wiki:MatrixProject

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)

Amino acid metabolism (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:0006520GO:0006310 DNA recombination NO_OVERLAP S.p; M.m; S.c.
GO:0006520GO: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:0006520GO:0006260 DNA replication NO_OVERLAP S.p; M. m {2 to report}; S.c {3 queried}
GO:0006520GO:0030437 ascospore formation NO_OVERLAP S.p; M.m {n/a}; S.c.
GO:0006520GO:0005975 carbohydrate metabolic process LATER S.p
GO:0006520GO: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:0006520GO: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:0006520GO: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:0006520GO: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:0006520GO:0007059 chromosome segregation GO:0023052 (signaling, upstream) S.p; M m.; S.c.
GO:0006520GO:0051186 cofactor metabolic process LATER S.p
GO:0006520GO:0000747 conjugation with cellular fusion NO_OVERLAP S.p; M.m {n/a}; S.c.
GO:0006520GO:0000910 cytokinesis NO_OVERLAP S.p; M.m {pending apc update uniprot}; S.c.
GO:0006520GO:0002181 cytoplasmic translation GO:0043039 (tRNA aminoacylation) S.p. M.m; S.c {NOTE check translation too}
GO:0006520GO:0007010 cytoskeleton organization GO:0023052 (signaling upstream) S.p; M.m; S.c.
GO:0006520GO:0007163 establishment or maintenance of cell polarity GO:0006355 (regulation of transcription DNA dependent) S.p; M.m.; S.c.
GO:0006520GO:0006091 generation of precursor metabolites and energy LATERS.p
GO:0006520GO: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:0006520GO:0016071 mRNA metabolic process NO_OVERLAP S.p; M.m {0 pending UniProt? feedback}; S.c.
GO:0006520GO:0007126 meiosis NO_OVERLAP S.p; M.m; S.c.
GO:0006520GO: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:0006520GO:0071941 nitrogen cycle metabolic process LATER S.p
GO:0006520GO:0055086 nucleobase-containing small molecule metabolic process LATER S.p
GO:0006520GO:0006913 nucleocytoplasmic transport NO_OVERLAP S.p; M.m {1 but should disappear pending response from Uniprot}
GO:0006520GO:0007031 peroxisome organization NO_OVERLAP S.p; M.m; S.c.
GO:0006520GO:0030163 protein catabolic process MOUSE LOTS GO:0006521 (regulation of amino acid metabolic process) S.p; S.c
GO:0006520GO:0006461 protein complex assembly MOUSE LOTS S.p; S.c
GO:0006520GO:0006457 protein folding NO_OVERLAP S.p; M.m {reported 1 anomaly to MGI}; S.c {queried 2 anomalies}
GO:0006520GO:0006486 protein glycosylation NO_OVERLAP S.p; S.c; M.m
GO:0006520GO:0051604 protein maturation NO_OVERLAP S.p;
GO:0006520GO: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:0006520GO:0006605 protein targeting NO_OVERLAPS.p; M.m; S.c
GO:0006520GO:0007346 regulation of mitotic cell cycle MOUSE LOTS S.p
GO:0006520GO:0042254 ribosome biogenesis NO_OVERLAP S.p; M.m; S.c.
GO:0006520GO:0023052 signaling LATER S.p; M.m; S.c
GO:0006520GO:0006399 tRNA metabolic process GO:0043039 OR GO:0031071 (tRNA aminoacylation OR cysteine desulphurase) S.p; M.m. S.c {some checks outstanding}
GO:0006520GO:0006351 transcription DNA-dependent GO:0006355 (regulation of transcription DNA dependent) S.p; M.m
GO:0006520GO:0055085 transmembrane transport MOUSE LOTS S.p; S.c {one ontology query}
GO:0006520GO:0007033 vacuole organization GO:0060627 (regulation of amino acid metabolism) S.p; S.c; M.m
GO:0006520GO: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:0006520GO: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}

Amino acid metabolism annotation updates

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
SGDGAP1ammonia 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 exocytosiserror
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

