The methods presented here provide a toolbox for the elucidation of protein interactions. In an organism with tens of thousands of genes, it is difficult to establish comprehensive protein–protein interaction data sets, because the total number of experiments is estimated to be far larger than for budding yeast. It will be necessary to analyze the experimental protein–protein interaction data together with publicly available information on mammalian protein–protein interaction. The diverse nature of the interactions discovered thus far illustrates that the methods presented here are highly complementary, and all are needed to cover the diverse protein synergies in the cell.
The mapping of protein interactions will be the key to better understanding of human protein function and diseases. Novel experimental and bioinformatics tools have accelerated the deciphering of protein interactions. In addition, emerging technologies such as protein micro-arrays, live cell microarrays, and RNAi hold the promise of systematically studying the entire human proteome. As high-throughput functional genomics and proteomics technology and bioinformatics develop concurrently, these technologies will become more accessible to the individual laboratory. Researchers will thus be empowered to ask increasingly more interesting and complex biological questions. Mapping protein complexes combined with other biological and genomic information will provide the framework of a physical map of the cell that can be filled in with ever-increasing details to encompass metabolic and signaling pathways. Given the advantages provided by an in silico approach, it seems reasonable to propose that it will become an essential tool for initially evaluating novel hypotheses and will offer an improved rationale for target prioritization. The goal is that only the most promising targets will be subjected to empirical testing.