Changes between Version 72 and Version 73 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 6:05:51 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v72 v73  
    112112        * Can also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc.
    113113
    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.
    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.
    116    * In contrast, for csk1 I just used the BP GO:0045944 'positive regulation of transcription from RNA polymerase II promoter' with IMP.
     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.
     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. In contrast, for csk1 I just used the BP GO:0045944 'positive regulation of transcription from RNA polymerase II promoter' with IMP.
    117116   * Full details in the [http://curation.pombase.org/pombe/curs/efb40309f7d22a73 curation session].
    118    * The phenotypes themselves are another hairball, since they're mainly effects on global transcription measured by microarrays. In theory we could do annotations with extensions for all affected genes, but that would be insane. Try to get data for browser track; in meantime I'm just annotating to "altered RNA level during cellular response to phosphate starvation" without extensions. (2014-03-10)
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