Identification of protein complexes and functional modules in integrated PPI networks

Yang Guo, Xuequn Shang, Qingping Zhu, Mingkui Huang, Zhanhuai Li

科研成果: 书/报告/会议事项章节会议稿件同行评审

3 引用 (Scopus)

摘要

Mining the protein complexes and functional modules from protein-protein interaction (PPI) networks is vital to understand the mechanism of cellular components and protein functions. Most of the proposed methods had solely focused on static properties of the PPI networks since the available PPI data are static. However, cellular systems are highly dynamic. That is, the interactions of proteins are responsive to environmental cues to accomplish diverse cellular functions. It is important to consider the dynamic inherent within the PPI networks to identify protein complexes and functional modules. In addition, most computational methods did not distinguish between protein complexes and functional modules. It is important to distinguish between them since they are different protein organizations. In this paper, we propose a novel framework to analyze the PPI networks in dynamic conditions by integrating time-series gene expression profiles data and subcelluar localization data. The algorithm, CBMI, is developed to identify protein complexes in integrated PPI networks. By investigating multiple perspectives of proteins in the PPI networks, we identify the 'dynamic' hubs in the PPI networks, and then present a new method to discover the functional modules in the PPI networks. The experimental results show that the integration of temporal gene expression data and subcelluar localization data with PPI data contributes to extracting the protein complexes more precisely. Comprehensive evaluations based on f-measure and functional annotations in MIPS database reveal that our algorithm, CBMI, outperforms other previous algorithms in identifying protein complexes, and the detected functional modules are statistically significant in terms of functional annotations. The proposed framework provides a new clue to distinguish between protein complexes and functional modules, and the developed algorithms can be an effective technique for the identification of them.

源语言英语
主期刊名Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
编辑Huiru Zheng, Xiaohua Tony Hu, Yadong Wang, Jin-Kao Hao, David Gilbert, Daniel Berrar, Kwang-Hyun Cho, Werner Dubitzky
出版商Institute of Electrical and Electronics Engineers Inc.
8-15
页数8
ISBN(电子版)9781479956692
DOI
出版状态已出版 - 29 12月 2014
活动2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, 英国
期限: 2 11月 20145 11月 2014

出版系列

姓名Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

会议

会议2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
国家/地区英国
Belfast
时期2/11/145/11/14

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