QC of GO annotation using annotation overlaps
Summary
This project identifies annotations which conflict with current biological knowledge.
Using biological process GO slim terms, each term is assessed for overlaps with each other. If no known overlaps exist, the overlap is described as "NULL" and any annotations to this intersection will be queried for validity. More specific rules are created by identifying specific processes, complexes or functions which *are* allowed in intersections. Rules can be extended to take account of new biology, or existing annotations in other organisms.
The template rules are defined after assessing the current annotation set for fission yeast, budding yeast and mouse.
The time consuming part is creating the rules, but once the rules are in place there should be a low maintenance overhead.
Method
Use
Matrix tool:
http://stove.lbl.gov:8899/cgi-bin/amigo/amigo_exp?mode=nmatrix
new test
http://amigo2.berkeleybop.org/cgi-bin/amigo2/matrix
new test
http://amigo2.berkeleybop.org/matrix
with GO slim list (template list at the bottom of this page
(Note that the tables must use the syntax described in the column headers for parsing)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006520 | GO:0006310 | DNA recombination | NO_OVERLAP | S.p; M.m; S.c.
|
| GO:0006520 | GO:0006281 | DNA repair | GO:0006521 OR GO:0006338 (regulation of cellular amino acid metabolic process -NOTE transcriptional OR chromatin remodelling- NOTE, this may be indirect for repair???) | S.p; M.m; S.c.
|
| GO:0006520 | GO:0006260 | DNA replication | NO_OVERLAP | S.p; M. m {2 to report}; S.c {3 queried}
|
| GO:0006520 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p; M.m {n/a}; S.c.
|
| GO:0006520 | GO:0005975 | carbohydrate metabolic process | LATER | S.p
|
| GO:0006520 | GO:0007155 | cell adhesion | GO:0006521 (regulation of cellular amino acid metabolic process) | S.p; M.m {0 pending responses from 2 Uniprot annotations}; S.c.
|
| GO:0006520 | GO:0071554 | cell wall organization or biogenesis | GO:0004360 OR GO:0004067 (glutamine-fructose-6-phosphate transaminase isomerizing activity OR asparaginase activity) | S.p; M.m {n/a}; S.c.
|
| GO:0006520 | GO:0016568 | chromatin modification | GO:0006521 OR GO:0006355 (regulation of cellular amino acid metabolic process- transcriptional OR regulation of transcription DNA dependent) | S.p; M.m.; S.c
|
| GO:0006520 | GO:0051276 | chromosome organization | GO:0023052 OR GO:0006521 (signaling, upstream OR regulation of cellular amino acid metabolic process- transcriptional) | S.p; M.m.; S.c.
|
| GO:0006520 | GO:0007059 | chromosome segregation | GO:0023052 (signaling, upstream) | S.p; M m.; S.c.
|
| GO:0006520 | GO:0051186 | cofactor metabolic process | LATER | S.p
|
| GO:0006520 | GO:0000747 | conjugation with cellular fusion | NO_OVERLAP | S.p; M.m {n/a}; S.c.
|
| GO:0006520 | GO:0000910 | cytokinesis | NO_OVERLAP | S.p; M.m {pending apc update uniprot}; S.c.
|
| GO:0006520 | GO:0002181 | cytoplasmic translation | GO:0043039 (tRNA aminoacylation) | S.p. M.m; S.c {NOTE check translation too}
|
| GO:0006520 | GO:0007010 | cytoskeleton organization | GO:0023052 (signaling upstream) | S.p; M.m; S.c.
|
| GO:0006520 | GO:0007163 | establishment or maintenance of cell polarity | GO:0006355 (regulation of transcription DNA dependent) | S.p; M.m.; S.c.
|
| GO:0006520 | GO:0006091 | generation of precursor metabolites and energy | LATER | S.p
|
| GO:0006520 | GO:0006629 | lipid metabolic process | GO:0006521 OR GO:0023052 (regulation of cellular amino acid metabolic process OR signaling-upstream) | S.p; M.m.; S.c
|
| GO:0006520 | GO:0016071 | mRNA metabolic process | NO_OVERLAP | S.p; M.m {0 pending UniProt? feedback}; S.c.
|
| GO:0006520 | GO:0007126 | meiosis | NO_OVERLAP | S.p; M.m; S.c.
|
| GO:0006520 | GO:0007005 | mitochondrion organization | GO:0043039 OR GO:0003994 (tRNA aminoacylation OR aconitate hydratase) | S.p {fusion proteins need column 17 annotations} {bifunctional enzyme ilv5- need to identify specific GO term to allow this}
|
| GO:0006520 | GO:0071941 | nitrogen cycle metabolic process | LATER | S.p
|
| GO:0006520 | GO:0055086 | nucleobase-containing small molecule metabolic process | LATER | S.p
|
| GO:0006520 | GO:0006913 | nucleocytoplasmic transport | NO_OVERLAP | S.p; M.m {1 but should disappear pending response from Uniprot}
|
| GO:0006520 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p; M.m; S.c.
|
| GO:0006520 | GO:0030163 | protein catabolic process | MOUSE LOTS GO:0006521 (regulation of amino acid metabolic process) | S.p; S.c
|
| GO:0006520 | GO:0006461 | protein complex assembly | MOUSE LOTS | S.p; S.c
|
| GO:0006520 | GO:0006457 | protein folding | NO_OVERLAP | S.p; M.m {reported 1 anomaly to MGI}; S.c {queried 2 anomalies}
|
| GO:0006520 | GO:0006486 | protein glycosylation | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0006520 | GO:0051604 | protein maturation | NO_OVERLAP | S.p;
|
| GO:0006520 | GO:0070647 | protein modification by small protein conjugation or removal | GO:0006521 (regulation of cellular amino acid metabolic process) | S.p; M.m {querying 3 annotations, one derived from uniprot human, and 2 MGI}; S.c {querying 1}
|
| GO:0006520 | GO:0006605 | protein targeting | NO_OVERLAP | S.p; M.m; S.c
|
| GO:0006520 | GO:0007346 | regulation of mitotic cell cycle | MOUSE LOTS | S.p
|
| GO:0006520 | GO:0042254 | ribosome biogenesis | NO_OVERLAP | S.p; M.m; S.c.
