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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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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. |
format | Online Article Text |
id | pubmed-5153870 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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