ArticleGenome biology2010
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers, 2 of them syntheses 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
141 citing papers in PubMed, 2 syntheses or guidelines pooled it, 273 citations in OpenAlex.
- Primary nitrate responses mediated by calcium signalling and diverse protein phosphorylation.Journal of experimental botany · 2020Pooled it
- A balancing act: how plants integrate nitrogen and water signals.Journal of experimental botany · 2020Pooled it
- Nitrate transiently rewires transcription in developing xylem of Populus wood to promote cell expansion via CRF4.The Plant cell · 2026Article
- Mechanistic and omics based integrative approaches reveal genetic and molecular basis of drought resilience in sesame (Sesamum indicum L.).Plant molecular biology · 2026Review
- HHO5 orchestrates dose-dependent feedback regulation of organic versus inorganic nitrogen signaling in Arabidopsis.The Plant cell · 2026Article
- An omnigenic interactome model to chart the genetic architecture of individual plants.Horticulture research · 2026Article
- A Predictive Computational Framework forPathogens (Basel, Switzerland) · 2026Article
- Antagonistic regulation of nitrogen and drought signaling mediated by NIN-like protein 7 transcription factor inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Modelling the short-term response to nitrogen that coordinates events in lateral root initiation.Quantitative plant biology · 2026Article
- Unraveling nitrogen uptake and metabolism: gene families, expression dynamics and functional insights in aspen (Populus tremula).Tree physiology · 2025Article
- Fluctuations in nitrate availability impact cytokinin biosynthesis through histone modifications of IPT3 in Arabidopsis roots for growth acclimation.Plant communications · 2025Article
- Evolutionary trajectory of the NPF6.3(NRT1.1/CHL1)-centered nitrate signaling regulatory network in plant roots.BMC plant biology · 2025Article
- Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.Plant communications · 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
- Characterization of nitrate use efficiency in tea plant (Horticulture research · 2025Article
- A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling.Molecular & cellular proteomics : MCP · 2024Article
- Transcription factor ZmEREB97 regulates nitrate uptake in maize (Zea mays) roots.Plant physiology · 2024Article
- AraLeTA: An Arabidopsis leaf expression atlas across diurnal and developmental scales.Plant physiology · 2024Article
81 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
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundNitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified.
resultsHere we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes and functions needed to prepare plants to use or reduce nitrate. A state-space model inferred from this microarray time-series data successfully predicts gene behavior in unlearnt conditions.
conclusionsThe experiments and methods allow us to propose a temporal working model for nitrate-driven gene networks. This network model is tested both in silico and experimentally. For example, the over-expression of a predicted gene hub encoding a transcription factor induced early in the cascade indeed leads to the modification of the kinetic nitrate response of sentinel genes such as NIR, NIA2, and NRT1.1, and several other transcription factors. The potential nitrate/hormone connections implicated by this time-series data are also evaluated.
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.