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PROPER: global protein interaction network alignment through percolation matching

BACKGROUND: The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different P...

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Detalles Bibliográficos
Autores principales: Kazemi, Ehsan, Hassani, Hamed, Grossglauser, Matthias, Pezeshgi Modarres, Hassan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5153870/
https://www.ncbi.nlm.nih.gov/pubmed/27955623
http://dx.doi.org/10.1186/s12859-016-1395-9
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author Kazemi, Ehsan
Hassani, Hamed
Grossglauser, Matthias
Pezeshgi Modarres, Hassan
author_facet Kazemi, Ehsan
Hassani, Hamed
Grossglauser, Matthias
Pezeshgi Modarres, Hassan
author_sort Kazemi, Ehsan
collection PubMed
description BACKGROUND: The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. RESULTS: In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. CONCLUSIONS: We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1395-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-51538702016-12-20 PROPER: global protein interaction network alignment through percolation matching Kazemi, Ehsan Hassani, Hamed Grossglauser, Matthias Pezeshgi Modarres, Hassan BMC Bioinformatics Research Article BACKGROUND: The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. RESULTS: In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. CONCLUSIONS: We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1395-9) contains supplementary material, which is available to authorized users. BioMed Central 2016-12-12 /pmc/articles/PMC5153870/ /pubmed/27955623 http://dx.doi.org/10.1186/s12859-016-1395-9 Text en © The Author(s) 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Kazemi, Ehsan
Hassani, Hamed
Grossglauser, Matthias
Pezeshgi Modarres, Hassan
PROPER: global protein interaction network alignment through percolation matching
title PROPER: global protein interaction network alignment through percolation matching
title_full PROPER: global protein interaction network alignment through percolation matching
title_fullStr PROPER: global protein interaction network alignment through percolation matching
title_full_unstemmed PROPER: global protein interaction network alignment through percolation matching
title_short PROPER: global protein interaction network alignment through percolation matching
title_sort proper: global protein interaction network alignment through percolation matching
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5153870/
https://www.ncbi.nlm.nih.gov/pubmed/27955623
http://dx.doi.org/10.1186/s12859-016-1395-9
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