Pentad

Pentad analyzes distance-dependent chromatin interactions from Hi-C matrices to quantify and visualize contact patterns within and between A (euchromatin) and B (heterochromatin) compartments across cis and trans genomic distances.

Key Features:

• Distance-Dependent Analysis: Computes average compartment-specific interactions from Hi-C matrices at specified cis, trans, and genomic distances.
• Comprehensive Visualization: Generates visualizations of contact frequency distributions to reveal changes within A (euchromatin) and B (heterochromatin) compartments.
• Quantitative Assessment: Quantifies compartment strength and detects redistribution patterns in chromatin contacts.

Scientific Applications:

• Cell differentiation and stimulus response analysis: Assesses how transcriptional and epigenetic changes during differentiation or following external stimuli alter chromatin compaction.
• Public Hi-C dataset analysis: Detects shifts in contact frequency within chromatin compartments in public Hi-C datasets to study dynamic genome organization.

Methodology:

Processes Hi-C matrices to compute and visualize average interactions at specified cis, trans, and genomic distances.