We would like to introduce www.wheat-expression.com where you can easily visualise and explore the homoeologue-specific expression patterns of your wheat genes of interest. We have added > 400 publicly available RNA-seq samples to an expression browser which can be dynamically filtered and sorted according to tissue, developmental stage, disease, abiotic stress and variety. We envisage this resource being useful for visualisation of single genes across studies, comparisons of homoeologue expression patterns and to identify genes of interest within QTL regions (up to 50 genes can be displayed simultaneously using heatmaps).
As a further community resource we have released a user-friendly version of the software underlying the website. expVIP (expression Visualisation and Integration Platform) software carries out all the stages of RNA-seq data analysis from mapping reads to creating a customizable data visualisation window. expVIP runs on a desktop computer and can be used on any species with a transcriptome to easily analyse and visualise RNA-seq data. expVIP can be used to compare private RNA-seq data to the public wheat samples already present at www.wheat-expression.com. expVIP is available at https://github.com/homonecloco/expvip-web/wiki/LoadingVM
For further information please see Borrill, Ramirez-Gonzalez and Uauy, 2016, Plant Physiology. http://dx.doi.org/10.1104/pp.15.01667
We would be delighted to received community feedback on how this resource could be improved.
Philippa Borrill, Ricardo Ramirez-Gonzalez and Cristobal Uauy