ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2017
Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 2 syntheses or guidelines pooled it, 42 citations in OpenAlex.
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
- Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine.Journal of visualized experiments : JoVE · 2017Pooled it
- A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.Frontiers in plant science · 2026Review
- Network-based identification of hub transcription factors associated with benzylisoquinoline alkaloid biosynthesis inBiochemistry and biophysics reports · 2025Article
- GAPDH Gene Family inInternational journal of molecular sciences · 2025Article
- Article
- Genome-Wide Characterization ofGenes · 2024Article
- Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L.Scientific reports · 2024Article
- Exploring the gene expression network involved in the heat stress response of a thermotolerant tomato genotype.BMC genomics · 2024Article
- Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.Horticulture research · 2024Article
- BnAP2-12 overexpression delays ramie flowering: evidence from AP2/ERF gene expression.Frontiers in plant science · 2024Article
- Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (International journal of molecular sciences · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- Genome-wide detection and classification of terpene synthase genes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response.Plant physiology · 2021Article
- Comparative transcriptome analyses between cultivated and wild grapes reveal conservation of expressed genes but extensive rewiring of co-expression networks.Plant molecular biology · 2021Article
- The Grapevine E3 Ubiquitin Ligase VriATL156 Confers Resistance against the Downy Mildew PathogenInternational journal of molecular sciences · 2021Article
- Red Chinese Cabbage Transcriptome Analysis Reveals Structural Genes and Multiple Transcription Factors Regulating Reddish Purple Color.International journal of molecular sciences · 2020Article
- Genome-Wide Analysis ofInternational journal of molecular sciences · 2019Article
- Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops.Frontiers in plant science · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coordinated transcriptional and metabolic reprogramming ensures a plant's continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters. Genes containing these CREs are enriched in a large repertoire of plant biological pathways. Large-scale transcriptome analyses also show that these CREs are highly implicated in grapevine development and stress response. Numerous CRE-driven modules in condition-specific gene co-expression networks (GCNs) were identified and many of these modules were highly enriched for plant biological functions. Several modules corroborate known roles of CREs in drought response, pathogen defense, cell wall metabolism, and fruit ripening, whereas others reveal novel functions in plants. Comparisons with Arabidopsis suggest a general conservation in promoter architecture, gene expression dynamics, and GCN structure across species. Systems analyses of CREs provide insights into the grapevine cis-regulatory code and establish a foundation for future genomic studies in grapevine.
Indexed as
Identifiers
What OpenQuestion holds
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.