Characterization of BioPlex network by topological properties. (21st November 2016)

• Record Type: Journal Article
• Authors: Yang, Lei; Wang, Shiyuan; Zhou, Meng; Chen, Xiaowen; Zuo, Yongchun; Lv, Yingli
• Is Part Of: Journal of theoretical biology. Volume 409(2016)
• Page Start: 148
• Page End: 154
• Publication Date: 2016-11-21
• Subjects: Protein interactions -- Topological pattern -- Random networks -- Correlation profile; Biology -- Periodicals; Biological Science Disciplines -- Periodicals; Biology -- Periodicals; Biologie -- Périodiques; Theoretische biologie; Biology; Periodicals; 571.05
• DOI: 10.1016/j.jtbi.2016.08.028
• Languages: English
• ISSNs: 0022-5193

Abstract

Abstract: Protein–protein interaction (PPI) networks are emerging as valuable prototypes to study important problems in molecular cellular biology and systems biomedicine. An analysis of the topological properties of a PPI network is very helpful for understanding the function and structure of networks. In this study, we analyzed the topological patterns in the BioPlex network containing interactions among 10, 961 proteins; most interactions were previously undocumented. The BioPlex network is a comprehensive map of human protein interactions and represents the first phase of a long-term effort to profile the entire human ORFEOME collection. Similar to other biological networks, we observed that the BioPlex network has several topological properties. We also quantified correlations profiles for the BioPlex network and compared them to randomized versions of the same network. We found that for the BioPlex network, edges between proteins with intermediate degrees were strongly suppressed, whereas edges between low-connected proteins were favored. Finally, the degrees of essential genes were compared with the degrees of non-essential genes and randomly selected proteins. There were no significant differences between the groups. Highlights: The BioPlex network is globally analyzed by utilizing in silico methods. The correlation profile is used to quantify the BioPlex network. The degrees of human essential and non-essential genes are compared in the BioPlex network.