EpiGRAPH

EpiGRAPH analyzes vertebrate genome and epigenome datasets to identify statistically significant associations between user-defined genomic regions and (epi-)genomic attributes such as DNA sequence, chromatin structure, epigenetic modifications, and evolutionary conservation using statistical testing and machine learning.

Key Features:

• Data Upload and Analysis: Tests user-provided sets of genomic regions against a comprehensive database of (epi-)genomic attributes including DNA sequence, chromatin structure, epigenetic modifications, and evolutionary conservation.
• Enrichment and Depletion Testing: Evaluates whether specific genomic attributes are enriched or depleted within the input regions using statistical tests.
• Predictive Identification: Applies machine learning algorithms to predict additional genomic regions that share attributes with the input set.
• Case Study Application: Demonstrated application to monoallelic gene expression to illustrate identification of associated genomic and epigenomic features.
• Reproducible Analysis: Implements an approach intended to support reproducible analyses across different studies and datasets.

Scientific Applications:

• Gene regulation: Integrates sequence and epigenetic data to investigate regulatory mechanisms affecting gene expression.
• Chromatin dynamics: Analyzes chromatin structure and epigenetic modifications to study chromatin state and dynamics.
• Evolutionary biology: Assesses evolutionary conservation in relation to genomic and epigenomic features.
• Predictive annotation and discovery: Predicts genomic regions with similar attributes to support hypothesis generation and discovery of novel functional regions.
• Monoallelic gene expression analysis: Identifies genomic and epigenomic correlates of monoallelic expression.

Methodology:

Performs systematic testing of input genomic regions against a comprehensive database of (epi-)genomic attributes using statistical enrichment/depletion tests and machine learning algorithms for predictive identification.