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.

• Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.