R: Pathway Information
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John Zhang ★ 2.9k
@john-zhang-6
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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
Genetics Pathways Cancer probe globaltest Genetics Pathways Cancer probe globaltest • 787 views
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@alexander-c-cambon-1251
Last seen 7.1 years ago
Just correct the typo from "steriods" to "steroids" and it works. Alex >>> "Alberto Goldoni" <alberto.goldoni at="" eurogene.org=""> 6/16/2005 11:43 AM >>> 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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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@alberto-goldoni-711
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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
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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 >
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