Protein-protein interaction networks and subnetworks in the biology of disease

The main goal of systems medicine is to provide predictive models of the patho-physiology of complex diseases as well as define healthy states. The reason is clear-we hope accurate models will ultimately lead to more specific and sensitive markers of disease that will help clinicians better stratify their patient populations and optimize treatment plans. In addition, we expect that these models will define novel targets for combating disease. However, for many complex diseases, particularly at the clinical level, it is becoming increasingly clear that one or a few genomic variations alone (e.g., simple models) cannot adequately explain the multiple phenotypes related to disease states, or the variable risks that attend disease progression. We suggest that models that account for the activities of many interacting proteins will explain a wider range of variability inherent in these phenotypes. These models, which encompass protein interaction networks dysregulated for specific diseases and specific patient sub-populations, will be constructed by integrating protein interaction data with multiple types of other relevant cellular information. Protein interaction databases are thus playing an increasingly important role in systems biology approaches to the study of disease. They present us with a static, but highly functional view of the cellular state, and thus give us a better understanding of not only the normal phenotype, but also the overall disease phenotype at the level of the whole organism when certain interactions become dysregulated. (C) 2010 John Wiley Sr Sons, Inc. WIREs Syst Biol Med 2011 3 357-367 DOI: 10.1002/wsbm.121