Changes between Version 70 and Version 71 of GOAnnotationGuidelines
- Timestamp:
- Feb 25, 2015, 5:58:58 PM (6 years ago)
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GOAnnotationGuidelines
v70 v71 97 97 === Molecular Function === 98 98 99 100 * [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments chromatin immunoprecipitation (ChIP) experiments NOT promoter binding]101 102 99 * Protein binding 103 100 * In !PomBase, we'll only annotate to a GO 'protein binding' GO:0005515 term if there's strong evidence that a physical interaction is direct, e.g. using purified proteins. Otherwise, just do the BioGRID interaction annotation. … … 106 103 107 104 * DNA binding - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above) 108 105 * update [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments chromatin immunoprecipitation (ChIP) experiments NOT promoter binding] 106 107 109 108 * Transcription factors - wherever possible (i.e. make exceptions only when data don't support this): 110 109 * transcription factor activity term (sequence-specific DNA binding transcription factor activity (GO:0003700) or a descendent) twith any target genes as has_regulation_target extensions and a 111 110 * DNA binding term, "transcription regulatory region sequence-specific DNA binding (GO:0000976)" or a descendent (most commonly RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000978) with any DNA binding motifs ar has_direct_input(SO:ID) 112 111 *-otherwise the TF won't be annotated to DNA binding, because the terms are connected by has_part in GO). 113 114 * To capture t on the transcription factor activity term 115 * Also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc. No need to make redundant BP annotations. 112 * Can also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc. 113 116 114 * Example: [http://www.ncbi.nlm.nih.gov/pubmed/23231582 PMID:23231582] describes transcription during phosphate starvation. Mutations in pho7 or csk1 affect the -phosphate expression profile. For pho7 they also do ChIP-Seq and TAP assays, and some assays with a reporter construct, to establish that it acts as a transcription factor. 117 115 * So I annotated pho7 to GO:0000978 (IPI with targets identified by ChIP-Seq) and GO:0001077 (IMP - Fig 4, plus can interpret Fig 2 ChIP-Seq as also supporting in light of Fig 4; have also thought about whether it might be good enough for IDA), with extensions on both to indicate phosphate starvation -- happens_during(GO:0016036) -- and the target genes highlighted in the text.