ArticleThe Plant cell2011
Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues.
Article in The Plant cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis 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
53 citing papers in PubMed, 1 synthesis or guideline pooled it, 104 citations in OpenAlex.
- Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea.Scientific reports · 2023Pooled it
- Comparative metabolomics of resistant and susceptible pecan leaflets uncovers early defense responses to scab infection.BMC plant biology · 2026Article
- Integrative Metabolomics and Machine Learning Approach to Uncover Scab Resistance Markers in Mature Pecan Trees.Journal of agricultural and food chemistry · 2026Article
- The Effects of Acorn Origin, Environmental Microbiomes and Local Adaptation on the Leaf Metabolome.Journal of chemical ecology · 2026Article
- Glutamine alleviates the toxicity of externally applied amino acids in Arabidopsis.Frontiers in plant science · 2026Article
- Multi-omics reveals DEAD-box RNA helicase 20 as key protein enhancing wilt resistance in transgenic chickpea.Plant cell reports · 2025Article
- Unraveling key genes and pathways involved in Verticillium wilt resistance by integrative GWAS and transcriptomic approaches in Upland cotton.Functional & integrative genomics · 2025Article
- Comparison of the Effects of UV-C Light in the Form of Flash or Continuous Exposure: A Transcriptomic Analysis onInternational journal of molecular sciences · 2024Article
- Systemic analysis of metabolome reconfiguration in Arabidopsis after abiotic stressors uncovers metabolites that modulate defense against pathogens.Plant communications · 2024Article
- NMR-Based Metabolomic Profiling of Mungbean Infected with Mungbean Yellow Mosaic India Virus.Applied biochemistry and biotechnology · 2022Article
- Alterations in Primary Carbon Metabolism in Cucumber Infected withInternational journal of molecular sciences · 2022Article
- Transcriptome Meta-Analysis Identifies Candidate Hub Genes and Pathways of Pathogen Stress Responses inBiology · 2022Article
- New Insight into Aspartate Metabolic Pathways inInternational journal of molecular sciences · 2022Article
- Morphological, Biochemical, and Proteomic Analyses to Understand the Promotive Effects of Plant-Derived Smoke Solution on Wheat Growth under Flooding Stress.Plants (Basel, Switzerland) · 2022Article
- Rice cellulose synthase-like protein OsCSLD4 coordinates the trade-off between plant growth and defense.Frontiers in plant science · 2022Article
- Identification of genes controlling compatible and incompatible reactions of pearl millet (Frontiers in plant science · 2022Article
- Primary Metabolite Adjustments Associated With Pinewood Nematode Resistance inFrontiers in plant science · 2021Article
- Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants.International journal of molecular sciences · 2020Review
- Functional Omics Identifies Serine Hydrolases That Mobilize Storage Lipids during Rice Seed Germination.Plant physiology · 2020Article
- Critical Role of Transcript Cleavage in Arabidopsis RNA Polymerase II Transcriptional Elongation.The Plant cell · 2020Article
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 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The expression pattern of any pair of genes may be negatively correlated, positively correlated, or not correlated at all in response to different stresses and even different progression stages of the stress. This makes it difficult to identify such relationships by classical statistical tools such as the Pearson correlation coefficient. Hence, dedicated bioinformatics approaches that are able to identify groups of cues in which there is a positive or negative expression correlation between pairs or groups of genes are called for. We herein introduce and discuss a bioinformatics approach, termed Gene Coordination, that is devoted to the identification of specific or multiple cues in which there is a positive or negative coordination between pairs of genes and can further incorporate additional coordinated genes to form large coordinated gene networks. We demonstrate the utility of this approach by providing a case study in which we were able to discover distinct expression behavior of the energy-associated gene network in response to distinct biotic and abiotic stresses. This bioinformatics approach is suitable to a broad range of studies that compare treatments versus controls, such as effects of various cues, or expression changes between a mutant and the control wild-type genotype.
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.