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Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC

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  • Jie Zhao
  • Xiujuan Lei
  • Fang-Xiang Wu

Abstract

Protein complexes play a critical role in understanding the biological processes and the functions of cellular mechanisms. Most existing protein complex detection algorithms cannot reflect dynamics of protein complexes. In this paper, a novel algorithm named Improved Cuckoo Search Clustering (ICSC) algorithm is proposed to detect protein complexes in weighted dynamic protein-protein interaction (PPI) networks. First, we constructed weighted dynamic PPI networks and detected protein complex cores in each dynamic subnetwork. Then, ICSC algorithm was used to cluster the protein attachments to the cores. The experimental results on both DIP dataset and Krogan dataset demonstrated that ICSC algorithm is more effective in identifying protein complexes than other competing methods.

Suggested Citation

  • Jie Zhao & Xiujuan Lei & Fang-Xiang Wu, 2017. "Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC," Complexity, Hindawi, vol. 2017, pages 1-11, August.
    • Handle: RePEc:hin:complx:4120506
    DOI: 10.1155/2017/4120506
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    References listed on IDEAS

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    1. Anne-Claude Gavin & Markus Bösche & Roland Krause & Paola Grandi & Martina Marzioch & Andreas Bauer & Jörg Schultz & Jens M. Rick & Anne-Marie Michon & Cristina-Maria Cruciat & Marita Remor & Christia, 2002. "Functional organization of the yeast proteome by systematic analysis of protein complexes," Nature, Nature, vol. 415(6868), pages 141-147, January.
    2. Yuen Ho & Albrecht Gruhler & Adrian Heilbut & Gary D. Bader & Lynda Moore & Sally-Lin Adams & Anna Millar & Paul Taylor & Keiryn Bennett & Kelly Boutilier & Lingyun Yang & Cheryl Wolting & Ian Donalds, 2002. "Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry," Nature, Nature, vol. 415(6868), pages 180-183, January.
    3. Hao Wu & Lin Gao & Jihua Dong & Xiaofei Yang, 2014. "Detecting Overlapping Protein Complexes by Rough-Fuzzy Clustering in Protein-Protein Interaction Networks," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-13, March.
    4. Nevan J. Krogan & Gerard Cagney & Haiyuan Yu & Gouqing Zhong & Xinghua Guo & Alexandr Ignatchenko & Joyce Li & Shuye Pu & Nira Datta & Aaron P. Tikuisis & Thanuja Punna & José M. Peregrín-Alvarez & Mi, 2006. "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae," Nature, Nature, vol. 440(7084), pages 637-643, March.
    5. Anne-Claude Gavin & Patrick Aloy & Paola Grandi & Roland Krause & Markus Boesche & Martina Marzioch & Christina Rau & Lars Juhl Jensen & Sonja Bastuck & Birgit Dümpelfeld & Angela Edelmann & Marie-Ann, 2006. "Proteome survey reveals modularity of the yeast cell machinery," Nature, Nature, vol. 440(7084), pages 631-636, March.
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    Cited by:

    1. Dhuha Abdulhadi Abduljabbar & Siti Zaiton Mohd Hashim & Roselina Sallehuddin, 2020. "Nature-inspired optimization algorithms for community detection in complex networks: a review and future trends," Telecommunication Systems: Modelling, Analysis, Design and Management, Springer, vol. 74(2), pages 225-252, June.

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