Individual skill
pathway-enrichment
Pathway and gene-set enrichment analysis — ORA, GSEA, background sets, and honest interpretation.
skills/pathway-enrichment/SKILL.md
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## Overview
pathway-enrichment covers testing whether gene lists or ranked gene profiles concentrate in
known pathways: over-representation analysis (ORA), gene set enrichment analysis (GSEA),
topology-aware methods, database choice (GO, KEGG, Reactome, MSigDB), and the interpretation
discipline that keeps enrichment from becoming story-telling. Enrichment generates hypotheses —
it doesn't confirm mechanisms.
## When to use
- Interpreting DE gene lists: which pathways are over-represented (ORA).
- Ranked-list analysis without thresholds: GSEA/fgsea.
- Choosing gene-set databases: GO, KEGG, Reactome, WikiPathways, MSigDB Hallmark.
- Background/universe selection and why it matters.