Question: How to find back the list of genes involved in pathways produced by a kegg analysis (kegga) with limma package
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gravatar for jambroise83
20 months ago by
jambroise8310
jambroise8310 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 • 298 views
ADD COMMENTlink written 20 months ago by jambroise8310
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