[BioC] get al microRNA target sites for a given gene

[James W. MacDonald]

Hi Javier,

On 10/15/2012 11:42 AM, Javier Pérez Florido wrote:
> Dear list,
> How can I obtain all microRNA target sites for a given gene?

Do you want miRNA target *sites* or target genes? Also, what do you mean 
by 'all'? To my knowledge, miRNA->mRNA mapping is based on sequence 
similarity, which implies a cutoff that can be varied (so 'all' is a 
relative term).

Anyway, you could use the microCosm files that you can download here:

http://www.ebi.ac.uk/enright-srv/microcosm/cgi-bin/targets/v5/download.pl

The files contain the Ensembl transcript ID, as well as the chr, start 
and end. So a simple tapply() (or by()) will give you the by-transcript 
miRNAs, and you can go from there.

Best,

Jim


> I've checked other packages such as miRBase, but it provides 
> information in the other way....(input is a microRNA).
>
> Thanks,
> Javier
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099