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PomBase curation
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IEA complexes to manually annotate #579

Closed pombase-admin closed 9 years ago

pombase-admin commented 9 years ago

Fix with EXP or ISS (I have taken about half and given you the DNA metabolism associated ones) A few more appear as different IEAs or TAS get supressed so it might take a couple of iterations to catch them all....

GO:0005663 DNA replication factor C complex SPBC23E6.07c rfc1 DNA replication factor C complex subunit Rfc1 IEA PomBase GO_REF:0000002 GO:0005665 DNA-directed RNA polymerase II, core complex SPBC28F2.12 rpb1 RNA polymerase II large subunit Rpb1 IEA,IEA PomBase GO_REF:0000002,GO_REF:0000002 GO:0005684 U2-type spliceosomal complex SPBP35G2.09 usp103 U1 snRNP-associated protein Usp103 ISO,IEA PomBase GO_REF:0000024,GO_REF:0000020 GO:0005760 gamma DNA polymerase complex SPCC24B10.22 pog1 mitochondrial DNA polymerase gamma IEA PomBase GO_REF:0000002 GO:0005852 eukaryotic translation initiation factor 3 complex SPAC821.05 tif38 translation initiation factor eIF3h (p40) IEA PomBase GO_REF:0000020 GO:0008180 COP9 signalosome SPAC1952.12c csn71 COP9/signalosome complex subunit 7a (predicted) IEA PomBase GO_REF:0000037 GO:0008180 COP9 signalosome SPAC22A12.03c csn4 COP9/signalosome complex subunit Csn4 IEA PomBase GO_REF:0000037 GO:0008180 COP9 signalosome SPAPB17E12.04c csn2 COP9/signalosome complex subunit Csn2 IEA PomBase GO_REF:0000037 GO:0008180 COP9 signalosome SPBC215.03c csn1 COP9/signalosome complex subunit Csn1 IEA PomBase GO_REF:0000037 GO:0008622 epsilon DNA polymerase complex SPBC25H2.13c cdc20 DNA polymerase epsilon catalytic subunit Pol2 IEA,IEA PomBase GO_REF:0000002,GO_REF:0000002 GO:0016591 DNA-directed RNA polymerase II, holoenzyme SPBC12D12.06 srb11 cyclin CycC, Srb mediator subunit Srb11 IEA PomBase GO_REF:0000002 GO:0016591 DNA-directed RNA polymerase II, holoenzyme SPBC28F2.12 rpb1 RNA polymerase II large subunit Rpb1 IEA PomBase GO_REF:0000002 GO:0032040 small-subunit processome SPAC18G6.06 utp11 U3 snoRNP-associated protein Utp11 (predicted) IEA PomBase GO_REF:0000002 GO:0032040 small-subunit processome SPAC57A7.06 utp14 U3 snoRNP protein Utp14 (predicted) IEA PomBase GO_REF:0000002 GO:0032040 small-subunit processome SPCC1672.07 SPCC1672.07 U3 snoRNP-associated protein Utp21 (predicted) IEA PomBase GO_REF:0000002 GO:0032040 small-subunit processome SPCC16A11.02 utp13 U3 snoRNP-associated protein Utp13 (predicted) IEA PomBase GO_REF:0000002 GO:0032777 Piccolo NuA4 histone acetyltransferase complex SPCC830.05c epl1 NuA4 histone acetyltransferase complex Epl1 IEA PomBase GO_REF:0000002 GO:0030870 Mre11 complex SPAC1556.01c rad50 DNA repair protein Rad50 IEA PomBase GO_REF:0000002 GO:0031011 Ino80 complex SPAC23D3.09 arp42 SWI/SNF and RSC complex subunit Arp42 IEA,IEA PomBase GO_REF:0000002,GO_REF:0000002 GO:0035267 NuA4 histone acetyltransferase complex SPAC23D3.09 arp42 SWI/SNF and RSC complex subunit Arp42 IEA PomBase GO_REF:0000002 GO:0042575 DNA polymerase complex SPBC25H2.13c cdc20 DNA polymerase epsilon catalytic subunit Pol2 IEA PomBase GO_REF:0000002 GO:0042575 DNA polymerase complex SPCC24B10.22 pog1 mitochondrial DNA polymerase gamma IEA PomBase GO_REF:0000002 GO:0043564 Ku70:Ku80 complex SPBC543.03c pku80 Ku domain protein Pku80 IEA PomBase GO_REF:0000002 GO:0043564 Ku70:Ku80 complex SPCC126.02c pku70 Ku domain protein Pku70 IEA PomBase GO_REF:0000002 GO:0043599 nuclear DNA replication factor C complex SPBC23E6.07c rfc1 DNA replication factor C complex subunit Rfc1 IEA,IEA PomBase GO_REF:0000002,GO_REF:0000002 GO:1990077 primosome complex SPAC6B12.10c spp1 DNA primase catalytic subunit Spp1 IEA,IEA PomBase GO_REF:0000037,GO_REF:0000037 GO:1990077 primosome complex SPBC17D11.06 spp2 DNA primase large subunit Spp2 IEA,IEA PomBase GO_REF:0000037,GO_REF:0000037

Original comment by: ValWood

pombase-admin commented 9 years ago

record of what I did

GO:0005663 DNA replication factor C complex SPBC23E6.07c rfc1 filtered - more specific ISO available

GO:0005665 DNA-directed RNA polymerase II, core complex SPBC28F2.12 rpb1 ISO done; filters GO:0016591

GO:0005760 gamma DNA polymerase complex SPCC24B10.22 pog1 added IPR002297 to /pombe-embl/goa-load-fixes/filtered_mappings rationale:suppress because PMID:20807588 says S.c. pol gamma acts as a monomer, not a complex, so in the absence of experimental evidence, there doesn't seem to be much reason to infer a complex annotation

GO:0005852 eukaryotic translation initiation factor 3 complex SPAC821.05 tif38 filtered - IDA added

GO:0008180 COP9 signalosome SPAC1952.12c csn71 GO:0008180 COP9 signalosome SPAC22A12.03c csn4 GO:0008180 COP9 signalosome SPAPB17E12.04c csn2 GO:0008180 COP9 signalosome SPBC215.03c csn1 ISOs added for now; experimental should come along in due course (PMIDs 10607571, 11854407)

GO:0008622 epsilon DNA polymerase complex SPBC25H2.13c cdc20 ISO done

GO:0016591 DNA-directed RNA polymerase II, holoenzyme SPBC12D12.06 srb11 IEA should disappear, because it's to an InterPro ID that no longer exists; mappings removed per GO SF https://sourceforge.net/p/geneontology/annotation-issues/1299/ from the SGD entry it looks like the annotation doesn't need to be restored (the existing GO:0016592 annotation will suffice)

GO:0016591 DNA-directed RNA polymerase II, holoenzyme SPBC28F2.12 rpb1 filtered - more specific ISO available

GO:0032040 small-subunit processome SPAC18G6.06 utp11 GO:0032040 small-subunit processome SPAC57A7.06 utp14 GO:0032040 small-subunit processome SPCC1672.07 SPCC1672.07 GO:0032040 small-subunit processome SPCC16A11.02 utp13 ISOs done

GO:0032777 Piccolo NuA4 histone acetyltransferase complex SPCC830.05c epl1 ISO done

GO:0030870 Mre11 complex SPAC1556.01c rad50 ISO added for now; experimental should follow eventually (refs cited in PMID:23188080)

GO:0031011 Ino80 complex SPAC23D3.09 arp42 ISO done

GO:0035267 NuA4 histone acetyltransferase complex SPAC23D3.09 arp42 ISO done

GO:0042575 DNA polymerase complex SPBC25H2.13c cdc20 filtered - more specific ISO available

GO:0042575 DNA polymerase complex SPCC24B10.22 pog1 should be suppressed: no experimental evidence that it's in a complex, and more specific IEA directly suppressed

GO:0043564 Ku70:Ku80 complex SPBC543.03c pku80 GO:0043564 Ku70:Ku80 complex SPCC126.02c pku70 ISO added for now; experimental should follow eventually

GO:0043599 nuclear DNA replication factor C complex SPBC23E6.07c rfc1 ISO added for now; experimental should follow eventually

GO:1990077 primosome complex SPAC6B12.10c spp1 GO:1990077 primosome complex SPBC17D11.06 spp2 ICs added (that's the best I can do; no ISO because the orthologs don't have experimental annotation to primosome)

Original comment by: mah11

pombase-admin commented 9 years ago

Diff:


--- old
+++ new
@@ -1,4 +1,3 @@
-
 Fix with EXP or ISS
 (I have taken about half and given you the DNA metabolism associated ones)
 A few more appear as different IEAs or TAS get supressed so it might take a couple of iterations to catch them all....

Original comment by: mah11