[ensembl-dev] Can you link TF-binding sites to the genes they are predicted to regulate in the funcgen database?

[Gordon Robertson]

GREAT appears to be a reasonable tool for the first type of method: http://great.stanford.edu/.  

Gordon


On 2012-02-17, at 7:04 AM, Ian Dunham wrote:

> Mark
> 
> We're kind of wondering this too :-)
> 
> Seriously this is significant aim for a lot of people in the field, and we'd like to be able to provide this through Ensembl.  There are different ways to do it, some of which are achievable now but which need careful interpretation, and others that will require good validated data. A brief synopsis of possibilities includes
> 
> 1. A simple method that is used in the field is to calculate the nearest gene, or more precisely the nearest 5' end of a gene to the TF binding site.  This assumes that the TF is likely to regulate a promoter closest to it, which is frequently but not always the case.  One can implement an approach to do this, but we haven't explicitly made this link on the grounds that it could be misleading since the biology may not always behave that way.
> 
> 2. Interaction mapping such as the various flavours of 3C, 4C, 5C and ChIA-PET should give sets of interactions between regulatory sites that we could use to imply regulation.  Interactions between promoters and distance sites in a cell found in this way would implicate regulation of that promoter in that site.  There are complications because it is possible for cell specific differences.  We're looking for good validated data that we can use in this way, we are aware of at least some data that could be used but there are caveats. Other methods that map looping interactions would also work here.
> 
> 3. Association analysis between signal intensity and, say, expression level by RNA-seq can also be used to infer a relationship between sites and genes.  There is data from several sources now that gives some of this.
> 
> At present our feeling is that neither of the second two is mature enough yet to implement within ensembl but we are monitoring this area, because it is something we want for several reasons.
> 
> We'd be interested in any other suggestions that are out there. I may have neglected some approaches in this brief reply.
> 
> Cheers
> Ian
> 
> Ian Dunham
> 
> 
> On 17/02/2012 14:50, Mark Aquino wrote:
>> Hi all,
>> 
>> I was wondering if it was possible to map the positions where binding factors are predicted to bind (in the funcgen database) to the genes they are predicted to regulate.  If anyone knows how to do this I would be very appreciative.
>> 
>> Best,
>> Mark
>> 
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> 
> 
> 
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--
Gordon Robertson
BC Cancer Agency Genome Sciences Centre
Vancouver BC Canada