BART3D

BART3D infers transcriptional regulators (TRs) associated with genome-wide differential chromatin interactions (DCIs).

Key Features:

• TR inference from DCIs: Identifies transcriptional regulators associated with genome-wide differential chromatin interactions (DCIs).
• Hi-C comparison: Compares two distinct Hi-C maps representing different biological states, such as TR perturbation or cell differentiation.
• Integration with ChIP-seq: Leverages publicly available ChIP-seq datasets from human and mouse to detect relevant TRs.
• Resolution-aware analysis: Accounts for Hi-C resolution limitations when inferring TR binding from chromatin interaction data.
• Implementation: Implemented in Python.

Scientific Applications:

• 3D genome data analysis: Associate changes in chromatin architecture with candidate transcriptional regulators.
• Functional genomics: Elucidate regulatory mechanisms underlying gene expression and cellular differentiation.
• Condition-specific TR discovery: Pinpoint TRs linked to chromatin interaction changes between biological states (e.g., perturbation versus control).

Methodology:

Compare two Hi-C maps from different biological states (for example TR perturbation or cell differentiation) and integrate publicly available human and mouse ChIP-seq datasets to infer transcriptional regulators associated with differential chromatin interactions; implemented in Python.