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GTEx MCP Server

Provides access to GTEx Portal data and 25 tools for expression, association, and reference analyses.

Installation

Add the following to your MCP client configuration file.

Configuration

{
  "mcpServers": {
    "augmented-nature-gtex-mcp-server": {
      "command": "node",
      "args": [
        "/path/to/gtex-server/build/index.js"
      ]
    }
  }
}

You can access GTEx Portal data through a complete MCP server that exposes 25 specialized tools across expression, association, and reference datasets. This server lets you query gene expression, eQTL/sQTL analyses, tissue metadata, and more, enabling AI assistants to perform comprehensive genomics research with GTEx data.

How to use

You interact with the GTEx MCP server via a client that speaks the MCP protocol. Use it to perform common genomics analyses such as retrieving gene expression across tissues, finding tissue-specific genes, exploring eQTL results, and looking up gene or variant information. You can run analyses individually or chain multiple tools to build complex workflows. When you issue a request, you specify the tool name and the required parameters (for example a gene identifier and tissue of interest). The server returns structured results that you can feed into downstream analyses, visualizations, or reports. You can also perform coordinate conversions between genome builds and fetch dataset-level metadata to understand what data is available and how it was collected.

How to install

Prerequisites: you need Node.js installed on your machine. You also need a compatible MCP client to talk to the server using MCP protocol messages.

Step 1: Install dependencies for the GTEx MCP server.

# Navigate to the server directory
cd gtex-server

# Install dependencies
npm install

Configuration and running

Step 2: Build the server before running in development or production mode.

npm run build

Step 3: Start the server for development or testing.

npm run dev
```

To inspect MCP interactions during development, you can also start the inspector tool if you are troubleshooting or validating tool registrations.

Example configuration for local MCP client

If you are configuring a local MCP client (such as Claude Desktop) to connect to this server, provide the following stdio configuration to launch the server from your client.

{
  "mcpServers": {
    "gtex-server": {
      "command": "node",
      "args": ["/path/to/gtex-server/build/index.js"]
    }
  }
}

Available tools

get_gene_expression

Retrieve gene expression data across tissues for specified genes, enabling tissue-wide expression profiling.

get_median_gene_expression

Return median expression levels for a gene across all tissues to summarize typical expression.

get_top_expressed_genes

Identify the top expressed genes within selected tissues to highlight tissue-dominant transcripts.

get_tissue_specific_genes

Find genes with tissue-specific expression patterns across the GTEx tissues.

get_clustered_expression

Provide clustered gene expression data suitable for visualization and heatmaps.

calculate_expression_correlation

Compute Pearson correlation of gene expression across tissues to assess co-expression.

get_differential_expression

Fetch differential expression results between tissue groups to compare conditions.

get_eqtl_genes

List genes with eQTL associations within specified genomic regions.

get_single_tissue_eqtls

Obtain single-tissue eQTL results for target genes.

calculate_dynamic_eqtl

Analyze how eQTL effects change across different tissues.

get_multi_tissue_eqtls

Retrieve meta-analysis eQTL results across multiple tissues.

get_sqtl_results

Fetch splicing QTL (sQTL) results for genes to study splicing regulation.

analyze_ld_structure

Assess linkage disequilibrium structure around given variants.

search_genes

Search for genes by symbol, name, or description to locate targets quickly.

get_gene_info

Get detailed information about a specific gene, including aliases and annotations.

get_variants

Retrieve genetic variants within specified genomic regions.

get_tissue_info

Fetch metadata about GTEx tissues and sample counts.

get_sample_info

Access GTEx sample metadata and demographics for analysis context.

get_subject_phenotypes

Obtain subject phenotype data and demographics for population-level insights.

validate_gene_id

Validate and normalize gene identifiers to ensure accurate queries.

validate_variant_id

Validate variant identifiers and genomic coordinates for queries.

get_dataset_info

Retrieve information about available GTEx datasets and versions.

search_transcripts

Search for transcripts and isoforms for a given gene.

get_gene_ontology

Fetch Gene Ontology annotations for a gene to support functional analysis.

convert_coordinates

Convert genomic coordinates between hg19 and hg38 builds.