Overview
What is Enrichr MCP Server?
A Model Context Protocol (MCP) server that provides gene set enrichment analysis using the Enrichr API. It supports hundreds of gene set libraries and returns only statistically significant results (adjusted p < 0.05) to reduce context usage.
How to use Enrichr MCP Server?
Install globally via npx -y enrichr-mcp-server and configure in your MCP client (e.g., .cursor/mcp.json). Use the enrichr_analysis tool for multi-library enrichment, or the query_enrichr_go_bp_tool / go_enrichment tools for GO Biological Process analysis. Custom default libraries can be set via CLI arguments (--libraries) or the ENRICHR_DEFAULT_LIBRARIES environment variable.
Key features of Enrichr MCP Server?
- Multi-library enrichment analysis with simultaneous queries
- Significance filtering (adjusted p < 0.05)
- Detailed results with p-values, z-scores, and combined scores
- Hundreds of gene set libraries supported
- Robust error handling with informative messages
- Specialized GO Biological Process tool
Use cases of Enrichr MCP Server
- Analyze cancer gene lists for enriched pathways and GO terms
- Discover disease associations using phenotype libraries (HPO, OMIM)
- Identify transcription factor targets from ChEA and ENCODE
- Evaluate drug-gene interactions via DrugMatrix and L1000
- Investigate microRNA targets using TargetScan and miRTarBase
FAQ from Enrichr MCP Server
What runtime is required?
Node.js 18+ and an internet connection for Enrichr API access.
Where does the enrichment data come from?
All results are fetched in real‑time from the public Enrichr API (https://maayanlab.cloud/Enrichr/).
Can I specify which libraries to use?
Yes, you can set default libraries via the --libraries CLI argument or the ENRICHR_DEFAULT_LIBRARIES environment variable.
Are results filtered before returning?
Yes, only terms with an adjusted p-value < 0.05 are returned
