Disease related signaling pathway

Question

[496527]

I want to download disease related signaling pathway in Kegg.

I tried r package KEGGREST but I don't know how to do it.

*how do i know interaction between two genes(in signaling pathway)

Please give me a help.

Thank you so much

[Benn]

Hi maybe it is wise to explain more what exactly you want to do. Just downloading seems a bit strange since you work in R. I mean downloading is not really something I use R for...

Answer 1

[Benn]

Let me first say that KEGG is not being updated in R, since it is not open access anymore (I guess since 2012 or so).

Having said that...

I think you want to know which pathways contain two genes of interest? Did I understand that correct?

I would recommend to make use of clusterProfiler. If you want e.g. to know in what pathways BRCA1 and BRCA2 both are involved use something like:

kk <- enrichKEGG(gene         = c("675","672"),
                 organism     = 'hsa',
                 pvalueCutoff = 1)

Where entrez ID are used.

summary(kk)

Will show you all pathways where one or both genes are present.

Hope this helps?