NetSets

NetSets compares biological networks by combining Venn-diagram-based set analysis with network visualization to identify shared and unique proteins, genes, nodes, and protein-protein interactions represented as edge-lists.

Key Features:

• Implementation: Implemented as a JavaScript framework for client-side compositional network analysis.
• Integrated visualization: Combines Venn diagrams with network diagrams to represent overlaps and relationships among nodes and edges.
• Compositional comparisons: Identifies common and exclusive nodes and edges across multiple networks using edge-list inputs.
• Visualization customization: Produces visual outputs that can highlight interactions present across all networks, shared between subsets, or exclusive to selected networks.
• Export capabilities: Exports network diagrams intended for publication-quality representation, with attention to detailed layouts for small networks.
• Cytoscape integration: Connects to the Cytoscape desktop application via Netsets-Cyapp for downstream analysis.

Scientific Applications:

• Microbiome networks: Demonstrated on microbiome networks for compositional and interaction comparisons.
• Gene interaction networks: Applied to gene interaction datasets to assess shared and unique gene relationships.
• Multiplex networks: Used on multiplex network data to compare layers and overlapping components.
• Protein-protein interaction networks: Employed for comparison of protein-protein interaction networks represented as edge-lists.

Methodology:

Operates independently of servers, uses simple edge-lists to perform compositional comparisons and generate combined Venn and network visualizations, and connects to Cytoscape via Netsets-Cyapp.