DynOVis

DynOVis visualizes dynamic dose-over-time effects in biological networks by creating force-directed graph visualizations and integrating pathway, disease, and gene annotations for temporal network analysis.

Key Features:

• Dynamic visualization capabilities: Animates node expression over time and provides frame-by-frame views of dynamic exposures to capture temporal changes.
• Integration with R and JavaScript: Combines R packages with JavaScript libraries to construct force-directed graph network visualizations.
• Network analysis methods: Supports multiple network methods, including degree thresholding for network filtering.
• Comprehensive data annotation: Augments nodes with pathway-to-gene associations from ConsensusPathDB, disease-to-gene associations from the Comparative Toxicogenomics Database, and gene metadata (Entrez gene ID, gene symbol, synonyms, type) from NCBI.

Scientific Applications:

• Dynamic dose-over-time analysis: Visualizes and analyzes dose-over-time effects within biological networks.
• Temporal perturbation analysis: Investigates temporal changes in networks to identify critical nodes with potential biological relevance.
• Annotation-driven interpretation: Correlates observed network dynamics with known pathways and disease associations from ConsensusPathDB and the Comparative Toxicogenomics Database.

Methodology:

Combines R packages with JavaScript libraries to build force-directed graph visualizations, animate node expression frame-by-frame, apply multiple network methods including degree thresholding, and integrate annotations from ConsensusPathDB, the Comparative Toxicogenomics Database, and NCBI (Entrez gene ID, gene symbol, synonyms, type).