TY - JOUR T1 - The Modular Organization of Protein Interactions in Escherichia coli A1 - Peregrín-Alvarez, José M. A1 - Xiong, Xuejian A1 - Su, Chong A1 - Parkinson, John Y1 - 2009/10/02 N2 - Author Summary Genes and their protein products do not operate in isolation, but form components of highly interconnected biological systems. Identifying the connections between components is therefore critical to understanding how these processes are organized and operate. E. coli is the leading model bacterium; however despite its importance in biological and medical discovery, an accurate atlas of these interactions is still lacking. On the other hand, several computational and experimental procedures have been applied on a high-throughput basis to provide collections of interaction data of varying quality and coverage. Using a sophisticated mathematical framework, we have combined and benchmarked these data to create a single, highly reliable set of interactions that encompasses almost 50% of the E. coli proteome. Organizing these data on the basis of their interactions, we identify groups of proteins representing functionally coordinated modules such as molecular machines (e.g., the flagellum) and biochemical pathways. Finally through examining the organization of E. coli interactions in the context of evolution, we propose a new model of bacterial network evolution that accounts for the integration of foreign genes acquired through horizontal gene transfer mechanisms. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 5 IS - 10 UR - https://doi.org/10.1371/journal.pcbi.1000523 SP - e1000523 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000523 ER -