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A core-attachment based method to detect protein complexes in PPI networks

BACKGROUND: How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complex...

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Detalles Bibliográficos
Autores principales: Wu, Min, Li, Xiaoli, Kwoh, Chee-Keong, Ng, See-Kiong
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701950/
https://www.ncbi.nlm.nih.gov/pubmed/19486541
http://dx.doi.org/10.1186/1471-2105-10-169
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author Wu, Min
Li, Xiaoli
Kwoh, Chee-Keong
Ng, See-Kiong
author_facet Wu, Min
Li, Xiaoli
Kwoh, Chee-Keong
Ng, See-Kiong
author_sort Wu, Min
collection PubMed
description BACKGROUND: How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complexes based solely on the observation that dense regions in PPI networks may correspond to protein complexes, but fail to consider the inherent organization within protein complexes. RESULTS: To provide insights into the organization of protein complexes, this paper presents a novel core-attachment based method (COACH) which detects protein complexes in two stages. It first detects protein-complex cores as the "hearts" of protein complexes and then includes attachments into these cores to form biologically meaningful structures. We evaluate and analyze our predicted protein complexes from two aspects. First, we perform a comprehensive comparison between our proposed method and existing techniques by comparing the predicted complexes against benchmark complexes. Second, we also validate the core-attachment structures using various biological evidence and knowledge. CONCLUSION: Our proposed COACH method has been applied on two different yeast PPI networks and the experimental results show that COACH performs significantly better than the state-of-the-art techniques. In addition, the identified complexes with core-attachment structures are demonstrated to match very well with existing biological knowledge and thus provide more insights for future biological study.
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spelling pubmed-27019502009-06-26 A core-attachment based method to detect protein complexes in PPI networks Wu, Min Li, Xiaoli Kwoh, Chee-Keong Ng, See-Kiong BMC Bioinformatics Methodology Article BACKGROUND: How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complexes based solely on the observation that dense regions in PPI networks may correspond to protein complexes, but fail to consider the inherent organization within protein complexes. RESULTS: To provide insights into the organization of protein complexes, this paper presents a novel core-attachment based method (COACH) which detects protein complexes in two stages. It first detects protein-complex cores as the "hearts" of protein complexes and then includes attachments into these cores to form biologically meaningful structures. We evaluate and analyze our predicted protein complexes from two aspects. First, we perform a comprehensive comparison between our proposed method and existing techniques by comparing the predicted complexes against benchmark complexes. Second, we also validate the core-attachment structures using various biological evidence and knowledge. CONCLUSION: Our proposed COACH method has been applied on two different yeast PPI networks and the experimental results show that COACH performs significantly better than the state-of-the-art techniques. In addition, the identified complexes with core-attachment structures are demonstrated to match very well with existing biological knowledge and thus provide more insights for future biological study. BioMed Central 2009-06-02 /pmc/articles/PMC2701950/ /pubmed/19486541 http://dx.doi.org/10.1186/1471-2105-10-169 Text en Copyright © 2009 Wu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Wu, Min
Li, Xiaoli
Kwoh, Chee-Keong
Ng, See-Kiong
A core-attachment based method to detect protein complexes in PPI networks
title A core-attachment based method to detect protein complexes in PPI networks
title_full A core-attachment based method to detect protein complexes in PPI networks
title_fullStr A core-attachment based method to detect protein complexes in PPI networks
title_full_unstemmed A core-attachment based method to detect protein complexes in PPI networks
title_short A core-attachment based method to detect protein complexes in PPI networks
title_sort core-attachment based method to detect protein complexes in ppi networks
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701950/
https://www.ncbi.nlm.nih.gov/pubmed/19486541
http://dx.doi.org/10.1186/1471-2105-10-169
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