eQTpLot

eQTpLot visualizes colocalization between expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) summary statistics to aid interpretation of gene-trait associations.

Key Features:

• Input Requirements: Accepts standard GWAS and eQTL summary statistics and optionally incorporates pairwise linkage disequilibrium (LD) information.
• Implementation: Implemented as an R package for processing and plotting summary statistic data.
• Customizable Multi-panel Plots: Generates a series of customizable plots that integrate multiple aspects of eQTL-GWAS data into single figure panels for specific gene-trait pairs.
• Colocalization Visualization: Displays colocalization between GWAS and eQTL signals at a locus.
• P-value Correlation: Plots correlation between GWAS and eQTL p-values.
• Enrichment Analysis: Performs enrichment analysis of eQTLs among trait-significant variants.
• LD Landscape Visualization: Visualizes the linkage disequilibrium landscape of the locus.
• Effect Direction Analysis: Analyzes the relationship between the direction of eQTL effects and colocalizing GWAS peaks.

Scientific Applications:

• Gene-trait association interpretation: Facilitates interpretation of how variation in gene expression correlates with phenotypic trait associations.
• Causal variant prioritization: Supports identification of potential causal variants through co-localized eQTL and GWAS signals.
• Mechanistic insight: Aids investigation of molecular mechanisms underlying trait associations by linking expression effects to GWAS peaks.

Methodology:

Processes GWAS and eQTL summary statistics, optionally incorporates pairwise LD information, and generates plots that depict colocalization, p-value correlations, eQTL enrichment among trait-significant variants, LD landscapes, and relationships between eQTL effect direction and colocalizing GWAS peaks.