hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast中心与网络主题组织模块化动态酵母的蛋白质相互作用网络.pdfVIP

Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast 1,2 1,2 1 3,4,5,6 Guangxu Jin , Shihua Zhang , Xiang-Sun Zhang *, Luonan Chen * 1 Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing, China, 2 Graduate University of Chinese Academy of Sciences, Beijing, China, 3 Institute of Systems Biology, Shanghai University, Shanghai, China, 4 Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan, 5 Exploratory Research for Advanced Technology (ERATO) Aihara Complexity Modelling Project, Japan Science and Technology Corporation (JST), Tokyo, Japan, 6 Institute of Industrial Science, The University of Tokyo, Tokyo, Japan Background. It has been recognized that modular organization pervades biological complexity. Based on network analysis, ‘party hubs’ and ‘date hubs’ were proposed to understand the basic principle of module organization of biomolecular networks. However, recent study on hubs has suggested that there is no clear evidence for coexistence of ‘party hubs’ and ‘date hubs’. Thus, an open question has been raised as to whether or not ‘party hubs’ and ‘date hubs’ truly exist in yeast interactome. Methodology. In contrast to previous studies focusing on the partners of a hub or the individual proteins around the hub, our work aims to study the network motifs of a hub or interactions among individual proteins including the hub and its neighbors. Depending on the relationship between a hub’s network motifs and protein complexes, we define two new types of hubs, ‘motif party hubs’ and ‘motif date hubs’, which have the same characteristics as the original ‘party hubs’ and ‘date hubs’ respectively. The network motifs of these two types of hubs d