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Question: Reactome pathway analysis using ReactomePA
0
gravatar for Deepak Tanwar
2.1 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 2.1 years ago by kmezhoud0 • written 2.1 years ago by Deepak Tanwar10
1
gravatar for Guangchuang Yu
2.1 years ago by
Hong Kong
Guangchuang Yu800 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,

http://bioconductor.org/packages/3.2/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

ADD COMMENTlink written 2.1 years ago by Guangchuang Yu800
0
gravatar for svlachavas
2.1 years ago by
svlachavas560
Greece/Athens/National Hellenic Research Foundation
svlachavas560 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:  http://amp.pharm.mssm.edu/Enrichr/ . It uses also various scoring methods to compute enrichment.

Best,

Efstathios

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by svlachavas560
0
gravatar for kmezhoud
2.1 years ago by
kmezhoud0
Tunisia
kmezhoud0 wrote:

Hi,

You can just add this line

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

Karim

ADD COMMENTlink written 2.1 years ago by kmezhoud0
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