Transcription jamboree

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Examples for discussion at electronic Transcription Jamboree

How much evidence is needed to make MF annotations

i) PMID 11486045 - Fig 2 I would like to annotate to the obsolete term GO:0016564 transcription repressor activity. How should this be annotated to the MF ontology with the new terms?


ii) We have

GO 0001102 RNA polymerase II activating transcription factor binding

and

GO:0001103 RNA polymerase II repressing transcription factor binding

Should we also have

RNA polymerase II activating/repressing transcription factor ACTIVITY?

Annotation to promoter/DNA binding terms

i) PMID 12270142 Based on figs 1 and 2 have annotated to

GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Based on fig 3 have annotated to

GO:2000679 positive regulation of transcription regulatory region DNA binding

Is this correct or are there other terms that should have been used instead?


ii) PMID 17332325 Is Fig 3 sufficient to support the following annotations?

GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity

GO:0070888 E-box binding