expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

• Published in: Plant physiology (Bethesda) 2016-04, Vol.170 (4), p.2172-2186
• Main Authors: Borrill, Philippa, Ramirez-Gonzalez, Ricardo, Uauy, Cristobal
• Format: Article
• Language: English
• Subjects: Gene Expression Profiling; Gene Expression Regulation, Plant; GENES, DEVELOPMENT AND EVOLUTION; Genes, Plant; Genetic Association Studies; Internet; Reference Standards; Reproducibility of Results; Sequence Analysis, RNA; Sequence Homology, Nucleic Acid; Software; Statistics as Topic; Stress, Physiological - genetics; Triticum - genetics; User-Computer Interface
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.15.01667

The majority of transcriptome sequencing (RNA-seq) expression studies in plants remain underutilized and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyze and visualize these data. We have developed expVIP, an expression visualization and integration platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyze public and user-specified data sets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom Web browser to visualize, sort, and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP's suitability for polyploid crops and evaluate its performance across a range of biologically relevant scenarios. To exemplify its use in crop research, we developed a flexible wheat (Triticum aestivum) expression browser (www.wheat-expression.com) that can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualization, and comparison of RNA-seq data across experiments.