Hi James,
Thanks for your reply.
What I want is something like this:
http://docs.bioinfo.cipf.es/projects/cellbase/wiki/Feature_rest_ws_api

Cellbase retrieves all microRNA targets sites for a given gene, for 
example, for BRCA2 gene:
*
http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/mirna_target



*I can use this webservice through R, but would like to know if some 
Bioconductor package can handle this....
Thanks again
Javier


On 15/10/12 17:53, James W. MacDonald wrote:
> 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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