Visualization and Analysis of Biological Networks

The study of the interactome—the totality of the protein–protein interactions taking place in a cell—has experienced an enormous growth in the last few years. Biological networks representation and analysis has become an everyday tool for many biologists and bioinformatics, as these interaction graphs allow us to map and characterize signaling pathways and predict the function of unknown proteins. However, given the size and complexity of interactome datasets, extracting meaningful information from interaction networks can be a daunting task. Many different tools and approaches can be used to build, represent, and analyze biological networks. In this chapter, we will use a practical example to guide novice users through this process. We will be making use of the popular open source tool Cytoscape and of other resources such as : the PSICQUIC client to access several protein interaction repositories and the BiNGO plugin to perform GO enrichment analysis of the resulting network.