The document discusses protein interaction networks and their use in large-scale data mining. It describes three phases: 1) constructing association networks using genomic context, co-expression, and curated protein interactions. 2) Building signaling networks using phosphoproteomics, sequence motifs, and prediction tools. 3) Analyzing dynamic networks using time course microarray data to study temporal networks and just-in-time assembly during the cell cycle. The goal is to integrate diverse data types to generate networks and make specific predictions about systems properties.