OmicsNet

OmicsNet constructs interactive three-dimensional molecular networks integrating omics-derived genes, proteins, miRNAs, metabolites, and transcription factors to support systems biology analyses.

Key Features:

• 3D WebGL rendering: Mitigates the "hairball" effect in large network visualizations via WebGL-based interactive three-dimensional rendering.
• Supported entity types: Represents genes, proteins, miRNAs, metabolites, and transcription factors and supports molecular interactions beyond protein–protein and metabolic networks.
• Network construction and merging: Constructs and merges networks from multiple molecular lists.
• Layout algorithms: Provides force-directed, multi-layered perspective, and spherical layouts for hierarchical and global network views.
• Visualization styling: Applies coloring and shading operations to differentiate node types and highlight pathways.
• Topology analysis: Computes network topology metrics including connectivity and centrality.
• Enrichment analysis: Identifies statistically over-represented elements to aid interpretation.

Scientific Applications:

• Systems biology network exploration: Integration and exploration of omics data within systems biology to analyze molecular interaction networks in three dimensions.
• Cross-omic interaction analysis: Investigation of interactions among genes, proteins, miRNAs, metabolites, and transcription factors.
• Hypothesis generation via enrichment: Identification of enriched pathways or molecular sets to generate biological hypotheses.
• Network topology studies: Analysis of connectivity and centrality to identify key nodes or modules.
• Hierarchical and global network interpretation: Visualization of hierarchical relationships with multi-layered perspective layouts and global structure with spherical layouts.

Methodology:

Constructs and merges networks from multiple molecular lists; renders networks in three dimensions using WebGL; applies force-directed, multi-layered perspective, and spherical layout algorithms; performs coloring/shading operations; computes topology metrics including connectivity and centrality; conducts enrichment analysis to identify over-represented elements.