ArticleFrontiers in plant science2016
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine.
Article in Frontiers in plant science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
- Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genomic and Bioinformatic Resources for Perennial Fruit Species.Current genomics · 2022Review
- GrapevineBiomolecules · 2022Article
- Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits.Frontiers in plant science · 2022Article
- Using genome-wide expression compendia to study microorganisms.Computational and structural biotechnology journal · 2022Review
- A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape.Frontiers in plant science · 2022Article
- Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks inBiomolecules · 2021Article
- Article
- Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines.Frontiers in plant science · 2021Review
- Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera 'Pinot Noir' and Vitis spp. genotypes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture.Molecular biology reports · 2020Review
- Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets.Genes · 2020Article
- PulmonDB: a curated lung disease gene expression database.Scientific reports · 2020Article
- First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.BMC bioinformatics · 2019Article
- Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops.Frontiers in plant science · 2019Review
- Linking Terpene Synthases to Sesquiterpene Metabolism in Grapevine Flowers.Frontiers in plant science · 2019Article
- Genome-wide identification and characterization of the 14-3-3 family in Vitis vinifera L. during berry development and cold- and heat-stress response.BMC genomics · 2018Article
- Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.