ArticleFrontiers in plant science2014
Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments.
Article in Frontiers in plant science, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 3 of them syntheses that pooled it.
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Who cites it
78 citing papers in PubMed, 3 syntheses or guidelines pooled it, 131 citations in OpenAlex.
- A balancing act: how plants integrate nitrogen and water signals.Journal of experimental botany · 2020Pooled it
- Primary nitrate responses mediated by calcium signalling and diverse protein phosphorylation.Journal of experimental botany · 2020Pooled it
- Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease.BMC plant biology · 2015Pooled it
- Systems-Level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation.Plant, cell & environment · 2026Article
- Calcium and Nitrogen Availability Controls Root Exudation in Hydroponically Cultured Barley.Plant, cell & environment · 2026Article
- Nitrogen Management in Crop-Soil-Environment Systems: Pathways Toward Sustainable and Climate-Resilient Agriculture.International journal of molecular sciences · 2026Review
- A feedback regulatory loop by MAPK-CCA1 engages auxin signalling to stimulate root foraging for nitrate.Nature plants · 2026Article
- An omnigenic interactome model to chart the genetic architecture of individual plants.Horticulture research · 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
- Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.Plant communications · 2025Article
- Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis.The Plant journal : for cell and molecular biology · 2025Article
- Nitrate attenuates abscisic acid signaling via NIN-LIKE PROTEIN8 in Arabidopsis seed germination.The Plant cell · 2025Article
- Nitrate activates an MKK3-dependent MAPK module via NLP transcription factors in Arabidopsis.The Plant journal : for cell and molecular biology · 2025Article
- The root hairless mutant buzz in Brachypodium distachyon shows increased nitrate uptake and signaling but does not affect overall nitrogen use efficiency.The Plant journal : for cell and molecular biology · 2024Article
- 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
- Nitrogen sensing and regulatory networks: it's about time and space.The Plant cell · 2024Review
- JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom.Nucleic acids research · 2023Article
- Integrated Transcriptome Analysis Identified Key Expansin Genes Associated with Wheat Cell Wall, Grain Weight and Yield.Plants (Basel, Switzerland) · 2023Article
- The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply.The Plant cell · 2023Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nitrogen (N) is an essential macronutrient for plant growth and development. Plants adapt to changes in N availability partly by changes in global gene expression. We integrated publicly available root microarray data under contrasting nitrate conditions to identify new genes and functions important for adaptive nitrate responses in Arabidopsis thaliana roots. Overall, more than 2000 genes exhibited changes in expression in response to nitrate treatments in Arabidopsis thaliana root organs. Global regulation of gene expression by nitrate depends largely on the experimental context. However, despite significant differences from experiment to experiment in the identity of regulated genes, there is a robust nitrate response of specific biological functions. Integrative gene network analysis uncovered relationships between nitrate-responsive genes and 11 highly co-expressed gene clusters (modules). Four of these gene network modules have robust nitrate responsive functions such as transport, signaling, and metabolism. Network analysis hypothesized G2-like transcription factors are key regulatory factors controlling transport and signaling functions. Our meta-analysis highlights the role of biological processes not studied before in the context of the nitrate response such as root hair development and provides testable hypothesis to advance our understanding of nitrate responses in plants.
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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.