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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2014
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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. |
format | Online Article Text |
id | pubmed-3996968 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
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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