tRNA metabolic process (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:0006399GO:0006310 DNA recombination NO_OVERLAPS.p.; M.m
GO:0006399GO:0006281 DNA repair NO_OVERLAPS.p.; M.m.
GO:0006399GO:0006260 DNA replication NO_OVERLAP S.p.; M.m
GO:0006399GO:0030437 ascospore formation NO_OVERLAP S.p. M.m {n/a}
GO:0006399GO:0005975 carbohydrate metabolic process NO_OVERLAP S.p.; M.m
GO:0006399GO:0007155 cell adhesion NO_OVERLAP S.p.; M.m.
GO:0006399GO:0006520 cellular amino acid metabolic process GO:0043039 OR GO:0031071 (tRNA aminoacylation OR cysteine desulphurase ) S.p; M.m
GO:0006399GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p.; M.m {n/a}
GO:0006399GO:0016568 chromatin modification GO:0033588 (elongator complex) S.p {check this, is elongator still thought to be histone acetyltransferase???};M.m
GO:0006399GO:0051276 chromosome organization GO:0033588 (elongator complex) S.p {check this, is elongator still thought to be histone acetyltransferase???}; M.m
GO:0006399GO:0007059 chromosome segregation NO_OVERLAP S.p; M.m.
GO:0006399GO:0051186 cofactor metabolic process GO:0006777 (Mo-molybdopterin cofactor biosynthetic process)S.p; M.m.
GO:0006399GO:0000747 conjugation with cellular fusion NO_OVERLAP S.p.; M.m {n/a}
GO:0006399GO:0000910 cytokinesis NO_OVERLAP S.p.; M.m
GO:0006399GO:0002181 cytoplasmic translation GO:0043039 (tRNA aminoacylation) S.p.; M.m.
GO:0006399GO:0007010 cytoskeleton organization NO_OVERLAP S.p; M.m.
GO:0006399GO:0007163 establishment or maintenance of cell polarity NO_OVERLAP S.p; M.m
GO:0006399GO:0006091 generation of precursor metabolites and energy NO_OVERLAP S.p; M.m.
GO:0006399GO:0006629 lipid metabolic process NO_OVERLAP S.p.; M.m.
GO:0006520GO:0016071 mRNA metabolic process LATER S.p; M.m.
GO:0006520GO:0007126 meiosis NO_OVERLAP S.p; M.m
GO:0006520GO:0007005 mitochondrion organization GO:0043039 (tRNA aminoacylation) S.p; M.m. {may need some more terms allowed in overlap}
GO:0006399GO:0071941 nitrogen cycle metabolic process NO_OVERLAP S.p; M.m.
GO:0006399GO:0055086 nucleobase-containing small molecule metabolic process LATERS.p.; M.m includes GO:0008479 {queuine tRNA-ribosyltransferase activity} GO:0003924 {GTPase activity, specifically IPR004520}
GO:0006399GO:0006913 nucleocytoplasmic transport NO_OVERLAP S.p.; M.m
GO:0006399GO:0007031 peroxisome organization NO_OVERLAP S.p.; M.m
GO:0006399GO:0030163 protein catabolic process NO_OVERLAP S.p.; M.m
GO:0006399GO:0006461 protein complex assembly NO_OVERLAP S.p.; M.m {need to deal with protein tetramerization}
GO:0006399GO:0006457 protein folding NO_OVERLAP S.p.; M.m
GO:0006399GO:0006486 protein glycosylation NO_OVERLAP S.p.; M.m.
GO:0006399GO:0051604 protein maturation NO_OVERLAP S.p; M.m
GO:0006399GO:0070647 protein modification by small protein conjugation or removal GO:0032447 (protein urmylation) S.p; M.m.
GO:0006399GO:0006605 protein targeting NO_OVERLAP S.p.; M.m
GO:0006399GO:0007346 regulation of mitotic cell cycle NO_OVERLAP S.p; M.m
GO:0006399GO:0042254 ribosome biogenesis LOTS (add details later) S.p.; M.m.
GO:0006399GO:0023052 signaling NO_OVERLAP S.p; M.m.
GO:0006399GO:0006351 transcription DNA-dependent LATER S.p.; M.m
GO:0006399GO:0055085 transmembrane transport NO_OVERLAP S.p.; M.m
GO:0006399GO:0007033 vacuole organization NO_OVERLAP S.p.; M.m.
GO:0006399GO:0016192 vesicle-mediated transport NO_OVERLAP S.p; M.m.
GO:0006399GO:0006766 vitamin metabolic process NO_OVERLAP S.p.; M.m

