Tool Helps Predict Gene Expression in Plants

Researchers from The John Innes Centre and The Genome Analysis Centre (TGAC), led by crop geneticist Dr Cristobal Uauy, have developed a free online tool, specifically designed to help crop scientists worldwide interpret data more effectively.ExpVIP (expression Visualisation and Integration Platform) can be used on any species, enabling scientists and breeders without advanced computer skills to know where and when genes are expressed in their favourite plants.  

Dr Uauy, said: “This new tool will accelerate scientific discoveries by enabling researchers and breeders to more easily place their discoveries in the context of previous knowledge.”

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 https://ilmt.co/PL/Y46B.

Ricardo Ramirez-Gonzalez, PhD student at TGAC and JIC and a member of the team who created the new tool, said: "ExpVIP makes the analysis of big data from expression experiments more accessible, enabling the research community to focus on the biology behind the experiments."

Philippa Borrill, a BBSRC Anniversary Future Leader Fellow and expVIP team member, envisages that: "the ability to visualise the expression patterns and infer the functions of genes presents a tremendous opportunity to improve major food crops".

This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC), the International Wheat Yield Partnership (IWYP) and from TGAC at Norwich Research Park.