RNA-Seq Pathway analysis in C. elegans, Gene name conversion issues

Question

[JPreston]

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/2015/12/tutorial-rna-seq-differential.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]
head(kegg.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_" E.g.,

$`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

Answer 1

[JPreston]

Nevermind, I figured it out!!

Needed to add the entrez option:

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

[GenoMax]

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