Evolution of biological interaction networks from models to real data.docVIP

Sun and Kim Genome Biology 2011,12:235 /2011/12/12/235 RE VIE W Evolution of biological interaction networks: from models to real data Mark GF Sun and Philip M Kim * 1 1,2,3,4 We review recent progress in the study of biological network evolution, with a particular focus on the PPI network, because this has been studied in more depth (other networks, such as the transcription factor-target network, are also available to varying degrees of comple- tion). While networks have been examined in the past using computational simulations [25,26], here we focus on studies based on experimental data primarily from high-throughput methods. e shift to using experi- mental data has enabled observation of di?erent proper- ties of network evolution. For instance, early studies suggested that certain interactions tend to be conserved, and this ?nding was used to transfer anno tation Abstract We are beginning to uncover common mechanisms leading to the evolution of biological networks. The driving force behind these advances is the increasing availability of comparative data in several species. Biological interaction networks have been the main focus of systems biology in recent years. ese interactions form a spectrum of biological networks, including protein- protein interaction (PPI), transcription factor-target regu- lation, genetic interaction and metabolic networks. Each of these networks provides insight into di?erent intra- knowledge and identify important cellular pathways cellular communication systems, from gene and post- translational regulation (transcription factor-target and between di?erent species. We also discuss network hubs and motifs, which are conserved elements whose members kinase-substrate phosphorylation networks, respect ively) are more likely to