* HOM:$sequence(7,0,9999999)$
02:12:2009 15:16
1.2
homology_and_related_concepts_in_biology
definition
namespace-id-rule
has_broad_synonym
database_cross_reference
has_exact_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
similarity
ECO:0000041
HOM:0000000
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
SO:similar_to
correspondence
homology_and_related_concepts_in_biology
resemblance
sameness
DOI:10.1007/BF02814479
correspondence
BGEE:curator
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
inferred from similarity
ECO:0000041
homology
HOM:0000001
Similarity that results from common evolutionary origin.
This broad definition encompasses all the working definitions proposed so far in the literature.
homology_and_related_concepts_in_biology
DOI:10.1002/bies.950180611
DOI:10.1002/jmor.1051730307
DOI:10.1007/BF02814480
Similarity that results from common evolutionary origin.
homoplasy
HOM:0000002
Similarity that results from independent evolution.
analogy
homology_and_related_concepts_in_biology
DOI:10.1016/j.jhevol.2006.11.010
Similarity that results from independent evolution.
homocracy
ECO:0000075
HOM:0000003
Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
homology_and_related_concepts_in_biology
inferred from gene expression similarity
ECO:0000075
DOI:10.1007/BF02814484
DOI:10.1007/s00427-003-0301-4
DOI:10.1186/1742-9994-2-15
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
convergence
Convergence usually implies a notion of adaptation.
HOM:0000004
Homoplasy that involves different underlying mechanisms or structures.
analogy
homology_and_related_concepts_in_biology
DOI:10.1016/j.jhevol.2006.11.010
Homoplasy that involves different underlying mechanisms or structures.
parallelism
Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
HOM:0000005
Homoplasy that involves homologous underlying mechanisms or structures.
homology_and_related_concepts_in_biology
parallel evolution
DOI:10.1016/j.jhevol.2006.11.010
Homoplasy that involves homologous underlying mechanisms or structures.
structural homology
ECO:0000071
HOM:0000006
Homology that is defined by similarity with regard to selected structural parameters.
MI:2163
homology_and_related_concepts_in_biology
idealistic homology
DOI:10.1016/j.jhevol.2006.11.014
DOI:10.1146/annurev.es.20.110189.000411
Homology that is defined by similarity with regard to selected structural parameters.
ISBN:0123195837
inferred from morphological similarity
ECO:0000071
by homology
MI:2163
historical homology
ECO:0000080
HOM:0000007
Homology that is defined by common descent.
RO_proposed_relation:homologous_to
SO:0000330
SO:0000853
SO:0000857
SO:homologous_to
TAO:homologous_to
cladistic homology
homology
homology_and_related_concepts_in_biology
phylogenetic homology
taxic homology
true homology
homologous
SO:0000857
conserved_region
SO:0000330
inferred from phylogeny
ECO:0000080
homologous_region
SO:0000853
DOI:10.1016/S0169-5347(97)01125-7
Homology that is defined by common descent.
ISBN:0123195837
biological homology
Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
ECO:0000067
HOM:0000008
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
homology_and_related_concepts_in_biology
transformational homology
inferred from developmental similarity
ECO:0000067
DOI:10.1016/S0169-5347(97)01125-7
DOI:10.1146/annurev.es.20.110189.000411
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
reversal
HOM:0000009
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
atavism
homology_and_related_concepts_in_biology
reversion
rudiment
DOI:10.1016/j.jhevol.2006.11.010
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
syntenic homology
HOM:0000010
MeSH:Synteny
SO:0000860
SO:0005858
Structural homology that is detected by similarity in content and organization between chromosomes.
homology_and_related_concepts_in_biology
synteny
syntenic_region
SO:0005858
syntenic
SO:0000860
MeSH:Synteny
Structural homology that is detected by similarity in content and organization between chromosomes.
paralogy
HOM:0000011
Historical homology that involves genes that diverged after a duplication event.
SO:0000854
SO:0000859
SO:paralogous_to
homology_and_related_concepts_in_biology
paralogous_region
SO:0000854
DOI:10.1016/S0168-9525(00)02005-9
DOI:10.1146/annurev.genet.39.073003.114725
Historical homology that involves genes that diverged after a duplication event.