tRNA metabolism annotation updates

Database gene update reason
SGD YHR020W removed chromatin organization added prolyl-tRNA aminoacylationlegacy 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:0006412GO: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:0006412GO: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:0006412GO:0006260 DNA replication LOTS IN MOUSE S.p.
GO:0006412GO:0030437 ascospore formation NO_OVERLAP S.p; S.c; M.m {n/a}
GO:0006412GO:0005975 carbohydrate metabolic process LOTS -
GO:0006412GO:0007155 cell adhesion LOTS IN MOUSE S.p.
GO:0006412GO:0006520 cellular amino acid metabolic process SEE ABOVE -
GO:0006412GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p; S.c; M.m
GO:0006412GO:0016568 chromatin modification LOTS -
GO:0006412GO:0051276 chromosome organization LOTS IN MOUSE -
GO:0006412GO:0007059 chromosome segregation NO_OVERLAP S.p; S.c; M.m
GO:0006412GO:0051186 cofactor metabolic process LOTS IN MOUSE S.p. {except fusion protein}
GO:0006412GO:0000747 conjugation with cellular fusion GO:0007165 S.p; S.c {DHH1 query} M.m
GO:0006412GO:0000910 cytokinesis GO:0018444 (translation release factor complex) S.p; S.c; M.m
GO:0006412GO:0007010 cytoskeleton organization LOTS, POSSIBLY ALL SIGNAL TRANSDUCTION -
GO:0006412GO:0007163 establishment or maintenance of cell polarity GO:0007165 (signal transduction) S.p.; M.m
GO:0006412GO:0006091 generation of precursor metabolites and energy GO:0007165 (signal transduction) S.p. {pending updates, except fusion protein}
GO:0006412GO:0006629 lipid metabolic process LOTS IN MOUSE, POSSIBLY ALL SIGNAL TRANSDUCTION -
GO:0006412GO:0016071 mRNA metabolic process LOTS IN MOUSE -
GO:0006412GO:0007126 meiosis LOTS IN MOUSE (mainly signal transduction) S.p.
GO:0006412GO:0007005 mitochondrion organization LOTS, mitochondrial translation -
GO:0006412GO:0071941 nitrogen cycle metabolic process NO_OVERLAP S.p; S.c; M.m
GO:0006412GO:0055086 nucleobase-containing small molecule metabolic process MOUSE LOTS -
GO:0006412GO:0006913 nucleocytoplasmic transport LOTS -
GO:0006412GO:0007031 peroxisome organization NO_OVERLAP S.p.; S.c; M.m
GO:0006412GO:0030163 protein catabolic process MOUSE LOTS S.p; S.c
GO:0006412GO:0006461 protein complex assembly MOUSE LOTS -
GO:0006412GO:0006457 protein folding LOTS -
GO:0006412GO:0006486 protein glycosylation NO_OVERLAP S.p; S.c; M.m {ontology parentage of glycosylation pending} |
GO:0006412GO:0051604 protein maturation LOTS -
GO:0006412GO:0070647 protein modification by small protein conjugation or removal LOTS -
GO:0006412GO:0006605 protein targeting NO_OVERLAP S.p. pending fixes
GO:0006412GO:0007346 regulation of mitotic cell cycle LOTS, probably all signal transduction -
GO:0006412GO:0042254 ribosome biogenesis LOTS -
GO:0006412GO:0023052 signaling LOTS -
GO:0006412GO:0006399 tRNA metabolic process LOTS -
GO:0006412GO:0006351 transcription DNA-dependent LOTS -
GO:0006412GO:0055085 transmembrane transport MOUSE LOTS CHECK AFTER ONTOLOGY UPDATE S.p. (pending updates)
GO:0006412GO:0007033 vacuole organization NO_OVERLAP S.p; S.c; M.m
GO:0006412GO:0016192 vesicle-mediated transport MOUSE LOTS S.p.
GO:0006412GO:0006766 vitamin metabolic process NO_OVERLAP S.p.; S.c; M.m

