The majority of RNA-seq expression studies in plants remain underutilised and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyse and visualise this data. Researchers from the John Innes Centre have developed expVIP, an expression Visualisation and Integration Platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyse public and user-specified datasets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom web browser to visualise, sort and filter the RNA-seq data and provides outputs for differential gene expression analysis. The researchers 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 they developed a flexible wheat expression browser (www.wheat-expression.com) which 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, visualisation and comparison of RNA-seq data across experiments.
Genes on chromosome 1A Genes on chromosome 1B Genes on chromosome 1D
Expression of genes with three homoeologous copies on chromosome 1 in nulli-tetrasomic wheat lines in shoots and roots. Genotypes for chromosome 1 are indicated by coloured squares: A genome in green, B in blue and D in purple. Squares listed in the bottom row (+) indicate extra copies (tetra), absence of squares indicates deletion (nulli) of entire chromosome.
Availability – The source code to prepare and setup the expVIP database and graphical interface are
524 available in Github: https://github.com/homonecloco/expvip-web
Detailed documentation on how to load metadata into expVIP is available online: https://github.com/homonecloco/expvip-web/wiki
More detail on the Wheat Expression Browser was presented at the PAG 2016 conference: