Gene Ontology Ontology Comparison Report ========================== Files used: - file 1 (old): go-2011-09-17.obo; date: 16:09:2011 13:48; CVS revision: 1.2262 - file 2 (new): go-2011-09-24.obo; date: 23:09:2011 13:54; CVS revision: 1.2279 NEW TERMS ========= ID name namespace GO:0036003 positive regulation of transcription from RNA polymerase II promoter in response to stress biological_process GO:0036004 GAF domain binding molecular_function GO:0036005 response to macrophage colony-stimulating factor stimulus biological_process GO:0036006 cellular response to macrophage colony-stimulating factor stimulus biological_process GO:0036007 scintillon cellular_component GO:0036008 sucrose catabolic process to fructose-6-phosphate and glucose-6-phosphate biological_process GO:0038033 vascular endothelial growth factor receptor signaling pathway involved in endothelial cell chemotaxis biological_process GO:0052747 sinapyl alcohol dehydrogenase activity molecular_function GO:0052748 baicalin beta-D-glucuronidase activity molecular_function GO:0052749 glucose-6-phosphate dehydrogenase (coenzyme F420) activity molecular_function GO:0052750 reactive-black-5:hydrogen-peroxide oxidoreductase activity molecular_function GO:0052751 GDP-mannose hydrolase activity molecular_function GO:0052752 reduced coenzyme F420:heterodisulfide oxidoreductase activity molecular_function GO:0052753 propan-2-ol:coenzyme F420 oxidoreductase activity molecular_function GO:0052754 GTP:coenzyme F420 guanyltransferase activity molecular_function GO:0052755 reduced coenzyme F420:2,3-dimethyl-1,4-naphthoquinone oxidoreductase activity molecular_function GO:0052756 sulfite reductase (coenzyme F420) activity molecular_function GO:0052757 aflatoxin reductase (coenzyme F420) activity molecular_function GO:0052758 F420H2:NADP+ oxidoreductase activity molecular_function GO:0097157 pre-mRNA intronic binding molecular_function GO:0097158 pre-mRNA intronic pyrimidine-rich binding molecular_function GO:0097159 organic cyclic compound binding molecular_function GO:0097160 polychlorinated biphenyl binding molecular_function GO:2001074 regulation of metanephric ureteric bud development biological_process GO:2001075 negative regulation of metanephric ureteric bud development biological_process GO:2001076 positive regulation of metanephric ureteric bud development biological_process GO:2001086 laminarabiose transport biological_process GO:2001087 sophorose transport biological_process GO:2001088 trisaccharide transport biological_process GO:2001089 maltotriose transport biological_process GO:2001090 maltotriulose transport biological_process GO:2001091 nigerotriose transport biological_process GO:2001092 arabinotriose transport biological_process GO:2001093 galactotriose transport biological_process GO:2001094 xylotriose transport biological_process GO:2001095 mannotriose transport biological_process GO:2001096 cellotriose transport biological_process GO:2001097 laminaritriose transport biological_process GO:2001098 tetrasaccharide transport biological_process GO:2001099 maltotetraose transport biological_process GO:2001100 pentasaccharide transport biological_process GO:2001101 maltopentaose transport biological_process GO:2001102 hexasaccharide transport biological_process GO:2001103 maltohexaose transport biological_process GO:2001104 heptasaccharide transport biological_process GO:2001105 maltoheptaose transport biological_process OBSOLETIONS =========== GO:0010131, sucrose catabolic process, using invertase or sucrose synthase (biological_process) This term was made obsolete because it describes two different routes of sucrose catabolism, both of which are represented by molecular functions. Consider: GO:0004564, GO:0005987, GO:0016157 GO:0019575, sucrose catabolic process, using beta-fructofuranosidase (biological_process) This term was made obsolete because beta-fructofuranosidase (also known as invertase) catalyzes the first step in multiple routes of sucrose catabolism. Consider: GO:0004564, GO:0036008 TERM MERGES =========== None TERM CHANGES ============ GO:0000083 : regulation of transcription involved in G1/S phase of mitotic cell cycle + intersection_of: GO:0006357 + intersection_of: part_of GO:0000082 GO:0000985 : bacterial-type RNA polymerase core promoter sequence-specific DNA binding - synonym: "bacterial-type RNA polymerase core promoter sequence-specific DNA binding" EXACT [] GO:0001054 : RNA polymerase I activity + intersection_of: GO:0003899 + intersection_of: part_of GO:0006360 GO:0001055 : RNA polymerase II activity + intersection_of: GO:0003899 + intersection_of: part_of GO:0006366 GO:0001056 : RNA polymerase III activity + intersection_of: GO:0003899 + intersection_of: part_of GO:0006383 GO:0001057 : RNA polymerase IV activity + intersection_of: GO:0003899 + intersection_of: part_of GO:0001059 GO:0001058 : RNA polymerase V activity + intersection_of: GO:0003899 + intersection_of: part_of GO:0001060 GO:0001976 : neurological system process involved in regulation of systemic arterial blood pressure + intersection_of: GO:0050877 + intersection_of: part_of GO:0003073 GO:0001985 : negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure + intersection_of: GO:0010459 + intersection_of: part_of GO:0001983 GO:0001988 : positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure + intersection_of: GO:0010460 + intersection_of: part_of GO:0001982 GO:0002379 : immunoglobulin biosynthetic process involved in immune response + intersection_of: GO:0002378 + intersection_of: part_of GO:0002381 GO:0002380 : immunoglobulin secretion involved in immune response + intersection_of: GO:0048305 + intersection_of: part_of GO:0002381 GO:0003267 : canonical Wnt receptor signaling pathway involved in positive regulation of secondary heart field cardioblast proliferation + intersection_of: GO:0061316 + intersection_of: part_of GO:0072513 GO:0003270 : Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation + intersection_of: GO:0007219 + intersection_of: part_of GO:0003266 GO:0004467 : long-chain fatty acid-CoA ligase activity - synonym: "long-chain fatty acid-CoA ligase activity" EXACT [] GO:0008046 : axon guidance receptor activity + intersection_of: GO:0004888 + intersection_of: part_of GO:0007411 GO:0008543 : fibroblast growth factor receptor signaling pathway + is_a: GO:0044344 GO:0008810 : cellulase activity - synonym: "avicelase activity" BROAD [EC:3.2.1.4] - synonym: "alkali cellulase activity" EXACT [EC:3.2.1.4] + synonym: "avicelase activity" RELATED [EC:3.2.1.4] + synonym: "alkali cellulase activity" NARROW [EC:3.2.1.4] GO:0010131 : sucrose catabolic process, using invertase or sucrose synthase - def: The chemical reactions and pathways resulting in the breakdown of sucrose by the enzymatic action of either invertase or sucrose synthase. + def: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sucrose by the enzymatic action of either invertase or sucrose synthase. + comment: This term was made obsolete because it describes two different routes of sucrose catabolism, both of which are represented by molecular functions. - is_a: GO:0005987 + is_obsolete: true + consider: GO:0004564 + consider: GO:0005987 + consider: GO:0016157 GO:0014065 : phosphatidylinositol 3-kinase cascade - is_a: GO:0035556 + is_a: GO:0048015 GO:0018532 : coenzyme F420-independent 5,10-methenyl-5,6,7,8-tetrahydromethanopterin dehydrogenase activity - name: F420-independent 5,10-methenyl-5,6,7,8-tetrahydromethanopterin dehydrogenase activity + name: coenzyme F420-independent 5,10-methenyl-5,6,7,8-tetrahydromethanopterin dehydrogenase activity + synonym: "5,10-methenyl-5,6,7,8-tetrahydromethanopterin dehydrogenase activity" BROAD [] GO:0018537 : coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity - def: Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F(420). + def: Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 1,5-dihydrocoenzyme F420 + 5,10-methylenetetrahydromethanopterin. 1,5-dihydrocoenzyme F420 is also known as reduced coenzyme F(420). GO:0019574 : sucrose catabolic process via 3'-ketosucrose - name: sucrose catabolic process, using glucoside 3-dehydrogenase + name: sucrose catabolic process via 3'-ketosucrose - def: The chemical reactions and pathways resulting in the breakdown of sucrose, catalyzed by the enzyme glucoside 3-dehydrogenase (EC:1.1.99.13). + def: The chemical reactions and pathways resulting in the breakdown of sucrose, which proceeds via the conversion of sucrose to 3'-ketosucrose. 