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Evolutionary analysis of functional modules in dynamic PPI networks

Published: 07 October 2012 Publication History

Abstract

Functional module detection in Protein-Protein Interaction (PPI) networks is essential to understanding the organization, evolution and interaction of the cellular systems. In recent years, most of the researches have focused on detecting the functional modules from the static PPI networks. However, sometimes the structure of the PPI networks changes in response to stimuli resulting in the changes of both the composition and functionality of these modules. These changes occur gradually and can be thought of as an evolution of the functional modules. In our opinions the evolutionary analysis of functional modules is a key to form important insights of the functional modules' underlying behaviors, particularly when targeting complex living systems.
In this paper, we propose a novel computational framework which integrates a PPI network with multiple dynamic gene coexpression networks to categorize and track the evolutionary pattern of functional modules over consecutive time-stamps. We first propose a method to construct dynamic PPI networks, and then design a new functional influence based algorithm to detect the functional modules from these dynamic PPI networks. Based on the results of this approach, we provide a simple but effective method to characterize and track the evolutionary patterns of dynamic modules, which involves detecting evolutionary events between modules found at consecutive timestamps. Extensive experiments on the fermentation process dataset of S. cerevisiae show that the proposed framework not only outperforms previous functional module detection methods, but also efficiently tracks the evolutionary patterns of functional modules.

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Cited By

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  • (2018)PCD-DPPI: Protein complex detection from dynamic PPI using shuffled frog-leaping algorithmGene Reports10.1016/j.genrep.2018.06.00212(89-98)Online publication date: Sep-2018
  • (2016)BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein ComplexesPLOS ONE10.1371/journal.pone.015992311:7(e0159923)Online publication date: 27-Jul-2016
  • (2016)Protein complex identification through Markov clustering with firefly algorithm on dynamic protein-protein interaction networksInformation Sciences: an International Journal10.1016/j.ins.2015.09.028329:C(303-316)Online publication date: 1-Feb-2016
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        cover image ACM Conferences
        BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
        October 2012
        725 pages
        ISBN:9781450316705
        DOI:10.1145/2382936
        Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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        Published: 07 October 2012

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        View all
        • (2018)PCD-DPPI: Protein complex detection from dynamic PPI using shuffled frog-leaping algorithmGene Reports10.1016/j.genrep.2018.06.00212(89-98)Online publication date: Sep-2018
        • (2016)BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein ComplexesPLOS ONE10.1371/journal.pone.015992311:7(e0159923)Online publication date: 27-Jul-2016
        • (2016)Protein complex identification through Markov clustering with firefly algorithm on dynamic protein-protein interaction networksInformation Sciences: an International Journal10.1016/j.ins.2015.09.028329:C(303-316)Online publication date: 1-Feb-2016
        • (2015)Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritisGenome Medicine10.1186/s13073-015-0227-27:1Online publication date: 24-Oct-2015
        • (2014)Detecting functional modules in dynamic protein-protein interaction networks using Markov Clustering and Firefly Algorithm2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2014.6999131(75-81)Online publication date: Nov-2014
        • (2013)Critical protein detection in dynamic PPI networks with multi-source integrated deep belief nets2013 IEEE International Conference on Bioinformatics and Biomedicine10.1109/BIBM.2013.6732606(29-36)Online publication date: Dec-2013

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