CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• Molecular interaction networks are crucial for understanding cellular processes.
• Visualizing these networks, especially with functional annotations like subcellular localization, aids biological discovery.
• Existing tools may lack flexibility or ease of integration for web-based applications.

Purpose of the Study:

• To develop a lightweight JavaScript plug-in, CerebralWeb, for interactive molecular network visualization.
• To enable stratification of networks based on subcellular localization or user-defined annotations.
• To facilitate easy integration into existing websites and databases.

Main Methods:

• CerebralWeb extends the Cytoscape.js library.
• It supports automatic retrieval of gene localizations via a web service for human, mouse, and bovine.
• Automated parsing of Cytoscape-compatible XGMML network files is enabled.

Main Results:

• Provides fast and interactive visualization of molecular interaction networks.
• Allows stratification of networks by subcellular localization or custom annotations.
• Supports seamless integration into web platforms, demonstrated on InnateDB and Allergy and Asthma Portal.

Conclusions:

• CerebralWeb enhances the visualization of molecular networks with functional annotations.
• Its lightweight design and integration capabilities make it a versatile tool for web-based biological data resources.
• Facilitates deeper insights into molecular interactions through customizable and interactive network displays.