3'-ketosucrose is hydrolyzed to 3-ketoglucose and fructose, and the 3-ketoglucose can then be converted to glucose. + synonym: "sucrose catabolic process to D-glucose" EXACT [GOC:bf, MetaCyc:SUCROSEUTIL2-PWY] + synonym: "sucrose catabolic process, using glucoside 3-dehydrogenase" EXACT [GOC:bf, MetaCyc:SUCROSEUTIL2-PWY] GO:0019575 : sucrose catabolic process, using beta-fructofuranosidase - def: The chemical reactions and pathways resulting in the breakdown of sucrose, catalyzed by the enzyme beta-fructofuranosidase (EC:3.2.1.26). + def: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sucrose, catalyzed by the enzyme beta-fructofuranosidase (EC:3.2.1.26). + comment: This term was made obsolete because beta-fructofuranosidase (also known as invertase) catalyzes the first step in multiple routes of sucrose catabolism. - is_a: GO:0005987 + is_obsolete: true + consider: GO:0004564 + consider: GO:0036008 GO:0023019 : signal transduction involved in regulation of gene expression + intersection_of: GO:0007165 + intersection_of: part_of GO:0010468 GO:0030268 : methylenetetrahydromethanopterin dehydrogenase activity - def: Catalysis of the reaction: 5,10-methylenetetrahydromethanopterin + coenzyme F420 + 2 H(+) = 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + reduced coenzyme F(420). + def: Catalysis of the reaction: 5,10-methylenetetrahydromethanopterin + coenzyme F420 + 2 H(+) = 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + 1,5-dihydrocoenzyme F420. 1,5-dihydrocoenzyme F420 is also known as reduced coenzyme F420. GO:0030733 : fatty acid O-methyltransferase activity - synonym: "fatty acid O-methyltransferase activity" EXACT [EC:2.1.1.15] GO:0034509 : centromeric core chromatin assembly - synonym: "centromeric core chromatin assembly" EXACT [] + synonym: "centric core chromatin assembly" EXACT [] GO:0035426 : extracellular matrix-cell signaling - synonym: "extracellular matrix-cell signaling" EXACT [] + synonym: "extracellular matrix-cell signalling" EXACT [] GO:0035446 : cysteine-glucosaminylinositol ligase activity GO:0035595 : N-acetylglucosaminylinositol deacetylase activity + synonym: "1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase activity" EXACT [EC:3.5.1.103] + synonym: "1-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol acetylhydrolase activity" EXACT [EC:3.5.1.103] GO:0035630 : bone mineralization involved in bone maturation - intersection_of: part_of GO:0070977 + intersection_of: part_of GO:0043931 GO:0035734 : intraflagellar transport involved in flagellum organisation + intersection_of: GO:0042073 + intersection_of: part_of GO:0043064 GO:0043738 : reduced coenzyme F420 dehydrogenase activity - name: F420H2 dehydrogenase activity + name: reduced coenzyme F420 dehydrogenase activity - def: Catalysis of the reaction: methanophenazine + reduced cofactor F420 = dihydromethanophenazine + cofactor F420. + def: Catalysis of the reaction: methanophenazine + 1,5-dihydrocoenzyme F420 = dihydromethanophenazine + coenzyme F420. 1,5-dihydrocoenzyme F420 is also known as reduced coenzyme F420. + synonym: "1,5-dihydrocoenzyme F420 dehydrogenase activity" EXACT [CHEBI:15823] + synonym: "F420H2 dehydrogenase activity" EXACT [] - xref: MetaCyc:CPLX-7105 + xref: MetaCyc:RXN-8106 GO:0043794 : formate dehydrogenase (coenzyme F420) activity - name: formate dehydrogenase (F420) activity + name: formate dehydrogenase (coenzyme F420) activity - def: Catalysis of the reaction: formate + coenzyme F420 = CO2 + reduced coenzyme F420. + def: Catalysis of the reaction: formate + coenzyme F420 = CO2 + 1,5-dihydrocoenzyme F420. 