NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through...

Area of Science:

• Bioinformatics
• Computational Biology
• Network Science

Background:

• Venn diagrams and network diagrams are used to compare biological datasets like gene and protein lists.
• Existing tools often require separate analyses for network nodes and edges, limiting compositional comparison.
• Visualizing shared or exclusive network interactions across datasets necessitates specialized workflows.

Purpose of the Study:

• To develop an integrated framework and web application for comparing biological network compositions.
• To enable simultaneous analysis of nodes and edges using Venn and network diagrams.
• To facilitate interactive visualization of common and exclusive network interactions.

Main Methods:

• Introduction of NetSets.js, a server-independent JavaScript framework.
• Development of a web application utilizing NetSets.js for compositional comparisons and network visualizations.
• Integration with Cytoscape desktop application via Netsets-Cyapp.

Main Results:

• NetSets.js integrates Venn and network diagrams into a single application.
• The web application allows compositional comparisons of nodes and edges from edge-lists.
• Interactive visualization of common/exclusive interactions and exportable network diagrams are provided.
• Demonstrated utility with real-world biological networks (microbiome, gene interaction, multiplex, PPI).

Conclusions:

• NetSets.js offers a unified approach for biological network comparison and visualization.
• The tool simplifies the analysis of common and exclusive network elements.
• Provides publication-ready network diagrams for small networks.