[DAS2] most up-to-date mouse das? (mm7)

[Steve Chervitz]

Ann,

Did you find a solution to your problem of mapping Entrez gene ids into
genomic coords? Some suggestions:

1) You can issue DAS/2 queries using gene names or accessions to retrieve
coordinate info, for example:

http://netaffxdas.affymetrix.com/das2/M_musculus_Aug_2005/features?name=ACTA
1
Or using refseq accession:
http://netaffxdas.affymetrix.com/das2/M_musculus_Aug_2005/features?name=NM_0
09606

2) You can¹t query the Affymetrix DAS/2 server using an Entrez gene id like
11459 (you could in principle, but it¹s not aware of these ids at present).
So you¹ll need to map from Entrez gene ids into accessions using data from
NCBI, such as ftp://ftp.ncbi.nih.gov/gene/gene2refseq.gz

3) There will likely be multiple mRNA sequences associated with a gene id,
so you may want to look up the genomic coordinates for each mRNA and take
the union of those to get a single location for each gene.

Steve

> From: Ann Loraine <aloraine at gmail.com>
> Date: Wed, 17 May 2006 23:20:47 -0500
> To: Steve Chervitz <Steve_Chervitz at affymetrix.com>
> Cc: DAS/2 <das2 at lists.open-bio.org>
> Subject: Re: most up-to-date mouse das? (mm7)
> 
> Hi Steve,
> 
> Thank you very much for the info!
> 
> Now I have another question...
> 
> I'd like to look up the genomic coordinates of a list of mouse genes
> using their numeric Entrez Gene ids.
> 
> If it's not too much bother, do you think you'd be able to give me
> some tips on how to do this using DAS?
> 
> btw, the DAS services have been hugely helpful to me in the last week.
> We have already found some interesting results with minimal coding.
> And the coding was actually fun because there was NO SCREEN-SCRAPING.
> Pure bliss.
> 
> -Ann
> 
> On 5/16/06, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
>> Hi Ann,
>> 
>> The list address has changed. It's now this: das2 at lists.open-bio.org
>> 
>> As for your question, check out the DAS registry server at the Sanger:
>> 
>> http://das.sanger.ac.uk/registry/
>> 
>> I don't think the registry provides an indication of how current the
>> annotations on each registered server for a given data source, such as
>> Entrez Gene. It would be a good piece of data to see, though.
>> 
>> As for the Affymetrix DAS/2 server, the mm7 annotations were last updated on
>> April 19 2006:
>> 
>> http://netaffxdas.affymetrix.com/das2/sources
>> 
>> The available annotations come from the UCSC server, and derive from the
>> knownGene, all_mrna, genscan, and refFlat files (called 'refseq' on the das
>> server). Looks like the knownGene data was last updated by UCSC on 15 Dec
>> 2005:
>> http://hgdownload.cse.ucsc.edu/goldenPath/mm7/database/
>> 
>> Technical note: The xml:base attribute in the das2xml features document
>> returned by the Affy DAS/2 server is currently incorrect. It should be
>> 
>> xml:base="http://netaffxdas.affymetrix.com/das2/M_musculus_Aug_2005/features
>> "
>> 
>> instead of
>> 
>> xml:base="http://127.0.0.1:9021/das2/M_musculus_Aug_2005/features"
>> 
>> This will be fixed in the near future.
>> 
>> Steve
>> 
>>> From: Ann Loraine <aloraine at gmail.com>
>>> Date: Tue, 16 May 2006 03:52:29 -0500
>>> To: Steve Chervitz <Steve_Chervitz at affymetrix.com>
>>> Subject: Fwd: most up-to-date mouse das? (mm7)
>>> 
>>> Hi Steve,
>>> 
>>> Would you post this to the DAS/2 list for me?
>>> 
>>> Sorry to bother you, but for some reason my message didn't appear on the
>>> list.
>>> 
>>> -Ann
>>> 
>>> ---------- Forwarded message ----------
>>> From: Ann Loraine <aloraine at gmail.com>
>>> Date: May 15, 2006 3:35 PM
>>> Subject: most up-to-date mouse das? (mm7)
>>> To: Andrew Dalke <dalke at dalkescientific.com>, DAS/2
>>> <das2 at portal.open-bio.org>
>>> 
>>> 
>>> Hi!
>>> 
>>> I working on a QTL study and need to get all the genes mapping to
>>> various regions under peaks.
>>> 
>>> I have the genomic coordinates for the regions so it should be very
>>> simple for me to get all accessions (feature ids) underneath those
>>> regions using DAS.
>>> 
>>> My question is: what is the most up-to-date server for mm7?
>>> 
>>> Here, of course, is UCSC:
>>> 
>>> http://genome.cse.ucsc.edu/cgi-bin/das/mm7/features?segment=chr1:3000000,400
>>> 00
>>> 00;type=knownGene
>>> 
>>> Ultimately, I'd like to get Entrez Gene ids for the genes under the
>>> peaks so that I can start sifting through the candidates using GO.
>>> 
>>> Any tips would be gratefully accepted!
>>> 
>>> All the best,
>>> 
>>> Ann
>>> 
>>> --
>>> Ann Loraine
>>> Assistant Professor
>>> Section on Statistical Genetics
>>> University of Alabama at Birmingham
>>> http://www.ssg.uab.edu
>>> http://www.transvar.org
>>> 
>>> 
>>> --
>>> Ann Loraine
>>> Assistant Professor
>>> Section on Statistical Genetics
>>> University of Alabama at Birmingham
>>> http://www.ssg.uab.edu
>>> http://www.transvar.org
>> 
>> 
> 
> 
> -- 
> Ann Loraine
> Assistant Professor
> Section on Statistical Genetics
> University of Alabama at Birmingham
> http://www.ssg.uab.edu
> http://www.transvar.org