Mining the modular structure of protein interaction networks.
BACKGROUND: Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithm...
| Autores: | , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2015 |
| País: | España |
| Institución: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repositorio: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:10230/25606 |
| Acceso en línea: | http://hdl.handle.net/10230/25606 http://dx.doi.org/10.1371/journal.pone.0122477 |
| Access Level: | acceso abierto |
| Palabra clave: | Bioinformàtica Proteïnes -- Estructura -- Simulació per ordinador |
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Mining the modular structure of protein interaction networks.Berenstein, Ariel JoséPiñero González, Janet, 1977-Furlong, Laura I., 1971-Chernomoretz, ArielBioinformàticaProteïnes -- Estructura -- Simulació per ordinadorBACKGROUND: Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. METHODOLOGY: We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. RESULTS: As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.This project has been made possible by CONICET (grant PIP0087), UBACyT (grant 20020110200314), ISCIII-FEDER (PI13/00082 and CP10/00524), IMI JU (grant agreements n° [115002] (eTOX) and n° [115191] (Open PHACTS)], resources of which are composed of financial contribution from the EU's FP7 (FP7/2007–2013) and EFPIA companies’ in kind contribution)Public Library of Science201620162015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/25606http://dx.doi.org/10.1371/journal.pone.0122477reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésPLoS One. 2015 Apr 9;10(4):e0122477info:eu-repo/grantAgreement/EC/FP7/115002info:eu-repo/grantAgreement/EC/FP7/115191© 2015 Berenstein et al. This is an open access article distributed under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/256062026-05-29T05:05:01Z |
| dc.title.none.fl_str_mv |
Mining the modular structure of protein interaction networks. |
| title |
Mining the modular structure of protein interaction networks. |
| spellingShingle |
Mining the modular structure of protein interaction networks. Berenstein, Ariel José Bioinformàtica Proteïnes -- Estructura -- Simulació per ordinador |
| title_short |
Mining the modular structure of protein interaction networks. |
| title_full |
Mining the modular structure of protein interaction networks. |
| title_fullStr |
Mining the modular structure of protein interaction networks. |
| title_full_unstemmed |
Mining the modular structure of protein interaction networks. |
| title_sort |
Mining the modular structure of protein interaction networks. |
| dc.creator.none.fl_str_mv |
Berenstein, Ariel José Piñero González, Janet, 1977- Furlong, Laura I., 1971- Chernomoretz, Ariel |
| author |
Berenstein, Ariel José |
| author_facet |
Berenstein, Ariel José Piñero González, Janet, 1977- Furlong, Laura I., 1971- Chernomoretz, Ariel |
| author_role |
author |
| author2 |
Piñero González, Janet, 1977- Furlong, Laura I., 1971- Chernomoretz, Ariel |
| author2_role |
author author author |
| dc.subject.none.fl_str_mv |
Bioinformàtica Proteïnes -- Estructura -- Simulació per ordinador |
| topic |
Bioinformàtica Proteïnes -- Estructura -- Simulació per ordinador |
| description |
BACKGROUND: Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. METHODOLOGY: We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. RESULTS: As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge. |
| publishDate |
2015 |
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2015 2016 2016 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
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http://hdl.handle.net/10230/25606 http://dx.doi.org/10.1371/journal.pone.0122477 |
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http://hdl.handle.net/10230/25606 http://dx.doi.org/10.1371/journal.pone.0122477 |
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Inglés |
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Inglés |
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PLoS One. 2015 Apr 9;10(4):e0122477 info:eu-repo/grantAgreement/EC/FP7/115002 info:eu-repo/grantAgreement/EC/FP7/115191 |
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http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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application/pdf application/pdf |
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Public Library of Science |
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Public Library of Science |
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reponame:Recercat. Dipósit de la Recerca de Catalunya instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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