Question: RNA-Seq Pathway analysis in C. elegans, Gene name conversion issues
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gravatar for JPreston
2.9 years ago by
JPreston10
Eugene, OR
JPreston10 wrote:

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]

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

rna-seq c. elegans pathview gage R • 1.2k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by JPreston10
0
gravatar for JPreston
2.9 years ago by
JPreston10
Eugene, OR
JPreston10 wrote:

Nevermind, I figured it out!!

Needed to add the entrez option:

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

ADD COMMENTlink written 2.9 years ago by JPreston10

Closing a post is an action that is generally used by moderators to close posts that are unsuitable/unrelated to the forum. Don't use it on a question that has been answered.

Since you have figured a solution out for your question go ahead and accept your own answer (use the check mark) to indicate that a solution has been found.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax75k
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