gmane.comp.lang.perl.bio.general

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

headers

Cook, Malcolm | 18 Sep 23:20

Re: Converting EnSeMBL Probe names to Gene Symbol with Bioperl

Gundala,

Here is an option - if you want a script...

http://research.stowers-institute.org/mec/software/scripts/affyprobeset2ensg/

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  It may be outdated due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

(Continue reading)

headers

Jason Stajich | 18 Sep 23:51

Re: 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/affyprobeset2ensg/
>
> 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  It may be outdated due to changes in  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,

(Continue reading)

headers

Cook, Malcolm | 19 Sep 15:06

Re: Converting EnSeMBL Probe names to Gene Symbol with Bioperl

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...
>

(Continue reading)

headers

Chris Fields | 18 Sep 23:48

Re: Converting EnSeMBL Probe names to Gene Symbol with Bioperl

You can probably use the Ensembl perl API alone or in combination with  
bioperl.  I'm not sure it is working with the latest code (bioperl- 
live), but it's worth a try:

http://www.ensembl.org/info/using/api/core/core_tutorial.html
http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_the_Perl_API_at_ENSEMBL

chris

On Sep 18, 2008, at 4:20 PM, Cook, Malcolm wrote:

> Gundala,
>
> Here is an option - if you want a script...
>
> http://research.stowers-institute.org/mec/software/scripts/affyprobeset2ensg/
>
> 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

(Continue reading)

headers

Cook, Malcolm | 19 Sep 15:09

Re: Converting EnSeMBL Probe names to Gene Symbol with Bioperl

Chris is right- the Ensembl perl API works fine. If you care to go this route and want to crib the code, you will
see that my script has a commented out implementation using Ensembl perl API - it suffered from being MUCH
TOO SLOOOOOOOOOO - accessing the tables directly was MUCH faster (unpublished correspondance with self)

However, the API is much more likely to be backwards compatible in the face of database schema changes at Ensembl....

Malcolm Cook

-----Original Message-----
From: Chris Fields [mailto:cjfields <at> illinois.edu]
Sent: Thursday, September 18, 2008 4:48 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

You can probably use the Ensembl perl API alone or in combination with bioperl.  I'm not sure it is working
with the latest code (bioperl- live), but it's worth a try:

http://www.ensembl.org/info/using/api/core/core_tutorial.html
http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_the_Perl_API_at_ENSEMBL

chris

On Sep 18, 2008, at 4:20 PM, Cook, Malcolm wrote:

> Gundala,
>
> Here is an option - if you want a script...
>

(Continue reading)