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Selection of organisms for the co-evolution-based study of protein interactions

BACKGROUND: The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms us...

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Autores principales: Herman, Dorota, Ochoa, David, Juan, David, Lopez, Daniel, Valencia, Alfonso, Pazos, Florencio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179974/
https://www.ncbi.nlm.nih.gov/pubmed/21910884
http://dx.doi.org/10.1186/1471-2105-12-363
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author Herman, Dorota
Ochoa, David
Juan, David
Lopez, Daniel
Valencia, Alfonso
Pazos, Florencio
author_facet Herman, Dorota
Ochoa, David
Juan, David
Lopez, Daniel
Valencia, Alfonso
Pazos, Florencio
author_sort Herman, Dorota
collection PubMed
description BACKGROUND: The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. RESULTS: We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. CONCLUSIONS: In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.
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spelling pubmed-31799742011-09-27 Selection of organisms for the co-evolution-based study of protein interactions Herman, Dorota Ochoa, David Juan, David Lopez, Daniel Valencia, Alfonso Pazos, Florencio BMC Bioinformatics Research Article BACKGROUND: The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. RESULTS: We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. CONCLUSIONS: In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest. BioMed Central 2011-09-12 /pmc/articles/PMC3179974/ /pubmed/21910884 http://dx.doi.org/10.1186/1471-2105-12-363 Text en Copyright ©2011 Herman 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 Research Article
Herman, Dorota
Ochoa, David
Juan, David
Lopez, Daniel
Valencia, Alfonso
Pazos, Florencio
Selection of organisms for the co-evolution-based study of protein interactions
title Selection of organisms for the co-evolution-based study of protein interactions
title_full Selection of organisms for the co-evolution-based study of protein interactions
title_fullStr Selection of organisms for the co-evolution-based study of protein interactions
title_full_unstemmed Selection of organisms for the co-evolution-based study of protein interactions
title_short Selection of organisms for the co-evolution-based study of protein interactions
title_sort selection of organisms for the co-evolution-based study of protein interactions
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179974/
https://www.ncbi.nlm.nih.gov/pubmed/21910884
http://dx.doi.org/10.1186/1471-2105-12-363
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