gtex-database
Access the GTEx portal's REST API to explore how genetic variants regulate gene expression across 54 human tissues. Find eQTL associations for your GWAS variants, retrieve tissue-specific expression levels, and identify splicing QTLs to uncover regulatory mechanisms underlying non-coding variants.
GTEx Database lets you query tissue-specific eQTLs and gene expression to interpret GWAS variants' regulatory effects.
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Install
LeonChaoX/qinyan-academic-skills/gtex-database · repository language: Python
git clone https://github.com/LeonChaoX/qinyan-academic-skills
cp -r qinyan-academic-skills/skills/12-科学数据库/gtex-database ~/.claude/skills/gtex-databaseFrequently asked questions
AI-generated answers based on this skill's SKILL.md and metadata
What is gtex-database and what can it help me find?
gtex-database provides access to the GTEx portal's REST API, enabling you to explore how genetic variants regulate gene expression across 54 human tissues. The skill helps you find eQTL associations for GWAS variants, retrieve tissue-specific expression levels in TPM units, identify splicing QTLs, and uncover regulatory mechanisms underlying non-coding variants. It's licensed under MIT.
How do I query eQTL variants for gene regulation using gtex-database?
gtex-database lets you query eQTL variants to discover gene regulation patterns. You can look up specific variants to find which genes they regulate, retrieve eGenes by tissue type, and map GWAS loci to their target genes through eQTL associations. The skill supports variant-to-gene mapping across all 54 tissues in the GTEx dataset.
Can gtex-database help me find tissue-specific expression levels?
Yes, gtex-database retrieves tissue-specific gene expression levels across GTEx's 54 human tissues. You can compare gene expression patterns across multiple tissues for annotation purposes, access TPM values for your genes of interest, and perform multi-tissue expression comparisons to understand tissue-dependent regulation.
What are splicing QTLs and how does gtex-database help discover them?
gtex-database helps you discover splicing QTLs (sQTLs)—genetic variants that affect gene isoform usage rather than overall expression levels. The skill identifies tissue-specific sQTL effects, allowing you to understand how variants influence alternative splicing patterns across different tissues and uncover regulatory mechanisms for non-coding variants.
How can gtex-database support GWAS variant interpretation?
gtex-database enables GWAS variant interpretation by finding eQTL associations that explain regulatory effects of your variants. You can map GWAS loci to regulated genes, perform multi-tissue eQTL colocalization analysis, and identify which tissues show the strongest regulatory effects for your variants of interest.
What data sources and formats does gtex-database provide access to?
gtex-database accesses the GTEx portal's comprehensive gene expression atlas covering 54 human tissues. It provides expression quantitative trait loci (eQTL) data, splicing QTL information, and tissue-specific expression measurements. The skill integrates with the GTEx REST API for programmatic queries and supports standard genomic variant identifiers for lookups.
SKILL.md
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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:
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skills/12-科学数据库/gtex-database/SKILL.md
skills/12-科学数据库/gtex-database/references/api_reference.md