Mining the modular structure of protein interaction networks.

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  • dc.contributor.author Berenstein, Ariel Joséca
  • dc.contributor.author Piñero González, Janet, 1977-ca
  • dc.contributor.author Furlong, Laura I., 1971-ca
  • dc.contributor.author Chernomoretz, Arielca
  • dc.date.accessioned 2016-01-20T11:20:27Z
  • dc.date.available 2016-01-20T11:20:27Z
  • dc.date.issued 2015
  • dc.description.abstract 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.ca
  • dc.description.sponsorship 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)
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Berenstein AJ, Piñero J, Furlong LI, Chernomoretz A. Mining the modular structure of protein interaction networks. PLoS One. 2015 Apr 9;10(4):e0122477. DOI: 10.1371/journal.pone.0122477.ca
  • dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0122477
  • dc.identifier.issn 1932-6203
  • dc.identifier.uri http://hdl.handle.net/10230/25606
  • dc.language.iso engca
  • dc.publisher Public Library of Scienceca
  • dc.relation.ispartof PLoS One. 2015 Apr 9;10(4):e0122477
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/115002
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/115191
  • dc.rights © 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.ca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/ca
  • dc.subject.other Bioinformàticaca
  • dc.subject.other Proteïnes -- Estructura -- Simulació per ordinadorca
  • dc.title Mining the modular structure of protein interaction networks.ca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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