PMID:5449325
paralogous
SO:0000859
syntenic paralogy
HOM:0000012
Paralogy that involves sets of syntenic blocks.
duplicon
homology_and_related_concepts_in_biology
paralogon
DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
DOI:10.1186/1471-213X-7-100
Paralogy that involves sets of syntenic blocks.
syntenic orthology
HOM:0000013
Syntenic homology that involves chromosomes of different species.
homology_and_related_concepts_in_biology
DOI:10.1101/gr.6380007
Syntenic homology that involves chromosomes of different species.
partial homology
HOM:0000014
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
fractional homology
homology_and_related_concepts_in_biology
mixed homology
modular homology
partial correspondence
percent homology
segmental homology
ISBN:0123195837
ISBN:978-0471984931
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
protein structural homology
HOM:0000015
MeSH:Structural Homology, Protein
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
homology_and_related_concepts_in_biology
DOI:10.1016/0022-2836(76)90195-9
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
non functional homology
HOM:0000016
SO:non_functional_homolog_of
Structural homology that involves a pseudogenic feature and its functional ancestor.
homology_and_related_concepts_in_biology
pseudogene
SO:non_functional_homolog_of
Structural homology that involves a pseudogenic feature and its functional ancestor.
orthology
ECO:00000060
HOM:0000017
Historical homology that involves genes that diverged after a speciation event.
SO:0000855
SO:0000858
SO:orthologous_to
The term is sometimes also used for anatomical structures.
homology_and_related_concepts_in_biology
DOI:10.1007/BF02814484
DOI:10.1016/S0168-9525(00)02005-9
DOI:10.1146/annurev.genet.39.073003.114725
Historical homology that involves genes that diverged after a speciation event.
PMID:5449325
inferred from sequence orthology
ECO:00000060
orthologous
SO:0000858
orthologous_region
SO:0000855
xenology
HOM:0000018
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
homology_and_related_concepts_in_biology
DOI:10.1016/S0168-9525(00)02005-9
DOI:10.1146/annurev.genet.39.073003.114725
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
1 to 1 homology
1:1 homology
HOM:0000019
Historical homology that involves two members sharing no other homologs in the lineages considered.
homology_and_related_concepts_in_biology
one-to-one homology
BGEE:curator
Historical homology that involves two members sharing no other homologs in the lineages considered.
1 to 1 orthology
1:1 orthology
HOM:0000020
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
homology_and_related_concepts_in_biology
one-to-one orthology
DOI:10.1007/BF02814484
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
http://www.ensembl.org/info/docs/compara/homology_method.html
allogeny
HOM:0000021
Relationship between recognizably corresponding characters that occurs in two or more taxa and have different generative bases.
generative homoplasy
homology_and_related_concepts_in_biology
true
DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
Relationship between recognizably corresponding characters that occurs in two or more taxa and have different generative bases.
ohnology
HOM:0000022
Paralogy that results from a whole genome duplication event.
homoeology
homology_and_related_concepts_in_biology
DOI:10.1038/75560
Paralogy that results from a whole genome duplication event.
in-paralogy
HOM:0000023
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
homology_and_related_concepts_in_biology
inparalogy
symparalogy
DOI:10.1146/annurev.genet.39.073003.114725
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
out-paralogy
HOM:0000024
Paralogy that results from a duplication preceding a given speciation event.
alloparalogy
homology_and_related_concepts_in_biology
outparalogy
DOI:10.1146/annurev.genet.39.073003.114725
Paralogy that results from a duplication preceding a given speciation event.
pro-orthology
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
HOM:0000025
homology_and_related_concepts_in_biology
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
DOI:10.1006/scdb.1999.0338
DOI:10.1038/nrg2099
semi-orthology
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
HOM:0000026
The converse of pro-orthologous.
homology_and_related_concepts_in_biology
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
DOI:10.1006/scdb.1999.0338
DOI:10.1038/nrg2099
serial homology
HOM:0000027
Iterative homology that involves structures arranged along the main body axis.
homology_and_related_concepts_in_biology
homonomy
DOI:10.1146/annurev.es.20.110189.000411
Iterative homology that involves structures arranged along the main body axis.
