Changes between Version 211 and Version 212 of MatrixProject


Ignore:
Timestamp:
Apr 23, 2013, 9:25:50 AM (8 years ago)
Author:
val_wood
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • MatrixProject

    v211 v212  
    499499||SGD|| TRX2|| removed regulation of DNA replication|| legacy annotation||
    500500||PomBase||trx1||regulation of DNA-dependent DNA replication|| removed unsupported ISO||
     501
     502
     503
     504
     505'''Protein glycosylation'''
     506
     507||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}||
     508|| GO:0006486||GO:0006310|| DNA recombination || NO OVERLAP || S.p;|| ||GO:0006486||GO:0006281|| DNA repair || NO OVERLAP || S.p;||
     509|| GO:0006486||GO:0006260|| DNA replication || NO OVERLAP || S.p;||
     510|| GO:0006486||GO:0030437|| ascospore formation || NO OVERLAP || S.p;||
     511|| GO:0006486||GO:0005975|| carbohydrate metabolic process || LOTS (makes sense - Is_a relationship between them) ||-||
     512|| GO:0006486||GO:0007155|| cell adhesion || - ||-||
     513|| GO:0006486||GO:0006520|| cellular amino acid metabolic process || NO OVERLAP || S.p;||
     514|| GO:0006486||GO:0070882|| cellular cell wall organization or biogenesis || NO OVERLAP || S.p;||
     515|| GO:0006486||GO:0016568|| chromatin modification || NO OVERLAP || S.p;||
     516|| GO:0006486||GO:0051276|| chromosome organization  || NO OVERLAP || S.p;||
     517|| GO:0006486||GO:0007059|| chromosome segregation || NO OVERLAP || S.p;||
     518|| GO:0006486||GO:0051186|| cofactor metabolic process  || NO OVERLAP || S.p;||
     519|| GO:0006486||GO:0000747|| conjugation with cellular fusion  || NO OVERLAP (actually 3 but see notes) || S.p;||
     520|| GO:0006486||GO:0000910|| cytokinesis || NO OVERLAP (see notes) ||-||
     521|| GO:0006486||GO:0002181|| cytoplasmic translation  || NO OVERLAP || S.p;||
     522|| GO:0006486||GO:0007010|| cytoskeleton organization  || NO OVERLAP || S.p;||
     523|| GO:0006486||GO:0007163|| establishment or maintenance of cell polarity  || NO OVERLAP || S.p;||
     524|| GO:0006486||GO:0006091|| generation of precursor metabolites and energy  || NO OVERLAP || S.p;||
     525|| GO:0006486||GO:0006629|| lipid metabolic process  || - || -||
     526|| GO:0006486||GO:0016071|| mRNA metabolic process  || NO OVERLAP || S.p;||
     527|| GO:0006486||GO:0007126|| meiosis  || NO OVERLAP || S.p;||
     528|| GO:0006486||GO:0007005|| mitochondrion organization  || NO OVERLAP || S.p;||
     529|| GO:0006486||GO:0071941|| nitrogen cycle metabolic process  || NO OVERLAP || S.p;||
     530|| GO:0006486||GO:0055086|| nucleobase-containing small molecule metabolic process  || - ||-||
     531|| GO:0006486||GO:0006913|| nucleocytoplasmic transport  || NO OVERLAP || S.p;||
     532|| GO:0006486||GO:0007031|| peroxisome organization  || NO OVERLAP || S.p;||
     533|| GO:0006486||GO:0030163|| protein catabolic process  || - ||-||
     534|| GO:0006486||GO:0006461|| protein complex assembly  || NO OVERLAP ||S.p;||
     535|| GO:0006486||GO:0006457|| protein folding  || NO OVERLAP || S.p;||
     536|| GO:0006486||GO:0051604|| protein maturation  || NO OVERLAP (none in pombe but probably should….)|| S.p;||
     537|| GO:0006486||GO:0070647|| protein modification by small protein conjugation or removal  || NO OVERLAP || S.p;||
     538|| GO:0006486||GO:0006605|| protein targeting  || NO OVERLAP || S.p;||
     539|| GO:0006486||GO:0007346|| regulation of mitotic cell cycle  || - ||-||
     540|| GO:0006486||GO:0042254|| ribosome biogenesis  || NO OVERLAP || S.p;||
