Mazimizing Modularity Density for Ezploring Modular Organization of Protein Interaction Networks

摘要：

The purpose of this study is to introduce a new quantitative measure modularity density into the field of biomolecular networks and develop new algorithms for detecting functional modules in protein-protein interaction (PPI) networks. Specifically, we adopt the simulated annealing (SA) to maximize the modularity density and evaluate its efficiency on simulated networks. In order to address the computational complexity of SA procedure, we devise a spectral method for optimizing the index and apply it to a yeast PPI network. Our analysis of resulted modules suggests that most of these modules have well biological significance in context of protein complexes. Comparison with the MCL and the modularity based methods shows the efficiency of our method.

关键词： Modular organization network clustering modularity density spectral method prorein interaction network

作者: Shihua Zhang Xuemei Ning Chris Ding

作者单位: Academy of Mathematics and Systems Science,CAS,Beijing 100190,China College of Science,Beijing Forestry University,Beijing 100083,China Department of Computer Science and Engineering,University of Texas at Arlington Arlington,TX 76019,U

会议类型: 国际会议

会议名称: The 3rd International Symposium on Optimization and System Biology(第三届最优化与系统生物学国际会议 OSB09)

会议地点: 张家界

会议语种:英文

页码: 361-370

在线出版日期: 2009-09-20（万方平台首次上网日期，不代表论文的发表时间）