|
| GO:0006520 | GO:0023052 | signaling | LATER | S.p; M.m; S.c
|
| GO:0006520 | GO:0006399 | tRNA metabolic process | GO:0043039 OR GO:0031071 (tRNA aminoacylation OR cysteine desulphurase) | S.p; M.m. S.c {some checks outstanding}
|
| GO:0006520 | GO:0006351 | transcription DNA-dependent | GO:0006355 (regulation of transcription DNA dependent) | S.p; M.m
|
| GO:0006520 | GO:0055085 | transmembrane transport | MOUSE LOTS | S.p; S.c {one ontology query}
|
| GO:0006520 | GO:0007033 | vacuole organization | GO:0060627 (regulation of amino acid metabolism) | S.p; S.c; M.m
|
| GO:0006520 | GO:0016192 | vesicle-mediated transport | GO:0006521 OR GO:0060627 (regulation of vesicle mediated transport & regulation of amino acid metabolism BOTH, via regulation of transcription) | S.p; S.c.; M.m
|
| GO:0006520 | GO:0006766 | vitamin metabolic process | GO:0004586 OR GO:0004372 (ornithine decarboxylase activity OR glycine hydroxymethyltransferase activity) | S.p; M.m {one query to fix}; S.c. {some SPKW to remove check sno1,2,3}
|
| Database | gene | update | reason
|
| PomBase | fmt1 | removed methionyl-tRNA aminoacylation | missannotation should be methionyl-tRNA to N-formyl-methionyl-tRNA
|
| PomBase | SPAC823.09 | waiting
|
| PomBase | hst4 | mitotic sister chromatid segregation | indirect
|
| PomBase | sla1 | removed regulation of conjugation with cellular fusion | indirect
|
| PomBase | sla1 | removed regulation of ascospore formation | indirect
|
| SGD | MET5 | removed fungal-type cell wall organization | indirect
|
| SGD | ARG7 | removed fungal-type cell wall organization | indirect
|
| SGD | GAP1 | ammonia assimilation cycle | indirect
|
| SGD | FMT1 | removed methionyl-tRNA aminoacylation | error, should be methionyl-tRNA to N-formyl-methionyl-tRNA
|
| SGD | ARG81 | replaced arginine metabolic process with "regulation of arginine metabolic process | upstream regulation
|
| SGD | ARG81 | removed negative regulation of calcium ion-dependent exocytosis | error
|
| SGD | CDC60 | removed DNA replication initiation | indirect
|
| SGD | MET18 | removed methionine metabolic process | indirect
|
| SGD | THR4 | removed endocytosis | indirect
|
| SGD | FPR1 | replaced arginine metabolic process with "regulation of arginine metabolic process | upstream regulation
|
| SGD | CBF1 | methionine biosynthetic process | indirect
|
| MGI | Sod1 | query nucleotide excision repair IMP | error, incorrect interpretation
|
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006399 | GO:0006310 | DNA recombination | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0006281 | DNA repair | NO_OVERLAP | S.p.; M.m.
|
| GO:0006399 | GO:0006260 | DNA replication | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p. M.m {n/a}
|
| GO:0006399 | GO:0005975 | carbohydrate metabolic process | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0007155 | cell adhesion | NO_OVERLAP | S.p.; M.m.
|
| GO:0006399 | GO:0006520 | cellular amino acid metabolic process | GO:0043039 OR GO:0031071 (tRNA aminoacylation OR cysteine desulphurase ) | S.p; M.m
|
| GO:0006399 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p.; M.m {n/a}
|
| GO:0006399 | GO:0016568 | chromatin modification | GO:0033588 (elongator complex) | S.p {check this, is elongator still thought to be histone acetyltransferase???};M.m
|
| GO:0006399 | GO:0051276 | chromosome organization | GO:0033588 (elongator complex) | S.p {check this, is elongator still thought to be histone acetyltransferase???}; M.m
|
| GO:0006399 | GO:0007059 | chromosome segregation | NO_OVERLAP | S.p; M.m.
|
| GO:0006399 | GO:0051186 | cofactor metabolic process | GO:0006777 (Mo-molybdopterin cofactor biosynthetic process) | S.p; M.m.
|
| GO:0006399 | GO:0000747 | conjugation with cellular fusion | NO_OVERLAP | S.p.; M.m {n/a}
|
| GO:0006399 | GO:0000910 | cytokinesis | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0002181 | cytoplasmic translation | GO:0043039 (tRNA aminoacylation) | S.p.; M.m.
|
| GO:0006399 | GO:0007010 | cytoskeleton organization | NO_OVERLAP | S.p; M.m.
|
| GO:0006399 | GO:0007163 | establishment or maintenance of cell polarity | NO_OVERLAP | S.p; M.m
|
| GO:0006399 | GO:0006091 | generation of precursor metabolites and energy | NO_OVERLAP | S.p; M.m.
|
| GO:0006399 | GO:0006629 | lipid metabolic process | NO_OVERLAP | S.p.; M.m.
|
| GO:0006520 | GO:0016071 | mRNA metabolic process | LATER | S.p; M.m.
|
| GO:0006520 | GO:0007126 | meiosis | NO_OVERLAP | S.p; M.m
|
| GO:0006520 | GO:0007005 | mitochondrion organization | GO:0043039 (tRNA aminoacylation) | S.p; M.m. {may need some more terms allowed in overlap}
|
| GO:0006399 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | S.p; M.m.
|
| GO:0006399 | GO:0055086 | nucleobase-containing small molecule metabolic process | LATER | S.p.; M.m includes GO:0008479 {queuine tRNA-ribosyltransferase activity} GO:0003924 {GTPase activity, specifically IPR004520}
|
| GO:0006399 | GO:0006913 | nucleocytoplasmic transport | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0030163 | protein catabolic process | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0006461 | protein complex assembly | NO_OVERLAP | S.p.; M.m {need to deal with protein tetramerization}
|
| GO:0006399 | GO:0006457 | protein folding | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0006486 | protein glycosylation | NO_OVERLAP | S.p.; M.m.
|
| GO:0006399 | GO:0051604 | protein maturation | NO_OVERLAP | S.p; M.m
|
| GO:0006399 | GO:0070647 | protein modification by small protein conjugation or removal | GO:0032447 (protein urmylation) | S.p; M.m.
|
| GO:0006399 | GO:0006605 | protein targeting | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0007346 | regulation of mitotic cell cycle | NO_OVERLAP | S.p; M.m
|
| GO:0006399 | GO:0042254 | ribosome biogenesis | LOTS (add details later) | S.p.; M.m.
|
| GO:0006399 | GO:0023052 | signaling | NO_OVERLAP | S.p; M.m.
|
| GO:0006399 | GO:0006351 | transcription DNA-dependent | LATER | S.p.; M.m
|
| GO:0006399 | GO:0055085 | transmembrane transport | NO_OVERLAP | S.p.; M.m
|
| GO:0006399 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p.; M.m.
|
| GO:0006399 | GO:0016192 | vesicle-mediated transport | NO_OVERLAP | S.p; M.m.
|
| GO:0006399 | GO:0006766 | vitamin metabolic process | NO_OVERLAP | S.p.; M.m
|
| Database | gene | update | reason
|
| SGD | YHR020W | removed chromatin organization added prolyl-tRNA aminoacylation | legacy annotation
|
translation (Term 1)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006412 | GO:0006310 | DNA recombination | GO:0000018 OR GO:0006417 (regulation of translation OR regulation of DNA recombination) | S.p.; M.m {2 ISO's from human to fix}; S.c
|
| GO:0006412 | GO:0006281 | DNA repair | NO_OVERLAP | S.p.; S.c {4 KW mapping queries and 1 annotation queries}; M.m {6 mappings ans 1 annotations to query}
|
| GO:0006412 | GO:0006260 | DNA replication | LOTS IN MOUSE | S.p.
|
| GO:0006412 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p; S.c; M.m {n/a}
|
| GO:0006412 | GO:0005975 | carbohydrate metabolic process | LOTS | -
|
| GO:0006412 | GO:0007155 | cell adhesion | LOTS IN MOUSE | S.p.
|
| GO:0006412 | GO:0006520 | cellular amino acid metabolic process | SEE ABOVE | -
|
| GO:0006412 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0006412 | GO:0016568 | chromatin modification | LOTS | -
|
| GO:0006412 | GO:0051276 | chromosome organization | LOTS IN MOUSE | -
|
| GO:0006412 | GO:0007059 | chromosome segregation | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0006412 | GO:0051186 | cofactor metabolic process | LOTS IN MOUSE | S.p. {except fusion protein}
|
| GO:0006412 | GO:0000747 | conjugation with cellular fusion | GO:0007165 | S.p; S.c {DHH1 query} M.m
|
| GO:0006412 | GO:0000910 | cytokinesis | GO:0018444 (translation release factor complex) | S.p; S.c; M.m
|
| GO:0006412 | GO:0007010 | cytoskeleton organization | LOTS, POSSIBLY ALL SIGNAL TRANSDUCTION | -
|
| GO:0006412 | GO:0007163 | establishment or maintenance of cell polarity | GO:0007165 (signal transduction) | S.p.; M.m
|
| GO:0006412 | GO:0006091 | generation of precursor metabolites and energy | GO:0007165 (signal transduction) | S.p. {pending updates, except fusion protein}
|
| GO:0006412 | GO:0006629 | lipid metabolic process | LOTS IN MOUSE, POSSIBLY ALL SIGNAL TRANSDUCTION | -
|
| GO:0006412 | GO:0016071 | mRNA metabolic process | LOTS IN MOUSE | -
|
| GO:0006412 | GO:0007126 | meiosis | LOTS IN MOUSE (mainly signal transduction) | S.p.
|
| GO:0006412 | GO:0007005 | mitochondrion organization | LOTS, mitochondrial translation | -
|
| GO:0006412 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0006412 | GO:0055086 | nucleobase-containing small molecule metabolic process | MOUSE LOTS | -
|
| GO:0006412 | GO:0006913 | nucleocytoplasmic transport | LOTS | -
|
| GO:0006412 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006412 | GO:0030163 | protein catabolic process | MOUSE LOTS | S.p; S.c
|
| GO:0006412 | GO:0006461 | protein complex assembly | MOUSE LOTS | -
|
| GO:0006412 | GO:0006457 | protein folding | LOTS | -
|
| GO:0006412 | GO:0006486 | protein glycosylation | NO_OVERLAP | S.p; S.c; M.m {ontology parentage of glycosylation pending} |
|
| GO:0006412 | GO:0051604 | protein maturation | LOTS | -
|
| GO:0006412 | GO:0070647 | protein modification by small protein conjugation or removal | LOTS | -
|
| GO:0006412 | GO:0006605 | protein targeting | NO_OVERLAP | S.p. pending fixes
|
| GO:0006412 | GO:0007346 | regulation of mitotic cell cycle | LOTS, probably all signal transduction | -
|
| GO:0006412 | GO:0042254 | ribosome biogenesis | LOTS | -
|
| GO:0006412 | GO:0023052 | signaling | LOTS | -
|
| GO:0006412 | GO:0006399 | tRNA metabolic process | LOTS | -
|
| GO:0006412 | GO:0006351 | transcription DNA-dependent | LOTS | -
|
| GO:0006412 | GO:0055085 | transmembrane transport | MOUSE LOTS CHECK AFTER ONTOLOGY UPDATE | S.p. (pending updates)
|
| GO:0006412 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0006412 | GO:0016192 | vesicle-mediated transport | MOUSE LOTS | S.p.
|
| GO:0006412 | GO:0006766 | vitamin metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
translation annotation updates
| Database | gene | update | reason
|
| SGD | SSL1 | removed translation initiation | legacy annotation - translation initiation isn't mentioned in any literature of the past decade (including papers from the authors who first made the conclusion)
|
| SGD | PAT1 | removed chromosome segregation | downstream effect
|
| SGD | DHH1 | removed cell morphogenesis involved in conjugation with cellular fusion | downstream effect
|
| SGD | MKT1 | positive regulation of translation | incorrect annotation
|
| PomBase? | pab1 | removed regulation of cytoplasmic translation ISO SGD:S000003158 | SGD no longer has this annotation
|
| SPAC8F11.04 | - | mapping to translation from IPR002143 | removed
|
ribosome biogenesis (Term 1)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0042254 | GO:0006310 | DNA recombination | GO:0000018 (regulation of DNA recombination) | S.p.; S.c; M.m
|
| GO:0042254 | GO:0006281 | DNA repair | GO:0031080 | S.p.; S.c
|
| GO:0042254 | GO:0006260 | DNA replication | LOTS | -
|
| GO:0042254 | GO:0030437 | ascospore formation | GO:0023052 (signaling, upstream) | S.p; S.c; M.m {n/a}
|
| GO:0042254 | GO:0005975 | carbohydrate metabolic process | GO:0023052 (signaling, upstream) | S.p.
|
| GO:0042254 | GO:0007155 | cell adhesion | MOUSE LOTS | S.p; S.c
|
| GO:0042254 | GO:0006520 | cellular amino acid metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0042254 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p.; S.c; M.m {n/a}
|
| GO:0042254 | GO:0016568 | chromatin modification | LOTS | -
|
| GO:0042254 | GO:0051276 | chromosome organization | LOTS | -
|
| GO:0042254 | GO:0007059 | chromosome segregation | LOTS | -
|
| GO:0042254 | GO:0051186 | cofactor metabolic process | LATER | -
|
| GO:0042254 | GO:0000747 | conjugation with cellular fusion | LATER | -
|
| GO:0042254 | GO:0000910 | cytokinesis | LATER, NOP15 | -
|
| GO:0042254 | GO:0002181 | cytoplasmic translation | SEE ABOVE | -
|
| GO:0042254 | GO:0007010 | cytoskeleton organization | LOTS | -
|
| GO:0042254 | GO:0007163 | establishment or maintenance of cell polarity | LATER | S.p.
|
| GO:0042254 | GO:0006091 | generation of precursor metabolites and energy | GO:0023052 (signaling, upstream) | S.p.; S.c; M.m
|
| GO:0042254 | GO:0006629 | lipid metabolic process | LATER GO:0019216 (regulation of lipid metabolic process) | S.p.; S.c.
