Gene Ontology: Ontology Comparison Report
Files used:
- file 1 (old): go-2011-12-03.obo; date: 02:12:2011 16:46; CVS revision: 1.2418
- file 2 (new): go-2011-12-10.obo; date: 09:12:2011 12:27; CVS revision: 1.2428
New terms
Obsoletions
| ID | name | namespace |
|---|---|---|
| GO:0003706 | ligand-regulated transcription factor activity
Consider: GO:0004879, GO:0038049 This term was made obsolete because it does not convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. |
molecular_function |
| GO:0034339 | regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor
Consider: GO:0004879, GO:0006357, GO:0030522, GO:0038049 This term was added by GO_REF:0000021. This term was made obsolete because it is unclear whether the term represents the action of the receptor or the entire process of transcription regulation. The term 'nuclear hormone receptor' is also misleading since many of these receptors reside in the cytoplasm until they are bound by a ligand. |
biological_process |
| GO:0072500 | negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor
Consider: GO:0000122, GO:0004879, GO:0030522, GO:0038049 This term was made obsolete because it is unclear whether the term represents the action of the receptor or the entire process of transcription regulation. The term 'nuclear hormone receptor' is also misleading since many of these receptors reside in the cytoplasm until they are bound by a ligand. |
biological_process |
Term merges
None
Term changes
| File 1 (02:12:2011 16:46, 1.2418) | File 2 (09:12:2011 12:27, 1.2428) |
|---|
| GO:0000038 : very long chain fatty acid metabolic process | |
|---|---|
|
name |
name very long chain fatty acid metabolic process |
| GO:0000908 : taurine dioxygenase activity | |
|---|---|
|
is_a |
is_a GO:0016706 |
| GO:0001503 : ossification | |
|---|---|
|
comment Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. | |
| GO:0001692 : histamine metabolic process | |
|---|---|
|
is_a |
is_a GO:0052803 |
| GO:0001695 : histamine catabolic process | |
|---|---|
|
is_a GO:0052805 | |
| GO:0003706 : ligand-regulated transcription factor activity | |
|---|---|
|
def is_a |
def OBSOLETE. Functions to enable the transcription of specific, or specific sets, of genes by RNA polymerase II in response to a ligand. comment This term was made obsolete because it does not convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. is_obsolete true consider GO:0004879 GO:0038049 |
| GO:0003708 : retinoic acid receptor activity | |
|---|---|
|
def |
def Combining with retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. Retinoic acid is one of the forms of vitamin A. |
| GO:0003832 : beta-alanyl-dopamine hydrolase activity | |
|---|---|
|
def |
def Catalysis of the reaction: N-beta-alanyl dopamine + H2O = dopamine + beta-alanine. |
| GO:0004402 : histone acetyltransferase activity | |
|---|---|
|
is_a |
is_a GO:0008080 |
| GO:0005040 : decoy death receptor activity | |
|---|---|
|
relationship |
|
| GO:0008486 : diphosphoinositol-polyphosphate diphosphatase activity | |
|---|---|
|
synonym |
synonym "diphospho-myo-inositol-polyphosphate diphosphohydrolase activity" EXACT [EC:3.6.1.52] "diphosphoinositol-polyphosphate phosphohydrolase activity" EXACT [EC:3.6.1.52] "DIPP activity" EXACT [EC:3.6.1.52] xref KEGG:R05777 |
| GO:0008810 : cellulase activity | |
|---|---|
|
synonym |
synonym "beta-1,4-endoglucan hydrolase activity" BROAD [EC:3.2.1.4] "endo-1,4-beta-D-glucanase activity" BROAD [EC:3.2.1.4] "endo-1,4-beta-D-glucanohydrolase activity" BROAD [EC:3.2.1.4] "endo-1,4-beta-glucanase activity" BROAD [EC:3.2.1.4] "endoglucanase activity" BROAD [EC:3.2.1.4] |
| GO:0008823 : cupric reductase activity | |
|---|---|
|
def |
def Catalysis of the reaction: Cu+ + NAD+ + H+ = Cu2+ + NADH. xref MetaCyc:R170-RXN |
| GO:0008849 : enterochelin esterase activity | |
|---|---|
|
def |
def Catalysis of the reaction: enterobactin + 3 H2O = 3 N-23-dihydroxybenzoyl-L-serine + 3 H+. xref MetaCyc:RXN0-1661 |
| GO:0016706 : oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors | |
|---|---|
|
def |
def Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor. synonym "2-oxoglutarate dioxygenase activity" EXACT [] |
| GO:0017099 : very-long-chain-acyl-CoA dehydrogenase activity | |
|---|---|
|
name def |
name very-long-chain-acyl-CoA dehydrogenase activity def Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a very long chain fatty acid residue. |
| GO:0018602 : 2,4-dichlorophenoxyacetate alpha-ketoglutarate dioxygenase activity | |
|---|---|
|
def |
def Catalysis of the reaction: 2,4-dichlorophenoxyacetate + 2-oxoglutarate + oxygen = 2,4-dichlorophenol + glyoxylate + succinate + CO2. |
| GO:0019797 : procollagen-proline 3-dioxygenase activity | |
|---|---|
|
synonym |
synonym "prolyl 3-hydroxylase activity" BROAD [EC:1.14.11.7] |
| GO:0030035 : microspike assembly | |
|---|---|
|
def |
def Formation of a microspike, a dynamic, actin-rich projection extending from the surface of a migrating animal cell. comment Although in some literature 'microspike' and 'filopodium' are used synonymously, in GO microspike refers to a cell projection that is distinct from a filopodium. For the assembly of filopodia, use 'filopodium assembly ; GO:0046847'. |
| GO:0030416 : methylamine metabolic process | |
|---|---|
|
def |
def The chemical reactions and pathways involving methylamine (CH3NH2). |
| GO:0030745 : dimethylhistidine N-methyltransferase activity | |
|---|---|
|
xref relationship |
|
| GO:0031217 : glucan 1,4-beta-glucosidase activity | |
|---|---|
|
synonym |
synonym "1,4-beta-D-glucan glucohydrolase activity" BROAD [EC:3.2.1.74] "beta-1,4-beta-glucanase activity" BROAD [EC:3.2.1.74] "beta-1,4-glucanase activity" BROAD [] |
| GO:0031543 : peptidyl-proline dioxygenase activity | |
|---|---|
|
def |
def Catalysis of the reaction: peptidyl L-proline + 2-oxoglutarate + O2 = peptidyl hydroxy-L-proline + succinate + CO2. |
| GO:0031964 : beta-alanyl-histamine hydrolase activity | |
|---|---|
|
def |
def Catalysis of the reaction: N-beta-alanyl histamine + H2O = histamine + beta-alanine. |
| GO:0033758 : clavaminate synthase activity | |
|---|---|
|
subset mf_needs_review | |
| GO:0033761 : mugineic-acid 3-dioxygenase activity | |
|---|---|
|
def |
def Catalysis of the reactions: mugineic acid + 2-oxoglutarate + O2 = 3-epihydroxymugineic acid + succinate + CO2. xref KEGG:R07186 MetaCyc:RXN-7982 RHEA:14512 |
| GO:0033946 : xyloglucan-specific endo-beta-1,4-glucanase activity | |
|---|---|
|
synonym |
synonym "1,4-beta-D-glucan glucanohydrolase activity" BROAD [EC:3.2.1.151] |
| GO:0034339 : regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor | |
|---|---|
|
def comment is_a |
def OBSOLETE. Any process in which a ligand-bound hormone receptor acts in the nucleus to modulate the frequency, rate or extent of transcription from an RNA polymerase II promoter. comment This term was added by GO_REF:0000021. This term was made obsolete because it is unclear whether the term represents the action of the receptor or the entire process of transcription regulation. The term 'nuclear hormone receptor' is also misleading since many of these receptors reside in the cytoplasm until they are bound by a ligand. is_obsolete true consider GO:0004879 GO:0006357 GO:0030522 GO:0038049 |
| GO:0043734 : DNA-N1-methyladenine dioxygenase activity | |
|---|---|
|
def |
def Catalysis of the oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA and RNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde. subset mf_needs_review |
| GO:0044374 : sequence-specific DNA binding, bending | |
|---|---|
|
is_a GO:0043565 | |
| GO:0045330 : aspartyl esterase activity | |
|---|---|
|
subset mf_needs_review | |
| GO:0045544 : gibberellin 20-oxidase activity | |
|---|---|
|
subset mf_needs_review | |
| GO:0046847 : filopodium assembly | |
|---|---|
|
def is_a |
def The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone. is_a GO:0030031 |
| GO:0047079 : deoxyuridine 1'-dioxygenase activity | |
|---|---|
|
name synonym |
name deoxyuridine 1'-dioxygenase activity synonym "pyrimidine-deoxynucleoside 1'-dioxygenase activity" BROAD [EC:1.14.11.10] "pyrimidine-deoxynucleoside,2-oxoglutarate 1'-dioxygenase activity" BROAD [EC:1.14.11.10] |