1,5-dihydrocoenzyme F420 is also known as reduced coenzyme F420. + synonym: "formate dehydrogenase (F420) activity" EXACT [] GO:0043910 : ATP:coenzyme F420 adenyltransferase activity - name: coenzyme F390 synthetase activity + name: ATP:coenzyme F420 adenyltransferase activity - def: Catalysis of the reaction: coenzyme F420 + ATP = coenzyme F390. + def: Catalysis of the reaction: ATP + factor gamma-F420-2 + H+ = coenzyme F390-A + diphosphate. - synonym: "ATP:coenzyme F420 adenyltransferase activity" EXACT [] + synonym: "coenzyme F390-A synthetase activity" EXACT [] + xref: MetaCyc:RXN-9385 GO:0044101 : (R)-citramalyl-CoA lyase activity - xref: MetaCyc:CPLX-7553 + xref: MetaCyc:RXN-8967 GO:0045168 : cell-cell signaling involved in cell fate commitment - synonym: "cell-cell signaling involved in cell fate commitment" EXACT [] + synonym: "cell-cell signaling during in cell fate commitment" EXACT [] GO:0046429 : 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity - synonym: "4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity" EXACT [EC:1.17.7.1] GO:0046568 : 3-methylbutanol:NAD(P) oxidoreductase activity - synonym: "3-methylbutanol:NAD(P) oxidoreductase activity" EXACT [] GO:0048017 : inositol lipid-mediated signaling - is_a: GO:0019932 + is_a: GO:0035556 GO:0048557 : embryonic digestive tract morphogenesis - synonym: "embryonic digestive tract morphogenesis" EXACT [] GO:0048699 : generation of neurons - synonym: "generation of neurons" EXACT [GOC:curators] + synonym: "neuron generation" EXACT [GOC:curators] GO:0050454 : coenzyme F420 hydrogenase activity - def: Catalysis of the reaction: coenzyme F420 + H(2) + H(+) = reduced coenzyme F(420). + def: Catalysis of the reaction: coenzyme F420 + H(2) + H(+) = 1,5-dihydrocoenzyme F420. 1,5-dihydrocoenzyme F420 is also known as reduced coenzyme F(420). GO:0052622 : ATP dimethylallyltransferase activity - synonym: "ATP dimethylallyltransferase activity" EXACT [EC:2.5.1.27] GO:0052623 : ADP dimethylallyltransferase activity - synonym: "ADP dimethylallyltransferase activity" EXACT [EC:2.5.1.27] GO:0052645 : F420-0 metabolic process + synonym: "F(420)-0 metabolic process" EXACT [CHEBI:59532] GO:0052741 : (R)-limonene 6-monooxygenase activity - synonym: "(R)-limonene 6-monooxygenase activity" EXACT [EC:1.14.13.80] GO:0060128 : corticotropin hormone secreting cell differentiation - synonym: "corticotropin hormone secreting cell differentiation" EXACT [] GO:0060131 : corticotropin hormone secreting cell development - synonym: "corticotropin hormone secreting cell development" EXACT [] GO:0060413 : atrial septum morphogenesis - synonym: "atrial septum morphogenesis" EXACT [] GO:0070036 : GTP-dependent helicase activity - is_a: GO:0042623 + is_a: GO:0003924 GO:0071930 : negative regulation of transcription involved in G1/S phase of mitotic cell cycle + intersection_of: GO:0000122 + intersection_of: part_of GO:0000082 GO:0071931 : positive regulation of transcription involved in G1/S phase of mitotic cell cycle + intersection_of: GO:0045944 + intersection_of: part_of GO:0000082 GO:0071935 : octopamine signaling pathway involved in response to food + intersection_of: GO:0071927 + intersection_of: part_of GO:0032094 GO:0071937 : barrier septum formation involved in cell cycle cytokinesis + intersection_of: GO:0000917 + intersection_of: part_of GO:0033205 GO:0071947 : protein deubiquitination involved in ubiquitin-dependent protein catabolic process + intersection_of: GO:0016579 + intersection_of: part_of GO:0006511 GO:0072000 : extracellular polysaccharide catabolic process involved in ascospore release from ascus + intersection_of: GO:0071999 + intersection_of: part_of GO:0071998 GO:0072037 : mesenchymal stem cell differentiation involved in nephron morphogenesis + intersection_of: GO:0072497 + intersection_of: part_of GO:0072028 GO:0072281 : mesenchymal stem cell differentiation involved in metanephric nephron morphogenesis + intersection_of: GO:0072497 + intersection_of: part_of GO:0072273 GO:0072316 : alpha-glucan catabolic process involved in ascospore release from ascus + intersection_of: GO:0030980 + intersection_of: part_of GO:0071998 GO:0072317 : glucan endo-1,3-beta-D-glucosidase activity involved in ascospore release from ascus + intersection_of: GO:0042973 + intersection_of: part_of GO:0071998 GO:0072335 : regulation of canonical Wnt receptor signaling pathway involved in neural crest cell differentiation + intersection_of: GO:0065007 + intersection_of: regulates GO:0044335 GO:0072336 : negative regulation of canonical Wnt receptor signaling pathway involved in neural crest cell differentiation + intersection_of: GO:0065007 + intersection_of: negatively_regulates GO:0044335 GO:0072381 : positive regulation of canonical Wnt receptor signaling pathway involved in neural crest cell differentiation + intersection_of: GO:0065007 + intersection_of: positively_regulates GO:0044335 GO:0072395 : signal transduction involved in cell cycle checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0000075 GO:0072398 : signal transduction involved in cytokinesis checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031565 GO:0072401 : signal transduction involved in DNA integrity checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031570 GO:0072404 : signal transduction involved in G1/S transition checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0071779 GO:0072407 : signal transduction involved in G2/M transition checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031576 GO:0072409 : detection of stimulus involved in meiotic cell cycle checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0033313 GO:0072411 : signal transduction involved in meiotic cell cycle checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0033313 GO:0072412 : detection of stimulus involved in mitotic cell cycle checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0007093 GO:0072413 : signal transduction involved in mitotic cell cycle checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0007093 GO:0072415 : detection of stimulus involved in spindle checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0031577 GO:0072416 : signal transduction involved in spindle checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031577 GO:0072418 : detection of stimulus involved in septin checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0000135 GO:0072419 : signal transduction involved in septin checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0000135 GO:0072422 : signal transduction involved in DNA damage checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0000077 GO:0072425 : signal transduction involved in G2/M transition DNA damage checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031572 GO:0072428 : signal transduction involved in intra-S DNA damage checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031573 GO:0072431 : signal transduction involved in mitotic cell cycle G1/S transition DNA damage checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031571 GO:0072436 : detection of stimulus involved in DNA replication checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0000076 GO:0072437 : signal transduction involved in DNA replication checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0000076 GO:0072442 : detection of stimulus involved in mitotic DNA replication checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0033314 GO:0072443 : signal transduction involved in mitotic DNA replication checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0033314 GO:0072448 : detection of stimulus involved in mitotic cell cycle G1/S transition size control checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0031568 GO:0072450 : signal transduction involved in mitotic cell cycle G1/S transition size control checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031568 GO:0072451 : detection of stimulus involved in G2/M transition size control checkpoint + intersection_of: GO:0051606 + intersection_of: part_of GO:0031569 GO:0072453 : signal transduction involved in G2/M transition size control checkpoint + intersection_of: GO:0035556 + intersection_of: part_of GO:0031569 GO:0080087 : callose binding - synonym: "callose binding" EXACT [] GO:0090388 : phagosome-lysosome docking involved in apoptotic cell clearance - intersection_of: GO:0090388 + intersection_of: GO:0090384 FILE STATS ========== Term counts for the old and new files Ontology Old file New file Change molecular function 9086 9103 +17 (9086 defined) (9103 defined) cellular component 2896 2897 +1 (2896 defined) (2897 defined) biological process 21406 21432 +26 (21406 defined) (21432 defined) Obsolete 1583 1585 +2 (4.5% of total) (4.5% of total) (+0.1%) Totals 33388 33432 +46 (+0.1%) 33388 (100.0%) defined 33432 (100.0%) defined 34971 inc. obs 35017 inc. obs