|
| GO:0042254 | GO:0016071 | mRNA metabolic process | MOUSE LOTS | -
|
| GO:0042254 | GO:0007126 | meiosis | GO:0023052 (signaling, upstream) | Sp; S.c. M.m
|
| GO:0042254 | GO:0007005 | mitochondrion organization | LOTS | -
|
| GO:0042254 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | M.m; S.p; S.c
|
| GO:0042254 | GO:0055086 | nucleobase-containing small molecule metabolic process | LOTS | -
|
| GO:0042254 | GO:0006913 | nucleocytoplasmic transport | LOTS | -
|
| GO:0042254 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0042254 | GO:0030163 | protein catabolic process | LATER | S.p.
|
| GO:0042254 | GO:0006461 | protein complex assembly | MOUSE LOTS | -
|
| GO:0042254 | GO:0006457 | protein folding | LATER S. c overlaps | S.p.
|
| GO:0042254 | GO:0006486 | protein glycosylation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0042254 | GO:0051604 | protein maturation | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0042254 | GO:0070647 | protein modification by small protein conjugation or removal | LATER | -
|
| GO:0042254 | GO:0006605 | protein targeting | LATER | -
|
| GO:0042254 | GO:0007346 | regulation of mitotic cell cycle | LATER | -
|
| GO:0042254 | GO:0023052 | signaling | LATER | -
|
| GO:0042254 | GO:0006399 | tRNA metabolic process | SEE ABOVE | -
|
| GO:0042254 | GO:0006351 | transcription DNA-dependent | LOTS | -
|
| GO:0042254 | GO:0055085 | transmembrane transport | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0042254 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p.; S.c; M.m.
|
| GO:0042254 | GO:0016192 | vesicle-mediated transport | LATER | S.p.
|
| GO:0042254 | GO:0006766 | vitamin metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
transmembrane transport (Term 1)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0055085 | GO:0006310 | DNA recombination | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0055085 | GO:0006281 | DNA repair | MOUSE HAS LOTS CHECK LATER | S.p.; S.c
|
| GO:0055085 | GO:0006260 | DNA replication | MOUSE HAS LOTS CHECK LATER | S.p.; S.c.
|
| GO:0055085 | GO:0030437 | ascospore formation | S. C LATER | S.p.; M.m(n/a)
|
| GO:0055085 | GO:0005975 | carbohydrate metabolic process | LOTS | -
|
| GO:0055085 | GO:0007155 | cell adhesion | MOUSE HAS LOTS CHECK LATER | S.p.; S.c.
|
| GO:0055085 | GO:0006520 | cellular amino acid metabolic process | LOTS | -
|
| GO:0055085 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0055085 | GO:0016568 | chromatin modification | NO_OVERLAP | S.p.; S.c; {11 MOUSE BUT SHOULD STOP WHEN ONTOLOGY FIXED}
|
| GO:0055085 | GO:0051276 | chromosome organization | MOUSE HAS LOTS | -
|
| GO:0055085 | GO:0007059 | chromosome segregation | 4 MOUSE BUT THESE MIGHT DISAPPEAR | S.p.; S.c
|
| GO:0055085 | GO:0051186 | cofactor metabolic process | S.C LOTS, LATER | S.p.
|
| GO:0055085 | GO:0000747 | conjugation with cellular fusion | LATER | -
|
| GO:0055085 | GO:0000910 | cytokinesis | GO:0023052 (signaling, upstream) | S.p; S.c; m.m
|
| GO:0055085 | GO:0002181 | cytoplasmic translation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0055085 | GO:0007010 | cytoskeleton organization | MOUSE LOTS | S.p.; S.c;
|
| GO:0055085 | GO:0007163 | establishment or maintenance of cell polarity | MOUSE LOTS | S.p.
|
| GO:0055085 | GO:0006091 | generation of precursor metabolites and energy | MOUSE LOTS | -
|
| GO:0055085 | GO:0006629 | lipid metabolic process | MOUSE LOTS | -
|
| GO:0055085 | GO:0016071 | mRNA metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0055085 | GO:0007126 | meiosis | LATER | S.p.
|
| GO:0055085 | GO:0007005 | mitochondrion organization | LOTS | -
|
| GO:0055085 | GO:0071941 | nitrogen cycle metabolic process | LATER | -
|
| GO:0055085 | GO:0055086 | nucleobase-containing small molecule metabolic process | LATER | -
|
| GO:0055085 | GO:0006913 | nucleocytoplasmic transport | allow protein folding (S.c. SSA1) | S.p; S.c. M.m {pending ontology changes}
|
| GO:0055085 | GO:0007031 | peroxisome organization | LOTS | -
|
| GO:0055085 | GO:0030163 | protein catabolic process | LOTS GO:0005784 (check again) | S.p;
|
| GO:0055085 | GO:0006461 | protein complex assembly | LOTS | -
|
| GO:0055085 | GO:0006457 | protein folding | LOTS CHECK | -
|
| GO:0055085 | GO:0006486 | protein glycosylation | LOTS | -
|
| GO:0055085 | GO:0051604 | protein maturation | LATER | -
|
| GO:0055085 | GO:0070647 | protein modification by small protein conjugation or removal | LATER | -
|
| GO:0055085 | GO:0006605 | protein targeting | LOTS | -
|
| GO:0055085 | GO:0007346 | regulation of mitotic cell cycle | LOTS | -
|
| GO:0055085 | GO:0042254 | ribosome biogenesis | SEE ABOVE | -
|
| GO:0055085 | GO:0023052 | signaling | LATER | -
|
| GO:0055085 | GO:0006399 | tRNA metabolic process | SEE ABOVE | S.p.
|
| GO:0055085 | GO:0006351 | transcription DNA-dependent | LOTS | -
|
| GO:0055085 | GO:0007033 | vacuole organization | LATER | S.p.
|
| GO:0055085 | GO:0016192 | vesicle-mediated transport | LOTS | -
|
| GO:0055085| GO:0006766 | vitamin metabolic process | LATER | -
|
transmembrane transport annotation updates
| Database | gene | update | reason
|
| SGD | MRS4 | removed RNA splicing | legacy annotation
|
| SGD | AAC3 | removed heme biosynthetic process | downstream process
|
| Pombase | yts12 | removed protein catabolic process IEA IPR005936
|
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006766 | GO:0006310 | DNA recombination | NO_OVERLAP | S.p.; S.c; M.m {1, looks dodgy ifn2 same paper as snai2 below}
|
| GO:0006766 | GO:0006281 | DNA repair | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0006260 | DNA replication | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p.; S.c; M.m (n/a)
|
| GO:0006766 | GO:0005975 | carbohydrate metabolic process | MOUSE LOTS | S.p.
