[BioC] RefSeq summary from biomaRt

[Gad Abraham]

On 26/6/09 2:15 PM, Steve Lianoglou wrote:
> Hi,
>
> On Jun 25, 2009, at 11:43 PM, Gad Abraham wrote:
>
>> Hi,
>>
>> Is it possible to get RefSeq summaries for a given gene using biomaRt
>> (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq
>> Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted Protein ID.
>>
>> Specifically, I'm looking for mentions of alternative splicing (e.g.,
>> "Alternatively spliced transcript variants encoding different isoforms
>> have been described").
>
>
> Would the presence of multiple ensembl_transcript_id's for one gene give
> you the information you need?
>
> For example:
>
> R> getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id',
> 'refseq_dna', 'transcript_start', 'transcript_end'),
> filters='hgnc_symbol', value='AKNA', mart=hmart)
> hgnc_symbol ensembl_transcript_id refseq_dna transcript_start
> transcript_end
> 1 AKNA ENST00000223791 116138266 116179065
> 2 AKNA ENST00000320310 116136257 116162197
> 3 AKNA ENST00000374074 116138266 116179736
> 4 AKNA ENST00000312033 116161188 116190182
> 5 AKNA ENST00000394574 116178067 116196506
> 6 AKNA ENST00000374075 116136257 116196506
> 7 AKNA ENST00000394582 116136257 116190037
> 8 AKNA ENST00000374088 NM_030767 116138228 116190064
> 9 AKNA ENST00000307564 116136257 116196506
> 10 AKNA ENST00000374079 116136257 116196506

Thanks Steve,

As far as I understand, having multiple splice variants doesn't in 
itself necessarily indicate that alternative splicing is important for 
the gene's function. My plan was to find such genes through the RefSeq 
description, and then if there is known alternative splicing, get the 
variants.

Gad

-- 
Gad Abraham
MEng Student, Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham