Question: Reactome pathway analysis using ReactomePA
gravatar for Deepak Tanwar
2.9 years ago by
McGill University, Canada
Deepak Tanwar10 wrote:

I want to use ReactomePA package for reactome pathway analysis.
Problem is, It takes EntrezID as input. Is there a way to use ReactomePA with Gene Symbols.
I know that I can map Gene Symbols with EntrezID, but I don't want to do that. I want to run analysis with Gene Symbols.

ADD COMMENTlink modified 2.8 years ago by kmezhoud10 • written 2.9 years ago by Deepak Tanwar10
gravatar for Guangchuang Yu
2.9 years ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

gene symbol is for human, while entrez gene ID for computer.

You can use bitr function in clusterProfiler to convert gene symbol to entrez gene ID. See the example in vignette,

ADD COMMENTlink written 2.9 years ago by Guangchuang Yu1.0k
gravatar for svlachavas
2.9 years ago by
Greece/Athens/National Hellenic Research Foundation
svlachavas610 wrote:

Dear Deepak,

i dont understand the reason why you don't want to use EntrezIDs instead of Gene Symbols. Anyway, if you are still willing to use as input Gene Symbols, then you could use the web tool Enrichr, which includes a gene-set library for Reactome 2015: . It uses also various scoring methods to compute enrichment.



ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by svlachavas610
gravatar for kmezhoud
2.8 years ago by
kmezhoud10 wrote:


You can just add this line

 GeneID<- unname(unlist(translate(GeneList, org.Hs.egSYMBOL2EG)))


ADD COMMENTlink written 2.8 years ago by kmezhoud10
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