ArticleScientific reports2017
Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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
20 citing papers in PubMed.
- Ranking Plant Network Nodes Based on Their Centrality Measures.Entropy (Basel, Switzerland) · 2023Article
- Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators inInternational journal of molecular sciences · 2023Article
- Protein-Protein Interaction Network Analysis Using NetworkX.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Protein-Protein Interaction Network Exploration Using Cytoscape.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Dynamic Enrichment for Evaluation of Protein Networks (DEEPN): A High Throughput Yeast Two-Hybrid (Y2H) Protocol to Evaluate Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Building Protein-Protein Interaction Graph Database Using Neo4j.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions.STAR protocols · 2022Article
- An interolog-based barley interactome as an integration framework for immune signaling.Genetics · 2022Article
- A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets.Computational and structural biotechnology journal · 2022Article
- Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity.Scientific reports · 2021Article
- Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis.iScience · 2020Article
- Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis.SSRN · 2020Article
- Article
- Network biology discovers pathogen contact points in host protein-protein interactomes.Nature communications · 2018Article
- Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence.NPJ systems biology and applications · 2018Article
- Compounds Released by the Biocontrol YeastFrontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The universal nature of networks' structural and physical properties across diverse systems offers a better prospect to elucidate the interplay between a system and its environment. In the last decade, several large-scale transcriptome and interactome studies were conducted to understand the complex and dynamic nature of interactions between Arabidopsis and its bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. We took advantage of these publicly available datasets and performed "-omics"-based integrative, and network topology analyses to decipher the transcriptional and protein-protein interaction activities of effector targets. We demonstrated that effector targets exhibit shorter distance to differentially expressed genes (DEGs) and possess increased information centrality. Intriguingly, effector targets are differentially expressed in a sequential manner and make for 1% of the total DEGs at any time point of infection with virulent or defense-inducing DC3000 strains. We revealed that DC3000 significantly alters the expression levels of 71% effector targets and their downstream physical interacting proteins in Arabidopsis interactome. Our integrative "-omics"--based analyses identified dynamic complexes associated with MTI and disease susceptibility. Finally, we discovered five novel plant defense players using a systems biology-fueled top-to-bottom approach and demonstrated immune-related functions for them, further validating the power and resolution of our network analyses.
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Registered trials
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