ArticleNature communications2019
Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Primary nitrate responses mediated by calcium signalling and diverse protein phosphorylation.Journal of experimental botany · 2020Pooled it
- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- The primary nitrate response TGA1 and TGA4 transcription factors are negative regulators of sulfate uptake and metabolism.Plant physiology · 2026Article
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- HHO5 orchestrates dose-dependent feedback regulation of organic versus inorganic nitrogen signaling in Arabidopsis.The Plant cell · 2026Article
- Cytokinin response factor 1 acts as a negative regulator of cytokinin-mediated developmental pathways in Arabidopsis.Planta · 2026Article
- B-GATA factors are required for nitrogen-responsive growth in Physcomitrium patens and Arabidopsis thaliana.The New phytologist · 2026Article
- Integrated Gene Regulatory Network Analysis Reveals Coordinated Transcriptional Reprogramming in thePlants (Basel, Switzerland) · 2026Article
- From binding to networks: methods for identifying transcription factor targets in plant systems.Frontiers in plant science · 2026Review
- Decoding nitrogen uptake efficiency in maize and sorghum: insights from comparative gene regulatory networks.The Plant journal : for cell and molecular biology · 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
- Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.Plant communications · 2025Article
- DSK2-mediated degradation of F-box protein LAO1 and class I TCPs modulates the nitrogen starvation response.EMBO reports · 2025Article
- Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits.The Plant cell · 2025Article
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis.The Plant journal : for cell and molecular biology · 2025Article
- Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The AP2/ERF Transcription Factor ERF56 Negatively Regulating Nitrate-Dependent Plant Growth inInternational journal of molecular sciences · 2025Article
- StCDF1: A 'jack of all trades' clock output with a central role in regulating potato nitrate reduction activity.The New phytologist · 2025Article
- Co-option of plant gene regulatory network in nutrient responses during terrestrialization.Nature plants · 2024Article
7 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
12 authors.
Funding
Abstract
Charting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated targets of 33 nitrogen (N)-early response TFs encompassing 88% of N-responsive Arabidopsis genes. We uncover a duality where each TF is an inducer and repressor, and in vitro cis-motifs are typically specific to regulation directionality. Validated TF-targets (71,836) are used to refine precision of a time-inferred root network, connecting 145 N-responsive TFs and 311 targets. These data are used to chart network paths from direct TF
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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.