Exploring Grapevine Gene Expression Patterns with VESPUCCI

In the era of high-throughput omics biology, the most used technologies for large-scale transcriptional studies are microarrays and RNA-Seq. These data are required to be deposited in public repositories upon publication. Such repositories have the enormous potential to provide a broad view of how different experimental conditions lead to expression changes, by comparing gene expression changes across all possible measured conditions. Unfortunately, this is not a task easily achievable due to differences among experimental platforms that make direct comparisons difficult. Using an adapted version of COLOMBOS technology (http://colombos.fmach.it/), geared towards eukaryotes and crop species in particular, we developed the Vitis Expression Studies Platform Using COLOMBOS Compendia Instances (VESPUCCI), a gene expression compendium for grapevine that integrates thousands of gene expression samples from several technological platforms, both microarray and RNA-Seq. Each sample has been manually annotated using a controlled vocabulary developed ad hoc to ensure both human readability and computational tractability. Expression data in the compendium can be visually explored using several tools provided by the web interface or can be programmatically accessed using the REST interface. VESPUCCI is freely accessible at http://vespucci.colombos.fmach.it.

References:

http://journal.frontiersin.org/article/10.3389/fpls.2016.00633/full