ArticlePlant physiology2015
Revealing shared and distinct gene network organization in Arabidopsis immune responses by integrative analysis.
Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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Who cites it
26 citing papers in PubMed, 72 citations in OpenAlex.
- Analysis of Gene Regulatory Networks of Taro (International journal of genomics · 2025Article
- Analysis of huanglongbing-associated RNA-seq data reveals disturbances in biological processes withinFrontiers in plant science · 2024Article
- Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications.Metabolites · 2023Review
- Data science approaches provide a roadmap to understanding the role of abscisic acid in defence.Quantitative plant biology · 2023Article
- Transcriptome Meta-Analysis Identifies Candidate Hub Genes and Pathways of Pathogen Stress Responses inBiology · 2022Article
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- Metatranscriptomic Comparison of Endophytic and PathogenicMolecular plant-microbe interactions : MPMI · 2021Article
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- Robustness of plant quantitative disease resistance is provided by a decentralized immune network.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Driving factors of epiphytic bacterial communities: A review.Journal of advanced research · 2019Review
- Dissecting R gene and host genetic background effect on the Brassica napus defense response to Leptosphaeria maculans.Scientific reports · 2019Article
- Proteomics of Rice-Frontiers in plant science · 2019Review
- Different Pathogen Defense Strategies inCells · 2018Review
- PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System.Genomics, proteomics & bioinformatics · 2018Article
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- Integrative network analyses of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility.Scientific reports · 2018Article
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- Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.Plant molecular biology · 2017Article
- Network Analysis Reveals a Common Host-Pathogen Interaction Pattern inFrontiers in plant science · 2017Article
Corrections and comments
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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
Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) are two main plant immune responses to counter pathogen invasion. Genome-wide gene network organizing principles leading to quantitative differences between PTI and ETI have remained elusive. We combined an advanced machine learning method and modular network analysis to systematically characterize the organizing principles of Arabidopsis (Arabidopsis thaliana) PTI and ETI at three network resolutions. At the single network node/edge level, we ranked genes and gene interactions based on their ability to distinguish immune response from normal growth and successfully identified many immune-related genes associated with PTI and ETI. Topological analysis revealed that the top-ranked gene interactions tend to link network modules. At the subnetwork level, we identified a subnetwork shared by PTI and ETI encompassing 1,159 genes and 1,289 interactions. This subnetwork is enriched in interactions linking network modules and is also a hotspot of attack by pathogen effectors. The subnetwork likely represents a core component in the coordination of multiple biological processes to favor defense over development. Finally, we constructed modular network models for PTI and ETI to explain the quantitative differences in the global network architecture. Our results indicate that the defense modules in ETI are organized into relatively independent structures, explaining the robustness of ETI to genetic mutations and effector attacks. Taken together, the multiscale comparisons of PTI and ETI provide a systems biology perspective on plant immunity and emphasize coordination among network modules to establish a robust immune response.
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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.