Reactome pathway analysis using ReactomePA
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@deepak-tanwar-8113
Last seen 23 months ago
McGill University, Canada

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.

reactomepa R bioconductor ReactomePA • 1.6k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

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

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svlachavas ▴ 780
@svlachavas-7225
Last seen 4 days ago
Germany/Heidelberg/German Cancer Resear…

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

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kmezhoud ▴ 10
@kmezhoud-6841
Last seen 2.5 years ago
Tunisia

Hi,

You can just add this line

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

Karim

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