Question: (Closed) How to identify the pathways that are enriched in up-regulated and downregulated genes from RNAseq?
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gravatar for bioinforesearchquestions
15 months ago by
United States
bioinforesearchquestions280 wrote:

Hi friends,

Which approach is correct to do GSEA and pathway analyses.

  • considering all ~20,000 genes as the input for Broad's GSEA tool

or

  • considering only the significantly (p.adj < 0.05) differentially expressed genes as the input for Broad's GSEA tool

My aim is to identify the pathways that are enriched in up-regulated and down-regulated genes.

ADD COMMENTlink written 15 months ago by bioinforesearchquestions280

Hello bioinforesearchquestions!

Questions similar to yours can already be found at:

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ADD REPLYlink written 15 months ago by ATpoint35k
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