Gene symbol to KEGG gene ids
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 7.1 years ago
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 MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** 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}}
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States
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 > >
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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}}
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@michael-watson-iah-c-378
Last seen 7.1 years ago
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@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 MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** 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:9}}
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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}}
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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@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 ************************************************************** 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:5}}
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Is Entrez ID = NCBI gene ID = KEGG ID ? On Fri, Apr 17, 2009 at 7:52 PM, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> wrote: > 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}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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