What is TomExpress?

The TomExpress RNA-Seq platform was developed to provide the tomato community with dedicated browser and tools for public RNA-Seq data handling, visualization and mining.

To avoid major biases resulting from the use of different processing methods, all RNA-Seq raw sequence were mapped on a unique tomato reference genome with accurate parameters. Following calculation of the number of counts per gene in each RNA-seq project, the same normalization method was applied to all counts available for the tomato as described in Maza et al.( 2013 ).

TomExpress database has been designed in a way that makes each expression value associated with the corresponding experimental details. This friendly web interface provides versatile data mining tools including output graphics showing barplots, heatmaps of hierarchically clustered expression data and identification and visualization of correlation networks of co-regulated gene groups. In addition, the expression patterns in different plant organs and tissues are provided as images suitable for visual and oral presentations.

How to cite?

Zouine M, Maza E, Djari A, Lauvernier M, Frasse P, Smouni A, Pirrello J, Bouzayen M.
TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks.
https://doi.org/10.1111/tpj.13711
Project Leader : Mohamed ZOUINE
Database and Web application engineering : Anis DJARI
Statistics and Data mining tools : Elie MAZA
Samples Annotation : Pierre FRASSE
'In Planta' pictures Design : Aziz SMOUNI
Complete Developpers List : Mathieu Lauvernier
Alexandre Wagner
Margot Zahm
Clement Folgoas
Marina Diaz Uzquiano

The TomExpress platform was developed by the Genomic and Biotechnology of the Fruit laboratory (GBF) , INRA/INPT-ENSAT, FRANCE