[BioC] Gene symbol to KEGG gene ids

[michael watson (IAH-C)]

Hi Daniel

Have a look at the KEGG ftp site.

Say your organism is chicken, then
ftp://ftp.genome.jp/pub/kegg/genes/organisms/gga/gga_ensembl.list links
KEGG gene IDs to ensembl gene IDs, and
ftp://ftp.genome.jp/pub/kegg/genes/organisms/gga/gga_ncbi-geneid.list
links KEGG gene IDs to NCBI gene IDs.  Both ensembl and the NCBI can
then provide the link from their ID to gene symbol.

The link from KEGG gene ID to KEGG pathway is in the file
ftp://ftp.genome.jp/pub/kegg/genes/organisms/gga/gga_pathway.list

Mick

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Daniel
Brewer
Sent: 17 April 2009 11:00
To: Bioconductor mailing list
Subject: [BioC] Gene symbol to KEGG gene ids

Hello,

The org.Hs.eg.db package provides annotations that link a gene to a
particular KEGG pathway.  What I would like to know is what is what are
the KEGG ids associated with this gene symbol.  This information does
not seem to be available in either KEGG.db or org.Hs.eg.db, but must be
used to construct the annotation files.  Does anyone know how to get
this info?

Thanks

Dan

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Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
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Tel: +44 (0) 20 8722 4109

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