translation annotation updates

Database gene update reason
SGD SSL1 removed translation initiationlegacy 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 translationincorrect 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:0042254GO:0006310 DNA recombination GO:0000018 (regulation of DNA recombination) S.p.; S.c; M.m
GO:0042254GO:0006281 DNA repair GO:0031080 S.p.; S.c
GO:0042254GO:0006260 DNA replication LOTS -
GO:0042254GO:0030437 ascospore formation GO:0023052 (signaling, upstream) S.p; S.c; M.m {n/a}
GO:0042254GO:0005975 carbohydrate metabolic process GO:0023052 (signaling, upstream) S.p.
GO:0042254GO:0007155 cell adhesion MOUSE LOTS S.p; S.c
GO:0042254GO:0006520 cellular amino acid metabolic process NO_OVERLAP S.p.; S.c; M.m
GO:0042254GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p.; S.c; M.m {n/a}
GO:0042254GO:0016568 chromatin modification LOTS -
GO:0042254GO:0051276 chromosome organization LOTS -
GO:0042254GO:0007059 chromosome segregation LOTS -
GO:0042254GO:0051186 cofactor metabolic process LATER -
GO:0042254GO:0000747 conjugation with cellular fusion LATER -
GO:0042254GO:0000910 cytokinesis LATER, NOP15 -
GO:0042254GO:0002181 cytoplasmic translation SEE ABOVE -
GO:0042254GO:0007010 cytoskeleton organization LOTS -
GO:0042254GO:0007163 establishment or maintenance of cell polarity LATER S.p.
GO:0042254GO:0006091 generation of precursor metabolites and energy GO:0023052 (signaling, upstream) S.p.; S.c; M.m
GO:0042254GO:0006629 lipid metabolic process LATER GO:0019216 (regulation of lipid metabolic process) S.p.; S.c.
GO:0042254GO:0016071 mRNA metabolic process MOUSE LOTS -
GO:0042254GO:0007126 meiosis GO:0023052 (signaling, upstream)Sp; S.c. M.m
GO:0042254GO:0007005 mitochondrion organization LOTS -
GO:0042254GO:0071941 nitrogen cycle metabolic process NO_OVERLAP M.m; S.p; S.c
GO:0042254GO:0055086 nucleobase-containing small molecule metabolic process LOTS -
GO:0042254GO:0006913 nucleocytoplasmic transport LOTS -
GO:0042254GO:0007031 peroxisome organization NO_OVERLAP S.p.; S.c; M.m
GO:0042254GO:0030163 protein catabolic process LATER S.p.
GO:0042254GO:0006461 protein complex assembly MOUSE LOTS -
GO:0042254GO:0006457 protein folding LATER S. c overlaps S.p.
GO:0042254GO:0006486 protein glycosylation NO_OVERLAP S.p.; S.c; M.m
GO:0042254GO:0051604 protein maturation NO_OVERLAP S.p; S.c; M.m
GO:0042254GO:0070647 protein modification by small protein conjugation or removal LATER -
GO:0042254GO:0006605 protein targeting LATER-
GO:0042254GO:0007346 regulation of mitotic cell cycle LATER -
GO:0042254GO:0023052 signaling LATER -
GO:0042254GO:0006399 tRNA metabolic process SEE ABOVE -
GO:0042254GO:0006351 transcription DNA-dependent LOTS -
GO:0042254GO:0055085 transmembrane transport NO_OVERLAP S.p.; S.c; M.m
GO:0042254GO:0007033 vacuole organization NO_OVERLAP S.p.; S.c; M.m.
GO:0042254GO:0016192 vesicle-mediated transport LATER S.p.
GO:0042254GO: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:0055085GO:0006310 DNA recombination NO_OVERLAP S.p.; S.c; M.m
GO:0055085GO:0006281 DNA repair MOUSE HAS LOTS CHECK LATER S.p.; S.c
GO:0055085GO:0006260 DNA replication MOUSE HAS LOTS CHECK LATER S.p.; S.c.
GO:0055085GO:0030437 ascospore formation S. C LATER S.p.; M.m(n/a)
GO:0055085GO:0005975 carbohydrate metabolic process LOTS -
GO:0055085GO:0007155 cell adhesion MOUSE HAS LOTS CHECK LATER S.p.; S.c.
GO:0055085GO:0006520 cellular amino acid metabolic process LOTS -
GO:0055085GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p; S.c; M.m
GO:0055085GO:0016568 chromatin modification NO_OVERLAP S.p.; S.c; {11 MOUSE BUT SHOULD STOP WHEN ONTOLOGY FIXED}
GO:0055085GO:0051276 chromosome organization MOUSE HAS LOTS -
GO:0055085GO:0007059 chromosome segregation 4 MOUSE BUT THESE MIGHT DISAPPEAR S.p.; S.c
GO:0055085GO:0051186 cofactor metabolic process S.C LOTS, LATER S.p.
GO:0055085GO:0000747 conjugation with cellular fusion LATER -
GO:0055085GO:0000910 cytokinesis GO:0023052 (signaling, upstream) S.p; S.c; m.m
GO:0055085GO:0002181 cytoplasmic translation NO_OVERLAP S.p.; S.c; M.m
GO:0055085GO:0007010 cytoskeleton organization MOUSE LOTS S.p.; S.c;
GO:0055085GO:0007163 establishment or maintenance of cell polarity MOUSE LOTS S.p.
GO:0055085GO:0006091 generation of precursor metabolites and energy MOUSE LOTS -
GO:0055085GO:0006629 lipid metabolic process MOUSE LOTS -
GO:0055085GO:0016071 mRNA metabolic process NO_OVERLAP S.p.; S.c; M.m
GO:0055085GO:0007126 meiosis LATERS.p.
GO:0055085GO:0007005 mitochondrion organization LOTS -
GO:0055085GO:0071941 nitrogen cycle metabolic process LATER -
GO:0055085GO:0055086 nucleobase-containing small molecule metabolic process LATER -
GO:0055085GO:0006913 nucleocytoplasmic transport allow protein folding (S.c. SSA1) S.p; S.c. M.m {pending ontology changes}
GO:0055085GO:0007031 peroxisome organization LOTS -
GO:0055085GO:0030163 protein catabolic process LOTS GO:0005784 (check again) S.p;
GO:0055085GO:0006461 protein complex assembly LOTS -
GO:0055085GO:0006457 protein folding LOTS CHECK -
GO:0055085GO:0006486 protein glycosylation LOTS -
GO:0055085GO:0051604 protein maturation LATER -
GO:0055085GO:0070647 protein modification by small protein conjugation or removal LATER -
GO:0055085GO:0006605 protein targeting LOTS -
GO:0055085GO:0007346 regulation of mitotic cell cycle LOTS -
GO:0055085GO:0042254 ribosome biogenesis SEE ABOVE -
GO:0055085GO:0023052 signaling LATER -
GO:0055085GO:0006399 tRNA metabolic process SEE ABOVE S.p.
GO:0055085GO:0006351 transcription DNA-dependent LOTS -
GO:0055085GO:0007033 vacuole organization LATER S.p.
GO:0055085GO: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