|
| GO:0006766 | GO:0007155 | cell adhesion | LATER | S.p.; S.c
|
| GO:0006766 | GO:0006520 | cellular amino acid metabolic process | LATER | -
|
| GO:0006766 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0016568 | chromatin modification | NO_OVERLAP | S.p.; M.m {1, looks dodgy, Snai2}
|
| GO:0006766 | GO:0051276 | chromosome organization | NO_OVERLAP | S.p.; S.c; M.m {1, looks dodgy, Snai2}
|
| GO:0006766 | GO:0007059 | chromosome segregation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0051186 | cofactor metabolic process | LOTS | -
|
| GO:0006766 | GO:0000747 | conjugation with cellular fusion | NO_OVERLAP | S.p.; S.c; M.m {n/a}
|
| GO:0006766 | GO:0000910 | cytokinesis | NO_OVERLAP | S.p.; M.m; S.c
|
| GO:0006766 | GO:0002181 | cytoplasmic translation | NO_OVERLAP | S.p.; S.c.; M.m
|
| GO:0006766 | GO:0007010 | cytoskeleton organization | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0007163 | establishment or maintenance of cell polarity | NO_OVERLAP | S.p.; M.m; S.c
|
| GO:0006766 | GO:0006091 | generation of precursor metabolites and energy | NO_OVERLAP | S.p.; M.m; S.c
|
| GO:0006766 | GO:0006629 | lipid metabolic process | MOUSE LOTS | S.p.
|
| GO:0006766 | GO:0016071 | mRNA metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0007126 | meiosis | LATER | S.p.; S.c
|
| GO:0006766 | GO:0007005 | mitochondrion organization | NO_OVERLAP | S.p.; M.m
|
| GO:0006766 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | M.m.; S.c; S.p
|
| GO:0006766 | GO:0055086 | nucleobase-containing small molecule metabolic process | LATER | -
|
| GO:0006766 | GO:0006913 | nucleocytoplasmic transport | NO_OVERLAP | S.p.; S.c; M.m {4 but snai2 and Ifng look dodgy}
|
| GO:0006766 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0030163 | protein catabolic process | GO:0070647 (glutamate-cycteine ligase activity) | S.p.; S.c; M.m {2 but look dodgy}
|
| GO:0006766 | GO:0006461 | protein complex assembly | NO_OVERLAP | S.p.; S.c; M.m {2 look dodgy}
|
| GO:0006766 | GO:0006457 | protein folding | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0006486 | protein glycosylation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0051604 | protein maturation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0070647 | protein modification by small protein conjugation or removal | GO:0070647 (glutamate-cycteine ligase activity) | S.p.; S.c; M.m
|
| GO:0006766 | GO:0006605 | protein targeting | NO_OVERLAP | S.p.; S.c; M.m {5 but look dodgy}
|
| GO:0006766 | GO:0007346 | regulation of mitotic cell cycle | NO_OVERLAP | S.p.; S.c; M.m {except tnf, check}
|
| GO:0006766 | GO:0042254 | ribosome biogenesis | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0023052 | signaling | MOUSE LOTS | S.p.; S.c
|
| GO:0006766 | GO:0006399 | tRNA metabolic process | SEE ABOVE | -
|
| GO:0006766 | GO:0006351 | transcription DNA-dependent | MOUSE LOTS | S.p.
|
| GO:0006766 | GO:0055085 | transmembrane transport | MOUSE LOTS | S.p.
|
| GO:0006766 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006766 | GO:0016192 | vesicle-mediated transport | NO_OVERLAP | S.p.; S.c; M.m
|
regulation of mitotic cell cycle (Term 1)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0007346 | GO:0006310 | DNA recombination | - | -
|
| GO:0007346 | GO:0006281 | DNA repair | - | -
|
| GO:0007346 | GO:0006260 | DNA replication | - | -
|
| GO:0007346 | GO:0030437 | ascospore formation | - | -
|
| GO:0007346 | GO:0005975 | carbohydrate metabolic process | NO_OVERLAP | S.p.
|
| GO:0007346 | GO:0007155 | cell adhesion | NO_OVERLAP | S.p.
|
| GO:0007346 | GO:0006520 | cellular amino acid metabolic process | NO_OVERLAP | S.p.
|
| GO:0007346 | GO:0071554 | cell wall organization or biogenesis | - | -
|
| GO:0007346 | GO:0016568 | chromatin modification | - | -
|
| GO:0007346 | GO:0051276 | chromosome organization | - | -
|
| GO:0007346 | GO:0007059 | chromosome segregation | - | -
|
| GO:0007346 | GO:0051186 | cofactor metabolic process | NO_OVERLAP | S.p.
|
| GO:0007346 | GO:0000747 | conjugation with cellular fusion | - | -
|
| GO:0007346 | GO:0000910 | cytokinesis | - | -
|
| GO:0007346 | GO:0002181 | cytoplasmic translation | - | M.m
|
| GO:0007346 | GO:0007010 | cytoskeleton organization | - | -
|
| GO:0007346 | GO:0007163 | establishment or maintenance of cell polarity | - | -
|
| GO:0007346 | GO:0006091 | generation of precursor metabolites and energy | NO_OVERLAP | S.p.
|
| GO:0007346 | GO:0006629 | lipid metabolic process | - | -
|
| GO:0007346 | GO:0016071 | mRNA metabolic process | - | -
|
| GO:0007346 | GO:0007126 | meiosis | - | -
|
| GO:0007346 | GO:0007005 | mitochondrion organization | S.c | -
|
| GO:0007346 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | S.p.; S.c.; ;M.m
|
| GO:0007346 | GO:0055086 | nucleobase-containing small molecule metabolic process | - | -
|
| GO:0007346 | GO:0006913 | nucleocytoplasmic transport | - | -
|
| GO:0007346 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0007346 | GO:0030163 | protein catabolic process | - | -
|
| GO:0007346 | GO:0006461 | protein complex assembly | - | -
|
| GO:0007346 | GO:0006457 | protein folding | - | M.m
|
| GO:0007346 | GO:0006486 | protein glycosylation | - | S.p; S.c; M.m
|
| GO:0007346 | GO:0051604 | protein maturation | NO_OVERLAP | S.p.; S.c.
|
| GO:0007346 | GO:0070647 | protein modification by small protein conjugation or removal | - | -
|
| GO:0007346 | GO:0006605 | protein targeting | - | -
|
| GO:0007346 | GO:0007346 | regulation of mitotic cell cycle | - | -
|
| GO:0007346 | GO:0042254 | ribosome biogenesis | - | -
|
| GO:0007346 | GO:0023052 | signaling | - | -
|
| GO:0007346 | GO:0006399 | tRNA metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0007346 | GO:0006351 | transcription DNA-dependent | - | -
|
| GO:0007346 | GO:0055085 | transmembrane transport | - | (S.p.- one annotation, checking)
|
| GO:0007346 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p.; M.m
|
| GO:0007346 | GO:0016192 | vesicle-mediated transport | - | -
|
| GO:0007346 | GO:0006766 | vitamin metabolic process | - | S.p. ; S.c
|
DNA repair (Term 1)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006281 | GO:0006310 | DNA recombination | - | -
|
| GO:0006281 | GO:0006281 | DNA repair | - | -
|
| GO:0006281 | GO:0006260 | DNA replication | - | -
|
| GO:0006281 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p.; M.m (n/a)
|
| GO:0006281 | GO:0005975 | carbohydrate metabolic process | - | S.p.
|
| GO:0006281 | GO:0007155 | cell adhesion | NO_OVERLAP | S.p.
|
| GO:0006281 | GO:0006520 | cellular amino acid metabolic process | - | S.c; M.m
|
| GO:0006281 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p.
|
| GO:0006281 | GO:0016568 | chromatin modification | - | -
|
| GO:0006281 | GO:0051276 | chromosome organization | - | -
|
| GO:0006281 | GO:0007059 | chromosome segregation | - | -
|
| GO:0006281 | GO:0051186 | cofactor metabolic process | NO_OVERLAP | S.p.; S.c
|
| GO:0006281 | GO:0000747 | conjugation with cellular fusion | NO_OVERLAP | S.p.; S.c; M.m (n/a)
|
| GO:0006281 | GO:0000910 | cytokinesis | NO_OVERLAP | S.p.
|
| GO:0006281 | GO:0002181 | cytoplasmic translation | NO_OVERLAP | S.p; M.m
|
| GO:0006281 | GO:0007010 | cytoskeleton organization | - | -
|
| GO:0006281 | GO:0007163 | establishment or maintenance of cell polarity | NO_OVERLAP | S.p.
|
| GO:0006281 | GO:0006091 | generation of precursor metabolites and energy | NO_OVERLAP | S.p.; S.c
|
| GO:0006281 | GO:0006629 | lipid metabolic process | NO_OVERLAP | S.p.
|
| GO:0006281 | GO:0016071 | mRNA metabolic process | - | -
|
| GO:0006281 | GO:0007126 | meiosis | - | -
|
| GO:0006281 | GO:0007005 | mitochondrion organization | - | -
|
| GO:0006281 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006281 | GO:0055086 | nucleobase-containing small molecule metabolic process | - | -
|
| GO:0006281 | GO:0006913 | nucleocytoplasmic transport | GO:0031080 | -
|
| GO:0006281 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p. ; S.c; M.m
|
| GO:0006281 | GO:0030163 | protein catabolic process | - | -
|
| GO:0006281 | GO:0006461 | protein complex assembly | - | -
|
| GO:0006281 | GO:0006457 | protein folding | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006281 | GO:0006486 | protein glycosylation | - | S.p.; S.c
|
| GO:0006281 | GO:0051604 | protein maturation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006281 | GO:0070647 | protein modification by small protein conjugation or removal | - | -
|
| GO:0006281 | GO:0006605 | protein targeting | - | S.p.
|
| GO:0006281 | GO:0007346 | regulation of mitotic cell cycle | - | -
|
| GO:0006281 | GO:0042254 | ribosome biogenesis | - | S.p.
|
| GO:0006281 | GO:0023052 | signaling | - | -
|
| GO:0006281 | GO:0006399 | tRNA metabolic process | - check s.c | S.p.; M.m
|
| GO:0006281 | GO:0006351 | transcription DNA-dependent | - | -
|
| GO:0006281 | GO:0055085 | transmembrane transport | NO_OVERLAP | S.p.; S.c; M.m (3 bad mappings)
|
| GO:0006281 | GO:0007033 | vacuole organization | - | S.p.; M.m
|
| GO:0006281 | GO:0016192 | vesicle-mediated transport | NO_OVERLAP | S.p.; M.m (4 mappings to remove)
|
| GO:0006281 | GO:0006766 | vitamin metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
DNA replication (Term 1)
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006260 | GO:0006310 | DNA recombination | - | -
|
| GO:0006260 | GO:0006281 | DNA repair | - | -
|
| GO:0006260 | GO:0006260 | DNA replication | - | -
|
| GO:0006260 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p.; M.m (n/a)
|
| GO:0006260 | GO:0005975 | carbohydrate metabolic process | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0007155 | cell adhesion | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006260 | GO:0006520 | cellular amino acid metabolic process | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0016568 | chromatin modification | - | -
|
| GO:0006260 | GO:0051276 | chromosome organization | - |
|
| GO:0006260 | GO:0007059 | chromosome segregation | - | -
|
| GO:0006260 | GO:0051186 | cofactor metabolic process | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0000747 | conjugation with cellular fusion | - | M.m
|
| GO:0006260 | GO:0000910 | cytokinesis | NO_OVERLAP | S.p.; S.c
|
| GO:0006260 | GO:0002181 | cytoplasmic translation | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006260 | GO:0007010 | cytoskeleton organization | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0007163 | establishment or maintenance of cell polarity | NO_OVERLAP | S.p.; S.c
|
| GO:0006260 | GO:0006091 | generation of precursor metabolites and energy | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0006629 | lipid metabolic process | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0016071 | mRNA metabolic process | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0007126 | meiosis | - | -
|
| GO:0006260 | GO:0007005 | mitochondrion organization | - | -
|
| GO:0006260 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | S.p.
