expVIP
RNA-Seq is a tool that enables the analysis of which genes are expressed under certain conditions in an organism. The difference in expression levels between conditions allows to find if a gene is linked to a function or not. In recent years, crop scientist have explored this technology and several datasets are publicly available. However, the complexity of crop genomes and the heterogeneity of the reported expression studies hinders the use of all the available resources. ExpVIP is a tool that enables the integration of different RNA-Seq studies by analysing the data uniformly across experiments and provides a web interface to query the data.
As a proof-of-concept, the scientists used expVIP to analyse publicly available data from wheat plants grown under a variety of growth conditions. Over 400 datasets which were previously separate and were not easily accessible to most breeders and researchers have now been opened up and linked thanks to this resource. This analysis and an explanation of the expVIP tool is available at http://www.wheat-expression.com/.
GitHub
Website
Paper
expVIP: a customisable RNA-seq data analysis and visualisation platform.
Philippa Borrill, Ricardo Ramirez-Gonzalez, and Cristobal Uauy. Plant Physiology 2016 : pp.15.01667v1-pp.01667.2015.