Transcription jamboree: Difference between revisions
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- 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? | - 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? | ||
= How much curator judgement is | = How much curator judgement is appropriate? = | ||
i) PMID 12270142 [VK] | i) PMID 12270142 [VK] | ||
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- How can we support curators in judging the part of the DNA region that is being bound, e.g. so that curators can more easily identify a proximal region? Could we include in the curation manuals a diagram of the promoter/regulatory regions which bind proteins - and identify the protein that bind to distinct regions? (perhaps from Karen's presentation, linked to this page?) | |||
- How | - How do you know where an element is located - if the authors do not specifically state it is located upstream? | ||
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Revision as of 12:28, 20 July 2011
Examples for discussion at electronic Transcription Jamboree
Resources for curators
- Karen's curation manual
When do we have enough data for a MF annotation?
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?
How much curator judgement is appropriate?
i) PMID 12270142 [VK] - as K/O of TWIST decreases expression of CBFA1, from figs 1 and 2 could we annotate to
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
- More generally, if a curator is trying to describe the up-regulation of a protein-encoding gene, then is it correct to assume that regulation of expression would necessarily be via the RNA polymerase II. We shouldn't need direct evidence demonstrating the involvement of RNA polymerase II in the experiment?
- Similarly, based on fig 3 could we annotate 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?
- How can we support curators in judging the part of the DNA region that is being bound, e.g. so that curators can more easily identify a proximal region? Could we include in the curation manuals a diagram of the promoter/regulatory regions which bind proteins - and identify the protein that bind to distinct regions? (perhaps from Karen's presentation, linked to this page?)
- How do you know where an element is located - if the authors do not specifically state it is located upstream?