VESPUCCI: exploring patterns of gene expression in grapevine
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 depo...
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Frontiers Media S.A.
2016-05-01
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Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00633/full |
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doaj-085570efd43f4ab7bb5f39067a41c3cc2020-11-24T22:08:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-05-01710.3389/fpls.2016.00633194986VESPUCCI: exploring patterns of gene expression in grapevineMarco eMoretto0Marco eMoretto1Paolo eSonego2Stefania ePilati3Giulia eMalacarne4Laura eCostantini5Lukasz eGrzeskowiak6Giorgia eBagagli7Maria Stella eGrando8Claudio eMoser9Kristof eEngelen10Fondazione Edmund MachUniversità degli Studi di PadovaFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachFondazione Edmund MachLarge-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.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00633/fullGene ExpressionMicroarraysRNA-Seqgrapevinecompendium |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Marco eMoretto Marco eMoretto Paolo eSonego Stefania ePilati Giulia eMalacarne Laura eCostantini Lukasz eGrzeskowiak Giorgia eBagagli Maria Stella eGrando Claudio eMoser Kristof eEngelen |
spellingShingle |
Marco eMoretto Marco eMoretto Paolo eSonego Stefania ePilati Giulia eMalacarne Laura eCostantini Lukasz eGrzeskowiak Giorgia eBagagli Maria Stella eGrando Claudio eMoser Kristof eEngelen VESPUCCI: exploring patterns of gene expression in grapevine Frontiers in Plant Science Gene Expression Microarrays RNA-Seq grapevine compendium |
author_facet |
Marco eMoretto Marco eMoretto Paolo eSonego Stefania ePilati Giulia eMalacarne Laura eCostantini Lukasz eGrzeskowiak Giorgia eBagagli Maria Stella eGrando Claudio eMoser Kristof eEngelen |
author_sort |
Marco eMoretto |
title |
VESPUCCI: exploring patterns of gene expression in grapevine |
title_short |
VESPUCCI: exploring patterns of gene expression in grapevine |
title_full |
VESPUCCI: exploring patterns of gene expression in grapevine |
title_fullStr |
VESPUCCI: exploring patterns of gene expression in grapevine |
title_full_unstemmed |
VESPUCCI: exploring patterns of gene expression in grapevine |
title_sort |
vespucci: exploring patterns of gene expression in grapevine |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2016-05-01 |
description |
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. |
topic |
Gene Expression Microarrays RNA-Seq grapevine compendium |
url |
http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00633/full |
work_keys_str_mv |
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