Dear group, I have 2 questions to ask: Question 1: Give a pathway name for KEGG, how do I get all the genes involved in that pathway. >library(KEGG) >wnt <- get("04310", KEGGPATHID2NAME) now how do I get gene names in wnt pathway. Here I am not interested in taking say HGU133a chip and map all probeset ids to wnt. I just need genes in wnt. Question 2: I have a vector of gene names as object 'mygenes'. I want to see if any genes in 'mygenes' are connected in wnt pathway. mygenes <- c("Wnt","FZD10","DVL1","p53","Ras") We know that Wnt,FZD10 and DVL1 are in linear order. Now is there any way to get the genes that are connected. from mygenes, I want to get Wnt, FZD10 and DVL1 are connected in order. Is this possible? Please help me Thanks Sri

Hi, Srini: try to answer your first question xx <- as.list(KEGGPATHID2EXTID) xx$hsa04310 HTH, Weiwei On 4/13/07, Srinivas Iyyer <srini_iyyer_bio at="" yahoo.com=""> wrote: > Dear group, > I have 2 questions to ask: > > Question 1: > Give a pathway name for KEGG, how do I get all the > genes involved in that pathway. > > >library(KEGG) > >wnt <- get("04310", KEGGPATHID2NAME) > > now how do I get gene names in wnt pathway. Here I am > not interested in taking say HGU133a chip and map all > probeset ids to wnt. I just need genes in wnt. > > > Question 2: > I have a vector of gene names as object 'mygenes'. > I want to see if any genes in 'mygenes' are connected > in wnt pathway. > > mygenes <- c("Wnt","FZD10","DVL1","p53","Ras") > > We know that Wnt,FZD10 and DVL1 are in linear order. > > Now is there any way to get the genes that are > connected. from mygenes, I want to get Wnt, FZD10 and > DVL1 are connected in order. Is this possible? > > Please help me > Thanks > Sri > > _______________________________________________ > 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 > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

As to your second question, I am not sure if "linearity" exists for a pathway. In our research, we created a "noodle" structure by hand but I assume KEGG pathway is a network instead of a linear noodle. So you might need to sacrifice your defn. of linear order or create noodles by yourself. my2cents, weiwei On 4/13/07, Srinivas Iyyer <srini_iyyer_bio at="" yahoo.com=""> wrote: > Dear group, > I have 2 questions to ask: > > Question 1: > Give a pathway name for KEGG, how do I get all the > genes involved in that pathway. > > >library(KEGG) > >wnt <- get("04310", KEGGPATHID2NAME) > > now how do I get gene names in wnt pathway. Here I am > not interested in taking say HGU133a chip and map all > probeset ids to wnt. I just need genes in wnt. > > > Question 2: > I have a vector of gene names as object 'mygenes'. > I want to see if any genes in 'mygenes' are connected > in wnt pathway. > > mygenes <- c("Wnt","FZD10","DVL1","p53","Ras") > > We know that Wnt,FZD10 and DVL1 are in linear order. > > Now is there any way to get the genes that are > connected. from mygenes, I want to get Wnt, FZD10 and > DVL1 are connected in order. Is this possible? > > Please help me > Thanks > Sri > > _______________________________________________ > 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 > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III