GeneOverlap

GeneOverlap assesses intersections between two gene lists and quantifies statistical significance to identify shared genes between GWAS loci and differentially expressed genes or proteins, facilitating cross-species comparison via human orthologs.

Key Features:

• Intersection Analysis: Calculates overlaps between gene sets and reports odds ratios (ORs) and P values for each intersection.
• Multiple Testing Correction: Adjusts P values using the Benjamini-Hochberg method to control the false discovery rate.
• Proximity Analysis: Compares orthologs to protein-coding genes located within 1 Mb, 500 kb, and 250 kb of human GWAS loci.
• Ortholog Mapping: Integrates with Ensembl's BioMart to identify human orthologs for genes differentially expressed in animal models.
• Visualization: Produces graphical representations of gene list comparison results.

Scientific Applications:

• GWAS integration: Compare GWAS loci with transcriptome or proteomics data to identify candidate genes near association signals.
• Cross-species analysis: Map differentially expressed genes or proteins from animal models to human orthologs to explore conserved biological mechanisms.
• Myopia and ocular trait studies: Investigate overlaps related to refractive error and axial length and genes differentially expressed during myopia induction.

Methodology:

Retrieve GWAS loci and differentially expressed genes or proteins from animal studies; identify human orthologs using Ensembl's BioMart; compare orthologs to protein-coding genes within 1 Mb, 500 kb, and 250 kb of GWAS loci; calculate odds ratios and P values and adjust P values using the Benjamini-Hochberg method.