|
| GO:0006260 | GO:0055086 | nucleobase-containing small molecule metabolic process | - | -
|
| GO:0006260 | GO:0006913 | nucleocytoplasmic transport | NO_OVERLAP | ??; S.c
|
| GO:0006260 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p.; S.c: M.m
|
| GO:0006260 | GO:0030163 | protein catabolic process | - | -
|
| GO:0006260 | GO:0006461 | protein complex assembly | - | -
|
| GO:0006260 | GO:0006457 | protein folding | - | -
|
| GO:0006260 | GO:0006486 | protein glycosylation | NO_OVERLAP | S.p.; S.c
|
| GO:0006260 | GO:0051604 | protein maturation | - | -
|
| GO:0006260 | GO:0070647 | protein modification by small protein conjugation or removal | - | -
|
| GO:0006260 | GO:0006605 | protein targeting | NO_OVERLAP | S.p.;
|
| GO:0006260 | GO:0007346 | regulation of mitotic cell cycle | - | -
|
| GO:0006260 | GO:0042254 | ribosome biogenesis | NO_OVERLAP | S.p.;M.m
|
| GO:0006260 | GO:0023052 | signaling | - | -
|
| GO:0006260 | GO:0006399 | tRNA metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006260 | GO:0006351 | transcription DNA-dependent | - | -
|
| GO:0006260 | GO:0055085 | transmembrane transport | NO_OVERLAP | S.p.; S.c; M.m
|
| GO:0006260 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p.; M.m
|
| GO:0006260 | GO:0016192 | vesicle-mediated transport | NO_OVERLAP | S.p.; M.m
|
| GO:0006260 | GO:0006766 | vitamin metabolic process | NO_OVERLAP | S.p.; S.c; M.m
|
DNA replication annotation updates
| Database | gene | update | reason
|
| SGD | TRX1 | removed regulation of DNA replication | legacy annotation
|
| SGD | TRX2 | removed regulation of DNA replication | legacy annotation
|
| PomBase? | trx1 | regulation of DNA-dependent DNA replication | removed unsupported ISO
|
| term ID 1 | term ID 2 | term name 2 | Exceptions GO:xxxxxxx (comments free text) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0005975 | GO:0006310 | DNA recombination | - | S.p
|
| GO:0005975 | GO:0006281 | DNA repair | - | S.p
|
| GO:0005975 | GO:0006260 | DNA replication | - | S.p
|
| GO:0005975 | GO:0030437 | ascospore formation | - | -
|
| GO:0005975 | GO:0005975 | carbohydrate metabolic process | - | -
|
| GO:0005975 | GO:0007155 | cell adhesion | - | S.p
|
| GO:0005975 | GO:0006520 | cellular amino acid metabolic process | - | -
|
| GO:0005975 | GO:0071554 | cell wall organization or biogenesis | - | -
|
| GO:0005975 | GO:0016568 | chromatin modification | - | S.p
|
| GO:0005975 | GO:0051276 | chromosome organization | - | S.p
|
| GO:0005975 | GO:0007059 | chromosome segregation | UPSTREAM REGULATORS OF BOTH | S.p S.c: M.m
|
| GO:0005975 | GO:0051186 | cofactor metabolic process | - | -
|
| GO:0005975 | GO:0000747 | conjugation with cellular fusion | - | -
|
| GO:0005975 | GO:0000910 | cytokinesis | - | -
|
| GO:0005975 | GO:0002181 | cytoplasmic translation | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0005975 | GO:0007010 | cytoskeleton organization | - | -
|
| GO:0005975 | GO:0007163 | establishment or maintenance of cell polarity | - | -
|
| GO:0005975 | GO:0006091 | generation of precursor metabolites and energy | - | -
|
| GO:0005975 | GO:0006629 | lipid metabolic process | - | -
|
| GO:0005975 | GO:0016071 | mRNA metabolic process | UPSTREAM REGULATORS OF BOTH | S.p; S.c; M.m
|
| GO:0005975 | GO:0007126 | meiosis | - | -
|
| GO:0005975 | GO:0007005 | mitochondrion organization | - | S.p ; S.c
|
| GO:0005975 | GO:0071941 | nitrogen cycle metabolic process | upstream regulation of both | S.p.; S.c; M.m
|
| GO:0005975 | GO:0055086 | nucleobase-containing small molecule metabolic process | - | -
|
| GO:0005975 | GO:0006913 | nucleocytoplasmic transport | LOTS OF MOUSE TO CHECK | S.p; S.c (REMOVE INTERPRO MAPPINGS FOR SOL1 & 2)
|
| GO:0005975 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0005975 | GO:0030163 | protein catabolic process | - | -
|
| GO:0005975 | GO:0006461 | protein complex assembly | - | S.p
|
| GO:0005975 | GO:0006457 | protein folding | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0005975 | GO:0006486 | protein glycosylation | - | -
|
| GO:0005975 | GO:0051604 | protein maturation | - | S.p.; S.c
|
| GO:0005975 | GO:0070647 | protein modification by small protein conjugation or removal | - | S.p
|
| GO:0005975 | GO:0006605 | protein targeting | - | -
|
| GO:0005975 | GO:0007346 | regulation of mitotic cell cycle | - | -
|
| GO:0005975 | GO:0042254 | ribosome biogenesis | - | S.p, M.m
|
| GO:0005975 | GO:0023052 | signaling | - | -
|
| GO:0005975 | GO:0006399 | tRNA metabolic process | NO_OVERLAP | S.p; S.c; M.m
|
| GO:0005975 | GO:0006351 | transcription DNA-dependent | - | -
|
| GO:0005975 | GO:0055085 | transmembrane transport | - | S.p.; S.c
|
| GO:0005975 | GO:0007033 | vacuole organization | - | S.p
|
| GO:0005975 | GO:0016192 | vesicle-mediated transport | - | -
|
| GO:0005975 | GO:0006766 | vitamin metabolic process | - | S.p; S.c recheck for mouse after ascorbic acid parentage fixed
|
queries to SGD
mail SGD
the following transporters are all annotated to carbohydrate metabolism. Is this indirect?
MPH3, MPH2, GAL2, YEA4, MAL31 , MAL11
query MDH2 protein import into peroxisome matrix
Protein glycosylation
| term ID 1 | term ID 2 | term name 2 | Exceptions GO:xxxxxxx (comments free text) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006486 | GO:0006310 | DNA recombination | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006281 | DNA repair | NO_OVERLAP | S.p; S.c
|
| GO:0006486 | GO:0006260 | DNA replication | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0030437 | ascospore formation | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0005975 | carbohydrate metabolic process | LOTS (makes sense - Is_a relationship between them) | -
|
| GO:0006486 | GO:0007155 | cell adhesion | - | -
|
| GO:0006486 | GO:0006520 | cellular amino acid metabolic process | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0071554 | cell wall organization or biogenesis | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0016568 | chromatin modification | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0051276 | chromosome organization | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007059 | chromosome segregation | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0051186 | cofactor metabolic process | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0000747 | conjugation with cellular fusion | NO_OVERLAP (actually 3 but see notes) | S.p;
|
| GO:0006486 | GO:0000910 | cytokinesis | NO_OVERLAP (see notes) | -
|
| GO:0006486 | GO:0002181 | cytoplasmic translation | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007010 | cytoskeleton organization | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007163 | establishment or maintenance of cell polarity | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006091 | generation of precursor metabolites and energy | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006629 | lipid metabolic process | - | -
|
| GO:0006486 | GO:0016071 | mRNA metabolic process | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007126 | meiosis | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007005 | mitochondrion organization | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0071941 | nitrogen cycle metabolic process | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0055086 | nucleobase-containing small molecule metabolic process | - | -
|
| GO:0006486 | GO:0006913 | nucleocytoplasmic transport | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007031 | peroxisome organization | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0030163 | protein catabolic process | - | -
|
| GO:0006486 | GO:0006461 | protein complex assembly | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006457 | protein folding | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0051604 | protein maturation | NO_OVERLAP (none in pombe but probably should….) | S.p;
|
| GO:0006486 | GO:0070647 | protein modification by small protein conjugation or removal | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006605 | protein targeting | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0007346 | regulation of mitotic cell cycle | - | -
|
| GO:0006486 | GO:0042254 | ribosome biogenesis | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0023052 | signaling | - | -
|
| GO:0006486 | GO:0006399 | tRNA metabolic process | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006351 | transcription, DNA-dependent | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0055085 | transmembrane transport | - | -
|
| GO:0006486 | GO:0007033 | vacuole organization | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0016192 | vesicle-mediated transport | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006766 | vitamin metabolic process | NO_OVERLAP | S.p;
|
Protein glycosylation updates
| database | gene | update | reason
|
| PomBase? | gms1 | protein galactosylation | indirect, phenotype only
|
| PomBase? | gms1 | conjugation with cellular fusion | indirect, phenotype only
|
| PomBase? | gms1 | galactose metabolic process | indirect, phenotype only
|
| PomBase? | gms1 | oligosaccharide metabolic process | indirect, phenotype only
|
| PomBase? | gms1 | galactomannan biosynthetic process | indirect, phenotype only
|
| PomBase? | gms1 | negative regulation of coflocculation via protein-carbohydrate interaction | indirect, phenotype only
|
| PomBase? | ogm1 | agglutination involved in conjugation with cellular fusion | indirect, phenotype only
|
| PomBase? | ogm4 | agglutination involved in conjugation with cellular fusion | indirect, phenotype only
|
| PomBase? | ogm1 | barrier septum assembly involved in cell cycle cytokinesis | indirect, phenotype only
|
| PomBase? | ogm4 | barrier septum assembly involved in cell cycle cytokinesis | indirect, phenotype only
|
| PomBase? | mpg4 | Pending Val | These are involved in the maturation of cell wall proteins in the ER so cytokinesis defects should be indirect and phenotype annotation?
|
| PomBase? (ISS) + cerevisiae | alg1 | Pending Val | lipid metabolic process - alg1 is involved in oligo-saccharide-lipid intermediate biosynthetic process. This I think is upstream of protein N-linked glycosylation (i.e. you synthesise the molecule that is going to be added to a protein, then a separate process actually adds it to the protein) (Check the 1983 reference)
|
| PomBase? | gp114 | Pending Val | lipid metabolic process - Does this attach the mannosyl residues to the protein or to the GPI anchor before it has been transferred to a protein? If the latter then the protein glycosylation term should be removed
|
| PomBase? | gpt2 | Pending Val | Protein N-linked glycosylation / N glycan processing – I think this protein is involved in the upstream process of synthesiszing a lipid-linked intermediate so should be annotated to a child of lipid metabolic process (is dolichyl Diphosphate biosynthetic process correct?)
|
| PomBase? | SPAC4D7.04c | Pending Val | I think this acts upstream from protein glycosylation in dolichol biosynthesis, but SGD has this as an IDA so check that reference
|
Nucleocytoplasmic transport
| term ID 1 | term ID 2 | term name 2 | Exceptions GO:xxxxxxx (comments free text) | checked in species S.p; etc {comments in curly brackets}
|
| GO:0006486 | GO:0006310 | DNA recombination | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006281 | DNA repair | NO_OVERLAP | S.p;
|
| GO:0006486 | GO:0006260 | DNA replication | NO_OVERLAP |
|
Nucleocytoplasmic transport updates
database | gene | update | reason
| PomBase? | ptr8 | nucleocytoplasmic transport | indirect, phenotype only accumulation not export
| | PomBase? | top2 | nucleocytoplasmic transport | indirect, phenotype only accumulation not export
|
'Cell wall organization or biogenesis
| term ID 1 | term ID 2 | term name 2 | Exceptions GO:xxxxxxx (comments free text) | checked in species S.p; etc {comments in curly brackets}
|
Cell wall organization or biogenesis updates
| database | gene | update | reason
| | PomBase? | act1 | cell wall org and biogenesis | indirect, (transport)
|
Misc sub processes
| term ID 1 | term ID 2 | term name 2 | exceptions format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) | checked in species S.p; etc {comments in curly brackets}
| | GO:0010498 | GO:0006914 | see PMID:22817709 | NO_OVERLAP | S.p.; S.c;
|
Template for process specific tables
| GO:0006310 | DNA recombination | - | -
| | GO:0006281 | DNA repair | - | -
| | GO:0006260 | DNA replication | - | -
| | GO:0030437 | ascospore formation | - | -
| | GO:0005975 | carbohydrate metabolic process | - | -
| | GO:0007155 | cell adhesion | - | -
| | GO:0006520 | cellular amino acid metabolic process | - | -
| | GO:0071554 | cell wall organization or biogenesis | - | -
| | GO:0016568 | chromatin modification | - | -
| | GO:0051276 | chromosome organization | - | -
| | GO:0007059 | chromosome segregation | - | -
| | GO:0051186 | cofactor metabolic process | - | -
| | GO:0000747 | conjugation with cellular fusion | - | -
| | GO:0000910 | cytokinesis | - | -
| | GO:0002181 | cytoplasmic translation | - | -
| | GO:0007010 | cytoskeleton organization | - | -
| | GO:0007163 | establishment or maintenance of cell polarity | - | -
| | GO:0006091 | generation of precursor metabolites and energy | - | -
| | GO:0006629 | lipid metabolic process | - | -
| | GO:0016071 | mRNA metabolic process | - | -
| | GO:0007126 | meiosis | - | -
| | GO:0007005 | mitochondrion organization | - | -
| | GO:0071941 | nitrogen cycle metabolic process | - | -
| | GO:0055086 | nucleobase-containing small molecule metabolic process | - | -
| | GO:0006913 | nucleocytoplasmic transport | - | -
| | GO:0007031 | peroxisome organization | - | -
| | GO:0030163 | protein catabolic process | - | -
| | GO:0006461 | protein complex assembly | - | -
| | GO:0006457 | protein folding | - | -
| | GO:0006486 | protein glycosylation | - | -
| | GO:0051604 | protein maturation | - | -
| | GO:0070647 | protein modification by small protein conjugation or removal | - | -
| | GO:0006605 | protein targeting | - | -
| | GO:0007346 | regulation of mitotic cell cycle | - | -
| | GO:0042254 | ribosome biogenesis | - | -
| | GO:0023052 | signaling | - | -
| | GO:0006399 | tRNA metabolic process | - | -
| | GO:0006351 | transcription DNA-dependent | - | -
| | GO:0055085 | transmembrane transport | - | -
| | GO:0007033 | vacuole organization | - | -
| | GO:0016192 | vesicle-mediated transport | - | -
| | GO:0006766 | vitamin metabolic process | - | -
|
Template to type into Matrix
GO:0006310
GO:0006281
GO:0006260
GO:0030437
GO:0005975
GO:0007155
GO:0006520
GO:0071554
GO:0016568
GO:0051276
GO:0007059
GO:0051186
GO:0000747
GO:0000910
GO:0002181
GO:0007010
GO:0007163
GO:0006091
GO:0006629
GO:0016071
GO:0007126
GO:0007005
GO:0071941
GO:0055086
GO:0006913
GO:0007031
GO:0030163
GO:0006461
GO:0006457
GO:0006486
GO:0051604
GO:0070647
GO:0006605
GO:0007346
GO:0042254
GO:0023052
GO:0006399
GO:0006351
GO:0055085
GO:0007033
GO:0016192
GO:0006766
to get rules
cat raw_rules.rtf |grep -v MOUSE | grep -v LATER | grep -v "SEE ABOVE" | grep -v LOTS | grep "GO:" | perl -pi -e 's/\|\|/,/g' | perl -pi -e 's/\(.*\)g' | cut -f 2,3,5 -d, | grep -v rm | perl -pi -e 's/, /,/g' | grep -v - >rules
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