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 ========= ID name namespace GO:0036043 microspike cellular_component GO:0044377 RNA polymerase II core promoter proximal region sequence-specific DNA binding, bending molecular_function GO:0044378 non-sequence-specific DNA binding, bending molecular_function GO:0044379 protein localization to actin cortical patch biological_process GO:0044381 glucose import in response to insulin stimulus biological_process GO:0052839 inositol diphosphate tetrakisphosphate kinase activity molecular_function GO:0052840 inositol diphosphate tetrakisphosphate diphosphatase activity molecular_function GO:0052841 inositol bisdiphosphate tetrakisphosphate diphosphatase activity molecular_function GO:0052842 inositol diphosphate pentakisphosphate diphosphatase activity molecular_function GO:0052843 inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity molecular_function GO:0052844 inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity molecular_function GO:0052845 inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity molecular_function GO:0052846 inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity molecular_function GO:0052847 inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity molecular_function GO:0052848 inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity molecular_function GO:0052849 NADPH-dependent curcurmin reductase activity molecular_function GO:0052850 NADPH-dependent dihydrocurcurmin reductase activity molecular_function GO:0052851 ferric-chelate reductase (NADPH) activity molecular_function GO:0052852 very-long-chain-(S)-2-hydroxy-acid oxidase activity molecular_function GO:0052853 long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity molecular_function GO:0052854 medium-chain-(S)-2-hydroxy-acid oxidase activity molecular_function GO:0052855 ADP-dependent NAD(P)H-hydrate dehydratase activity molecular_function GO:0052856 NADHX epimerase activity molecular_function GO:0052857 NADPHX epimerase activity molecular_function GO:0052858 peptidyl-lysine N-acetyltransferase activity molecular_function GO:0052859 glucan endo-1,4-beta-glucosidase activity molecular_function GO:0052860 2'-deoxymugineic-acid 3-dioxygenase activity molecular_function GO:0052861 glucan endo-1,3-beta-glucanase activity, C-3 substituted reducing group molecular_function GO:0052862 glucan endo-1,4-beta-glucanase activity, C-3 substituted reducing group molecular_function GO:0052863 1-deoxy-D-xylulose 5-phosphate metabolic process biological_process GO:0052864 1-deoxy-D-xylulose 5-phosphate catabolic process biological_process GO:0052865 1-deoxy-D-xylulose 5-phosphate biosynthetic process biological_process GO:0072694 cell cycle arrest in response to caffeine biological_process GO:0097198 histone H3-K36 trimethylation biological_process OBSOLETIONS =========== GO:0003706, ligand-regulated transcription factor activity (molecular_function) 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. Consider: GO:0004879, GO:0038049 GO:0034339, regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor (biological_process) 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. Consider: GO:0004879, GO:0006357, GO:0030522, GO:0038049 GO:0072500, negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor (biological_process) 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. Consider: GO:0000122, GO:0004879, GO:0030522, GO:0038049 TERM MERGES =========== None TERM CHANGES ============ GO:0000038 : very long chain fatty acid metabolic process - name: very long-chain fatty acid metabolic process + name: very long chain fatty acid metabolic process GO:0000908 : taurine dioxygenase activity - is_a: GO:0000907 + 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: GO:0046483 + is_a: GO:0052803 GO:0001695 : histamine catabolic process + is_a: GO:0052805 GO:0003706 : ligand-regulated transcription factor activity - def: Functions to enable the transcription of specific, or specific sets, of genes by RNA polymerase II in response to a ligand. + 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_a: GO:0003674 + is_obsolete: true + consider: GO:0004879 + consider: GO:0038049 GO:0003708 : retinoic acid receptor activity - 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\npolymerase II. Retinoic acid is one of the forms of vitamin A. + 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: Catalysis of the conversion of beta-alanyl dopamine to dopamine (3,4-dihydroxyphenylethylamine). + def: Catalysis of the reaction: N-beta-alanyl dopamine + H2O = dopamine + beta-alanine. GO:0004402 : histone acetyltransferase activity - is_a: GO:0004468 + is_a: GO:0008080 GO:0005040 : decoy death receptor activity - relationship: has_part GO:0005488 GO:0008486 : diphosphoinositol-polyphosphate diphosphatase