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Gene Set Enrichment Analysis (GSEA)

GSEA identifies whether predefined sets of genes show statistically significant, coordinated differences between your experimental conditions.

Running GSEA

Section titled “Running GSEA”
  1. Complete DESeq2 analysis first
  2. Navigate to the GSEA step
  3. Click Run GSEA

What GSEA Does

Section titled “What GSEA Does”

Instead of looking at individual genes, GSEA tests whether groups of related genes (gene sets) are enriched at the top or bottom of your ranked gene list.

Output

Section titled “Output”
  • Enrichment plots — Visualize the enrichment score for each gene set
  • Results table — Enriched pathways with normalized enrichment scores and FDR values
  • Leading edge genes — Key genes driving the enrichment

Interpreting Results

Section titled “Interpreting Results”
  • Positive NES — Gene set is upregulated in treatment
  • Negative NES — Gene set is downregulated in treatment
  • FDR < 0.25 — Considered significant for GSEA (less strict than DESeq2)