[DAS2] most up-to-date mouse das? (mm7)
Ann Loraine
aloraine at gmail.com
Thu Jun 8 01:43:14 UTC 2006
Thanks Steve!
We ended up looking up the genomic positions in a bit of a grueling way.
We had a list of gene names from a paper that we thought could
influence our eQTLs and then used those to look up (by hand) the
corresponding Entrez Gene ids.
We used gene2refseq.gz to get RefSeq ids mapping onto the gene ids.
Then we used 'bed' files downloaded from UC Santa Cruz to get the
genomic coordinates of the RefSeq ids (alignments) and then checked
them against our list of genomic regions (peaks).
Clearly we could have used DAS to get the positions, which would have
saved coding!
Live and learn :-)
-Ann
On 6/7/06, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
>
> 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=ACTA1
> Or using refseq accession:
> http://netaffxdas.affymetrix.com/das2/M_musculus_Aug_2005/features?name=NM_009606
>
> 2) You can't query the Affymetrix DAS/2 server using an Entrez gene id like
> 11459 (you could in principle, but it's not aware of these ids at present).
> So you'll 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
>
--
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org
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