the other place to look for pathways is in the cMAP package - they are set up a bit differently, so you will need to do a bit more work (I think), but any reports on what did or did not work - to the list please - would be helpful. cMAP has both KEGG and BioCarta pathway data. Robert Alberto Goldoni wrote: > Now it works! > > get(paste("hsa", get("Biosynthesis of steroids", KEGGPATHNAME2ID),sep= > ""),KEGGPATHID2EXTID) > [1] "10654" "10682" "1717" "1728" "2222" "2224" "3156" "3422" > "4047" "4597" "4598" "4835" "51302" "6309" "6713" "79001" "91734" > "9420" "9453" > > but if now i would like to create a file ex CVS in which i can have: > > "10654" ----> pathway1..... > "10682"-----> pathway2 > > > > "9420"------->pathwayN > > how can i obtain it? > > thanks > > -----Messaggio originale----- > Da: John Zhang [mailto:jzhang at jimmy.harvard.edu] > Inviato: gioved? 16 giugno 2005 17.56 > A: jzhang at jimmy.harvard.edu; michael.auer at meduniwien.ac.at; > rhaddad at genetics.wayne.edu; alberto.goldoni at eurogene.org > Cc: bioconductor at stat.math.ethz.ch > Oggetto: Re: R: [BioC] Pathway Information > > Sorry for the typo. steriods should be steroids. > > >>X-Original-To: jzhang at jimmy.harvard.edu >>Delivered-To: jzhang at jimmy.harvard.edu >>From: "Alberto Goldoni" <alberto.goldoni at="" eurogene.org=""> >>To: "'John Zhang'" <jzhang at="" jimmy.harvard.edu="">, > > <michael.auer at="" meduniwien.ac.at="">, > <rhaddad at="" genetics.wayne.edu=""> > >>Cc: <bioconductor at="" stat.math.ethz.ch=""> >>Subject: R: [BioC] Pathway Information >>Date: Thu, 16 Jun 2005 17:43:49 +0200 >>MIME-Version: 1.0 >>Content-Transfer-Encoding: quoted-printable >>X-Priority: 3 (Normal) >>X-MSMail-Priority: Normal >>X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1506 >>Importance: Normal >>X-Virus-Scanned: Cineca AppOs 0.86 at poster.unibo.it >>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > > pascal.dfci.harvard.edu > >>X-Spam-Level: >>X-Spam-Status: No, score=-1.3 required=3.0 tests=AWL,BAYES_00 > > autolearn=ham > version=3.0.1 > >>Sorry but it doesn't work: >> >> >>>get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), >> >>sep= ""),KEGGPATHID2EXTID) >>Error in get(x, envir, mode, inherits) : variable "Biosynthesis of >>steriods" not find >> >>-----Messaggio originale----- >>Da: bioconductor-bounces at stat.math.ethz.ch >>[mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di John Zhang >>Inviato: gioved? 16 giugno 2005 16.55 >>A: michael.auer at meduniwien.ac.at; rhaddad at genetics.wayne.edu >>Cc: bioconductor at stat.math.ethz.ch >>Oggetto: Re: [BioC] Pathway Information >> >>Suppose you are looking for gene that are involved in human >>"Biosynthesis of >>steriods" pathway, the following will give you a vector of Entrez Gene >>ids: >> >> >>>library(KEGG) >>>get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep >> >>= ""), >>KEGGPATHID2EXTID) >> >> >> >>>X-Original-To: jzhang at jimmy.harvard.edu >>>Delivered-To: jzhang at jimmy.harvard.edu >>>From: Ramsi Haddad <rhaddad at="" genetics.wayne.edu=""> >>>To: michael.auer at meduniwien.ac.at >>>Mime-Version: 1.0 >>>Date: 16 Jun 2005 09:58:13 -0400 >>>Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is >> >>authenticated by a >>trusted mechanism) >> >>>Received-SPF: none (hypatia: domain of rhaddad at genetics.wayne.edu does >> >>not >>designate permitted sender hosts) >> >>>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >>>Cc: bioconductor mailing list <bioconductor at="" stat.math.ethz.ch=""> >>>Subject: Re: [BioC] Pathway Information >>>X-BeenThere: bioconductor at stat.math.ethz.ch >>>X-Mailman-Version: 2.1.6 >>>List-Id: The Bioconductor Project Mailing List >> >><bioconductor.stat.math.ethz.ch> >> >>>List-Unsubscribe: > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >> >>>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >>>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >>>List-Help: > > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > >>>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >> >>>Content-Transfer-Encoding: 7bit >>>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on >> >>pascal.dfci.harvard.edu >> >>>X-Spam-Level: >>>X-Spam-Status: No, score=-2.2 required=3.0 tests=AWL,BAYES_00 >> >>autolearn=ham >>version=3.0.1 >> >>> >>>Dear Michael, >>> There is a pretty good description in the globaltest vignette. >> >>Most of >> >>>the stuff shown below is based on it: >>> >>>library(mgu74av2) >>>library(KEGG) >>> >>>### this next line generates a list of kegg pathways and all >>>### the probe sets that belong in a given pathway. >>>mouse.kegg.sets <- as.list(mgu74av2PATH2PROBE) >>> >>>### the next 3 lines give the names of the pathways from their >>>### kegg ID numbers >>>all.kegg.ids <- ls(KEGGPATHID2NAME) >>>all.kegg.names <- mget(all.kegg.ids, KEGGPATHID2NAME) >>>table.of.keggs <- as.matrix(unlist(all.kegg.names)) >>>write.table(table.of.keggs, "keggs.csv", sep=",",col.names=NA, >>>row.names=T) >>> >>>### here's how to get the name of a given kegg pathway: >>>what.is.00010 <- get("00010", KEGGPATHID2NAME) ## this is glycolysis. >>> >>>### here's how to get the probesets in the Glycolysis Path from the >>>mouse array: >>>glycolysis.affyIDs <- get("00010", mgu74av2PATH2PROBE) ## there are 68 >>>such probe sets. >>>another.glycolysis.affyIDs <- mouse.kegg.sets[["00010"]] ## more than >>>one way to skin a cat >>> >>>### here's how to get the kegg pathway numbers for anything with >>>"Cholera" >>>colera.kegg.paths.index <- grep("Cholera", table.of.keggs) ## this >>>provides the index >>>colera.keggs <- table.of.keggs[colera.kegg.paths] >>>### here it is in one step: >>>### table.of.keggs[grep("Cholera", table.of.keggs)] >>> >>>hope that gets you started. >>> >>>Ramsi >>> >>> >>> >>> >>> >>>>Hi >>>> >>>>Can anybody tell me the following >>>> >>>>I want to identify genes which are located on a certain pathway NF >> >>Kappa. >> >>>>How can I obtain such an information. Which package is appropriate >> >>and >> >>>>which commands are needed. If any body ever encounterd the same >> >>problem >> >>>>please let me know. >>>> >>>>Michael >>> >>>-- >>>Ramsi Haddad, Ph.D. >>>Center for Molecular Medicine and Genetics. >>>Functional Genomics Laboratory, >>>Perinatology Research Branch, NICHD, NIH. >>>259 Mack Avenue, >>>Room 3146 Applebaum Bldg. >>>Detroit, MI 48201, USA. >>> >>>phone:(313) 577-2569 / fax:(313) 577-7736 >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>Jianhua Zhang >>Department of Medical Oncology >>Dana-Farber Cancer Institute >>44 Binney Street >>Boston, MA 02115-6084 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >