FunCoup Cytoscape App

FunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape to visualize and analyze gene interaction networks across 640 species.

Key Features:

• Network Expansion Algorithms: Supports group gene search, independent gene search, MaxLink, and TOPAS algorithms for network construction and expansion.
• Multi-Species Support: Enables gene interaction network analysis and visualization for 640 species through the FunCoup web service API.
• Customizable Search Parameters: Allows users to input gene identifiers and customize search parameters for network queries.
• Detailed Annotation Display: Provides detailed node and link information, including tissue and pathway gene annotations.
• Cytoscape Plugin Integration: Integrates with Cytoscape plugins such as ClusterMaker2 to enhance analytical capabilities.

Scientific Applications:

• Disease Module Identification: Enables identification of disease modules and potential new therapeutic targets, as demonstrated by the identification of the Myasthenia gravis disease module.
• Genome-Wide Network Analysis: Facilitates analysis and visualization of genome-wide functional association networks for complex gene interaction studies.

Methodology:

The app is developed using the Java OSGi framework with Java Swing UI components and Maven build support, integrating the FunCoup web service API with Cytoscape.