[BioC] Gene symbol to KEGG gene ids

[michael watson (IAH-C)]

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... ;)

Mick

-----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

Dan

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
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
> 

-- 
**************************************************************
Daniel Brewer, Ph.D.

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