Protein–Protein Interaction Network Exploration Using Cytoscape

As the protein-protein interaction (PPI) data increase exponentially, the development and usage of computational methods to analyze these datasets have become a new research horizon in systems biology. The PPI network analysis and visualization can help identify functional modules of the network, pathway genes involved in common cellular functions, and functional annotations of novel genes. Currently, a variety of tools are available for network graph visualization and analysis. Cytoscape, an open-source software tool, is one of them. It provides an interactive visualization interface along with other core features to import, navigate, filter, cluster, search, and export networks. It comes with hundreds of in-built Apps in App Manager to resolve research questions related to network visualization and integration. This chapter aims to illustrate the Cytoscape application to visualize and analyze the PPI network using Arabidopsis interactome-1 main (AI-1MAIN) PPI network dataset from Plant Interactome Database.