[ensembl-dev] Can you link TF-binding sites to the genes they are predicted to regulate in the funcgen database?
Ian Dunham
dunham at ebi.ac.uk
Fri Feb 17 15:04:54 GMT 2012
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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