| GO:0047080 : deoxyuridine 2'-dioxygenase activity | |
|---|---|
|
name synonym |
name deoxyuridine 2'-dioxygenase activity synonym "pyrimidine deoxyribonucleoside 2'-hydroxylase activity" BROAD [EC:1.14.11.3] "pyrimidine-deoxynucleoside 2'-dioxygenase activity" BROAD [EC:1.14.11.3] "pyrimidine-deoxynucleoside,2-oxoglutarate 2'-dioxygenase activity" BROAD [EC:1.14.11.3] "thymidine 2'-hydroxylase activity" RELATED [EC:1.14.11.3] "thymidine 2-oxoglutarate dioxygenase activity" RELATED [EC:1.14.11.3] "thymidine dioxygenase activity" RELATED [EC:1.14.11.3] |
| GO:0047453 : ATP-dependent NAD(P)H-hydrate dehydratase activity | |
|---|---|
|
synonym |
synonym "reduced nicotinamide adenine dinucleotide hydrate dehydratase activity" BROAD [EC:4.2.1.93] |
| GO:0050353 : trimethyllysine dioxygenase activity | |
|---|---|
|
def |
def Catalysis of the reaction: 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysine + O(2) = 3-hydroxy-N(6),N(6),N(6)-trimethyl-L-lysine + CO(2) + succinate. |
| GO:0050590 : desacetoxyvindoline 4-hydroxylase activity | |
|---|---|
|
xref KEGG:R05857 RHEA:18976 | |
| GO:0052704 : ergothioneine biosynthesis from histidine via N-alpha,N-alpha,N-alpha-trimethyl-L-histidine | |
|---|---|
|
relationship has_part GO:0052707 has_part GO:0052711 | |
| GO:0052705 : methylhistidine N-methyltransferase activity | |
|---|---|
|
relationship |
|
| GO:0052706 : histidine N-methyltransferase activity | |
|---|---|
|
relationship |
|
| GO:0052707 : N-alpha,N-alpha,N-alpha-trimethyl-L-histidine biosynthesis from histidine | |
|---|---|
|
relationship |
relationship has_part GO:0030745 has_part GO:0052705 has_part GO:0052706 |
| GO:0052711 : ergothioneine biosynthesis from N-alpha,N-alpha,N-alpha-trimethyl-L-histidine | |
|---|---|
|
relationship |
|
| GO:0052773 : diacetylchitobiose deacetylase activity | |
|---|---|
|
relationship |
|
| GO:0052774 : glucosyl-N-acetylglucosamine glucosaminidase activity | |
|---|---|
|
relationship |
|
| GO:0052776 : diacetylchitobiose catabolic process to glucosamine and acetate | |
|---|---|
|
relationship has_part GO:0052773 has_part GO:0052774 has_part GO:0052790 | |
| GO:0052790 : chitooligosaccharide deacetylase activity | |
|---|---|
|
relationship |
|
| GO:0052803 : imidazole-containing compound metabolic process | |
|---|---|
|
name |
name imidazole-containing compound metabolic process |
| GO:0052805 : imidazole-containing compound catabolic process | |
|---|---|
|
name |
name imidazole-containing compound catabolic process |
| GO:0072500 : negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor | |
|---|---|
|
def is_a |
def OBSOLETE. Any process in which a ligand-bound hormone receptor acts in the nucleus to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. comment This term was made obsolete because it is unclear whether the term represents the action of the receptor or the entire process of transcription regulation. The term 'nuclear hormone receptor' is also misleading since many of these receptors reside in the cytoplasm until they are bound by a ligand. is_obsolete true consider GO:0000122 GO:0004879 GO:0030522 GO:0038049 |
| GO:0080182 : histone H3-K4 trimethylation | |
|---|---|
|
def |
def The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone. |
| GO:2000190 : negative regulation of regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor | |
|---|---|
|
replaced_by |
consider GO:0000122 GO:0004879 GO:0030522 GO:0038049 |
File Stats
| Ontology | Old file | New file | Change |
|---|---|---|---|
| molecular function |
9168 9168 (100.0%) defined |
9193 9193 (100.0%) defined |
+25 |
| cellular component |
2926 2926 (100.0%) defined |
2927 2927 (100.0%) defined |
+1 |
| biological process |
21659 21659 (100.0%) defined |
21664 21664 (100.0%) defined |
+5 |
| Obsolete | 1603 (4.5% of total) |
1606 (4.5% of total) |
+3 (+0.2%) |
| Totals |
33753 33753 (100.0%) defined 35356 inc. obsoletes |
33784 33784 (100.0%) defined 35390 inc. obsoletes |
+34 (+0.1%) |