vitamin metabolic process (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:0006766GO:0006310 DNA recombination NO_OVERLAP S.p.; S.c; M.m {1, looks dodgy ifn2 same paper as snai2 below}
GO:0006766GO:0006281 DNA repair NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0006260 DNA replication NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0030437 ascospore formation NO_OVERLAP S.p.; S.c; M.m (n/a)
GO:0006766GO:0005975 carbohydrate metabolic process MOUSE LOTS S.p.
GO:0006766GO:0007155 cell adhesion LATER S.p.; S.c
GO:0006766GO:0006520 cellular amino acid metabolic process LATER-
GO:0006766GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0016568 chromatin modification NO_OVERLAP S.p.; M.m {1, looks dodgy, Snai2}
GO:0006766GO:0051276 chromosome organization NO_OVERLAP S.p.; S.c; M.m {1, looks dodgy, Snai2}
GO:0006766GO:0007059 chromosome segregation NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0051186 cofactor metabolic process LOTS -
GO:0006766GO:0000747 conjugation with cellular fusion NO_OVERLAP S.p.; S.c; M.m {n/a}
GO:0006766GO:0000910 cytokinesis NO_OVERLAP S.p.; M.m; S.c
GO:0006766GO:0002181 cytoplasmic translation NO_OVERLAP S.p.; S.c.; M.m
GO:0006766GO:0007010 cytoskeleton organization NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0007163 establishment or maintenance of cell polarity NO_OVERLAP S.p.; M.m; S.c
GO:0006766GO:0006091 generation of precursor metabolites and energy NO_OVERLAP S.p.; M.m; S.c
GO:0006766GO:0006629 lipid metabolic process MOUSE LOTS S.p.
GO:0006766GO:0016071 mRNA metabolic process NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0007126 meiosis LATER S.p.; S.c
GO:0006766GO:0007005 mitochondrion organization NO_OVERLAP S.p.; M.m
GO:0006766GO:0071941 nitrogen cycle metabolic process NO_OVERLAP M.m.; S.c; S.p
GO:0006766GO:0055086 nucleobase-containing small molecule metabolic process LATER -
GO:0006766GO:0006913 nucleocytoplasmic transport NO_OVERLAP S.p.; S.c; M.m {4 but snai2 and Ifng look dodgy}
GO:0006766GO:0007031 peroxisome organization NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0030163 protein catabolic process GO:0070647 (glutamate-cycteine ligase activity) S.p.; S.c; M.m {2 but look dodgy}
GO:0006766GO:0006461 protein complex assembly NO_OVERLAP S.p.; S.c; M.m {2 look dodgy}
GO:0006766GO:0006457 protein folding NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0006486 protein glycosylation NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0051604 protein maturation NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0070647 protein modification by small protein conjugation or removal GO:0070647 (glutamate-cycteine ligase activity) S.p.; S.c; M.m
GO:0006766GO:0006605 protein targeting NO_OVERLAP S.p.; S.c; M.m {5 but look dodgy}
GO:0006766GO:0007346 regulation of mitotic cell cycle NO_OVERLAP S.p.; S.c; M.m {except tnf, check}
GO:0006766GO:0042254 ribosome biogenesis NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO:0023052 signaling MOUSE LOTS S.p.; S.c
GO:0006766GO:0006399 tRNA metabolic process SEE ABOVE -
GO:0006766GO:0006351 transcription DNA-dependent MOUSE LOTS S.p.
GO:0006766GO:0055085 transmembrane transport MOUSE LOTS S.p.
GO:0006766GO:0007033 vacuole organization NO_OVERLAP S.p.; S.c; M.m
GO:0006766GO: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:0007346GO:0006310 DNA recombination - -
GO:0007346GO:0006281 DNA repair - -
GO:0007346GO:0006260 DNA replication - -
GO:0007346GO:0030437 ascospore formation - -
GO:0007346GO:0005975 carbohydrate metabolic process NO_OVERLAP S.p.
GO:0007346GO:0007155 cell adhesion NO_OVERLAP S.p.
GO:0007346GO:0006520 cellular amino acid metabolic process NO_OVERLAP S.p.
GO:0007346GO:0071554 cell wall organization or biogenesis - -
GO:0007346GO:0016568 chromatin modification - -
GO:0007346GO:0051276 chromosome organization - -
GO:0007346GO:0007059 chromosome segregation - -
GO:0007346GO:0051186 cofactor metabolic process NO_OVERLAP S.p.
GO:0007346GO:0000747 conjugation with cellular fusion - -
GO:0007346GO:0000910 cytokinesis - -
GO:0007346GO:0002181 cytoplasmic translation - M.m
GO:0007346GO:0007010 cytoskeleton organization - -
GO:0007346GO:0007163 establishment or maintenance of cell polarity - -
GO:0007346GO:0006091 generation of precursor metabolites and energy NO_OVERLAP S.p.
GO:0007346GO:0006629 lipid metabolic process - -
GO:0007346GO:0016071 mRNA metabolic process - -
GO:0007346GO:0007126 meiosis --
GO:0007346GO:0007005 mitochondrion organization S.c -
GO:0007346GO:0071941 nitrogen cycle metabolic process NO_OVERLAP S.p.; S.c.; ;M.m
GO:0007346GO:0055086 nucleobase-containing small molecule metabolic process - -
GO:0007346GO:0006913 nucleocytoplasmic transport - -
GO:0007346GO:0007031 peroxisome organization NO_OVERLAP S.p.; S.c; M.m
GO:0007346GO:0030163 protein catabolic process - -
GO:0007346GO:0006461 protein complex assembly - -
GO:0007346GO:0006457 protein folding - M.m
GO:0007346GO:0006486 protein glycosylation - S.p; S.c; M.m
GO:0007346GO:0051604 protein maturation NO_OVERLAP S.p.; S.c.
GO:0007346GO:0070647 protein modification by small protein conjugation or removal - -
GO:0007346GO:0006605 protein targeting - -
GO:0007346GO:0007346 regulation of mitotic cell cycle - -
GO:0007346GO:0042254 ribosome biogenesis - -
GO:0007346GO:0023052 signaling - -
GO:0007346GO:0006399 tRNA metabolic process NO_OVERLAP S.p.; S.c; M.m
GO:0007346GO:0006351 transcription DNA-dependent - -
