Hi Fabrice, suppose you are using human genes and that you have gene symbols then you could do something like this: library("org.Hs.eg.db") twoGenes <- c("ATM", "TP53") ## convert them to Entrez Gene ids twoGenesEG <- unlist(mget(twoGenes, org.Hs.egSYMBOL2EG)) twoGenesEGkegg <- mget(twoGenesEG, org.Hs.egPATH) commonKegg <- intersect(twoGenesEGkegg[[1]], twoGenesEGkegg[[2]]) print(commonKegg) ##[1] "04110" "04115" "04210" ## what are these pathways library("KEGG.db") mget(commonKegg, KEGGPATHID2NAME) ##$`04110` ##[1] "Cell cycle" ## ##$`04115` ##[1] "p53 signaling pathway" ## ##$`04210` ##[1] "Apoptosis" HTH, J. On 05/21/2011 01:39 PM, Fabrice Tourre wrote: > If just using Gene symbol is OK or should convert Gene symbol to KEGG > gene ids first? > > > > On Sat, May 21, 2011 at 12:58 PM, Fabrice Tourre<fabrice.ciup at="" gmail.com=""> wrote: >> Dear list, >> Is there some packages can quikly know whether two genes are in the >> same pathway or not? For example, kegg pathway. >> Thanks. >> > > _______________________________________________ > 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 >