Transcription jamboree: Difference between revisions

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iii) PMID 19342457 [YAF]
iii) PMID 19342457 [YAF]
Based on Figs 1 and 3 I have annotated to:
Based on Figs 1 and 3 I have annotated to:
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
GO:0000122 negative regulation of transcription from RNA polymerase II promoter

Revision as of 09:41, 22 June 2011

Examples for discussion at electronic Transcription Jamboree

Resources for curators

  • Karen's curation manual

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


iii) PMID 19342457 [YAF] Based on Figs 1 and 3 I have annotated to:

GO:0000987 core promoter proximal region sequence-specific DNA binding GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription GO:0000122 negative regulation of transcription from RNA polymerase II promoter