Changes between Version 88 and Version 89 of GOAnnotationGuidelines


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Timestamp:
Apr 28, 2015, 11:40:30 AM (6 years ago)
Author:
mah79
Comment:

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  • GOAnnotationGuidelines

    v88 v89  
    9797 * Protein binding
    9898  * 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.
    99   * We do not use gene product specific, or protein family specific, or GO function specific GO protein binding descendents (this would take  too long, and can be done with a query)
    100   * However we do use "domain specific' GO binding terms to specify binding toa specific region in a target protein
    101  * DNA binding  - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above)
    102   * Don't use "promoter binding" terms if the only evidence is chromatin immunoprecipitation (ChIP); use a "chromatin" cellular component term instead. See the [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments GO wiki page on ChIP experiments]. Specify where with 'coincident_with(SO:nnn)' extensions.
     99  * We do not use gene product-specific, protein family-specific, or GO function-specific GO protein binding descendants (this would take too long, and can be done with a query)
     100  * However, we do use "domain-specific" GO binding terms to specify binding to a specific region in a target protein
     101 * DNA binding - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above). The rationale is that the bound substrate is the whole DNA molecule, and the SO extension indicates the region where binding takes place.
     102  * If you don't know whether a gene product is binding to DNA or protein (or both) in chromatin, you can use "chromatin binding" again with 'occurs_at(SO:nnn)' extensions ... BUT:
     103  * Don't use "promoter binding" terms if the only evidence is chromatin immunoprecipitation (ChIP). In fact, it's safer not to use a binding term at all; use a "chromatin" cellular component term instead. See the [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments GO wiki page on ChIP experiments]. Specify where with 'coincident_with(SO:nnn)' extensions.
    103104 * Transcription factors - wherever possible make annotation to both:
    104   * 1. a transcription factor activity term (sequence-specific DNA binding transcription factor activity (GO:0003700) or a descendent) with any target genes as has_regulation_target extensions, and optionally a promoter in an occurs_at(SO:nnn) extension; and a
    105   * 2. a 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)
     105  * 1. a transcription factor activity term (sequence-specific DNA binding transcription factor activity (GO:0003700) or a descendant) with any target genes as has_regulation_target extensions, and optionally a promoter in an occurs_at(SO:nnn) extension; and a
     106  * 2. a 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). Capture DNA binding specificity (e.g. motifs) with 'occurs_at(SO:nnn)' extensions
    106107  * 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)
    107108   * Can also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc.
    108109   * 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.
    109110    * 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].
     111 * RNA binding - can use has_direct_input(SO:nnn) extensions
     112  * The difference between extensions on 'RNA binding' versus 'DNA binding' is that with RNA, the SO terms usually represent different RNA molecules (the ones we tend to use are in the "transcript" branch of SO, and we should eventually switch to the "SO molecule" ontology if and when it becomes more than a clever idea).
    110113 
    111114=== Gene Product Forms, or "Column 17" ===