Off topic:How to identify the pathways that are enriched in up-regulated and downregulated genes from RNAseq?
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5.1 years ago

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.
RNA-Seq DEGs pathway analysis GSEA • 594 views
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