WashU Epigenome Browser

WashU Epigenome Browser visualizes and integrates epigenomic datasets to enable exploration of one-dimensional genomic features, two-dimensional chromatin interactions (Hi-C), three-dimensional genome structures, and four-dimensional time-series dynamics.

Key Features:

• 1D genomic features: Displays one-dimensional genomic annotation features and numerical value tracks.
• 2D chromatin interactions: Visualizes two-dimensional chromatin interaction data, including Hi-C contact maps.
• 3D genome viewer: Provides a dedicated 3D genome viewer module for structural representation of genome organization.
• 4D Dynamic tracks: Implements Dynamic tracks that animate time-series data to show temporal changes in genomic regions or gene activity.
• Data integration: Integrates annotation features, numerical values, and chromatin interaction datasets within the same visualization framework.
• Microscopy imaging: Supports incorporation and display of imaging data from microscopy experiments alongside sequencing-based data.
• Plugin track types: Supports plugin track types such as qBed and dynseq to extend track functionality.

Scientific Applications:

• Epigenomic exploration: Exploration and visualization of epigenomic datasets across 1D–4D modalities.
• Temporal dynamics analysis: Identification of candidate regions or genes based on temporal dynamics using Dynamic tracks.
• Chromatin interaction analysis: Analysis of chromatin architecture and interactions using Hi-C and other interaction datasets.
• 3D genome structure analysis: Investigation of three-dimensional genome organization via the 3D viewer.
• Integrative imaging and sequencing: Integration of microscopy imaging data with sequencing-derived epigenomic datasets.
• Virus and comparative genomics: Support for virus genome analyses (WashU Virus Genome Browser) relevant to COVID-19 research and comparative genomics (Comparative Genome Browser).
• Consortia data visualization: Hosting and visualization of datasets from consortia including 4DN, Roadmap Epigenomics, TaRGET, and ENCODE.

Methodology:

Provides a dedicated 3D genome viewer module, a Dynamic track mode for animated time-series display, and support for plugin track types including qBed and dynseq.