ArticleGenome biology2007
Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 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
120 citing papers in PubMed, 1 synthesis or guideline pooled it, 236 citations in OpenAlex.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Article
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- Improving rice eating and cooking quality by enhancing endogenous expression of a nitrogen-dependent floral regulator.Plant biotechnology journal · 2023Article
- Plants' Response to Abiotic Stress: Mechanisms and Strategies.International journal of molecular sciences · 2023Review
- Bacterial Volatiles (mVOC) Emitted by the PhytopathogenAntioxidants (Basel, Switzerland) · 2023Article
- Article
- Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice.Frontiers in plant science · 2023Article
- Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types.Methods in molecular biology (Clifton, N.J.) · 2023Article
- High Recovery from Either Waterlogging or Drought Overrides Any Beneficial Acclimation ofPlants (Basel, Switzerland) · 2022Article
- Interplay between ARABIDOPSIS Gβ and WRKY transcription factors differentiates environmental stress responses.Plant physiology · 2022Article
- Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line.Life (Basel, Switzerland) · 2022Article
- Mutations that alter Arabidopsis flavonoid metabolism affect the circadian clock.The Plant journal : for cell and molecular biology · 2022Article
- Metabolic Pathway of Natural Antioxidants, Antioxidant Enzymes and ROS Providence.Antioxidants (Basel, Switzerland) · 2022Review
- Modeling temporal and hormonal regulation of plant transcriptional response to wounding.The Plant cell · 2022Article
- Abiotic stress responses in plants.Nature reviews. Genetics · 2022Review
- R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses.Frontiers in plant science · 2022Article
- Transcriptome Meta-Analysis Associated Targeting Hub Genes and Pathways of Drought and Salt Stress Responses in Cotton (Frontiers in plant science · 2022Article
- Identification of miRNA and their target genes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Combined Abiotic Stresses Repress Defense and Cell Wall Metabolic Genes and Render Plants More Susceptible to Pathogen Infection.Plants (Basel, Switzerland) · 2021Article
60 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundArabidopsis thaliana transcript profiles indicate effects of abiotic and biotic stresses and tissue-specific and cell-specific gene expression. Organizing these datasets could reveal the structure and mechanisms of responses and crosstalk between pathways, and in which cells the plants perceive, signal, respond to, and integrate environmental inputs.
resultsWe clustered Arabidopsis transcript profiles for various treatments, including abiotic, biotic, and chemical stresses. Ubiquitous stress responses in Arabidopsis, similar to those of fungi and animals, employ genes in pathways related to mitogen-activated protein kinases, Snf1-related kinases, vesicle transport, mitochondrial functions, and the transcription machinery. Induced responses to stresses are attributed to genes whose promoters are characterized by a small number of regulatory motifs, although secondary motifs were also apparent. Most genes that are downregulated by stresses exhibited distinct tissue-specific expression patterns and appear to be under developmental regulation. The abscisic acid-dependent transcriptome is delineated in the cluster structure, whereas functions that are dependent on reactive oxygen species are widely distributed, indicating that evolutionary pressures confer distinct responses to different stresses in time and space. Cell lineages in roots express stress-responsive genes at different levels. Intersections of stress-responsive and cell-specific profiles identified cell lineages affected by abiotic stress.
conclusionBy analyzing the stress-dependent expression profile, we define a common stress transcriptome that apparently represents universal cell-level stress responses. Combining stress-dependent and tissue-specific and cell-specific expression profiles, and Arabidopsis 5'-regulatory DNA sequences, we confirm known stress-related 5' cis-elements on a genome-wide scale, identify secondary motifs, and place the stress response within the context of tissues and cell lineages in the Arabidopsis root.
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.