title: VESPUCCI: Exploring Patterns of Gene Expression in Grapevine.
abstract: Large-scale transcriptional studies aim to decipher the dynamic cellular responses to a stimulus, like different environmental conditions. In the era of high-throughput omics biology, the most used technologies for these purposes are microarray and RNA-Seq, whose data are usually required to be deposited in public repositories upon publication. Such repositories have the enormous potential to provide a comprehensive view of how different experimental conditions lead to expression changes, by comparing gene expression across all possible measured conditions. Unfortunately, this task is greatly impaired by differences among experimental platforms that make direct comparisons difficult. In this paper, we present the Vitis Expression Studies Platform Using COLOMBOS Compendia Instances (VESPUCCI), a gene expression compendium for grapevine which was built by adapting an approach originally developed for bacteria, and show how it can be used to investigate complex gene expression patterns. We integrated nearly all publicly available microarray and RNA-Seq expression data: 1608 gene expression samples from 10 different technological platforms. 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.
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund MachTrento, Italy; Department of Biology, University of PadovaPadova, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Moretto
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Sonego
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Pilati
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Malacarne
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Costantini
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Grzeskowiak
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Giorgia
authors.initials: G
authors.lastname: Bagagli
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Maria Stella
authors.initials: MS
authors.lastname: Grando
authors.affiliation: Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Moser
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach Trento, Italy.
authors.forename: Kristof
authors.initials: K
authors.lastname: Engelen
keywords: RNA-Seq; compendium; gene expression; grapevine; microarray; transcriptomics