GO:0007346GO:0055085 transmembrane transport - (S.p.- one annotation, checking)
GO:0007346GO:0007033 vacuole organization NO_OVERLAP S.p.; M.m
GO:0007346GO:0016192 vesicle-mediated transport - -
GO:0007346GO: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:0006281GO:0006310 DNA recombination - -
GO:0006281GO:0006281 DNA repair - -
GO:0006281GO:0006260 DNA replication - -
GO:0006281GO:0030437 ascospore formation NO_OVERLAP S.p.; M.m (n/a)
GO:0006281GO:0005975 carbohydrate metabolic process - S.p.
GO:0006281GO:0007155 cell adhesion NO_OVERLAP S.p.
GO:0006281GO:0006520 cellular amino acid metabolic process - S.c; M.m
GO:0006281GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p.
GO:0006281GO:0016568 chromatin modification - -
GO:0006281GO:0051276 chromosome organization - -
GO:0006281GO:0007059 chromosome segregation - -
GO:0006281GO:0051186 cofactor metabolic process NO_OVERLAP S.p.; S.c
GO:0006281GO:0000747 conjugation with cellular fusion NO_OVERLAPS.p.; S.c; M.m (n/a)
GO:0006281GO:0000910 cytokinesis NO_OVERLAP S.p.
GO:0006281GO:0002181 cytoplasmic translation NO_OVERLAP S.p; M.m
GO:0006281GO:0007010 cytoskeleton organization - -
GO:0006281GO:0007163 establishment or maintenance of cell polarity NO_OVERLAP S.p.
GO:0006281GO:0006091 generation of precursor metabolites and energy NO_OVERLAP S.p.; S.c
GO:0006281GO:0006629 lipid metabolic process NO_OVERLAP S.p.
GO:0006281GO:0016071 mRNA metabolic process - -
GO:0006281GO:0007126 meiosis --
GO:0006281GO:0007005 mitochondrion organization - -
GO:0006281GO:0071941 nitrogen cycle metabolic process NO_OVERLAP S.p.; S.c; M.m
GO:0006281GO:0055086 nucleobase-containing small molecule metabolic process - -
GO:0006281GO:0006913 nucleocytoplasmic transport GO:0031080 -
GO:0006281GO:0007031 peroxisome organization NO_OVERLAP S.p. ; S.c; M.m
GO:0006281GO:0030163 protein catabolic process - -
GO:0006281GO:0006461 protein complex assembly - -
GO:0006281GO:0006457 protein folding NO_OVERLAPS.p.; S.c; M.m
GO:0006281GO:0006486 protein glycosylation - S.p.; S.c
GO:0006281GO:0051604 protein maturation NO_OVERLAP S.p.; S.c; M.m
GO:0006281GO:0070647 protein modification by small protein conjugation or removal - -
GO:0006281GO:0006605 protein targeting - S.p.
GO:0006281GO:0007346 regulation of mitotic cell cycle - -
GO:0006281GO:0042254 ribosome biogenesis - S.p.
GO:0006281GO:0023052 signaling - -
GO:0006281GO:0006399 tRNA metabolic process - check s.c S.p.; M.m
GO:0006281GO:0006351 transcription DNA-dependent - -
GO:0006281GO:0055085 transmembrane transport NO_OVERLAP S.p.; S.c; M.m (3 bad mappings)
GO:0006281GO:0007033 vacuole organization - S.p.; M.m
GO:0006281GO:0016192 vesicle-mediated transport NO_OVERLAP S.p.; M.m (4 mappings to remove)
GO:0006281GO: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:0006260GO:0006310 DNA recombination - -
GO:0006260GO:0006281 DNA repair - -
GO:0006260GO:0006260 DNA replication - -
GO:0006260GO:0030437 ascospore formation NO_OVERLAP S.p.; M.m (n/a)
GO:0006260GO:0005975 carbohydrate metabolic process NO_OVERLAP S.p.
GO:0006260GO:0007155 cell adhesion NO_OVERLAP S.p.; S.c; M.m
GO:0006260GO:0006520 cellular amino acid metabolic process NO_OVERLAP S.p.
GO:0006260GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p.
GO:0006260GO:0016568 chromatin modification - -
GO:0006260GO:0051276 chromosome organization -
GO:0006260GO:0007059 chromosome segregation - -
GO:0006260GO:0051186 cofactor metabolic process NO_OVERLAP S.p.
GO:0006260GO:0000747 conjugation with cellular fusion - M.m
GO:0006260GO:0000910 cytokinesis NO_OVERLAP S.p.; S.c
GO:0006260GO:0002181 cytoplasmic translation NO_OVERLAP S.p.; S.c; M.m
GO:0006260GO:0007010 cytoskeleton organization NO_OVERLAP S.p.
GO:0006260GO:0007163 establishment or maintenance of cell polarity NO_OVERLAP S.p.; S.c
GO:0006260GO:0006091 generation of precursor metabolites and energy NO_OVERLAP S.p.
GO:0006260GO:0006629 lipid metabolic process NO_OVERLAP S.p.
GO:0006260GO:0016071 mRNA metabolic process NO_OVERLAP S.p.
GO:0006260GO:0007126 meiosis --
GO:0006260GO:0007005 mitochondrion organization - -
GO:0006260GO:0071941 nitrogen cycle metabolic process NO_OVERLAP S.p.
GO:0006260GO:0055086 nucleobase-containing small molecule metabolic process - -
GO:0006260GO:0006913 nucleocytoplasmic transport NO_OVERLAP ??; S.c
GO:0006260GO:0007031 peroxisome organization NO_OVERLAP S.p.; S.c: M.m
GO:0006260GO:0030163 protein catabolic process - -
GO:0006260GO:0006461 protein complex assembly - -
GO:0006260GO:0006457 protein folding - -
GO:0006260GO:0006486 protein glycosylation NO_OVERLAP S.p.; S.c
GO:0006260GO:0051604 protein maturation - -
GO:0006260GO:0070647 protein modification by small protein conjugation or removal - -
GO:0006260GO:0006605 protein targeting NO_OVERLAP S.p.;
GO:0006260GO:0007346 regulation of mitotic cell cycle - -
GO:0006260GO:0042254 ribosome biogenesis NO_OVERLAP S.p.;M.m
GO:0006260GO:0023052 signaling - -
GO:0006260GO:0006399 tRNA metabolic process NO_OVERLAP S.p.; S.c; M.m
GO:0006260GO:0006351 transcription DNA-dependent - -
GO:0006260GO:0055085 transmembrane transport NO_OVERLAP S.p.; S.c; M.m
GO:0006260GO:0007033 vacuole organization NO_OVERLAP S.p.; M.m
GO:0006260GO:0016192 vesicle-mediated transport NO_OVERLAP S.p.; M.m
GO:0006260GO: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?trx1regulation of DNA-dependent DNA replication removed unsupported ISO

Carbohydrate metabolic process

term ID 1 term ID 2term name 2Exceptions GO:xxxxxxx (comments free text) checked in species S.p; etc {comments in curly brackets}
GO:0005975GO:0006310 DNA recombination - S.p
GO:0005975GO:0006281 DNA repair - S.p
GO:0005975GO:0006260 DNA replication - S.p
GO:0005975GO:0030437 ascospore formation - -
GO:0005975GO:0005975 carbohydrate metabolic process - -
GO:0005975GO:0007155 cell adhesion - S.p
GO:0005975GO:0006520 cellular amino acid metabolic process - -
GO:0005975GO:0071554 cell wall organization or biogenesis - -
GO:0005975GO:0016568 chromatin modification - S.p
GO:0005975GO:0051276 chromosome organization - S.p
GO:0005975GO:0007059 chromosome segregation UPSTREAM REGULATORS OF BOTHS.p S.c: M.m
GO:0005975GO:0051186 cofactor metabolic process - -
GO:0005975GO:0000747 conjugation with cellular fusion - -
GO:0005975GO:0000910 cytokinesis - -
GO:0005975GO:0002181 cytoplasmic translation NO_OVERLAP S.p; S.c; M.m
GO:0005975GO:0007010 cytoskeleton organization - -
GO:0005975GO:0007163 establishment or maintenance of cell polarity - -
GO:0005975GO:0006091 generation of precursor metabolites and energy - -
GO:0005975GO:0006629 lipid metabolic process - -
GO:0005975GO:0016071 mRNA metabolic process UPSTREAM REGULATORS OF BOTH S.p; S.c; M.m
GO:0005975GO:0007126 meiosis --
GO:0005975GO:0007005 mitochondrion organization - S.p ; S.c
GO:0005975GO:0071941 nitrogen cycle metabolic process upstream regulation of both S.p.; S.c; M.m
GO:0005975GO:0055086 nucleobase-containing small molecule metabolic process - -
GO:0005975GO:0006913 nucleocytoplasmic transport LOTS OF MOUSE TO CHECK S.p; S.c (REMOVE INTERPRO MAPPINGS FOR SOL1 & 2)
GO:0005975GO:0007031 peroxisome organization NO_OVERLAP S.p; S.c; M.m
GO:0005975GO:0030163 protein catabolic process - -
GO:0005975GO:0006461 protein complex assembly - S.p
GO:0005975GO:0006457 protein folding NO_OVERLAP S.p; S.c; M.m
GO:0005975GO:0006486 protein glycosylation - -
GO:0005975GO:0051604 protein maturation - S.p.; S.c
GO:0005975GO:0070647 protein modification by small protein conjugation or removal - S.p
GO:0005975GO:0006605 protein targeting - -
GO:0005975GO:0007346 regulation of mitotic cell cycle - -
GO:0005975GO:0042254 ribosome biogenesis - S.p, M.m
GO:0005975GO:0023052 signaling - -
GO:0005975GO:0006399 tRNA metabolic process NO_OVERLAP S.p; S.c; M.m
GO:0005975GO:0006351 transcription DNA-dependent - -
GO:0005975GO:0055085 transmembrane transport - S.p.; S.c
GO:0005975GO:0007033 vacuole organization - S.p
GO:0005975GO:0016192 vesicle-mediated transport - -
GO:0005975GO: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 2term name 2Exceptions GO:xxxxxxx (comments free text) checked in species S.p; etc {comments in curly brackets}
GO:0006486GO:0006310 DNA recombination NO_OVERLAP S.p;
GO:0006486GO:0006281 DNA repair NO_OVERLAP S.p; S.c
GO:0006486GO:0006260 DNA replication NO_OVERLAP S.p;
GO:0006486GO:0030437 ascospore formation NO_OVERLAP S.p;
GO:0006486GO:0005975 carbohydrate metabolic process LOTS (makes sense - Is_a relationship between them) -
GO:0006486GO:0007155 cell adhesion - -
GO:0006486GO:0006520 cellular amino acid metabolic process NO_OVERLAP S.p;
GO:0006486GO:0071554 cell wall organization or biogenesis NO_OVERLAP S.p;
GO:0006486GO:0016568 chromatin modification NO_OVERLAP S.p;
GO:0006486GO:0051276 chromosome organization NO_OVERLAP S.p;
GO:0006486GO:0007059 chromosome segregation NO_OVERLAP S.p;
GO:0006486GO:0051186 cofactor metabolic process NO_OVERLAP S.p;
GO:0006486GO:0000747 conjugation with cellular fusion NO_OVERLAP (actually 3 but see notes) S.p;
GO:0006486GO:0000910 cytokinesis NO_OVERLAP (see notes) -
GO:0006486GO:0002181 cytoplasmic translation NO_OVERLAP S.p;
GO:0006486GO:0007010 cytoskeleton organization NO_OVERLAP S.p;
GO:0006486GO:0007163 establishment or maintenance of cell polarity NO_OVERLAP S.p;
GO:0006486GO:0006091 generation of precursor metabolites and energy NO_OVERLAP S.p;
GO:0006486GO:0006629 lipid metabolic process - -
GO:0006486GO:0016071 mRNA metabolic process NO_OVERLAP S.p;
GO:0006486GO:0007126 meiosis NO_OVERLAP S.p;
GO:0006486GO:0007005 mitochondrion organization NO_OVERLAP S.p;
GO:0006486GO:0071941 nitrogen cycle metabolic process NO_OVERLAP S.p;
GO:0006486GO:0055086 nucleobase-containing small molecule metabolic process - -
GO:0006486GO:0006913 nucleocytoplasmic transport NO_OVERLAP S.p;
GO:0006486GO:0007031 peroxisome organization NO_OVERLAP S.p;
GO:0006486GO:0030163 protein catabolic process - -
GO:0006486GO:0006461 protein complex assembly NO_OVERLAP S.p;
GO:0006486GO:0006457 protein folding NO_OVERLAP S.p;
GO:0006486GO:0051604 protein maturation NO_OVERLAP (none in pombe but probably should….) S.p;
GO:0006486GO:0070647 protein modification by small protein conjugation or removal NO_OVERLAP S.p;
GO:0006486GO:0006605 protein targeting NO_OVERLAP S.p;
GO:0006486GO:0007346 regulation of mitotic cell cycle - -
GO:0006486GO:0042254 ribosome biogenesis NO_OVERLAP S.p;
GO:0006486GO:0023052 signaling - -
GO:0006486GO:0006399 tRNA metabolic process NO_OVERLAP S.p;
GO:0006486GO:0006351 transcription, DNA-dependent NO_OVERLAP S.p;
GO:0006486GO:0055085 transmembrane transport - -
GO:0006486GO:0007033 vacuole organization NO_OVERLAP S.p;
GO:0006486GO:0016192 vesicle-mediated transport NO_OVERLAP S.p;
GO:0006486GO:0006766 vitamin metabolic process NO_OVERLAP S.p;

Protein glycosylation updates

databasegeneupdatereason
PomBase?gms1protein galactosylation indirect, phenotype only
PomBase?gms1conjugation with cellular fusion indirect, phenotype only
PomBase?gms1galactose metabolic process indirect, phenotype only
PomBase?gms1oligosaccharide metabolic process indirect, phenotype only
PomBase?gms1galactomannan biosynthetic process indirect, phenotype only
PomBase?gms1negative regulation of coflocculation via protein-carbohydrate interaction indirect, phenotype only
PomBase?ogm1agglutination involved in conjugation with cellular fusion indirect, phenotype only
PomBase?ogm4agglutination involved in conjugation with cellular fusion indirect, phenotype only
PomBase?ogm1barrier septum assembly involved in cell cycle cytokinesis indirect, phenotype only
PomBase?ogm4barrier septum assembly involved in cell cycle cytokinesis indirect, phenotype only
PomBase? mpg4Pending ValThese are involved in the maturation of cell wall proteins in the ER so cytokinesis defects should be indirect and phenotype annotation?
PomBase? (ISS) + cerevisiaealg1Pending Vallipid 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?gp114Pending 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?gpt2Pending ValProtein 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?SPAC4D7.04cPending ValI 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 2term name 2Exceptions GO:xxxxxxx (comments free text) checked in species S.p; etc {comments in curly brackets}
GO:0006486GO:0006310 DNA recombination NO_OVERLAP S.p;
GO:0006486GO:0006281 DNA repair NO_OVERLAP S.p;
GO:0006486GO:0006260 DNA replication NO_OVERLAP

Nucleocytoplasmic transport updates

databasegeneupdatereason

PomBase?ptr8nucleocytoplasmic transport indirect, phenotype only accumulation not export
PomBase?top2nucleocytoplasmic transport indirect, phenotype only accumulation not export

'Cell wall organization or biogenesis

term ID 1 term ID 2term name 2Exceptions GO:xxxxxxx (comments free text) checked in species S.p; etc {comments in curly brackets}

Cell wall organization or biogenesis updates

databasegeneupdatereason
PomBase?act1cell 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

Last modified 6 years ago Last modified on Feb 6, 2015, 10:35:46 AM