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Topology analysis and visualization of Potyvirus protein-protein interaction network

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Topology analysis and visualization of Potyvirus protein-protein interaction network

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dc.contributor.author Bosque, Gabriel es_ES
dc.contributor.author Folch Fortuny, Abel es_ES
dc.contributor.author Picó Marco, Jesús Andrés es_ES
dc.contributor.author Ferrer, Alberto es_ES
dc.contributor.author Elena Fito, Santiago Fco es_ES
dc.date.accessioned 2016-04-06T11:05:43Z
dc.date.available 2016-04-06T11:05:43Z
dc.date.issued 2014-11-20
dc.identifier.issn 1752-0509
dc.identifier.uri http://hdl.handle.net/10251/62283
dc.description.abstract Background: One of the central interests of Virology is the identification of host factors that contribute to virus infection. Despite tremendous efforts, the list of factors identified remains limited. With omics techniques, the focus has changed from identifying and thoroughly characterizing individual host factors to the simultaneous analysis of thousands of interactions, framing them on the context of protein-protein interaction networks and of transcriptional regulatory networks. This new perspective is allowing the identification of direct and indirect viral targets. Such information is available for several members of the Potyviridae family, one of the largest and more important families of plant viruses. Results: After collecting information on virus protein-protein interactions from different potyviruses, we have processed it and used it for inferring a protein-protein interaction network. All proteins are connected into a single network component. Some proteins show a high degree and are highly connected while others are much less connected, with the network showing a significant degree of dissortativeness. We have attempted to integrate this virus protein-protein interaction network into the largest protein-protein interaction network of Arabidopsis thaliana, a susceptible laboratory host. To make the interpretation of data and results easier, we have developed a new approach for visualizing and analyzing the dynamic spread on the host network of the local perturbations induced by viral proteins. We found that local perturbations can reach the entire host protein-protein interaction network, although the efficiency of this spread depends on the particular viral proteins. By comparing the spread dynamics among viral proteins, we found that some proteins spread their effects fast and efficiently by attacking hubs in the host network while other proteins exert more local effects. Conclusions: Our findings confirm that potyvirus protein-protein interaction networks are highly connected, with some proteins playing the role of hubs. Several topological parameters depend linearly on the protein degree. Some viral proteins focus their effect in only host hubs while others diversify its effect among several proteins at the first step. Future new data will help to refine our model and to improve our predictions. es_ES
dc.description.sponsorship This work was supported by the Spanish Ministerio de Economia y Competitividad grants BFU2012-30805 (to SFE), DPI2011-28112-C04-02 (to AF) and DPI2011-28112-C04-01 (to JP). The first two authors are recipients of fellowships from the Spanish Ministerio de Economia y Competitividad: BES-2012-053772 (to GB) and BES-2012-057812 (to AF-F). en_EN
dc.language Inglés es_ES
dc.publisher BioMed Central es_ES
dc.relation Spanish Ministerio de Economia y Competitividad BFU2012-30805 DPI2011-28112-C04-02 DPI2011-28112-C04-01 BES-2012-053772 BES-2012-057812 es_ES
dc.relation.ispartof BMC Systems Biology es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Amplification of perturbations es_ES
dc.subject Network biology es_ES
dc.subject Potyvirus es_ES
dc.subject Protein interaction network es_ES
dc.subject Systems biology es_ES
dc.subject Virology es_ES
dc.subject.classification ESTADISTICA E INVESTIGACION OPERATIVA es_ES
dc.subject.classification INGENIERIA DE SISTEMAS Y AUTOMATICA es_ES
dc.title Topology analysis and visualization of Potyvirus protein-protein interaction network es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12918-014-0129-8
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Automática e Informática Industrial - Institut Universitari d'Automàtica i Informàtica Industrial es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Estadística e Investigación Operativa Aplicadas y Calidad - Departament d'Estadística i Investigació Operativa Aplicades i Qualitat es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ingeniería de Sistemas y Automática - Departament d'Enginyeria de Sistemes i Automàtica es_ES
dc.description.bibliographicCitation Bosque, G.; Folch Fortuny, A.; Picó Marco, JA.; Ferrer, A.; Elena Fito, SF. (2014). Topology analysis and visualization of Potyvirus protein-protein interaction network. BMC Systems Biology. 129(8):1-15. doi:10.1186/s12918-014-0129-8 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1186/s12918-014-0129-8 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 15 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 129 es_ES
dc.description.issue 8 es_ES
dc.relation.senia 278675 es_ES
dc.identifier.pmid 25409737 en_EN
dc.identifier.pmcid PMC4251984 en_EN
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