     541|| GO:0006486||GO:0023052|| signaling  || - ||-||
     542|| GO:0006486||GO:0006399|| tRNA metabolic process  || NO OVERLAP || S.p;||
     543|| GO:0006486||GO:0006351|| transcription, DNA-dependent  || NO OVERLAP || S.p;||
     544|| GO:0006486||GO:0055085|| transmembrane transport  || - ||-||
     545|| GO:0006486||GO:0007033|| vacuole organization  || NO OVERLAP || S.p;||
     546|| GO:0006486||GO:0016192|| vesicle-mediated transport  || NO OVERLAP || S.p;||
     547|| GO:0006486||GO:0006766|| vitamin metabolic process  || NO OVERLAP || S.p;||
     548
     549Protein glycosylation updates
     550||database||gene||update||reason||
     551||PomBase||gms1||Pending me knowing what embl file to modify||protein galactosylation – this is upstream so should be removed||
     552||PomBase||gms1||Pending Val||conjugation with cellular fusion – this protein is a transporter that provides the substrate for galactosylation. If surface proteins are not galactosylated cells cannot agglutinate. So this is upstream right?||
     553||PomBase||gms1/ogm1/ogm4||Pending Val||ogm1 and ogm4 annotated to agglutination involved in conjugation with cellular fusion (PMID:15809069). These proteins are involved in mannosylation of cell wall mannoproteins. Without them cells cannot agglutinate. I think this is upstream because the proteins are not modified correctly to start with and that this annotation should be changed to phenotype (it is the mannoprotein that should have the annotation agglutination involved in conjugation with cellular fusion)||
     554||PomBase||omg1, omg4, 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?||
     555||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)||
     556||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||
     557||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?)||
     558||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||
     559
     560
    501561
    502562
     
    602662cat 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
    603663
    604 '''Protein glycosylation'''
    605 
    606 ||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}||
    607 || GO:0006486||GO:0006310|| DNA recombination || NO OVERLAP || S.p;|| ||GO:0006486||GO:0006281|| DNA repair || NO OVERLAP || S.p;||
    608 || GO:0006486||GO:0006260|| DNA replication || NO OVERLAP || S.p;||
    609 || GO:0006486||GO:0030437|| ascospore formation || NO OVERLAP || S.p;||
    610 || GO:0006486||GO:0005975|| carbohydrate metabolic process || LOTS (makes sense - Is_a relationship between them) ||-||
    611 || GO:0006486||GO:0007155|| cell adhesion || - ||-||
    612 || GO:0006486||GO:0006520|| cellular amino acid metabolic process || NO OVERLAP || S.p;||
    613 || GO:0006486||GO:0070882|| cellular cell wall organization or biogenesis || NO OVERLAP || S.p;||
    614 || GO:0006486||GO:0016568|| chromatin modification || NO OVERLAP || S.p;||
    615 || GO:0006486||GO:0051276|| chromosome organization  || NO OVERLAP || S.p;||
    616 || GO:0006486||GO:0007059|| chromosome segregation || NO OVERLAP || S.p;||
    617 || GO:0006486||GO:0051186|| cofactor metabolic process  || NO OVERLAP || S.p;||
    618 || GO:0006486||GO:0000747|| conjugation with cellular fusion  || NO OVERLAP (actually 3 but see notes) || S.p;||
    619 || GO:0006486||GO:0000910|| cytokinesis || NO OVERLAP (see notes) ||-||
    620 || GO:0006486||GO:0002181|| cytoplasmic translation  || NO OVERLAP || S.p;||
    621 || GO:0006486||GO:0007010|| cytoskeleton organization  || NO OVERLAP || S.p;||
