Gene Symbol to KEGG Pathway
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@srinivasan-ramachandran-1922
Last seen 8.1 years ago
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Dear Ramachandran, The process is: gene symbols --> Entrez Gene ID --> KEGG pathway ID --> KEGG pathway names. You can get the first step done via Entrez Gene database, and get the rest done via KEGG database. If you want to make it work in bioconductor, there is a far-from- elegant way: ## gene symbols --> Entrez Gene ID library(biomaRt) ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl") eg <- getBM(attributes=c("hgnc_symbol","entrezgene"), filters="hgnc_symbol", values=symbols, mart=ensembl) ## clean up the result a bit eg <- split(eg[,2], eg[,1]) eg <- lapply(eg, function(x) { unique(x)[1] }) ## Entrez Gene ID --> KEGG pathway ID library(KEGG) kegg <- mget(as.character(eg), KEGGEXTID2PATHID, ifnotfound=list(NA)) ## KEGG pathway ID --> KEGG pathway name i <- which(!is.na(kegg)) kegg[i] <- lapply(kegg[i], function(x) { x <- sub("hsa", "", x) unlist(mget(x, KEGGPATHID2NAME, ifnotfound=list(NA))) }) names(kegg) <- names(eg) hope it is helpful nianhua ======================================= Dear Colleagues, I have a list of Human Gene Symbols and I need to get the corresponding KEGG pathways. Can anyone show me the Bioconductor function to accomplish this? Many Thanks in Advance Ramachandran Dr. S. Ramachandran Scientist E I G.N. Ramachandran Knowledge Centre for Genome Informatics Institute of Genomics and Integrative Biology Mall Road, Delhi 110 007 Tel: 091-11-2766-6156 Fax: 091-11-2766-7471
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