RAD

RAD identifies differentially expressed genes (DEGs) associated with proximal and distal genomic regions to link genomic regions of interest (gROI) to gene expression changes.

Key Features:

• Comprehensive Analysis: Maps up- and down-regulated genes to specified genomic regions of interest (gROI) across proximal and distal distances.
• Regulatory Function Inference: Analyzes distances between gROIs and DEGs to infer potential regulatory relationships of genomic regions.
• Visualization and Statistical Tools: Generates visualizations and applies statistical inference to assess the significance of gROI–DEG associations.

Scientific Applications:

• Chromatin accessibility: Associates chromatin accessibility regions with nearby and distal differential gene expression.
• Transcription factor binding sites: Links transcription factor binding sites to changes in gene expression via distance-based association.
• Epigenetic modifications: Investigates relationships between epigenetic modifications and differential gene expression across distances.
• Gene regulation studies: Supports analysis of gene regulation mechanisms and their implications in biological processes and disease contexts.

Methodology:

Maps DEGs to gROIs, analyzes distances between gROIs and DEGs to assign proximal and distal associations, performs statistical inference to assess association significance, and generates visualizations.