[Bioperl-l] Converting EnSeMBL Probe names to Gene Symbol with Bioperl

Cook, Malcolm MEC at stowers-institute.org
Fri Sep 19 09:06:08 EDT 2008


Jason,

Yes .... Biomart .... If I remember correctly, at the time I wrote the script, the problem with using biomart interactively for this task was that though you could query for genes or transcripts by affy id, the results would not include the term you queried with, so, you just get a list of genes that match any of your affyids without knowing which goes with which.

But perhaps I was wrong.  Certainly I see now that it is possible interactively to return the affyid for any gene for many standard probesets.

Cheers,

Malcolm Cook

-----Original Message-----
From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason Stajich
Sent: Thursday, September 18, 2008 4:52 PM
To: Cook, Malcolm
Cc: 'Gundala Viswanath'; 'bioperl-l at lists.open-bio.org'
Subject: Re: [Bioperl-l] Converting EnSeMBL Probe names to Gene Symbol with Bioperl

seems like something that biomart was designed for? There is a scripting interface too.
http://biomart.org/

On Sep 18, 2008, at 2:20 PM, Cook, Malcolm wrote:

> Gundala,
>
> Here is an option - if you want a script...
>
> http://research.stowers-institute.org/mec/software/scripts/affyprobese
> t2ensg/
>
> It is not bioperl.   It is perl.  It uses DBI to query the ensembl
> MySQL database using SQL.  It may be outdated due to changes in
> Ensembl schema.
>
> Good luck,
>
> Malcolm Cook
> Stowers Institute for Medical Research - Kansas City, Missouri
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org
> ] On Behalf Of Gundala Viswanath
> Sent: Thursday, September 18, 2008 3:52 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Converting EnSeMBL Probe names to Gene Symbol
> with Bioperl
>
> Dear all,
>
> Is there a way I can convert such EnSeMBL probe names into Gene Symbol
> with BioPerl?
>
> ENSG00000000003_at
> ENSG00000000005_at
> ENSG00000000419_at
> ENSG00000000457_at
> ENSG00000000460_at
> ENSG00000000938_at
> ENSG00000000971_at
> ENSG00000001036_at
> ENSG00000001084_at
> ENSG00000001167_at
> ENSG00000001461_at
> ENSG00000001497_at
> ENSG00000001561_at
> ... etc ...
>
> Or perhaps there is a flat file for conversion?
>
>
>
> - Gundala Viswanath
> Jakarta - Indonesia
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Jason Stajich
jason at bioperl.org






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