Gene Enrichment and Pathway Analysis

Perform comprehensive gene enrichment analysis including Gene Ontology (GO), KEGG, Reactome, WikiPathways, and MSigDB enrichment using both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). Integrates local computation via gseapy with ToolUniverse pathway databases for cross-validated, publication-ready results.

IMPORTANT: Always use English terms in tool calls (gene names, pathway names, organism names), even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language.

When to Use This Skill

Apply when users:

• Ask about gene enrichment analysis (GO, KEGG, Reactome, etc.)
• Have a gene list from differential expression, clustering, or any experiment
• Want to know which biological processes, molecular functions, or cellular components are enriched
• Need KEGG or Reactome pathway enrichment analysis
• Ask about GSEA (Gene Set Enrichment Analysis) with ranked gene lists
• Want over-representation analysis (ORA) with Fisher's exact test
• Need multiple testing correction (Benjamini-Hochberg, Bonferroni)
• Ask about enrichGO, gseapy, clusterProfiler-style analyses