research-article

Regularizing predicted complexes by mutually exclusive protein-protein interactions

Authors:

Osamu Maruyama,

Limsoon WongAuthors Info & Claims

ASONAM '15: Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2015

Pages 1068 - 1075

https://doi.org/10.1145/2808797.2808817

Published: 25 August 2015 Publication History

Abstract

Protein complexes are key entities in the cell responsible for various cellular mechanisms and biological processes. We propose here a method for predicting protein complexes from a protein-protein interaction (PPI) network, using information on mutually exclusive PPIs. If two interactions are mutually exclusive, they are not allowed to exist simultaneously in the same predicted complex. We introduce a new regularization term which checks whether predicted complexes are connected by mutually exclusive PPIs. This regularization term is added into the scoring function of our earlier protein complex prediction tool, PPSampler2. We show that PPSampler2 with mutually exclusive PPIs outperforms the original one. Furthermore, the performance is superior to well-known representative conventional protein complex prediction methods. Thus, it is is effective to use mutual exclusiveness of PPIs in protein complex prediction.

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Cited By

Wu ZLiao QLiu B(2019)A comprehensive review and evaluation of computational methods for identifying protein complexes from protein–protein interaction networksBriefings in Bioinformatics10.1093/bib/bbz085Online publication date: 18-Oct-2019
https://doi.org/10.1093/bib/bbz085
Zhang ZSong JTang JXu XGuo F(2018)Detecting complexes from edge-weighted PPI networks via genes expression analysisBMC Systems Biology10.1186/s12918-018-0565-y12:S4Online publication date: 24-Apr-2018
https://doi.org/10.1186/s12918-018-0565-y
Maruyama OKuwahara Y(2017)RocSampler: regularizing overlapping protein complexes in protein-protein interaction networksBMC Bioinformatics10.1186/s12859-017-1920-518:S15Online publication date: 6-Dec-2017
https://doi.org/10.1186/s12859-017-1920-5

Regularizing predicted complexes by mutually exclusive protein-protein interactions
1. Applied computing
  1. Life and medical sciences
2. Human-centered computing
  1. Human computer interaction (HCI)
    1. Interaction paradigms

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cover image ACM Conferences

ASONAM '15: Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2015

August 2015

835 pages

ISBN:9781450338547

DOI:10.1145/2808797

Copyright © 2015 ACM.

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: 25 August 2015

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ASONAM '15: Advances in Social Networks Analysis and Mining 2015

August 25 - 28, 2015

Paris, France

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Cited By

Wu ZLiao QLiu B(2019)A comprehensive review and evaluation of computational methods for identifying protein complexes from protein–protein interaction networksBriefings in Bioinformatics10.1093/bib/bbz085Online publication date: 18-Oct-2019
https://doi.org/10.1093/bib/bbz085
Zhang ZSong JTang JXu XGuo F(2018)Detecting complexes from edge-weighted PPI networks via genes expression analysisBMC Systems Biology10.1186/s12918-018-0565-y12:S4Online publication date: 24-Apr-2018
https://doi.org/10.1186/s12918-018-0565-y
Maruyama OKuwahara Y(2017)RocSampler: regularizing overlapping protein complexes in protein-protein interaction networksBMC Bioinformatics10.1186/s12859-017-1920-518:S15Online publication date: 6-Dec-2017
https://doi.org/10.1186/s12859-017-1920-5

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