Dear Bioconductor users, i have RefSeq gene descriptions and also UniProt identifiers. How can i map this onto KO numbers (KEGG Orthology), e.g. K03120 ?

Hi Alla, Alla Bulashevska wrote: > Dear Bioconductor users, > i have RefSeq gene descriptions and also UniProt > identifiers. > How can i map this onto KO numbers (KEGG Orthology), e.g. > K03120 ? I would use the org.Xx.eg.db package for your organism. Here is an example using the human package. First convert UniProt IDs to Entrez Gene IDs egs <- mget(<uniprot ids="">, revmap(org.Hs.eg.dbUNIPROT)) you should check the resulting list for any missing or duplicate values and deal with those in whatever manner you find useful. You then need to convert to a character vector using e.g., unlist() Now convert Entrez Gene IDs to KEGG IDs kegg <- mget(<entrez gene="" id="" vector="">, org.Hs.egPATH) again, you may need to deal with duplicates. Best, Jim > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues