Transcription jamboree
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 [VK] - 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) [VK] 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 [VK] 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 [VK] 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 REST_HUMAN (Q13127) 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
iv) PMID 17130167 [YAF] Based on Figs 2, 5 and 6, I have tentatively annotated to
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
GO:0045892 negative regulation of transcription, DNA-dependent
Possible full papers for jamboree
PMID 18062917 [VK]