alterlab-gtex

GTEx Database

Overview

The Genotype-Tissue Expression (GTEx) project provides a comprehensive resource for studying tissue-specific gene expression and genetic regulation across 54 non-diseased human tissues from nearly 1,000 individuals. GTEx v10 (the latest release) enables researchers to understand how genetic variants regulate gene expression (eQTLs) and splicing (sQTLs) in a tissue-specific manner, which is critical for interpreting GWAS loci and identifying regulatory mechanisms.

Key resources:

• GTEx Portal: https://gtexportal.org/
• GTEx API v2: https://gtexportal.org/api/v2/
• Data downloads: https://gtexportal.org/home/downloads/adult-gtex/
• Documentation: https://gtexportal.org/home/documentationPage

When to Use This Skill

Use GTEx when:

• GWAS locus interpretation: Identifying which gene a non-coding GWAS variant regulates via eQTLs
• Tissue-specific expression: Comparing gene expression levels across 54 human tissues
• eQTL colocalization: Testing if a GWAS signal and an eQTL signal share the same causal variant
• Multi-tissue eQTL analysis: Finding variants that regulate expression in multiple tissues
• Splicing QTLs (sQTLs): Identifying variants that affect splicing ratios
• Tissue specificity analysis: Determining which tissues express a gene of interest
• Gene expression exploration: Retrieving normalized expression levels (TPM) per tissue

Core Capabilities

1. GTEx REST API v2

Base URL: https://gtexportal.org/api/v2/

The API returns JSON and does not require authentication. All endpoints support pagination.

import requests

BASE_URL = "https://gtexportal.org/api/v2"

def gtex_get(endpoint, params=None):
    """Make a GET request to the GTEx API."""
    url = f"{BASE_URL}/{endpoint}"
    response = requests.get(url, params=params, headers={"Accept": "application/json"})
    response.raise_for_status()
    return response.json()

2. Gene Expression by Tissue

import requests
import pandas as pd

def get_gene_expression_by_tissue(gene_id_or_symbol, dataset_id="gtex_v10"):
    """Get median gene expression across all tissues."""
    url = "https://gtexportal.org/api/v2/expression/medianGeneExpression"
    params = {
        "gencodeId": gene_id_or_symbol,
        "datasetId": dataset_id,
        "itemsPerPage": 100
    }
    response = requests.get(url, params=params)
    data = response.json()

    records = data.get("data", [])
    df = pd.DataFrame(records)
    if not df.empty:
        # v2 returns tissueSiteDetailId (not a display-name column), median, unit, geneSymbol
        df = df[["geneSymbol", "tissueSiteDetailId", "median", "unit"]].sort_values(
            "median", ascending=False
        )
    return df

# Example: get expression of APOE across tissues (v10 = GENCODE v39; APOE keeps .10 here)
df = get_gene_expression_by_tissue("ENSG00000130203.10")  # APOE GENCODE ID
print(df.head(10))
# Output: tissueSiteDetailId, median TPM, sorted by highest expression