tooluniverse-gene-enrichment

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

NOT for (use other skills instead):

• Network pharmacology / drug repurposing → Use tooluniverse-network-pharmacology
• Disease characterization → Use tooluniverse-multiomic-disease-characterization
• Single gene function lookup → Use tooluniverse-disease-research
• Spatial omics analysis → Use tooluniverse-spatial-omics-analysis
• Protein-protein interaction analysis only → Use tooluniverse-protein-interactions

---

Input Parameters

Parameter	Required	Description	Example
gene_list	Yes	List of gene symbols, Ensembl IDs, or Entrez IDs	["TP53", "BRCA1", "EGFR"]
organism	No	Organism (default: human). Supported: human, mouse, rat, fly, worm, yeast, zebrafish	human
analysis_type	No	ORA (default) or GSEA	ORA
enrichment_databases	No	Which databases to query. Default: all applicable	["GO_BP", "GO_MF", "GO_CC", "KEGG", "Reactome"]
gene_id_type	No	Input ID type: symbol, ensembl, entrez, uniprot (auto-detected if omitted)	symbol
p_value_cutoff	No	Significance threshold (default: 0.05)	0.05
correction_method	No	Multiple testing: BH (Benjamini-Hochberg, default), bonferroni, fdr	BH
background_genes	No	Custom background gene set (default: genome-wide)	["GENE1", "GENE2", ...]
ranked_gene_list	No	For GSEA: gene-to-score mapping (e.g., log2FC)	{"TP53": 2.5, "BRCA1": -1.3, ...}

---