CHiCP

CHiCP visualizes promoter capture Hi-C (PCHi-C) datasets to map genome-wide physical interactions between gene promoters and distal regulatory elements for studying chromatin-mediated gene regulation.

Key Features:

• PCHi-C interaction mapping: Generates chromosome interaction maps from promoter capture Hi-C (PCHi-C) data that depict physical contacts between promoters and distal genomic regions.
• Integration with genomic datasets: Integrates PCHi-C interaction maps with public genomic datasets and user-provided data for combined analyses.
• Annotation overlay: Overlays interaction maps with genomic annotations to provide multi-layered views of promoters, regulatory elements, and chromatin organization.
• Tissue-context support: Supports analysis of promoter–regulatory element interactions across multiple tissue contexts.

Scientific Applications:

• Regulatory architecture elucidation: Visualizes promoter–distal interactions to infer regulatory networks and relationships between regulatory elements and target genes.
• Tissue-specific expression studies: Identifies tissue-specific promoter interactions to aid interpretation of tissue-dependent gene expression patterns.
• Chromatin organization research: Assists investigation of how chromatin spatial organization relates to gene regulation in health and disease.
• Functional genomics hypothesis generation: Provides interaction-based evidence to support hypothesis generation and testing in functional genomics.

Methodology:

Generates interaction maps from PCHi-C data that depict physical contacts between genomic regions and integrates these maps with genomic annotations to produce multi-layered regulatory views.