    622 || GO:0006486||GO:0007163|| establishment or maintenance of cell polarity  || NO OVERLAP || S.p;||
    623 || GO:0006486||GO:0006091|| generation of precursor metabolites and energy  || NO OVERLAP || S.p;||
    624 || GO:0006486||GO:0006629|| lipid metabolic process  || - || -||
    625 || GO:0006486||GO:0016071|| mRNA metabolic process  || NO OVERLAP || S.p;||
    626 || GO:0006486||GO:0007126|| meiosis  || NO OVERLAP || S.p;||
    627 || GO:0006486||GO:0007005|| mitochondrion organization  || NO OVERLAP || S.p;||
    628 || GO:0006486||GO:0071941|| nitrogen cycle metabolic process  || NO OVERLAP || S.p;||
    629 || GO:0006486||GO:0055086|| nucleobase-containing small molecule metabolic process  || - ||-||
    630 || GO:0006486||GO:0006913|| nucleocytoplasmic transport  || NO OVERLAP || S.p;||
    631 || GO:0006486||GO:0007031|| peroxisome organization  || NO OVERLAP || S.p;||
    632 || GO:0006486||GO:0030163|| protein catabolic process  || - ||-||
    633 || GO:0006486||GO:0006461|| protein complex assembly  || NO OVERLAP ||S.p;||
    634 || GO:0006486||GO:0006457|| protein folding  || NO OVERLAP || S.p;||
    635 || GO:0006486||GO:0051604|| protein maturation  || NO OVERLAP (none in pombe but probably should….)|| S.p;||
    636 || GO:0006486||GO:0070647|| protein modification by small protein conjugation or removal  || NO OVERLAP || S.p;||
    637 || GO:0006486||GO:0006605|| protein targeting  || NO OVERLAP || S.p;||
    638 || GO:0006486||GO:0007346|| regulation of mitotic cell cycle  || - ||-||
    639 || GO:0006486||GO:0042254|| ribosome biogenesis  || NO OVERLAP || S.p;||
    640 || GO:0006486||GO:0023052|| signaling  || - ||-||
    641 || GO:0006486||GO:0006399|| tRNA metabolic process  || NO OVERLAP || S.p;||
    642 || GO:0006486||GO:0006351|| transcription, DNA-dependent  || NO OVERLAP || S.p;||
    643 || GO:0006486||GO:0055085|| transmembrane transport  || - ||-||
    644 || GO:0006486||GO:0007033|| vacuole organization  || NO OVERLAP || S.p;||
    645 || GO:0006486||GO:0016192|| vesicle-mediated transport  || NO OVERLAP || S.p;||
    646 || GO:0006486||GO:0006766|| vitamin metabolic process  || NO OVERLAP || S.p;||
    647 
    648 Protein glycosylation updates
    649 ||database||gene||update||reason||
    650 ||PomBase||gms1||Pending me knowing what embl file to modify||protein galactosylation – this is upstream so should be removed||
    651 ||PomBase||gms1||Pending Val||conjugation with cellular fusion – this protein is a transporter that provides the substrate for galactosylation. If surface proteins are not galactosylated cells cannot agglutinate. So this is upstream right?||
    652 ||PomBase||gms1/ogm1/ogm4||Pending Val||ogm1 and ogm4 annotated to agglutination involved in conjugation with cellular fusion (PMID:15809069). These proteins are involved in mannosylation of cell wall mannoproteins. Without them cells cannot agglutinate. I think this is upstream because the proteins are not modified correctly to start with and that this annotation should be changed to phenotype (it is the mannoprotein that should have the annotation agglutination involved in conjugation with cellular fusion)||
    653 ||PomBase||omg1, omg4, 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?||
    654 ||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)||
    655 ||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||
    656 ||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?)||
    657 ||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||
    658 
    659