lamm-mit GTEx Database Skill Summary
Purpose
This skill enables querying the Genotype-Tissue Expression (GTEx) portal to investigate tissue-specific gene expression, expression quantitative trait loci (eQTLs), and splicing QTLs—critical for connecting GWAS variants to regulatory mechanisms.
Primary Use Cases
The documentation identifies several key applications:
- Linking non-coding GWAS variants to regulated genes via eQTL analysis
- Comparing expression patterns across 54 human tissues
- Testing whether GWAS and eQTL signals share causal variants
- Identifying variants affecting RNA splicing ratios
Core Technical Components
API Foundation: The GTEx REST API v2 (base: https://gtexportal.org/api/v2/) provides JSON responses without authentication and supports pagination.
Key Endpoints:
- Gene expression lookup returns median TPM values per tissue
- eQTL queries retrieve significant variant-gene associations with p-values and effect sizes
- Variant-based searches identify all genes regulated by a specific SNP
- Tissue lists provide available samples with metadata
Data Format: The skill uses GENCODE identifiers for genes and employs a standardized variant ID format: chr{chrom}_{pos}_{ref}_{alt}_b38.
Practical Implementation
The documentation provides Python examples demonstrating pagination handling, DataFrame filtering, and multi-tissue aggregation. It emphasizes using GRCh38 coordinates and notes that FDR < 0.05 defines GTEx significance thresholds.
License
The skill is distributed under CC-BY-4.0, authored by Kuan-lin Huang.