Search, Retrieve, Visualize, and Analyze Protein-Protein Interactions from Multiple Databases: A Guide for Experimental Biologists.

Functional annotation is lacking for over half of the proteins encoded in genomes and model or representative organisms are not an exception to this trend. One of the popular ways of assigning putative functions to uncharacterized proteins is based on the functions of well-characterized proteins that physically interact with them, i.e., guilt-by-association or functional context approach. In the last two decades, several powerful experimental and computational techniques have been used to determine protein-protein interactions (PPIs) at genome level and are made available through many public databases. The PPI data are often complex and heterogeneously represented across databases posing unique challenges in retrieving, integrating, and analyzing the data even for trained computational biologists, the end users-experimental biologists often struggle to work around the data for the protein of their interests. This chapter provides stepwise protocols to import interaction network of the protein of interest in Cytoscape using PSICQUIC, stringApp, and IntAct App. These are next-generation applications that import PPI from multiple databases/resources and provide seamless functions to study the protein of interest and its functional context directly in Cytoscape.