TADCompare

"TADCompare" is a computational method designed for the differential analysis of the boundaries of topologically associated domains (TADs) and smaller chromatin loops, collectively referred to as "interacting domains," across different Hi-C datasets. The dynamic behavior of these domains is crucial for understanding genomic regulation, as they often exhibit changes during development, disease progression, and under different cellular conditions.

Core Features:

- Eigenvector Gap Measurement: TADCompare utilizes a spectral clustering-derived measure, known as the eigenvector gap, to facilitate a precise loci-by-loci comparison of boundary differences between interacting domains. This innovative approach allows for the detailed analysis of how domain boundaries shift or change across different conditions or cell types.

- Differential and Consensus Boundaries Identification: The tool introduces methods for identifying both differential and consensus boundaries of interacting domains. This capability enables researchers to track which boundaries remain consistent across conditions and which ones differ, providing insights into the stability and variability of genome organization.

- Boundary Changes Classification Framework: TADCompare proposes a novel framework for systematically classifying boundary changes. This framework helps categorize the types of observed modifications, enhancing the understanding of their potential biological implications.

- Biological Functionality Analysis: TADCompare can associate distinct biological functions with different boundary changes through colocalization and gene enrichment analyses. This feature underscores the biological relevance of observed changes in interacting domain boundaries.