ChiCMaxima

ChiCMaxima identifies chromatin loops in Capture Hi-C (CHi-C) promoter data to detect promoter-centered DNA looping interactions and reduce false positives arising from technical biases in Hi-C or 4C-like analyses.

Key Features:

• Targeted data support: Operates on promoter-targeted Capture Hi-C (CHi-C) contact profiles.
• Local maxima detection: Detects chromatin loops by identifying local maxima in CHi-C contact profiles.
• Limited filtering strategies: Implements limited filtering to reduce spurious calls while preserving true interaction signals.
• Biological replicate integration: Integrates data from multiple biological replicates to increase stringency and robustness of loop calls.
• Noise discrimination: Uses local maxima focus to distinguish genuine chromatin interactions from background noise.
• Bias accommodation: Addresses differing technical bias assumptions that can impair traditional Hi-C or 4C-like loop detection.

Scientific Applications:

• Genome organization: Maps promoter-centered chromatin loops to study 3D genome organization.
• Chromatin architecture: Identifies looping interactions to characterize local and distal chromatin architecture.
• Gene regulation: Links promoters to distal regulatory elements via detected promoter-loop interactions to inform gene regulatory studies.
• Promoter-centric interaction mapping: Provides promoter-focused interaction calls for analyses requiring promoter contact profiles.

Methodology:

Detects local maxima in CHi-C contact profiles, applies limited filtering strategies, and combines signals across biological replicates to call significant chromatin loops.