SIGNORApp: a Cytoscape 3 application to access SIGNOR data

Area of Science:

• Systems Biology
• Bioinformatics
• Network Biology

Background:

• Biological interactions and pathways are complex.
• Understanding causal relationships is crucial for biological research.
• Existing tools may lack comprehensive causal interaction data.

Purpose of the Study:

• To introduce SIGNORApp, a Cytoscape application for accessing and visualizing causal interactions from the SIGNOR resource.
• To provide users with tools for building and exploring biological networks based on curated causal data.
• To facilitate the study of post-translational modifications within biological networks.

Main Methods:

• Developed as a Cytoscape 3 application (3.8 and later) in Java.
• Utilizes the SIGNOR database of curated causal interactions.
• Implements network visualization with options for weighted, signed, directed graphs.
• Offers query functionalities for single/multiple entities, pathway browsing, and interactome extraction.
• Provides two visualization modes: entity interactions and emphasis on post-translational modifications.

Main Results:

• SIGNORApp allows users to construct networks representing causal interactions.
• The application supports querying and browsing pathways and the entire causal interactome.
• Two distinct visualization modes enhance the exploration of biological networks and post-translational modifications.
• Causal information is available for human, mouse, and rat.

Conclusions:

• SIGNORApp provides a valuable resource for researchers studying causal biological interactions.
• The application enhances network visualization and exploration capabilities within Cytoscape.
• It supports systems biology research by integrating curated causal data and facilitating network analysis.