Changes between Version 73 and Version 74 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 6:06:45 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v73 v74  
    111111        * Otherwise the TF won't be annotated to DNA binding, because the terms are connected by has_part in GO).  (YOu might need to use ISS or IC to get both)
    112112        * Can also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc.
    113 
    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.
    116    * Full details in the [http://curation.pombase.org/pombe/curs/efb40309f7d22a73 curation session].
     113           * 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.
     114           * 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. Full details in the [http://curation.pombase.org/pombe/curs/efb40309f7d22a73 curation session].
    117115 
    118116