heterochronous homology
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
HOM:0000028
heterochrony
homology_and_related_concepts_in_biology
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
ISBN:978-0674639416
paedomorphorsis
HOM:0000029
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
homology_and_related_concepts_in_biology
juvenification
pedomorphosis
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
ISBN:978-0674639416
http://en.wikipedia.org/wiki/Pedomorphosis
peramorphosis
HOM:0000030
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
homology_and_related_concepts_in_biology
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
http://en.wikipedia.org/wiki/Peramorphosis
progenesis
HOM:0000031
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
homology_and_related_concepts_in_biology
ISBN:978-0674639416
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
http://en.wikipedia.org/wiki/Progenesis
neoteny
HOM:0000032
Paedomorphosis that is produced by a retardation of somatic development.
homology_and_related_concepts_in_biology
juvenilization
ISBN:978-0674639416
Paedomorphosis that is produced by a retardation of somatic development.
http://en.wikipedia.org/wiki/Neoteny
mimicry
2009-07-30T11:28:41Z
Convergence that results from co-evolution usually involving an evolutionary arms race.
HOM:0000033
admin
homology_and_related_concepts_in_biology
Convergence that results from co-evolution usually involving an evolutionary arms race.
http:://en.wikipedia.org/wiki/Mimicry
1 to many orthology
1:many orthology
HOM:0000034
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
co-orthology
homology_and_related_concepts_in_biology
many to 1 orthology
one-to-many orthology
DOI:10.1038/415741a
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
http://www.ensembl.org/info/docs/compara/homology_method.html
many to many homology
HOM:0000036
Historical homology that involves two members of a larger set of homologs.
homology_and_related_concepts_in_biology
many-to-many homology
many:many homology
DOI:10.1093/molbev/msp002
Historical homology that involves two members of a larger set of homologs.
1 to many homology
1:many homology
HOM:0000037
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
homology_and_related_concepts_in_biology
one-to-many homology
BGEE:curator
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
apomorphy
HOM:0000042
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
homology_and_related_concepts_in_biology
synapomorphy
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
ISBN:978-0252068140
plesiomorphy
HOM:0000043
Historical homology that is based on distant shared ancestry.
This term is usually contrasted to apomorphy.
homology_and_related_concepts_in_biology
symplesiomorphy
Historical homology that is based on distant shared ancestry.
ISBN:978-0252068140
deep homology
HOM:0000044
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
Used for structures in distantly related taxa.
deep genetic homology
generative homology
homoiology
homology_and_related_concepts_in_biology
DOI:10.1007/BF02814485
DOI:10.1038/nature07891
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
hemiplasy
HOM:0000045
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
homology_and_related_concepts_in_biology
DOI:10.1073/pnas.0807433105
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
gametology
HOM:0000046
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
homology_and_related_concepts_in_biology
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
PMID:11110898
chromosomal homology
HOM:0000047
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
MeSH:Chromosome Pairing
homology_and_related_concepts_in_biology
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
ISBN:0195307615
many to many orthology
HOM:0000048
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
co-orthology
homology_and_related_concepts_in_biology
many-to-many orthology
many:many orthology
trans-homology
trans-orthology
DOI:10.1038/415741a
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
http://www.ensembl.org/info/docs/compara/homology_method.html
within-species paralogy
HOM:0000049
Paralogy that involves genes from the same species.
homology_and_related_concepts_in_biology
Paralogy that involves genes from the same species.
http://www.ensembl.org/info/docs/compara/homology_method.html
between-species paralogy
HOM:0000050
Paralogy that involves genes from different species.
The genes have diverged before a speciation event.
homology_and_related_concepts_in_biology
Paralogy that involves genes from different species.
http://www.ensembl.org/info/docs/compara/homology_method.html
postdisplacement
HOM:0000051
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
homology_and_related_concepts_in_biology
post-displacement
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
http://en.wikipedia.org/wiki/Pedomorphosis
hypermorphosis
HOM:0000052
Peramorphosis that is produced by a delay in the offset of development.
homology_and_related_concepts_in_biology
ISBN:978-0674639416
Peramorphosis that is produced by a delay in the offset of development.
http://en.wikipedia.org/wiki/Peramorphosis
synology
HOM:0000053
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
homology_and_related_concepts_in_biology
DOI:10.1007/BF00173425
DOI:10.1016/S0168-9525(00)02005-9
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
isoorthology
ECO:0000080
HOM:0000054
Orthology that involves functional equivalent genes with retention of the ancestral function.
homology_and_related_concepts_in_biology
DOI:10.1016/S0168-9525(00)02005-9
Orthology that involves functional equivalent genes with retention of the ancestral function.
inferred from phylogeny
ECO:0000080
tandem paralogy
HOM:0000055
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
homology_and_related_concepts_in_biology
iterative paralogy
serial paralogy
DOI:10.1016/S0168-9525(00)02005-9
ISBN:978-0878932665
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
latent homology
HOM:0000057
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
Used for structures in closely related taxa.
apomorphic tendency
cryptic homology
homoiology
homology_and_related_concepts_in_biology
homoplastic tendency
re-awakening
underlying synapomorphy
DOI:10.1007/BF02814485
DOI:10.1016/j.jhevol.2006.11.010
DOI:10.1186/1742-9994-2-15
ISBN:0199141118
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
syngeny
Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
HOM:0000058
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
generative homology
homology_and_related_concepts_in_biology
DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
DOI:10.1186/1742-9994-2-15
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
apparent orthology
1:1 paralogy
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
HOM:0000060
The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
apparent 1:1 orthology
homology_and_related_concepts_in_biology
pseudoorthology
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
DOI:10.1146/annurev.genet.39.073003.114725
http://www.ensembl.org/info/docs/compara/homology_method.html
pseudoparalogy
HOM:0000061
These genes may come out as paralogs in a single-genome analysis.
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
homology_and_related_concepts_in_biology
DOI:10.1146/annurev.genet.39.073003.114725
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
equivalogy
HOM:0000062
Historical homology that involves functional equivalent genes with retention of the ancestral function.
This may include examples of orthology, paralogy and xenology.
homology_and_related_concepts_in_biology
DOI:10.1093/nar/gkl1043
Historical homology that involves functional equivalent genes with retention of the ancestral function.
interology
HOM:0000063
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
homology_and_related_concepts_in_biology
DOI:10.1101/gr.1774904
DOI:10.1126/science.287.5450.116
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
functional equivalence
HOM:0000065
Similarity that is characterized by interchangeability in function.
functional similarity
homology_and_related_concepts_in_biology
DOI:10.1007/BF02814484
DOI:10.1038/415741a
Similarity that is characterized by interchangeability in function.
iterative homology
Biological homology that involves parts of the same organism.
HOM:0000066
homology_and_related_concepts_in_biology
Biological homology that involves parts of the same organism.
DOI:10.1146/annurev.es.20.110189.000411
paraxenology
HOM:0000068
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
duplicate xenology
homology_and_related_concepts_in_biology
multiple xenology
PMID:3065587
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
plerology
HOM:0000069
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
This phenomenon is usually due to gene conversion process.
homology_and_related_concepts_in_biology
PMID:3065587
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
homotopy
HOM:0000071
Structural homology that involves structures with the same or similar relative positions.
Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
homology_and_related_concepts_in_biology
DOI:10.1007/BF02814484
DOI:10.1007/BF02814485
ISBN:0123195837
Structural homology that involves structures with the same or similar relative positions.
homeosis
Biological homology that involves an ectopic structure and the normally positioned structure.
HOM:0000072
heterotopy
homology_and_related_concepts_in_biology
Biological homology that involves an ectopic structure and the normally positioned structure.
DOI:10.1007/BF02814485
DOI:10.1016/j.cell.2008.06.030
homoeology
HOM:0000073
On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
Synology that results from allopolyploidy.
homology_and_related_concepts_in_biology
DOI:10.1073/pnas.0505156102
Synology that results from allopolyploidy.
paramorphism
HOM:0000074
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
axis paramorphism
homology_and_related_concepts_in_biology
DOI:10.1007/s10441-007-9023-8
DOI:10.1046/j.1525-142x.2000.00054.x
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
regulogy
HOM:0000075
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
homology_and_related_concepts_in_biology
DOI:10.1101/gr.1774904
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.