Pathway Enrichment Overview Enrichment analysis answers "what biology is over-represented in my genes?" It is the standard last step after differential expression, a screen, or clustering. There are two core methods, and choosing correctly is the single most important decision: - ORA (over-representation analysis) — take a thresholded gene list (e.g., padj < 0.05) and test which gene sets it overlaps more than chance, using Fisher's exact / hypergeometric tests. Tools: Enrichr, g:Profiler. - GSEA (gene set enrichment analysis) — take the whole ranked list of genes (no threshold) and test whet…