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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Nature Portfolio
2017
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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) |
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Medicine R Science Q Ujjwal Maulik Srinka Basu Sumanta Ray Identifying protein complexes in PPI network using non-cooperative sequential game |
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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 |
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