ArticleThe Plant cell2014
Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress.
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 40 papers, 1 of them a synthesis that pooled it.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it, 80 citations in OpenAlex.
- Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum.BMC genomics · 2022Pooled it
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- Integrated physiological characterisation and transcriptomics reveals drought tolerance differences between two cultivars of A. sinensis at seedling stage.Molecular biology reports · 2025Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- MENTOR: Multiplex Embedding of Networks for Team-Based Omics Research.bioRxiv : the preprint server for biology · 2024Article
- Evaluation of single-sample network inference methods for precision oncology.NPJ systems biology and applications · 2024Article
- MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework.Bioinformatics (Oxford, England) · 2023Article
- Construction of a Hierarchical Gene Regulatory Network to Reveal the Drought Tolerance Mechanism of Shanxin Poplar.International journal of molecular sciences · 2022Article
- GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress.Plant physiology · 2022Article
- Silencing GhJUB1L1 (JUB1-like 1) reduces cotton (Gossypium hirsutum) drought tolerance.PloS one · 2021Article
- Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance.Frontiers in genetics · 2021Article
- Network-based approaches for understanding gene regulation and function in plants.The Plant journal : for cell and molecular biology · 2020Review
- Gene Regulatory Network Guided Investigations and Engineering of Storage Root Development in Root Crops.Frontiers in plant science · 2020Review
- Article
- Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling.Frontiers in genetics · 2020Review
- Transcription Factor Networks in Leaves ofPlants (Basel, Switzerland) · 2019Article
- Identification and validation of four hub genes involved in the plaque deterioration of atherosclerosis.Aging · 2019Article
- ANAC032 regulates root growth through the MYB30 gene regulatory network.Scientific reports · 2019Article
- Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to HPlant physiology · 2019Article
- SlNAC2 overexpression in Arabidopsis results in enhanced abiotic stress tolerance with alteration in glutathione metabolism.Protoplasma · 2019Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary reverse-engineering solutions through average rank aggregation on an Arabidopsis thaliana microarray expression compendium. This ensemble performed the most robustly in benchmarking and greatly expands upon the availability of interactions currently reported. Besides recovering 1182 known regulatory interactions, cis-regulatory motifs and coherent functionalities of target genes corresponded with the predicted transcription factors. We provide a valuable resource of 572 abiotic stress modules of coregulated genes with functional and regulatory information, from which we deduced functional relationships for 1966 uncharacterized genes and many regulators. Using gain- and loss-of-function mutants of seven transcription factors grown under control and salt stress conditions, we experimentally validated 141 out of 271 predictions (52% precision) for 102 selected genes and mapped 148 additional transcription factor-gene regulatory interactions (49% recall). We identified an intricate core oxidative stress regulatory network where NAC13, NAC053, ERF6, WRKY6, and NAC032 transcription factors interconnect and function in detoxification. Our work shows that ensemble reverse-engineering can generate robust biological hypotheses of gene regulation in a multicellular eukaryote that can be tested by medium-throughput experimental validation.
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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.