Protein–protein interactions: from global to local analyses

For the increasing number of species with complete genome sequences, the task of elucidating their complete proteomes and interactomes has attracted much recent interest. Although the proteome describes the complete repertoire of proteins expressed, the interactome comprises the pairwise protein–protein interactions that occur, or could occur, within an organism, and forms a large-scale sparse network. Here we discuss the challenges provided by present data, and outline a route from global analysis to more detailed and focused studies of protein–protein interactions. Carefully using protein-interaction data allows us to explore its potential fully alongside the evaluation of mechanistic hypotheses about biological systems.