GenomeFlow

GenomeFlow reconstructs, stores, analyzes, and annotates three-dimensional (3D) genome models from Hi-C chromosomal conformation capture data to investigate genome organization and its relationship to functional genomics.

Key Features:

• Data Mapping and Normalization: Maps Hi-C data to one-dimensional (1D) reference genomes and generates and normalizes two-dimensional (2D) chromosomal contact maps.
• 3D Model Reconstruction: Reconstructs 3D models of chromosomes and whole genomes from normalized Hi-C contact maps.
• Visualization of 3D Structures: Produces visual representations of reconstructed 3D genome structures for inspection and interpretation.
• Integration with Functional Genomics: Overlays gene annotation, gene expression, and genome methylation data onto 3D genome models.
• Spatial Interaction Analysis: Performs analyses of spatial genomic interactions to assess functional implications of 3D organization.
• Model Storage and Annotation: Stores reconstructed 3D genome models and supports annotation of structural features.

Scientific Applications:

• 3D Genome Organization Studies: Investigating the structural organization of chromosomes and whole genomes using Hi-C data.
• Gene Regulation and Functional Genomics: Exploring how 3D genome architecture relates to gene expression and epigenetic marks such as DNA methylation.
• Spatial Chromatin Interaction Analysis: Characterizing spatial genomic interactions to study regulatory contacts and chromatin architecture.

Methodology:

Maps Hi-C reads to one-dimensional reference genomes, generates and normalizes two-dimensional chromosomal contact maps, and reconstructs, stores, and annotates three-dimensional genome models.