# Gtex Database

Use when you want to retrieve quantitative RNA expression data and variant eQTL...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill gtex-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill gtex-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill gtex-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill gtex-database -g -a gemini-cli -y`

## Description

Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# GTEx Database Integration

This skill retrieves transcriptomics data (RNA expression baselines) and
expression Quantitative Trait Loci (eQTLs) from the GTEx Portal API V2. It
provides access to median TPM (Transcripts Per Million) values for genes and
significant eQTLs for variants across 54 human tissue sites.

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/gtex_database_LICENSE.txt does not
    already exist in the workspace root directory then (1) prominently notify
    the user to check the terms at https://gtexportal.org/home/license and
    https://gtexportal.org/home/documentationPage#gtexApi, then (2) create the
    file recording the notification text and timestamp.

## When to Use

**Use this skill when you need to:**

-   Map a gene symbol to its Versioned GENCODE ID.
-   Retrieve the baseline median expression level (in TPM) of a gene across
    various tissues.
-   Find the top tissues where a particular gene is most highly expressed.
-   Fetch significant single-tissue eQTLs for a variant or within a chromosomal
    window.
-   Get all significant eQTLs associated with a specific gene.
-   Contextualise a variant within GWAS loci using eQTL data.

**Do NOT use when you need to:**

-   Query for protein-level expression or post-translational modifications
    (PTMs). GTEx only measures mRNA abundance.
-   Query gene expression in diseased tissues (e.g., tumor samples, cirrhosis).
    GTEx is a baseline atlas of normal, non-diseased tissues.
-   Query embryonic or fetal gene expression. GTEx donors are adults only.

## Core Rules

**CRITICAL**: You MUST respect GTEx Portal API Terms of Use.

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/gtex_database/SKILL.md