NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome

Next Generation Sequencing technologies (NGS) unexpectedly pushed forward the capability of solving genome organization and of widely depicting gene expression. However, although the flourishing of tools to process the NGS data, versatile and user-friendly computational environments for integrative and comparative analyses of the results from the increasing amount of collections are still required.

Here we present the architecture and the facilities of NexGenEx-, a web based platform that offers processed NGS transcriptome collections and enables immediate analyses of the results. The platform allows gene expression investigations, profiling and comparisons, and exploits different resources.

In the current version, NexGenEx-Tom includes processed and normalized NGS expression data from three collections covering several tissue/stages from different genotypes. Beyond providing a user-friendly interface, the platform was designed with the aim to easily be expanded to include other NGS based transcriptome collections. It can also integrate different genome releases, possibly from different cultivars or genotypes, but even from different species. The platform is proposed as an example effort in tomato, and is described as a profitable approach for the exploitation of these challenging and precious datasets.