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To avoid major biases resulting from the use of different mapping and statistical processings for available expression profiling data, all RNA-seq raw sequence data available in public databases (SRA/EMBL-EBI-ENA) were mapped de novo on a unique tomato reference genome using the most popular mapping software (TopHat-Bowtie) and accurate mapping parameters. Following calculation of the count number per gene in each RNA-seq project, the same normalization method was applied to all counts available for the tomato as described in the article by MAZA et al. (2013).

The 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 clusters. In addition, gene expression patterns in different plant organs and tissues are provided as images suitable for visual and oral presentations.

The developed pipeline allows easy updating of the database with newly published RNA-seq data.