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Mapping Rat gene entries to GO

Simon Twigger simont at mcw.edu
Mon Jul 2 11:54:22 PDT 2001


Dear Group,

Here at the Rat Genome Database we've been lurking on the GO Friends list for
a while as we've been looking into GO and planning how to move forward to
incorporate GO annotations into RGD. I've been making our first foray into
annotation via GO entries already attached to genes in other databases and I
would welcome the group's comments and suggestions on how to move forward.

Approach #1 took RGD rat genes with MGD-curated mouse homologs and using the
MGI number of the mouse homolog attached the GO annotation from the Mouse gene
to its rat homolog. This gave us annotations for 964 genes in RGD, 2881
annotations in total. I havent had a chance to break these numbers down into
Biological Process, Molecular Function, Cellular Component yet and the files
still need work to get all the information for a full blown GO record.

Proposed Approach #2: use the EMBL/InterPro/InterPro2GO mappings to get a more
complete dataset. A preliminary plan might be:

For each RGD Gene, match its Genbank DNA sequence accession to the
corresponding EMBL record, retrieve EMBL record with associated InterPro
numbers, map InterPro to GO and use these GO terms to annotate RGD gene
record.

There may well be problems with these approaches that we havent seen and very
likely a more direct route to annotating our rat gene entries that others are
aware of. We would welcome any advice the group can give us as we start to
develop this resource and hopefully we will have more information on progress
to present at the GO meeting later this month.

Cheers,

    Simon,

--
--------------------------------------------------
Simon Twigger, Ph.D.

Assistant Professor
Bioinformatics Research Center
Medical College of Wisconsin,
8701 Watertown Plank Road,
Milwaukee, WI, 53226

tel. 414-456-8802               fax. 414-456-6516
--------------------------------------------------



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