circular transcripts generated when a pre-mRNA undergoes “backsplicing” to join a splice donor to an upstream splice acceptor. They can originate from exons, introns or lncRNAs.
Licata
2021-12-15T11:55:10Z
circRNA
PSI-MI
MI:2405
circular RNA
Circular RNAs are stable circular transcripts generated when a pre-mRNA undergoes “backsplicing” to join a splice donor to an upstream splice acceptor. They can originate from exons, introns or lncRNAs.
PMID:23446348
circRNA
Ribozymes (ribonucleic acid enzymes) are folded catalytic RNA molecules that perform important biological functions.
Licata
2022-03-01T16:49:20Z
ribozyme
PSI-MI
MI:2406
ribozyme
Ribozymes (ribonucleic acid enzymes) are folded catalytic RNA molecules that perform important biological functions.
PMID:34415304
ribozyme
Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage.
https://www.ebi.ac.uk/ols/ontologies/uberon
Licata
uberon
PSI-MI
MI:2407
Uberon
Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage.
https://www.ebi.ac.uk/ols/ontologies/uberon
PMID:22293552
uberon
The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
https://www.ebi.ac.uk/ols/ontologies/COVOC
Licata
COVID-19 Vocabulary
CoVoc
PSI-MI
MI:2408
CoVoc Coronavirus Vocabulary
COVID-19 Vocabulary
CoVoc
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
https://www.ebi.ac.uk/ols/ontologies/po
Licata
PO
plant ontology
PSI-MI
MI:2409
Plant Ontology
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
https://www.ebi.ac.uk/ols/ontologies/po
PMID:23220694
PO
plant ontology
A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.
https://www.ebi.ac.uk/ols/ontologies/mondo
Licata
2022-06-30T16:05:45Z
mondo
PSI-MI
MI:2410
mondo
A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.
https://www.ebi.ac.uk/ols/ontologies/mondo
PMID:31701156
mondo
mondo
The protein of interest is expressed as a fusion to a MAC-tag, which contains a twin-strep affinity tag and BirA* in one construct, requires generation of only one isogenic cell line and allows one-step protein purification by Strep-Tactin matrix for both AP–MS and BioID pipelines.
Licata
2022-07-28T16:04:45Z
mac-tag
PSI-MI
MI:2411
mac tag
The protein of interest is expressed as a fusion to a MAC-tag, which contains a twin-strep affinity tag and BirA* in one construct, requires generation of only one isogenic cell line and allows one-step protein purification by Strep-Tactin matrix for both AP–MS and BioID pipelines.
PMID:32778839
mac-tag
mac-tag
Protein complementation methods specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
Licata
2022-02-03T16:27:45Z
MTH
PSI-MI
MI:2412
membrane two hybrid
Protein complementation methods specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
PMID:24658140
MTH
PSI-MI-short
A membrane bait protein is tagged with the C-terminal half of ubiquitin (Cub) and a chimeric transcription factor, and a cytosolic or membrane-bound prey is tagged with the N-terminal half of ubiquitin (Nub). Upon interaction of bait and prey, the split halves form pseudoubiquitin, which is recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor and expression of a reporter gene.
Licata
2023-02-03T10:18:35Z
MAMTH
PSI-MI
MI:2413
mammalian membrane two hybrid
A membrane bait protein is tagged with the C-terminal half of ubiquitin (Cub) and a chimeric transcription factor, and a cytosolic or membrane-bound prey is tagged with the N-terminal half of ubiquitin (Nub). Upon interaction of bait and prey, the split halves form pseudoubiquitin, which is recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor and expression of a reporter gene.
PMID:24658140
MAMTH
The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research.
Licata
2023-02-04T11:18:35Z
cellosaurus
PSI-MI
MI:2414
Cellosaurus
The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research.
PMID:29805321
cellosaurus
The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.
Licata
2023-02-04T11:50:35Z
CLO
Cell Line Ontology
PSI-MI
MI:2415
cell line ontology
The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.
PMID:25852852
CLO
Cell Line Ontology
Ensembl Bacteria is a browser for bacterial and archaeal genomes.
https://bacteria.ensembl.org/
Licata
2023-02-04T12:00:05Z
Ensembl Bacteria
ensembl bacteria
PSI-MI
MI:2416
ensemblbacteria
Ensembl Bacteria is a browser for bacterial and archaeal genomes.
https://bacteria.ensembl.org/
PMID:34791415
Ensembl Bacteria
ensembl bacteria
Ensembl Fungi is a browser for fungal genomes. https://fungi.ensembl.org/
Licata
2023-02-04T12:10:25Z
Ensembl Fungi
ensembl fungi
PSI-MI
MI:2417
ensemblfungi
Ensembl Fungi is a browser for fungal genomes. https://fungi.ensembl.org/
PMID:34791415
Ensembl Fungi
ensembl fungi
Ensembl Metazoa is a is a browser for genomes of metazoan species of scientific interest. https://metazoa.ensembl.org/
Licata
2023-02-04T12:20:05Z
Ensembl Metazoa
ensembl metazoa
PSI-MI
MI:2418
ensemblmetazoa
Ensembl Metazoa is a is a browser for genomes of metazoan species of scientific interest. https://metazoa.ensembl.org/
PMID:34791415
Ensembl Metazoa
ensembl metazoa
Ensembl Plants is a browser for plant genomes.
https://plants.ensembl.org/
Licata
2023-02-04T12:33:15Z
Ensembl Plants
ensembl plants
PSI-MI
MI:2419
ensemblplants
Ensembl Plants is a browser for plant genomes.
https://plants.ensembl.org/
PMID:27987162
Ensembl Plants
ensembl plants
Ensembl Protists is a browser for protist genomes. https://protists.ensembl.org/
Licata
2023-02-04T12:40:07Z
Ensembl Protists
ensembl protists
PSI-MI
MI:2420
ensemblprotists
Ensembl Protists is a browser for protist genomes. https://protists.ensembl.org/
PMID:34791415
Ensembl Protists
ensembl protists
SubtiList is the reference database dedicated to the genome of Bacillus subtilis, the paradigm of Gram-positive endospore-forming bacteria.
http://genolist.pasteur.fr/SubtiList/
Licata
Subtilist
PSI-MI
MI:2421
subtilist
SubtiList is the reference database dedicated to the genome of Bacillus subtilis, the paradigm of Gram-positive endospore-forming bacteria.
http://genolist.pasteur.fr/SubtiList/
PMID:11752255
Subtilist
Mass photometry measures mass at the single molecule level in solution and enables the quantification of protein–protein interactions in solution with sufficient sensitivity to accurately determine stoichiometry and rate of reactions.
Licata
2023-19-07T11:19:50Z
mass photometry
PSI-MI
MI:2422
mass photometry
Mass photometry measures mass at the single molecule level in solution and enables the quantification of protein–protein interactions in solution with sufficient sensitivity to accurately determine stoichiometry and rate of reactions.
PMID:32167227
mass photometry
Licata
reference to the gene producing this interactor.
gene reference
PSI-MI
MI:2423
gene ref
reference to the gene producing this interactor.
PMID:14755292
gene reference