ALEA

ALEA analyzes allele-specific epigenomic signals from next-generation sequencing data (ChIP-seq, RNA-seq) to link allelic variation to DNA methylation, histone modifications, and chromatin accessibility in human and mouse samples.

Key Features:

• Integration of allelic variation: Incorporates allelic variation information into genomic analyses to detect associations between specific variants and epigenetic changes such as DNA methylation, histone modifications, and chromatin accessibility.
• Sequencing support: Processes next-generation sequencing data types explicitly including ChIP-seq and RNA-seq for allele-specific analysis.
• Customizable command-line pipeline: Provides a configurable pipeline to process raw sequencing data and produce allele-specific outputs for downstream analysis.
• Allelic disambiguation: Distinguishes reads by allele using known allelic variation databases to assign signals to specific alleles.
• Allele-specific epigenomic analysis: Identifies epigenetic modifications and differential signals associated with each allele.
• Output generation for visualization: Produces separate allelic tracks suitable for visualization on genome browsers.
• Validation across species: Validated using ChIP-seq and RNA-seq data from human cells and hybrid mouse models.

Scientific Applications:

• Gene regulation: Dissects how specific alleles affect gene expression through differential epigenetic modifications.
• Disease mechanisms: Investigates allelic contributions to disease phenotypes by linking variants to allele-specific epigenomic changes.
• Developmental biology: Explores interactions between genetic variation and epigenetic regulation during development in model organisms such as mice.

Methodology:

Inputs raw sequencing data (ChIP-seq, RNA-seq); performs allelic disambiguation leveraging known allelic variation databases; conducts allele-specific epigenomic analyses to identify allele-associated modifications; generates separate allelic tracks for genome browser visualization.