KEGG REST: retrieving genes
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 3 days ago
Wageningen University, Wageningen, the …
Hi, I am exploring the package KEGG REST. I would like to retrieve the genes that belong to a specific pathway, e.g. all human genes that are in the Arachidonic Acid Metabolism pathway (= map00590). For now the topology of the pathway is not of relevance to me. I have checked the KEGG REST vignette but could not find how to do this, so if this is possible a pointer would be appreciated. Thanks, Guido As a side node (for the maintainer): I noticed that the API has recently been updated (18 January 2013); a.o. KGML files can now be retrieved and also conversion options from/to KEGG IDs has been expanded. > sessionInfo() R Under development (unstable) (2012-11-21 r61136) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGGREST_0.99.1 loaded via a namespace (and not attached): [1] BiocGenerics_0.5.6 Biostrings_2.27.10 digest_0.6.2 httr_0.2 [5] IRanges_1.17.30 parallel_2.16.0 png_0.1-4 RCurl_1.91-1.1 [9] stats4_2.16.0 stringr_0.6.2 tools_2.16.0 > [[alternative HTML version deleted]]
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 6 days ago
United States
Hi Guido, On Tue, Jan 29, 2013 at 2:24 PM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > Hi, > I am exploring the package KEGG REST. > I would like to retrieve the genes that belong to a specific pathway, e.g. all human genes that are in the Arachidonic Acid Metabolism pathway (= map00590). For now the topology of the pathway is not of relevance to me. > I have checked the KEGG REST vignette but could not find how to do this, so if this is possible a pointer would be appreciated. > Normally the answer would be: keggGet("map00590")[[1]]$GENE But it looks like KEGG does not have gene data for this particular pathway (see the underlying URL, http://rest.kegg.jp/get/path:map00590, we expect a GENE section like you'd see in a different pathway, such as http://rest.kegg.jp/get/path:hsa05200) You can find some (possibly outdated) genes for this pathway by doing the following: library(org.Hs.eg.db) select(org.Hs.eg.db, "00590", cols=c("ENTREZID","SYMBOL"), keytype="PATH") This is old KEGG data and I do not know why their REST interface doesn't contain this data. > Thanks, > Guido > > As a side node (for the maintainer): I noticed that the API has recently been updated (18 January 2013); a.o. KGML files can now be retrieved and also conversion options from/to KEGG IDs has been expanded. Thanks! I will update the package. Dan > >> sessionInfo() > R Under development (unstable) (2012-11-21 r61136) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KEGGREST_0.99.1 > > loaded via a namespace (and not attached): > [1] BiocGenerics_0.5.6 Biostrings_2.27.10 digest_0.6.2 httr_0.2 > [5] IRanges_1.17.30 parallel_2.16.0 png_0.1-4 RCurl_1.91-1.1 > [9] stats4_2.16.0 stringr_0.6.2 tools_2.16.0 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Dan, Actually, after a slight modification your suggestion does work! I realized that the pathways referred to as 'mapxxxxx' are actually the reference pathways; to retrieve the genes for a specific organism 'map' has to be replaced by the abbreviation of that specific organism, e.g. 'hsa' or 'mmu'. Thus, all human genes that are in the Arachidonic Acid Metabolism pathway: > head(keggGet("hsa00590")[[1]]$GENE) 8399 "PLA2G10; phospholipase A2, group X [KO:K01047] [EC:3.1.1.4]" 26279 "PLA2G2D; phospholipase A2, group IID [KO:K01047] [EC:3.1.1.4]" 30814 "PLA2G2E; phospholipase A2, group IIE [KO:K01047] [EC:3.1.1.4]" 50487 "PLA2G3; phospholipase A2, group III [KO:K01047] [EC:3.1.1.4]" 64600 "PLA2G2F; phospholipase A2, group IIF [KO:K01047] [EC:3.1.1.4]" 81579 "PLA2G12A; phospholipase A2, group XIIA [KO:K01047] [EC:3.1.1.4]" > Thanks, Guido -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wednesday, January 30, 2013 00:47 To: Hooiveld, Guido Cc: bioconductor at r-project.org Subject: Re: [BioC] KEGG REST: retrieving genes Hi Guido, On Tue, Jan 29, 2013 at 2:24 PM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > Hi, > I am exploring the package KEGG REST. > I would like to retrieve the genes that belong to a specific pathway, e.g. all human genes that are in the Arachidonic Acid Metabolism pathway (= map00590). For now the topology of the pathway is not of relevance to me. > I have checked the KEGG REST vignette but could not find how to do this, so if this is possible a pointer would be appreciated. > Normally the answer would be: keggGet("map00590")[[1]]$GENE But it looks like KEGG does not have gene data for this particular pathway (see the underlying URL, http://rest.kegg.jp/get/path:map00590, we expect a GENE section like you'd see in a different pathway, such as http://rest.kegg.jp/get/path:hsa05200) You can find some (possibly outdated) genes for this pathway by doing the following: library(org.Hs.eg.db) select(org.Hs.eg.db, "00590", cols=c("ENTREZID","SYMBOL"), keytype="PATH") This is old KEGG data and I do not know why their REST interface doesn't contain this data. > Thanks, > Guido > > As a side node (for the maintainer): I noticed that the API has recently been updated (18 January 2013); a.o. KGML files can now be retrieved and also conversion options from/to KEGG IDs has been expanded. Thanks! I will update the package. Dan > >> sessionInfo() > R Under development (unstable) (2012-11-21 r61136) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United > States.1252 [3] LC_MONETARY=English_United States.1252 [4] > LC_NUMERIC=C [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KEGGREST_0.99.1 > > loaded via a namespace (and not attached): > [1] BiocGenerics_0.5.6 Biostrings_2.27.10 digest_0.6.2 httr_0.2 > [5] IRanges_1.17.30 parallel_2.16.0 png_0.1-4 RCurl_1.91-1.1 > [9] stats4_2.16.0 stringr_0.6.2 tools_2.16.0 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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