[BioC] RefSeq summary from biomaRt

[Steve Lianoglou]

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

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos