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

ID name namespace
GO:0010131 sucrose catabolic process, using invertase or sucrose synthase
Consider: GO:0004564, GO:0005987, GO:0016157
This term was made obsolete because it describes two different routes of sucrose catabolism, both of which are represented by molecular functions. 		biological_process
GO:0019575 sucrose catabolic process, using beta-fructofuranosidase
Consider: GO:0004564, GO:0036008
This term was made obsolete because beta-fructofuranosidase (also known as invertase) catalyzes the first step in multiple routes of sucrose catabolism. 		biological_process

Term merges

None

Term changes

Changes in term-related data
File 1 (16:09:2011 13:48, 1.2262) File 2 (23:09:2011 13:54, 1.2279)
GO:0000083 : regulation of transcription involved in G1/S phase of mitotic cell cycle
intersection_of
GO:0006357
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
part_of GO:0006360
GO:0001055 : RNA polymerase II activity
intersection_of
GO:0003899
part_of GO:0006366
GO:0001056 : RNA polymerase III activity
intersection_of
GO:0003899
part_of GO:0006383
GO:0001057 : RNA polymerase IV activity
intersection_of
GO:0003899
part_of GO:0001059
GO:0001058 : RNA polymerase V activity
intersection_of
GO:0003899
part_of GO:0001060
GO:0001976 : neurological system process involved in regulation of systemic arterial blood pressure
intersection_of
GO:0050877
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
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
part_of GO:0001982
GO:0002379 : immunoglobulin biosynthetic process involved in immune response
intersection_of
GO:0002378
part_of GO:0002381
GO:0002380 : immunoglobulin secretion involved in immune response
intersection_of
GO:0048305
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
part_of GO:0072513
GO:0003270 : Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation
intersection_of
GO:0007219
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
part_of GO:0007411
GO:0008543 : fibroblast growth factor receptor signaling pathway
is_a
GO:0044344
GO:0008810 : cellulase activity
synonym
"alkali cellulase activity" EXACT [EC:3.2.1.4]
"avicelase activity" BROAD [EC:3.2.1.4]
 synonym
"alkali cellulase activity" NARROW [EC:3.2.1.4]
"avicelase activity" RELATED [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.
is_a
GO:0005987
 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_obsolete
true
consider
GO:0004564
GO:0005987
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
def
The chemical reactions and pathways resulting in the breakdown of sucrose, catalyzed by the enzyme glucoside 3-dehydrogenase (EC:1.1.99.13).
 name
sucrose catabolic process via 3'-ketosucrose
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]
"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).
is_a
GO:0005987
 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_obsolete
true
consider
GO:0004564
GO:0036008
GO:0023019 : signal transduction involved in regulation of gene expression
intersection_of
GO:0007165
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
"1-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol acetylhydrolase activity" EXACT [EC:3.5.1.103]
"1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase 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
part_of GO:0043064
GO:0043738 : reduced coenzyme F420 dehydrogenase activity
name
F420H2 dehydrogenase activity
def
Catalysis of the reaction: methanophenazine + reduced cofactor F420 = dihydromethanophenazine + cofactor F420.
xref
MetaCyc:CPLX-7105
 name
reduced coenzyme F420 dehydrogenase activity
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]
"F420H2 dehydrogenase activity" EXACT []
xref
MetaCyc:RXN-8106
GO:0043794 : formate dehydrogenase (coenzyme F420) activity
name
formate dehydrogenase (F420) activity
def
Catalysis of the reaction: formate + coenzyme F420 = CO2 + reduced coenzyme F420.
 name
formate dehydrogenase (coenzyme F420) activity
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
def
Catalysis of the reaction: coenzyme F420 + ATP = coenzyme F390.
synonym
"ATP:coenzyme F420 adenyltransferase activity" EXACT []
 name
ATP:coenzyme F420 adenyltransferase activity
def
Catalysis of the reaction: ATP + factor gamma-F420-2 + H+ = coenzyme F390-A + diphosphate.
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
part_of GO:0000082
GO:0071931 : positive regulation of transcription involved in G1/S phase of mitotic cell cycle
intersection_of
GO:0045944
part_of GO:0000082
GO:0071935 : octopamine signaling pathway involved in response to food
intersection_of
GO:0071927
part_of GO:0032094
GO:0071937 : barrier septum formation involved in cell cycle cytokinesis
intersection_of
GO:0000917
part_of GO:0033205
GO:0071947 : protein deubiquitination involved in ubiquitin-dependent protein catabolic process
intersection_of
GO:0016579
part_of GO:0006511
GO:0072000 : extracellular polysaccharide catabolic process involved in ascospore release from ascus
intersection_of
GO:0071999
part_of GO:0071998
GO:0072037 : mesenchymal stem cell differentiation involved in nephron morphogenesis
intersection_of
GO:0072497
part_of GO:0072028
GO:0072281 : mesenchymal stem cell differentiation involved in metanephric nephron morphogenesis
intersection_of
GO:0072497
part_of GO:0072273
GO:0072316 : alpha-glucan catabolic process involved in ascospore release from ascus
intersection_of
GO:0030980
part_of GO:0071998
GO:0072317 : glucan endo-1,3-beta-D-glucosidase activity involved in ascospore release from ascus
intersection_of
GO:0042973
part_of GO:0071998
GO:0072335 : regulation of canonical Wnt receptor signaling pathway involved in neural crest cell differentiation
intersection_of
GO:0065007
regulates GO:0044335
GO:0072336 : negative regulation of canonical Wnt receptor signaling pathway involved in neural crest cell differentiation
intersection_of
GO:0065007
negatively_regulates GO:0044335
GO:0072381 : positive regulation of canonical Wnt receptor signaling pathway involved in neural crest cell differentiation
intersection_of
GO:0065007
positively_regulates GO:0044335
GO:0072395 : signal transduction involved in cell cycle checkpoint
intersection_of
GO:0035556
part_of GO:0000075
GO:0072398 : signal transduction involved in cytokinesis checkpoint
intersection_of
GO:0035556
part_of GO:0031565
GO:0072401 : signal transduction involved in DNA integrity checkpoint
intersection_of
GO:0035556
part_of GO:0031570
GO:0072404 : signal transduction involved in G1/S transition checkpoint
intersection_of
GO:0035556
part_of GO:0071779
GO:0072407 : signal transduction involved in G2/M transition checkpoint
intersection_of
GO:0035556
part_of GO:0031576
GO:0072409 : detection of stimulus involved in meiotic cell cycle checkpoint
intersection_of
GO:0051606
part_of GO:0033313
GO:0072411 : signal transduction involved in meiotic cell cycle checkpoint
intersection_of
GO:0035556
part_of GO:0033313
GO:0072412 : detection of stimulus involved in mitotic cell cycle checkpoint
intersection_of
GO:0051606
part_of GO:0007093
GO:0072413 : signal transduction involved in mitotic cell cycle checkpoint
intersection_of
GO:0035556
part_of GO:0007093
GO:0072415 : detection of stimulus involved in spindle checkpoint
intersection_of
GO:0051606
part_of GO:0031577
GO:0072416 : signal transduction involved in spindle checkpoint
intersection_of
GO:0035556
part_of GO:0031577
GO:0072418 : detection of stimulus involved in septin checkpoint
intersection_of
GO:0051606
part_of GO:0000135
GO:0072419 : signal transduction involved in septin checkpoint
intersection_of
GO:0035556
part_of GO:0000135
GO:0072422 : signal transduction involved in DNA damage checkpoint
intersection_of
GO:0035556
part_of GO:0000077
GO:0072425 : signal transduction involved in G2/M transition DNA damage checkpoint
intersection_of
GO:0035556
part_of GO:0031572
GO:0072428 : signal transduction involved in intra-S DNA damage checkpoint
intersection_of
GO:0035556
part_of GO:0031573
GO:0072431 : signal transduction involved in mitotic cell cycle G1/S transition DNA damage checkpoint
intersection_of
GO:0035556
part_of GO:0031571
GO:0072436 : detection of stimulus involved in DNA replication checkpoint
intersection_of
GO:0051606
part_of GO:0000076
GO:0072437 : signal transduction involved in DNA replication checkpoint
intersection_of
GO:0035556
part_of GO:0000076
GO:0072442 : detection of stimulus involved in mitotic DNA replication checkpoint
intersection_of
GO:0051606
part_of GO:0033314
GO:0072443 : signal transduction involved in mitotic DNA replication checkpoint
intersection_of
GO:0035556
part_of GO:0033314
GO:0072448 : detection of stimulus involved in mitotic cell cycle G1/S transition size control checkpoint
intersection_of
GO:0051606
part_of GO:0031568
GO:0072450 : signal transduction involved in mitotic cell cycle G1/S transition size control checkpoint
intersection_of
GO:0035556
part_of GO:0031568
GO:0072451 : detection of stimulus involved in G2/M transition size control checkpoint
intersection_of
GO:0051606
part_of GO:0031569
GO:0072453 : signal transduction involved in G2/M transition size control checkpoint
intersection_of
GO:0035556
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
9086 (100.0%) defined 		9103
9103 (100.0%) defined 		+17
cellular component 2896
2896 (100.0%) defined 		2897
2897 (100.0%) defined 		+1
biological process 21406
21406 (100.0%) defined 		21432
21432 (100.0%) defined 		+26
Obsolete 1583
(4.5% of total)		 1585
(4.5% of total)		 +2 (+0.1%)
Totals 33388
33388 (100.0%) defined
34971 inc. obsoletes 		33432
33432 (100.0%) defined
35017 inc. obsoletes 		+46 (+0.1%)

Ontology report info