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Question: How to find back the list of genes involved in pathways produced by a kegg analysis (kegga) with limma package
0
11 months ago by
jambroise830 wrote:

Hello,

I used edger to detect differentially expressed genes based on my RNA-seq data from Rattus Norvegicus samples.

I obtained a list of DE genes and I used the 'kegga' function from the limma package in order to detect kegg pathways with abnormal number of DE genes.

In the result, I obtain a list of kegg pathway and the corresponding number of DE genes and associated p-values.

For some of these pathways (e.g. rno05166), I can not find the list of the genes that are implicated in this pathway so I can not find out if these genes tend to be up- or down- regulated.

library(Rattus.norvegicus)
ENTREZ <- keys(Rattus.norvegicus,keytype = 'ENTREZID')
annot.path <- select(Rattus.norvegicus,keytype = 'ENTREZID',keys=ENTREZ,columns = 'PATH')
select(Rattus.norvegicus,keytype = 'PATH',keys='03030',columns = 'ENTREZID')
select(Rattus.norvegicus,keytype = 'PATH',keys='05166',columns = 'ENTREZID')

For pathway '05166', the following error message is produced:

None of the keys entered are valid keys for 'PATH'. Please use the keys method to see a listing of valid arguments.


How to explain that the 'kegga' function found some genes in the pathway while this pathway is absent in the Rattus.norvegicus annotation package?

Many thanks

Jérôme

edger kegg • 177 views