Transcription jamboree

Examples for discussion at electronic Transcription Jamboree

Resources for curators

• TxnOverhaulKChristie.ppt Karen's transcription presentation

• 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

Not sure if these are correct.

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

v) PMID 17984088 Based on Fig 1 I have annotated REST_H Q13127 to

GO:0001047 core promoter binding

GO:0045892 negative regulation of transcription, DNA-dependent

GO:0045893 positive regulation of transcription, DNA-dependent

and based on Fig 4 I have annotated BRM_H P51531 to

GO:0045893 positive regulation of transcription, DNA-dependent

GO:0001105 RNA polymerase II transcription coactivator activity

GO:0044212 transcription regulatory region DNA binding

Possible full papers for jamboree

PMID 18062917 [VK]