EpiCompare

EpiCompare identifies and characterizes genomic regions with tissue- or cell type-specific epigenomic features to pinpoint regulatory promoters and enhancers unique to specific human tissues and cell types.

Key Features:

• Integration with Roadmap Epigenomics Data: Leverages the Human Reference Epigenome Map from the Roadmap Epigenomics Consortium comprising thousands of genome-wide epigenomic datasets to annotate regulatory elements such as promoters and enhancers across human tissues and cell types.
• Dynamic comparison: Allows selection of specific combinations of epigenomes to compare tissue- and cell type-specific epigenomic patterns.
• Classification algorithms: Applies classification algorithms to identify genomic regions that are unique to or shared among selected tissue and cell types.
• Data input support: Supports analysis using publicly available Roadmap Epigenomics data and user-provided datasets.
• Quality assessment: Provides quality assessment metrics for predicted tissue- or cell type-specific epigenomic regions.
• Visualization: Enables visualization and further exploration of results within the WashU Epigenome Browser.

Scientific Applications:

• Lineage-specific regulatory element discovery: Detection of lineage-specific enhancers and other regulatory elements implicated in cell type identity.
• Regulatory genomics of differentiation: Comparative epigenomic analysis to investigate regulatory features underlying tissue and cell type differentiation and function.

Methodology:

Selects specific combinations of epigenomes and applies classification algorithms to identify regions with unique or common epigenomic features.