MCP server · Research

Enrichr MCP server

Lets your AI run gene set enrichment analysis on a list of genes using the Enrichr service.

Research For science and research Search & Data Extraction

This is a helper that connects your AI assistant to Enrichr, a free online service used by biologists to make sense of gene lists. You give your AI a list of genes, and it can ask Enrichr which biological pathways, diseases, or cell types those genes are linked to. It is handy for anyone doing life science research who wants quick answers without clicking through a website.

What is an MCP server? The 30-second version

On its own, your AI can only chat with you using what it already knows. An MCP server is a small helper program that gives your AI a new skill, in this case a connection to Enrichr. Once it is set up, your AI can send your gene list to Enrichr, get the results back, and explain them to you in plain words. You just ask in the chat, and the helper does the back and forth with Enrichr for you.

What this MCP server does

You type a request in your AI chat, like asking which pathways a set of genes belongs to. Your AI passes the gene list to this helper. The helper sends the list to Enrichr and asks it to compare your genes against large collections of known gene sets. Enrichr sends back the matching terms with statistics, and the helper hands them to your AI. Your AI then shows you the significant results and can talk them through with you.

Flow diagram: you ask your AI “Which pathways do TP53, BRCA1, ATM and CHEK2 belong to?”, the Enrichr MCP server connects it to Enrichr, and you get back matching terms with statistics.

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What you can do with it

Find biological pathways linked to a list of genes
Check which diseases or traits your genes are associated with
Suggest the best Enrichr libraries for your research topic
Compare your genes against your own background list instead of the whole genome
Save the full results to a TSV file you can open in a spreadsheet
Adjust how much detail you get back to keep answers short or long

Try asking your AI

“Run enrichment analysis on TP53, BRCA1, ATM, and CHEK2 using the GO Biological Process library”
“Which Enrichr libraries would be best for a study on breast cancer drug resistance”
“Analyze these genes against KEGG and Reactome and show me the top pathways”
“Use my expressed genes as the background and re-run the analysis on this list”

What it gives back to you

You get back a list of significant terms, each with its name, p-values, odds ratio, combined score, and the genes from your list that overlap with that term. Your AI can show this as a readable summary in the chat, and it can also give you the full data in a structured form. If you asked for a file, the complete results are saved as a TSV you can open in Excel or similar tools. If background correction could not be applied, the result is clearly flagged with a warning instead of being quietly presented as corrected.

Before you start

What you need

An MCP client such as Claude Desktop, Cursor, VS Code, or Claude Code
Node.js 18 or newer installed on your computer
An internet connection so the helper can reach the Enrichr service
A list of gene symbols to analyze, at least two

Good to know

The analysis is only as good as the gene list and background you give it, so double-check your inputs before drawing conclusions.

Install it with your AI

Add Enrichr MCP server to your AI, no technical skills needed

You don't install anything by hand. You copy one prompt, paste it into an AI that can work on your computer, and it checks, installs and connects the server for you, asking you when it needs something.

Sign in to get the install prompt

Members get a ready-made prompt that lets the Claude desktop app check Enrichr MCP server, install it and connect it for them, step by step. You don't need any technical skills: you copy, paste and answer a few questions. Your connected AI can also find and install any of the 4,066 MCP servers here for you.