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

[James W. MacDonald]

Hi Javier,

On 10/16/2012 3:06 AM, Javier Pérez Florido wrote:
> 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....

There is the mirbase.db package, but you would need to poke around to 
see what it can do - I have never found it particularly helpful for my 
use cases.

Best,

Jim


> 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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>>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099