Transcription jamboree: Difference between revisions
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i) PMID 11486045 [VK] - Fig 2 | i) PMID 11486045 [VK] - Fig 2 | ||
=How much evidence is needed to make MF annotations = | |||
i) PMID 11486045 [VK] - Fig 2 | |||
- this data would have been previously annotated to the now obsolete term GO:0016564 transcription repressor activity. | |||
GO | - can we can we annotate to anything more than the biological process: 'GO:00045892; negative regulation of transcription, DNA-dependent', and 'DNA binding' | ||
as the molecular function? | |||
- There is no indication anymore in the available MF terms of a proteins repressor activity, concerns about losing this information. | |||
GO | - if we can discribe the binding of a protein as activating transcription in the molecular function ontology (GO 0001102 RNA polymerase II activating transcription factor binding ), why are we no longer able state that a transcription factor is activating or repressing in its activity? | ||
=Annotation to promoter/DNA binding terms = | =Annotation to promoter/DNA binding terms = |
Revision as of 12:10, 20 July 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
How much evidence is needed to make MF annotations
i) PMID 11486045 [VK] - Fig 2 - this data would have been previously annotated to the now obsolete term GO:0016564 transcription repressor activity.
- can we can we annotate to anything more than the biological process: 'GO:00045892; negative regulation of transcription, DNA-dependent', and 'DNA binding' as the molecular function?
- There is no indication anymore in the available MF terms of a proteins repressor activity, concerns about losing this information.
- if we can discribe the binding of a protein as activating transcription in the molecular function ontology (GO 0001102 RNA polymerase II activating transcription factor binding ), why are we no longer able state that a transcription factor is activating or repressing in its 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
vi) PMID 20590529 [RH]
Based on Fig. 3 (p240) have annotated MEF2A (Q02078) and MEF2D (Q14814) to;
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
(may not be enough evidence for the second annotation; extract: "we performed a time-course analysis of c-Jun expression in PMA-differentiated cells.MEF2A and MEF2D proteins were induced within 2 h of treatment, before c-Jun, whose up-regulation was seen after 4 h (Figure 3B). These data support the idea that c-Jun is regulated by MEF2 in HL60 cells."
Possible full papers for jamboree
PMID 18062917 [VK]