TADreg

TADreg performs regression-based identification, differential analysis, and prediction of rearranged three-dimensional (3D) genomic structures focused on topologically associating domains (TADs) to study genome organization and its effects on gene regulation, DNA repair, and replication.

Key Features:

• Fast and accurate TAD identification: Performs rapid, accurate identification of topologically associating domains (TADs) from chromatin conformation data.
• Differential analysis of TAD borders: Detects differential TAD borders across biological conditions.
• Prediction of 3D genome reorganization: Predicts how chromosomal rearrangements alter 3D genome structure.
• Identification of TAD facilitators: Identifies novel genomic features termed "TAD facilitators" that are enriched for specific transcription factors.
• Role of cell-type-specific transcription factors: Highlights the contribution of cell-type-specific transcription factors to the formation of new TAD borders during processes such as neuronal differentiation.
• Comparison with state-of-the-art methods: Compares predictive performance against existing methods for rearranged 3D genome prediction.

Scientific Applications:

• Genomic research: Enables investigation of TAD alterations associated with disease, including cancer.
• Gene expression studies: Supports analyses linking 3D genome organization to gene expression patterns.
• Developmental biology: Facilitates study of cellular differentiation processes, including neuronal development and the role of transcription factors in TAD formation.

Methodology:

Implements a regression framework for TAD identification, performs differential analysis of TAD borders, predicts rearranged 3D genome structures, identifies TAD facilitators enriched for transcription factors, and compares results to other methods.