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  • KEGG pathway analysis with C. elegans data: Gene name issues

    Hi,

    I want to do a KEGG pathway analysis with C. elegans data using Pathview/Gage in R. I've done this previously with mouse data, using this great tutorial: http://www.gettinggeneticsdone.com/2...ferential.html

    However C. elegans isn't one of the 4 supported genomes that allow the "data(kegg.sets.hs)" command.

    I've found that the following commands can give me KEGG sets for C.elegans:

    kg.cel=kegg.gsets("cel")

    kegg.gs=kg.cel$kg.sets[kg.cel$sigmet.idx]

    headkegg.gs)

    However, the gene names are in a format that I'm unfamiliar with. The gene names I recognize, but they are all starting with "CELE_" Eg. $cel03015 mRNA surveillance pathway [1] "CELE_C01F6.5" "CELE_C02B10.4" "CELE_C03D6.3" "CELE_C05C10.2"

    I can format my expression data to have the gene names, without the "CELE_" part, but can't figure out how to get the "CELE_" onto every single gene name. Is there an easy way to do this?

    Thanks so much!! -Jessica

  • #2
    Figured it out!!

    Needed to specify "entrez id" durind the kegg.gsets step:

    kg.cel=kegg.gsets("cel", id.type = "entrez")

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