Enrichr MCP Server

Q: What runtime is required?

Node.js 18+ and an internet connection for Enrichr API access.

Q: Where does the enrichment data come from?

All results are fetched in real‑time from the public Enrichr API (`https://maayanlab.cloud/Enrichr/`).

Q: 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.

Q: Are results filtered before returning?

Yes, only terms with an adjusted p-value < 0.05 are returned

@tianqitang1

Repository

About Enrichr MCP Server

No overview available yet

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "enrichr-go-only": {
      "command": "npx",
      "args": [
        "-y",
        "enrichr-mcp-server",
        "--libraries",
        "GO_Biological_Process_2025"
      ]
    },
    "enrichr-pathways": {
      "command": "npx",
      "args": [
        "-y",
        "enrichr-mcp-server",
        "-l",
        "GO_Biological_Process_2025,KEGG_2021_Human,Reactome_2022"
      ]
    },
    "enrichr-disease": {
      "command": "npx",
      "args": [
        "-y",
        "enrichr-mcp-server",
        "--libraries",
        "Human_Phenotype_Ontology,OMIM_Disease,ClinVar_2019"
      ]
    }
  }
}

Tools

Perform gene set enrichment analysis using Enrichr across multiple gene set libraries. Returns only statistically significant terms (adjusted p < 0.05). Configured default libraries: - GO_Biological_Process_2025: Gene Ontology terms describing biological objectives accomplished by gene products. Any library in Enrichr's live catalog is accepted. Enrichr adds and retires libraries continuously, so do not rely on a memorized list: call suggest_libraries, or read the enrichr://libraries resource, to discover the libraries that currently exist. Pass 'background' to test against a custom background gene set (for example, only the genes expressed in your assay) instead of Enrichr's whole-genome default. This is the statistically correct choice whenever the gene list was drawn from a restricted universe, and it matters: the whole-genome default can overstate significance by many orders of magnitude. Each library's result reports 'backgroundCorrected'. If Enrichr's background service is unavailable the result falls back to uncorrected whole-genome p-values, flagged with a warning — treat those numbers as inflated and re-run rather than reporting them as background-corrected.

Suggest relevant Enrichr libraries for a research question. Use this before enrichr_analysis to pick the best libraries for a specific topic.

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

Frequently asked questions

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

Comments

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