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Updated: Mar 20, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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VESPUCCI: Exploring Patterns of Gene Expression in Grapevine.

Marco Moretto1, Paolo Sonego2, Stefania Pilati3

  • 1Department of Computational Biology, Research and Innovation Center, Fondazione Edmund MachTrento, Italy; Department of Biology, University of PadovaPadova, Italy.

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|June 1, 2016
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Summary

This study introduces VESPUCCI, a grapevine gene expression compendium integrating diverse data. It enables robust analysis of transcriptional responses across various conditions and platforms.

Keywords:
RNA-Seqcompendiumgene expressiongrapevinemicroarraytranscriptomics

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Area of Science:

  • Plant biology
  • Genomics
  • Bioinformatics

Background:

  • Large-scale transcriptional studies are crucial for understanding cellular responses to stimuli.
  • Microarray and RNA-Seq technologies generate vast amounts of gene expression data.
  • Data integration across different experimental platforms is challenging due to technical variability.

Purpose of the Study:

  • To develop a comprehensive gene expression compendium for grapevine (Vitis).
  • To facilitate the comparison and analysis of gene expression data from diverse sources.
  • To enable the investigation of complex gene expression patterns in grapevine.

Main Methods:

  • Integration of 1608 publicly available grapevine microarray and RNA-Seq samples from 10 platforms.
  • Manual annotation of each sample using a controlled vocabulary for human readability and computational tractability.
  • Adaptation of a bacterial data integration approach for grapevine.

Main Results:

  • Creation of the Vitis Expression Studies Platform Using COLOMBOS Compendia Instances (VESPUCCI).
  • Successful integration of heterogeneous gene expression data, overcoming platform differences.
  • Development of web and REST interfaces for data exploration and programmatic access.

Conclusions:

  • VESPUCCI provides a valuable resource for grapevine research, enabling cross-platform gene expression analysis.
  • The compendium facilitates a deeper understanding of grapevine's dynamic cellular responses.
  • VESPUCCI is freely accessible, promoting collaborative research in grapevine genomics.