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msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks

Dynamics of protein-protein interactions (PPIs) reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses...

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Detalles Bibliográficos
Autores principales: Zhang, Yuan, Du, Nan, Li, Kang, Feng, Jinchao, Jia, Kebin, Zhang, Aidong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996968/
https://www.ncbi.nlm.nih.gov/pubmed/24800204
http://dx.doi.org/10.1155/2014/138410
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author Zhang, Yuan
Du, Nan
Li, Kang
Feng, Jinchao
Jia, Kebin
Zhang, Aidong
author_facet Zhang, Yuan
Du, Nan
Li, Kang
Feng, Jinchao
Jia, Kebin
Zhang, Aidong
author_sort Zhang, Yuan
collection PubMed
description Dynamics of protein-protein interactions (PPIs) reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses on identifying these critical proteins exhibiting dramatic structural changes in dynamic PPI networks. First, a comprehensive way of modeling the dynamic PPIs is presented which simultaneously analyzes the activity of proteins and assembles the dynamic coregulation correlation between proteins at each time point. Second, a novel method is proposed, named msiDBN, which models a common representation of multiple PPI networks using a deep belief network framework and analyzes the reconstruction errors and the variabilities across the time courses in the biological process. Experiments were implemented on data of yeast cell cycles. We evaluated our network construction method by comparing the functional representations of the derived networks with two other traditional construction methods. The ranking results of critical proteins in msiDBN were compared with the results from the baseline methods. The results of comparison showed that msiDBN had better reconstruction rate and identified more proteins of critical value to yeast cell cycle process.
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spelling pubmed-39969682014-05-05 msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks Zhang, Yuan Du, Nan Li, Kang Feng, Jinchao Jia, Kebin Zhang, Aidong Biomed Res Int Research Article Dynamics of protein-protein interactions (PPIs) reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses on identifying these critical proteins exhibiting dramatic structural changes in dynamic PPI networks. First, a comprehensive way of modeling the dynamic PPIs is presented which simultaneously analyzes the activity of proteins and assembles the dynamic coregulation correlation between proteins at each time point. Second, a novel method is proposed, named msiDBN, which models a common representation of multiple PPI networks using a deep belief network framework and analyzes the reconstruction errors and the variabilities across the time courses in the biological process. Experiments were implemented on data of yeast cell cycles. We evaluated our network construction method by comparing the functional representations of the derived networks with two other traditional construction methods. The ranking results of critical proteins in msiDBN were compared with the results from the baseline methods. The results of comparison showed that msiDBN had better reconstruction rate and identified more proteins of critical value to yeast cell cycle process. Hindawi Publishing Corporation 2014 2014-04-02 /pmc/articles/PMC3996968/ /pubmed/24800204 http://dx.doi.org/10.1155/2014/138410 Text en Copyright © 2014 Yuan Zhang et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhang, Yuan
Du, Nan
Li, Kang
Feng, Jinchao
Jia, Kebin
Zhang, Aidong
msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
title msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
title_full msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
title_fullStr msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
title_full_unstemmed msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
title_short msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
title_sort msidbn: a method of identifying critical proteins in dynamic ppi networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996968/
https://www.ncbi.nlm.nih.gov/pubmed/24800204
http://dx.doi.org/10.1155/2014/138410
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