Construction of dynamic probabilistic protein interaction networks for protein complex identification.
BACKGROUND
Recently, high-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data which can construct large complex PPI networks for numerous organisms. System biology attempts to understand cellular organization and function by analyzing these PPI networks. However, most studies still focus on static PPI networks which neglect the dynamic information of PPI.


RESULTS
The gene expression data under different time points and conditions can reveal the dynamic information of proteins. In this study, we used an active probability-based method to distinguish the active level of proteins at different active time points. We constructed dynamic probabilistic protein networks (DPPN) to integrate dynamic information of protein into static PPI networks. Based on DPPN, we subsequently proposed a novel method to identify protein complexes, which could effectively exploit topological structure as well as dynamic information of DPPN. We used three different yeast PPI datasets and gene expression data to construct three DPPNs. When applied to three DPPNs, many well-characterized protein complexes were accurately identified by this method.


CONCLUSIONS
The shift from static PPI networks to dynamic PPI networks is essential to accurately identify protein complex. This method not only can be applied to identify protein complex, but also establish a framework to integrate dynamic information into static networks for other applications, such as pathway analysis.
College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116023, China. zhyj@dlut.edu.cn.
Yijia
Y
Zhang
College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116023, China.
Hongfei
H
Lin
College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116023, China.
Zhihao
Z
Yang
College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116023, China.
Jian
J
Wang
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
D029701:Saccharomyces cerevisiae Proteins
Dynamic networks; Gene expression data; Protein complex identification; Protein-protein interaction networks