Folch-Fortuny, A.; Bosque-Chacon, G.; Picó, J.; Ferrer, A.; Elena, S. (2016). Fusion of genomic, proteomic and phenotypic data: the case of potyviruses. Molecular BioSystems. 12(1):253-261. https://doi.org/10.1039/c5mb00507h
Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/76327
Título:
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Fusion of genomic, proteomic and phenotypic data: the case of potyviruses
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Autor:
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Folch-Fortuny, A.
BOSQUE-CHACON, GABRIEL
Picó, Jesús
Ferrer, A.
Elena, S.F.
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Entidad UPV:
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Universitat Politècnica de València. Escuela Técnica Superior de Ingenieros Industriales - Escola Tècnica Superior d'Enginyers Industrials
Universitat Politècnica de València. Departamento de Estadística e Investigación Operativa Aplicadas y Calidad - Departament d'Estadística i Investigació Operativa Aplicades i Qualitat
Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
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Fecha difusión:
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Resumen:
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Data fusion has been widely applied to analyse different sources of information, combining all of them in a single multivariate model. This methodology is mandatory when different omic data sets must be integrated to fully ...[+]
Data fusion has been widely applied to analyse different sources of information, combining all of them in a single multivariate model. This methodology is mandatory when different omic data sets must be integrated to fully understand an organism using a systems biology approach. Here, a data fusion procedure is presented to combine genomic, proteomic and phenotypic data sets gathered for Tobacco etch virus (TEV). The genomic data correspond to random mutations inserted in most viral genes. The proteomic data represent both the effect of these mutations on the encoded proteins and the perturbation induced by the mutated proteins to their neighbours in the protein protein interaction net- work (PPIN). Finally, the phenotypic trait evaluated for each mutant virus is replicative fitness. To analyse these three sources of information a Partial Least Squares (PLS) regression model is fitted in order to extract the latent variables from data that explain (and relate) the significant variables to the fitness of TEV. The final output of this methodology is a set of functional modules of the PPIN relating topology and mutations with fitness. Throughout the re-analysis of these diverse TEV data, we generated valuable information on the mechanism of action of certain mutations and how they translate into organismal fitness. Results show that the effect of some mutations goes beyond the protein they directly affect and spreads on the PPIN to neighbour proteins, thus defining functional modules.
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Palabras clave:
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YEAST 2-HYBRID SYSTEM
,
COMPLEX NETWORKS
,
VIRUS
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CHEMOMETRICS
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REGRESSION
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TUTORIAL
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CULTURE
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Derechos de uso:
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Reserva de todos los derechos
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Fuente:
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Molecular BioSystems. (issn:
1742-206X
) (eissn:
1742-2051
)
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DOI:
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10.1039/c5mb00507h
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Editorial:
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Royal Society of Chemistry
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Versión del editor:
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http://dx.doi. org/10.1039/c5mb00507h
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Código del Proyecto:
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info:eu-repo/grantAgreement/MICINN//DPI2011-28112-C04-02/ES/MONITORIZACION, INFERENCIA, OPTIMIZACION Y CONTROL MULTI-ESCALA: DE CELULAS A BIORREACTORES. (MULTISCALES)/ /
info:eu-repo/grantAgreement/GVA//PROMETEOII%2F2014%2F021/ES/Comparative systems biology of host-virus interactions/
info:eu-repo/grantAgreement/MINECO//BFU2012-30805/ES/EVOLUTIONARY SYSTEMS VIROLOGY: EPISTASIS AND THE RUGGEDNESS OF ADAPTIVE LANDSCAPES, MUTATIONS IN REGULATORY SEQUENCES, AND THE HOST DETERMINANTS OF VIRAL FITNESS/
info:eu-repo/grantAgreement/MINECO//DPI2014-55276-C5-1-R/ES/BIOLOGIA SINTETICA PARA LA MEJORA EN BIOPRODUCCION: DISEÑO, OPTIMIZACION, MONITORIZACION Y CONTROL/
info:eu-repo/grantAgreement/MINECO//BES-2012-053772/ES/BES-2012-053772/
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Agradecimientos:
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This work was supported by the Spanish Ministerio de Economia y Competitividad grants BFU2012-30805 (to SFE), and DPI2011-28112-C04-02, DPI2011-28112-C04-01, DPI2014-55276-C5-1-R (to AF and JP) and by Generalitat Valenciana ...[+]
This work was supported by the Spanish Ministerio de Economia y Competitividad grants BFU2012-30805 (to SFE), and DPI2011-28112-C04-02, DPI2011-28112-C04-01, DPI2014-55276-C5-1-R (to AF and JP) and by Generalitat Valenciana grant PROMETEOII/2014/021 (to SFE). 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).
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Tipo:
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Artículo
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