expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN]
By P. Borrill, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy. Plant Physiology, 2016
367 citations recorded by the source corpus.
expVIP is an adaptable platform to create an integrated gene expression interface for any species with a transcriptome assembly. 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.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/598055bf22798a8c75918dea40e5cfafe233319f
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Citations in the corpus
- Breeding for increased grain protein and micronutrient content in wheat: Ten years of the GPC-B1 gene (2017, background): “Expression studies consistently show that GPC-B1 is expressed only after anthesis (Avni et al., 2014; Borrill et al., 2016; Cantu et al., 2011; Pearce et al., 2015, 2014; Uauy et al., 2006a, b).”