wiki:GOslims

Standard PomBase? GO slim IDs

See http://preview.pombase.org/browse-curation/fission-yeast-go-slim-terms

GO:0140053 GO:0007031 GO:0030437 GO:0023052 GO:0030036 GO:0006520 GO:0032200 GO:0016074 GO:0005975 GO:0070647 GO:0000070 GO:0002181 GO:0030163 GO:0055086 GO:0006351 GO:0006260 GO:0071554 GO:0140013 GO:0065003 GO:0071941 GO:0006355 GO:0006399 GO:0042254 GO:0006457 GO:0006486 GO:0016071 GO:0007005 GO:0006310 GO:1901135 GO:0000747 GO:0006091 GO:0006914 GO:0098754 GO:0016192 GO:0051186 GO:0007163 GO:0006605 GO:0061024 GO:0006629 GO:0006281 GO:0000281 GO:0051604 GO:0007155 GO:0006766 GO:0006325 GO:0000226 GO:0016073 GO:0006915 GO:0006790 GO:0055065 GO:0140056 GO:0055085 GO:0006913

Slim Set used for unknown project

The PomBase? slim set is too specific for many organisms annotation

Swapped

  • GO:0002181 cytoplasmic translation for GO:0006412 translation
  • GO:0030036 actin cytoskeleton organization and GO:0000226 microtubule cytoskeleton organization for GO:0007010 cytoskeleton organization
  • GO:0000070 mitotic sister chromatid segregation and GO:0007059 chromosome segregation
  • GO:0006605 protein targetting GO:0006913 nucleocytoplasmic transport GO:0055085 transmembrane transport for GO:0006810 transport
  • GO:1901990 regulation of mitotic cell cycle phase transition for GO:0000278 mitotic cell cycle
  • GO:0000281 mitotic cytokinesis for cytokinesis GO:0000910

GO:0140053 GO:0000278 GO:0006810 GO:0007010 GO:0006412 GO:0007031 GO:0030437 GO:0023052 GO:0006520 GO:0032200 GO:0016074 GO:0005975 GO:0070647 GO:0007059 GO:0030163 GO:0055086 GO:0006351 GO:0006260 GO:0071554 GO:1901990 GO:0140013 GO:0065003 GO:0071941 GO:0006355 GO:0006399 GO:0042254 GO:0006457 GO:0006486 GO:0016071 GO:0007005 GO:0006310 GO:1901135 GO:0000747 GO:0006913 GO:0006091 GO:0006914 GO:0098754 GO:0016192 GO:0051186 GO:0007163 GO:0061024 GO:0006629 GO:0006281 GO:0000910 GO:0051604 GO:0007155 GO:0055085 GO:0006766 GO:0006325 GO:0016073 GO:0006915 GO:0006790 GO:0055065 GO:0140056

Added these terms with small numbers of annotations not mapped to slim in either or both organisms

  • GO:0000920 cell separation after cytokinesis
  • GO:0000493 box H/ACA snoRNP assembly
  • GO:0070941 eisosome assembly
  • GO:0007124 pseudohyphal growth
  • GO:0009305 protein biotinylation (should not be needed soon)
  • GO:0018342 protein prenylation
  • GO:0000128 flocculation
  • GO:0034389 lipid particle organization
  • GO:0034276 kynurenic acid biosynthetic process
  • GO:0007032 endosome organisation
  • GO:0030091 protein repair ( needs a new slim term )
  • GO:0018345 protein palmitoylation

Uninformative terms/annotations in SGD slim

  • GO:0042221 response to chemical
  • GO:0070417 cellular response to cold
  • GO:0006974 cellular response to DNA damage stimulus
  • GO:0006979 response to oxidative stress
  • GO:0006970 response to osmotic stress
  • GO:0009408 response to heat
  • GO:0042594 response to starvation
  • GO:0031399 regulation of protein modification process
  • GO:0018193 peptidyl-amino acid modification
  • GO:0070647 protein modification by small protein conjugation or removal
  • GO:0016570 histone modification
  • GO:0006468 protein phosphorylation
  • GO:0006470 protein dephosphorylation
  • GO:0043543 protein acylation
  • GO:0016310 phosphorylation
  • GO:0016311 dephosphorylation
  • GO:0055114 oxidation-reduction process
  • GO:0006464 cellular protein modification process
  • GO:0043086 negative regulation of catalytic activity
  • GO:0006796 phosphate-containing compound metabolic process

Other non-specific terms to filter

  • cellular response to water deprivation
  • Response to drug
  • Response to copper ion
  • Proteolysis
  • cellular aldehyde metabolic process
  • response to stress
  • peptidyl-lysine methylation
  • cellular response to salt stress
  • metabolic process
  • phosphate-containing compound metabolic process
  • nitrogen compound metabolic process
  • peptidyl-lysine trimethylation
  • nitrogen compound metabolic process

Slim Set used for Matrix project including uninformative terms and specific terms

Non specific terms

GO:0042221 GO:0006974 GO:0006979 GO:0006970 GO:0009408 GO:0042594 GO:0031399 GO:0018193 GO:0070647 GO:0016570 GO:0006468 GO:0006470 GO:0043543 GO:0016310 GO:0016311 GO:0055114 GO:0006464 GO:0043086 GO:0070417 GO:0006796

standard slim with swaps GO:0140053 GO:0000278 GO:0006810 GO:0007010 GO:0006412 GO:0007031 GO:0030437 GO:0023052 GO:0006520 GO:0032200 GO:0016074 GO:0005975 GO:0070647 GO:0007059 GO:0030163 GO:0055086 GO:0006351 GO:0006260 GO:0071554 GO:1901990 GO:0140013 GO:0065003 GO:0071941 GO:0006355 GO:0006399 GO:0042254 GO:0006457 GO:0006486 GO:0016071 GO:0007005 GO:0006310 GO:1901135 GO:0000747 GO:0006913 GO:0006091 GO:0006914 GO:0098754 GO:0016192 GO:0051186 GO:0007163 GO:0061024 GO:0006629 GO:0006281 GO:0000910 GO:0051604 GO:0007155 GO:0055085 GO:0006766 GO:0006325 GO:0016073 GO:0006915 GO:0006790 GO:0055065 GO:0140056

add for greater coverage for "unknowns" project

GO:0000920 GO:0000493 GO:0070941 GO:0007124 GO:0009305 GO:0018342 GO:0000128 GO:0034389 GO:0034276 GO:0007032 GO:0030091 GO:0018345 GO:0006797 GO:0006089 GO:0072659 protein localization to plasma membrane GO:0019413 acetate biosynthetic process GO:0009436 glyoxylate catabolic process GO:0034079 butanediol biosynthetic process (energy generation) GO:1901426 response to furfural (these are really detoxification) GO:0018890 cyanamide metabolic process (really cellular detoxification) GO:0006276 plasmid maintenance GO:2000001 regulation of DNA damage checkpoint GO:0009636 response to toxic substance YNR064C, YMR074C, YOL052C-A, YHL010C (really detoxification) GO:2000001 regulation of DNA damage checkpoint GO:0071218 cellular response to misfolded protein GO:0046210 nitric oxide catabolic process

Last modified 3 years ago Last modified on Feb 21, 2018, 10:58:22 AM