TFHAZ

TFHAZ identifies transcription factor (TF) high accumulation DNA zones (DNA high occupancy target, HOT, zones) to map dense TF binding regions for analysis of gene regulatory architecture and disease-associated regulatory changes.

Key Features:

• Dual Methodology: Implements two alternative HOT-zone identification methods, "binding regions" and "overlaps", for comparative analysis of TF binding patterns.
• Resolution Flexibility: Provides three types of accumulation analysis enabling single-base resolution or broader region-oriented scales.
• Moving Window Technique: Applies a moving window to assess the influence of neighboring bases on accumulation at each examined base.
• Parametric Algorithm and Implementation: Uses a computationally efficient parametric algorithm implemented as an R/Bioconductor package.

Scientific Applications:

• Mapping TF binding density: Generates maps of dense TF binding across genomes to characterize transcriptional regulatory architecture.
• Comparative genomics across cells and tissues: Enables analysis of TF accumulation patterns across different cells and tissues to identify context-specific regulatory regions.
• Disease-related regulatory analysis: Supports investigation of alterations in HOT zones associated with disease processes, including cancer.
• Large-scale functional studies: Facilitates replicable analyses across diverse biological samples to elucidate functional roles of HOT zones.

Methodology:

Starting from datasets of genomic positions of TF binding regions, TFHAZ computes TF accumulation at each base of selected chromosomes using a parametric algorithm; it implements two identification methods ("binding regions" and "overlaps"), supports three accumulation-resolution types including single-base and region-level analyses, and applies a moving window to assess neighboring-base influence, with the software implemented in R/Bioconductor.