EAGLE

EAGLE detects gene-by-environment (GxE) interaction effects on the transcriptome using allele-specific expression (ASE) quantified from RNA-seq data.

Key Features:

• Hierarchical Bayesian Model: Employs a hierarchical Bayesian model to identify associations between environmental variables and allele-specific expression.
• Allele-Specific Expression (ASE) Analysis: Quantifies ASE from RNA-seq data to measure allele-level expression differences across environmental contexts.
• Environmental Annotations and Whole-blood RNA-seq Integration: Integrates comprehensive environmental annotations with whole-blood RNA-seq data for joint analysis of environment and ASE.
• Enhanced Detection Capability: In a study of 922 human individuals, identified 35 GxE interactions compared to four detected by standard GxE interaction testing methods.

Scientific Applications:

• GxE discovery in transcriptomics: Detecting gene-by-environment interactions at allele resolution in transcriptome data.
• Functional genomics of environmental response: Linking environmental variables to allele-specific regulatory effects in whole-blood RNA-seq.
• Phenotype and disease studies: Investigating how environmental modulation of ASE contributes to phenotypic diversity and disease susceptibility.

Methodology:

Quantifies ASE from RNA-seq, combines ASE measures with comprehensive environmental annotations, and models GxE interactions using a hierarchical Bayesian approach.