Identifying protein complexes in PPI network using non-cooperative sequential game

Abstract Identifying protein complexes from protein-protein interaction (PPI) network is an important and challenging task in computational biology as it helps in better understanding of cellular mechanisms in various organisms. In this paper we propose a noncooperative sequential game based model f...

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Auteurs principaux:	Ujjwal Maulik, Srinka Basu, Sumanta Ray
Format:	article
Langue:	EN
Publié:	Nature Portfolio 2017
Sujets:	Medicine R Science Q
Accès en ligne:	https://doaj.org/article/ab245d748d8f4e92828172db375f1d53
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spelling	oai:doaj.org-article:ab245d748d8f4e92828172db375f1d532021-12-02T15:18:52ZIdentifying protein complexes in PPI network using non-cooperative sequential game10.1038/s41598-017-08760-x2045-2322https://doaj.org/article/ab245d748d8f4e92828172db375f1d532017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08760-xhttps://doaj.org/toc/2045-2322Abstract Identifying protein complexes from protein-protein interaction (PPI) network is an important and challenging task in computational biology as it helps in better understanding of cellular mechanisms in various organisms. In this paper we propose a noncooperative sequential game based model for protein complex detection from PPI network. The key hypothesis is that protein complex formation is driven by mechanism that eventually optimizes the number of interactions within the complex leading to dense subgraph. The hypothesis is drawn from the observed network property named small world. The proposed multi-player game model translates the hypothesis into the game strategies. The Nash equilibrium of the game corresponds to a network partition where each protein either belong to a complex or form a singleton cluster. We further propose an algorithm to find the Nash equilibrium of the sequential game. The exhaustive experiment on synthetic benchmark and real life yeast networks evaluates the structural as well as biological significance of the network partitions.Ujjwal MaulikSrinka BasuSumanta RayNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ujjwal Maulik Srinka Basu Sumanta Ray Identifying protein complexes in PPI network using non-cooperative sequential game
description	Abstract Identifying protein complexes from protein-protein interaction (PPI) network is an important and challenging task in computational biology as it helps in better understanding of cellular mechanisms in various organisms. In this paper we propose a noncooperative sequential game based model for protein complex detection from PPI network. The key hypothesis is that protein complex formation is driven by mechanism that eventually optimizes the number of interactions within the complex leading to dense subgraph. The hypothesis is drawn from the observed network property named small world. The proposed multi-player game model translates the hypothesis into the game strategies. The Nash equilibrium of the game corresponds to a network partition where each protein either belong to a complex or form a singleton cluster. We further propose an algorithm to find the Nash equilibrium of the sequential game. The exhaustive experiment on synthetic benchmark and real life yeast networks evaluates the structural as well as biological significance of the network partitions.
format	article
author	Ujjwal Maulik Srinka Basu Sumanta Ray
author_facet	Ujjwal Maulik Srinka Basu Sumanta Ray
author_sort	Ujjwal Maulik
title	Identifying protein complexes in PPI network using non-cooperative sequential game
title_short	Identifying protein complexes in PPI network using non-cooperative sequential game
title_full	Identifying protein complexes in PPI network using non-cooperative sequential game
title_fullStr	Identifying protein complexes in PPI network using non-cooperative sequential game
title_full_unstemmed	Identifying protein complexes in PPI network using non-cooperative sequential game
title_sort	identifying protein complexes in ppi network using non-cooperative sequential game
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/ab245d748d8f4e92828172db375f1d53
work_keys_str_mv	AT ujjwalmaulik identifyingproteincomplexesinppinetworkusingnoncooperativesequentialgame AT srinkabasu identifyingproteincomplexesinppinetworkusingnoncooperativesequentialgame AT sumantaray identifyingproteincomplexesinppinetworkusingnoncooperativesequentialgame
_version_	1718387467215699968

Identifying protein complexes in PPI network using non-cooperative sequential game

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