ArticleBiomolecules2021
Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in
Article in Biomolecules, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 24 citations in OpenAlex.
- Heat waves reveal additive genetic effects leading to sunburn resilience of grapevine berries.Frontiers in plant science · 2025Article
- Genotyping-by-sequencing-based high-resolution mapping reveals a single candidate gene for the grapevine veraison locus Ver1.Plant physiology · 2024Article
- NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine.Journal of experimental botany · 2024Article
- Molecular regulation of apple and grape ripening: exploring common and distinct transcriptional aspects of representative climacteric and non-climacteric fruits.Journal of experimental botany · 2023Review
- Temperature affects organic acid, terpene and stilbene metabolisms in wine grapes during postharvest dehydration.Frontiers in plant science · 2023Article
- GrapevineBiomolecules · 2022Article
- Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits.Frontiers in plant science · 2022Article
- A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape.Frontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.
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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.