Changes between Version 70 and Version 71 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 5:58:58 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v70 v71  
    9797=== Molecular Function ===
    9898   
    99  
    100    * [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments chromatin immunoprecipitation (ChIP) experiments NOT promoter binding]
    101    
    10299  * Protein binding
    103100    * 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.
     
    106103 
    107104  * 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
    109108  * Transcription factors - wherever possible (i.e. make exceptions only when data don't support this):
    110109     * 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
    111110     * 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)
    112111        *-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
    116114  * 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.
    117115   * 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.