ArticleNucleic acids research2016
Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 78 citations in OpenAlex.
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- Bridging scales: integrated multi-omics and deep phenotyping for climate resilience in crop plants.Frontiers in plant science · 2026Review
- Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses.The Plant journal : for cell and molecular biology · 2025Article
- Integrative analysis of coding and non-coding RNAs in rice reveals conserved molecular response signatures to heat, drought, and salt stresses.Journal of biosciences · 2025Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
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- Gene communities in co-expression networks across different tissues.PLoS computational biology · 2023Article
- Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response.BMC genomics · 2023Article
- Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis.Plant direct · 2023Article
- Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression.PLoS computational biology · 2023Article
- The PtoTCP20-miR396d-PtoGRF15 module regulates secondary vascular development in Populus.Plant communications · 2023Article
- Transcriptional control of hydrogen peroxide homeostasis regulates ground tissue patterning in theFrontiers in plant science · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection ofInternational journal of molecular sciences · 2021Article
- Co-expression network analysis of protein phosphatase 2A (PP2A) genes with stress-responsive genes in Arabidopsis thaliana reveals 13 key regulators.Scientific reports · 2020Article
- Using single-plant-omics in the field to link maize genes to functions and phenotypes.Molecular systems biology · 2020Article
- Transcriptome Profiles Reveal the Growth-Promoting Mechanisms ofFrontiers in microbiology · 2020Article
- Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling.Frontiers in genetics · 2020Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plant Arabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness against cis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.
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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.