ArticleThe Plant cell2014
Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it, 128 citations in OpenAlex.
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
- Dissecting gene regulatory networks driving grape berry ripening using comparative systems biology across nonclimacteric fleshy fruits: the NAC-centered hierarchy revisited.Horticulture research · 2026Review
- The role of miR-335-5p in the redifferentiation of BRAF p.V600E thyroid cancers.Molecular oncology · 2026Article
- Traversing the effects of ploidy changes in different Eragrostis curvula genotypes through high-throughput RNA sequencing.The plant genome · 2026Article
- A two-phase clustering procedure based on allele specific expression.BMC bioinformatics · 2026Article
- Identification of Disease-miRNA Networks Across Different Human Complex Diseases Using SWIM and MIENTURNET Tools.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Grape ripening speed slowed down using natural variation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Optimized Protocol for High-Quality RNA Extraction from Grape Berry Skins Using Sorbitol Pre-Wash.Plants (Basel, Switzerland) · 2025Article
- Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression.BMC plant biology · 2025Article
- VvFHY3 links auxin and endoplasmic reticulum stress to regulate grape anthocyanin biosynthesis at high temperatures.The Plant cell · 2024Article
- Genotyping-by-sequencing-based high-resolution mapping reveals a single candidate gene for the grapevine veraison locus Ver1.Plant physiology · 2024Article
- Berry shrivel in grapevine: a review considering multiple approaches.Journal of experimental botany · 2024Review
- 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
- The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine.Plant physiology · 2023Article
- Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development.Molecular plant pathology · 2023Article
- An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.G3 (Bethesda, Md.) · 2023Article
- Dissecting the effect of soil on plant phenology and berry transcriptional plasticity in two Italian grapevine varieties (Horticulture research · 2023Article
- Dissection of the Pearl of Csaba pedigree identifies key genomic segments related to early ripening in grape.Plant physiology · 2023Article
- Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.
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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.