Question

GSEA analysis and pathway mapping

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5.7 years ago

ps1212 • 0

Hi,

I have a set of DE genes from a GSEA. I would like to know how to map the genes to pathways in R? This is from Limma's pipeline output. I also have a set of normalized gene counts. How do I make sense of this table to map genes to specific pathways?

pathway R RNA-Seq • 1.4k views

ADD COMMENT • link updated 9 months ago by liux.bio ▴ 360 • written 5.7 years ago by ps1212 • 0

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What do you mean by "map genes to specific pathways"?

ADD REPLY • link 5.7 years ago by h.mon 35k

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Im trying to figure out which genes are part of a certain KEGG pathway.

ADD REPLY • link 5.7 years ago by ps1212 • 0

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Gene Set Clustering based on Functional annotation (GeneSCF)

ADD REPLY • link 5.7 years ago by EagleEye 7.5k

score 1 · Answer 1 · 2023-07-27

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9 months ago

liux.bio ▴ 360

You can use EnrichMiner. It performs GSEA analysis and highlights genes on KEGG pathway map according to expression values.

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ADD COMMENT • link 9 months ago by liux.bio ▴ 360