Construction and analysis of protein–protein interaction networks

Protein–protein interactions form the basis for a vast majority of cellular events, including signal transduction and transcriptional regulation. It is now understood that the study of interactions between cellular macromolecules is fundamental to the understanding of biological systems. Interactions between proteins have been studied through a number of high-throughput experiments and have also been predicted through an array of computational methods that leverage the vast amount of sequence data generated in the last decade. In this review, I discuss some of the important computational methods for the prediction of functional linkages between proteins. I then give a brief overview of some of the databases and tools that are useful for a study of protein–protein interactions. I also present an introduction to network theory, followed by a discussion of the parameters commonly used in analysing networks, important network topologies, as well as methods to identify important network components, based on perturbations.