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gtex-database

Retrieve GTEx baseline RNA expression and single-tissue eQTL associations for genes and genomic regions.

2.7k|283|Updated May 13, 2026
Search Tags:#api integration#transcriptomics#gtex#genomics data#expression profiling#eQTL mapping#gene identifier resolution
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill gtex-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gtex-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill gtex-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

GTEx users need an efficient way to obtain consistent baseline mRNA expression (TPM) and variant–gene eQTL associations across many human tissues without manually navigating the GTEx portal.

Core Features & Use Cases

  • Gene symbol to GTEx-ready identifier: Convert a gene symbol into the correct Versioned GENCODE ID needed for GTEx API V2 queries.
  • Expression profiling across tissues: Retrieve median gene expression (TPM) across all 54 non-diseased tissue sites or a user-specified tissue subset.
  • eQTL discovery for genes and variants: Fetch significant single-tissue eQTLs for a gene and retrieve eQTLs within a chromosomal window for a chosen tissue.

Quick Start

Use the gtex-database skill to resolve the gene symbol TNF to its Versioned GENCODE ID and write the JSON output to /tmp.

Frequently Asked Questions about gtex-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve GTEx median TPM expression values for a specific gene across all tissues?▼

You can retrieve GTEx baseline RNA expression by using the provided scripts to query the API V2. The skill resolves a standard gene symbol to a Versioned GENCODE ID and fetches median TPM values across 54 non-diseased tissues, outputting the results as JSON files.

What is the best way to query significant single-tissue eQTLs for a gene?▼

To query significant single-tissue eQTLs, use this skill to fetch variant-gene associations for a specific gene via the GTEx API V2. It also supports retrieving eQTLs within specified chromosomal windows of up to 8Mb.

Do I need a Versioned GENCODE ID to fetch eQTL associations and expression profiling from GTEx?▼

Yes, the GTEx API V2 requires a Versioned GENCODE ID for expression and eQTL queries. This skill handles gene identifier resolution by automatically mapping your standard gene symbol to the correct Versioned GENCODE ID.

Can I retrieve eQTLs within a chromosomal window instead of querying by gene identifier?▼

Yes, you can retrieve eQTLs within a chromosomal window. The skill supports querying significant single-tissue eQTL associations within up to 8Mb windows for a chosen tissue without needing a specific gene identifier.

How do I ensure my genomics data queries respect GTEx Portal API rate limits?▼

To respect GTEx Portal API terms of use and rate limits, you must use the provided scripts included in this skill. These scripts manage the API integration securely and write the retrieved expression or eQTL outputs as JSON files to your filesystem.

What are the limitations when mapping gene symbols to GTEx-ready identifiers?▼

The main limitation is that gene identifier resolution must match the exact Versioned GENCODE ID required by the GTEx API V2. Additionally, eQTL mapping is restricted to single-tissue associations and specific chromosomal windows of up to 8Mb.

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