[BioC] Gene symbol to KEGG gene ids

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Apr 17 14:15:46 CEST 2009

Hi Dan

In all cases I have seen so far, the NCBI gene ID is the same as the
KEGG gene ID.  However, I like to err on the side of caution, as it only
takes one case where they don't match... ;)


-----Original Message-----
From: Daniel Brewer [mailto:daniel.brewer at icr.ac.uk] 
Sent: 17 April 2009 12:53
To: michael watson (IAH-C)
Cc: Bioconductor mailing list
Subject: Re: [BioC] Gene symbol to KEGG gene ids

In the case of humans it seems that the KEGG ID equals the ncbi gene ID.

Many thanks


michael watson (IAH-C) wrote:
> 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
> 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
> 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
> used to construct the annotation files.  Does anyone know how to get
> this info?
> Thanks
> Dan

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7

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