activity - synonym: "diphosphoinositol-polyphosphate phosphohydrolase activity" EXACT [EC:3.6.1.52e] - synonym: "diphospho-myo-inositol-polyphosphate diphosphohydrolase activity" EXACT [EC:3.6.1.52e] - synonym: "DIPP activity" EXACT [EC:3.6.1.52e] + synonym: "diphosphoinositol-polyphosphate phosphohydrolase activity" EXACT [EC:3.6.1.52] + synonym: "DIPP activity" EXACT [EC:3.6.1.52] + synonym: "diphospho-myo-inositol-polyphosphate diphosphohydrolase activity" EXACT [EC:3.6.1.52] + xref: KEGG:R05777 GO:0008810 : cellulase activity - synonym: "endo-1,4-beta-glucanase activity" EXACT [EC:3.2.1.4] - synonym: "endo-1,4-beta-D-glucanase activity" EXACT [EC:3.2.1.4] - synonym: "beta-1,4-endoglucan hydrolase activity" EXACT [EC:3.2.1.4] - synonym: "endo-1,4-beta-D-glucanohydrolase activity" EXACT [EC:3.2.1.4] - synonym: "endoglucanase activity" EXACT [EC:3.2.1.4] + synonym: "endoglucanase activity" BROAD [EC:3.2.1.4] + synonym: "endo-1,4-beta-D-glucanase activity" BROAD [EC:3.2.1.4] + synonym: "endo-1,4-beta-glucanase activity" BROAD [EC:3.2.1.4] + synonym: "beta-1,4-endoglucan hydrolase activity" BROAD [EC:3.2.1.4] + synonym: "endo-1,4-beta-D-glucanohydrolase activity" BROAD [EC:3.2.1.4] GO:0008823 : cupric reductase activity - def: Catalysis of the reaction: Cu+ + NAD+ = Cu2+ + NADH. + def: Catalysis of the reaction: Cu+ + NAD+ + H+ = Cu2+ + NADH. + xref: MetaCyc:R170-RXN GO:0008849 : enterochelin esterase activity - def: Catalysis of the hydrolysis of the enterochelin group of ferric-enterochelin to yield ultimately three molecules of N-2,3-dihydroxybenzoylserine. + 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: Catalysis of 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. + 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: very long-chain-acyl-CoA dehydrogenase activity + 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. + 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: Catalysis of the reaction: 2,4-dichlorophenoxyacetic acid = glyoxylate + 2,4-dichlorophenol. + 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: "prolyl 3-hydroxylase activity" EXACT [EC:1.14.11.7] + synonym: "prolyl 3-hydroxylase activity" BROAD [EC:1.14.11.7] GO:0030035 : microspike assembly - def: Formation of a microspike, a thin, stiff projection extended from the surface of a migrating cell. + 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: The chemical reactions and pathways involving methylamine (CH3NH2), a flammable, explosive gas, used in tanning and in organic synthesis and produced naturally in some decaying fish, certain plants, and crude methanol. + def: The chemical reactions and pathways involving methylamine (CH3NH2). GO:0030745 : dimethylhistidine N-methyltransferase activity - xref: RHEA:RHEA\:11107 - relationship: has_part GO:0052707 GO:0031217 : glucan 1,4-beta-glucosidase activity - synonym: "beta-1,4-beta-glucanase activity" EXACT [EC:3.2.1.74] - synonym: "1,4-beta-D-glucan glucohydrolase activity" EXACT [EC:3.2.1.74] - synonym: "beta-1,4-glucanase activity" EXACT [] + synonym: "beta-1,4-beta-glucanase activity" BROAD [EC:3.2.1.74] + synonym: "1,4-beta-D-glucan glucohydrolase activity" BROAD [EC:3.2.1.74] + synonym: "beta-1,4-glucanase activity" BROAD [] GO:0031543 : peptidyl-proline dioxygenase activity - def: Catalysis of the transfer of a hydroxyl group from 2-oxoglutarate to a prolyl residue in a protein. + 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: Catalysis of the conversion of beta-alanyl-histamine to histamine. + 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: Catalysis of the reactions: mugineic acid + 2-oxoglutarate + O2 = 3-epihydroxymugineic acid + succinate + CO2, and 2'-deoxymugineic acid + 2-oxoglutarate + O2 = 3-epihydroxy-2'-deoxymugineic acid + succinate + CO2. + def: Catalysis of the reactions: mugineic acid + 2-oxoglutarate + O2 = 3-epihydroxymugineic acid + succinate + CO2. + xref: MetaCyc:RXN-7982 + xref: KEGG:R07186 + xref: RHEA:14512 GO:0033946 : xyloglucan-specific endo-beta-1,4-glucanase activity - synonym: "1,4-beta-D-glucan glucanohydrolase activity" EXACT [EC:3.2.1.151] + 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: 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. + 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. + 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_a: GO:0006357 + is_obsolete: true + consider: GO:0004879 + consider: GO:0006357 + consider: GO:0030522 + consider: GO:0038049 GO:0043734 : DNA-N1-methyladenine dioxygenase activity - 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 methylgroup on N1-methyladenine and N3-methylcytosine as formaldehyde. + 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: The assembly of a filopodium, a very long microspike extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or by the growth cone of a developing nerve cell axon. + 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:0030035 + is_a: GO:0030031 GO:0047079 : deoxyuridine 1'-dioxygenase activity - name: pyrimidine-deoxynucleoside 1'-dioxygenase activity + name: deoxyuridine 1'-dioxygenase activity - synonym: "pyrimidine-deoxynucleoside,2-oxoglutarate 1'-dioxygenase activity" EXACT [EC:1.14.11.10] - synonym: "deoxyuridine-uridine 1'-dioxygenase activity" EXACT [EC:1.14.11.10] + synonym: "pyrimidine-deoxynucleoside 1'-dioxygenase activity" BROAD [EC:1.14.11.10] + synonym: "pyrimidine-deoxynucleoside,2-oxoglutarate 1'-dioxygenase activity" BROAD [EC:1.14.11.10] GO:0047080 : deoxyuridine 2'-dioxygenase activity - name: pyrimidine-deoxynucleoside 2'-dioxygenase activity + name: deoxyuridine 2'-dioxygenase activity - synonym: "thymidine 2'-hydroxylase activity" NARROW [EC:1.14.11.3] - synonym: "pyrimidine-deoxynucleoside,2-oxoglutarate 2'-dioxygenase activity" EXACT [EC:1.14.11.3] - synonym: "thymidine dioxygenase activity" NARROW [EC:1.14.11.3] - synonym: "pyrimidine deoxyribonucleoside 2'-hydroxylase activity" EXACT [EC:1.14.11.3] - synonym: "deoxyuridine 2'-dioxygenase activity" EXACT [EC:1.14.11.3] - synonym: "thymidine 2-oxoglutarate dioxygenase activity" NARROW [EC:1.14.11.3] + synonym: "pyrimidine-deoxynucleoside 2'-dioxygenase activity" BROAD [EC:1.14.11.3] + synonym: "thymidine 2-oxoglutarate dioxygenase activity" RELATED [EC:1.14.11.3] + synonym: "pyrimidine deoxyribonucleoside 2'-hydroxylase activity" BROAD [EC:1.14.11.3] + synonym: "thymidine dioxygenase activity" RELATED [EC:1.14.11.3] + synonym: "thymidine 2'-hydroxylase activity" RELATED [EC:1.14.11.3] + synonym: "pyrimidine-deoxynucleoside,2-oxoglutarate 2'-dioxygenase activity" BROAD [EC:1.14.11.3] GO:0047453 : ATP-dependent NAD(P)H-hydrate dehydratase activity - synonym: "reduced nicotinamide adenine dinucleotide hydrate dehydratase activity" EXACT [EC:4.2.1.93] + synonym: "reduced nicotinamide adenine dinucleotide hydrate dehydratase activity" BROAD [EC:4.2.1.93] GO:0050353 : trimethyllysine dioxygenase activity - 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. + 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: RHEA:18976 + xref: KEGG:R05857 GO:0052704 : ergothioneine biosynthesis from histidine via N-alpha,N-alpha,N-alpha-trimethyl-L-histidine + relationship: has_part GO:0052707 + relationship: has_part GO:0052711 GO:0052705 : methylhistidine N-methyltransferase activity - relationship: has_part GO:0052707 GO:0052706 : histidine N-methyltransferase activity - relationship: has_part GO:0052707 GO:0052707 : N-alpha,N-alpha,N-alpha-trimethyl-L-histidine biosynthesis from histidine - relationship: has_part GO:0052704 + relationship: has_part GO:0052705 + relationship: has_part GO:0030745 + relationship: has_part GO:0052706 GO:0052711 : ergothioneine biosynthesis from N-alpha,N-alpha,N-alpha-trimethyl-L-histidine - relationship: has_part GO:0052704 GO:0052773 : diacetylchitobiose deacetylase activity - relationship: has_part GO:0052776 GO:0052774 : glucosyl-N-acetylglucosamine glucosaminidase activity - relationship: has_part GO:0052776 GO:0052776 : diacetylchitobiose catabolic process to glucosamine and acetate + relationship: has_part GO:0052773 + relationship: has_part GO:0052774 + relationship: has_part GO:0052790 GO:0052790 : chitooligosaccharide deacetylase activity - relationship: has_part GO:0052776 GO:0052803 : imidazole-containing compound metabolic process - name: imidazole metabolic process + name: imidazole-containing compound metabolic process GO:0052805 : imidazole-containing compound catabolic process - name: imidazole catabolic process + name: imidazole-containing compound catabolic process GO:0072500 : negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor - def: 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. + 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_a: GO:0034339 + is_obsolete: true + consider: GO:0000122 + consider: GO:0004879 + consider: GO:0030522 + consider: GO:0038049 GO:0080182 : histone H3-K4 trimethylation - def: The modification of histone H4 by addition of three methyl groups to lysine at position 4 of the histone. + 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: GO:0072500 + consider: GO:0000122 + consider: GO:0004879 + consider: GO:0030522 + consider: GO:0038049 FILE STATS ========== Term counts for the old and new files Ontology Old file New file Change molecular function 9168 9193 +25 (9168 defined) (9193 defined) cellular component 2926 2927 +1 (2926 defined) (2927 defined) biological process 21659 21664 +5 (21659 defined) (21664 defined) Obsolete 1603 1606 +3 (4.5% of total) (4.5% of total) (+0.2%) Totals 33753 33784 +34 (+0.1%) 33753 (100.0%) defined 33784 (100.0%) defined 35356 inc. obs 35390 inc. obs