Transcription jamboree: Difference between revisions
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i) PMID 12270142 [VK] | i) PMID 12270142 [VK] | ||
Based on figs 1 and 2 have annotated to | Based on figs 1 and 2 have annotated to | ||
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ii) PMID 17332325 [VK] | ii) PMID 17332325 [VK] | ||
Is Fig 3 sufficient to support the following annotations? | Is Fig 3 sufficient to support the following annotations? | ||
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iii) PMID 19342457 [YAF] | iii) PMID 19342457 [YAF] | ||
Based on Figs 1 and 3 I have annotated REST_HUMAN (Q13127) to: | Based on Figs 1 and 3 I have annotated REST_HUMAN (Q13127) to: | ||
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iv) PMID 17130167 [YAF] | iv) PMID 17130167 [YAF] | ||
Based on Figs 2, 5 and 6, I have tentatively annotated to | Based on Figs 2, 5 and 6, I have tentatively annotated to | ||
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v) PMID 17984088 | v) PMID 17984088 [YAF] | ||
Based on Fig 1 I have annotated REST_H Q13127 to | Based on Fig 1 I have annotated REST_H Q13127 to | ||
Revision as of 10:50, 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 [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 [YAF]
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]