ArticleNature plants2021
Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.
Article in Nature plants, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 96 citations in OpenAlex.
- The transcriptional cascade CiERF023Horticulture research · 2026Article
- Large-scale comparative analysis of the nuclear factor-Y transcription factors across 320 horticultural and other plants.Horticulture research · 2026Article
- MINI-EX Version 2: Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell Transcriptomics Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Inferring Gene Networks from High-Throughput Transcriptomes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- bHLH35 mediates specificity in plant responses to multiple stress conditions.Science advances · 2025Article
- Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato.Plant communications · 2025Article
- Article
- Unlocking gene regulatory networks for crop resilience and sustainable agriculture.Nature biotechnology · 2025Review
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Function diversification of CONSTANS-like genes in Pyrus and regulatory mechanisms in response to different light quality.BMC plant biology · 2025Article
- Article
- BADDADAN: Mechanistic modelling of time-series gene module expression.Quantitative plant biology · 2025Article
- Systems genomics of salinity stress response in rice.bioRxiv : the preprint server for biology · 2024Article
- Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean.Genome biology · 2024Article
- Perception and processing of stress signals by plant mitochondria.The Plant journal : for cell and molecular biology · 2024Review
- Arabidopsis transcription factor ANAC102 predominantly expresses a nuclear protein and acts as a negative regulator of methyl viologen-induced oxidative stress responses.Journal of experimental botany · 2024Article
- Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana.Bioinformatics (Oxford, England) · 2024Article
- Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model.Plants (Basel, Switzerland) · 2024Article
- Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). This iGRN outperforms the different input networks to predict known regulatory interactions and has a similar performance to recover functional interactions compared to state-of-the-art experimental methods. The iGRN correctly inferred known functions for 681 TFs and predicted new gene functions for hundreds of unknown TFs. For regulators predicted to be involved in reactive oxygen species (ROS) stress regulation, we confirmed in total 75% of TFs with a function in ROS and/or physiological stress responses. This includes 13 ROS regulators, previously not connected to any ROS or stress function, that were experimentally validated in our ROS-specific phenotypic assays of loss- or gain-of-function lines. In conclusion, the presented iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants by integrating different experimental data types.
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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.