Fusion of genomic, proteomic and phenotypic data: the case of potyviruses

TitleFusion of genomic, proteomic and phenotypic data: the case of potyviruses
Publication TypeJournal Article
Year of Publication2016
AuthorsFolch-Fortuny A, Bosque G, Picó J, Ferrer A, Elena SF
JournalMolecular Biosystems
Abstract
  1. Background: 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.

  2. Results: 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 in the encoded proteins and the perturbation induced by the mutated proteins to its neighbours in the protein-protein interaction network (PPIN). Finally, the phenotypic trait evaluated for each mutant virus was 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 phenotypic fitness.

  3. Conclusions: 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 go beyond the protein they directly affect and spread on the PPIN to neighbour proteins, thus defining functional modules. 

Project: