Hi Marc, Many thanks for that. The process you describe gives you the pathway KEGG ID rather than the KEGG gene ID. This information is currently not available in the org.Hs.eg.db package. I have manage to get a satisfactory solution from other replies. Thanks for your time and the interesting insight. Dan Marc Carlson wrote: > Hi Daniel, > > To get get the KEGG IDs associated with a particular gene symbol you > must first convert the gene symbols from the org.Hs.eg.db package into > Entrez Gene IDs. There are two reasons for this. The 1st is that we > never want to use gene symbols as primary identifiers because they are > not unique. And the 2nd reason is because the org.Hs.eg.db package is > Entrez Gene centric. So if you have an Entrez Gene ID, then you can get > to every other piece of information in the org.Hs.eg.db package database. > > To achieve this we can do the following: > > library(org.Hs.eg.db) > > ##Toy example symbols: > sym = c("AKT3","CDH1") > > ##Get the Entrez gene IDs associated with those symbols > EG_IDs = mget(sym, revmap(org.Hs.egSYMBOL),ifnotfound=NA) > > ##Then get the KEGG IDs associated with those entrez genes. > KEGG_IDs = mget(as.character(EG_IDs), org.Hs.egPATH,ifnotfound=NA) > > > Please let me know if you have more questions. > > > Marc > > > > > Daniel Brewer wrote: >> 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 ************************************************************** 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 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

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 ************************************************************** 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 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}