ArticleScientific reports2016
Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish.Nature ecology & evolution · 2024Article
- The fusiform gyrus exhibits differential gene-gene co-expression in Alzheimer's disease.Frontiers in aging neuroscience · 2023Article
- Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession.International journal of molecular sciences · 2022Article
- Integrative omics approaches for biosynthetic pathway discovery in plants.Natural product reports · 2022Review
- Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana.Genome biology and evolution · 2021Article
- Filtering of the Gene Signature as the Predictors of Cisplatin-Resistance in Ovarian Cancer.Iranian journal of biotechnology · 2021Article
- Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava.Scientific reports · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- Article
- Review
- Expression correlation attenuates within and between key signaling pathways in chronic kidney disease.BMC medical genomics · 2020Article
- Systemic lipid dysregulation is a risk factor for macular neurodegenerative disease.Scientific reports · 2020Article
- Metric learning on expression data for gene function prediction.Bioinformatics (Oxford, England) · 2020Article
- Recent advances in gene function prediction using context-specific coexpression networks in plants.F1000Research · 2019Review
- Differential coexpression in human tissues and the confounding effect of mean expression levels.Bioinformatics (Oxford, England) · 2019Article
- PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System.Genomics, proteomics & bioinformatics · 2018Article
- Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity.Scientific reports · 2017Article
- Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.Plant molecular biology · 2017Article
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5 authors.
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Abstract
Plant defense responses to pathogens involve massive transcriptional reprogramming. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. syringae through differential coexpression analysis. Overall, we found that differential coexpression was a common phenomenon of plant immunity. Genes that were frequently involved in differential coexpression tend to be related to plant immune responses. Importantly, many of those genes have similar average expression levels between normal plant growth and pathogen infection but have different coexpression partners. By integrating the Arabidopsis regulatory network into our analysis, we identified several transcription factors that may be regulators of differential coexpression during plant immune responses. We also observed extensive differential coexpression between genes within the same metabolic pathways. Several metabolic pathways, such as photosynthesis light reactions, exhibited significant changes in expression correlation between normal growth and pathogen infection. Taken together, differential coexpression analysis provides a new strategy for analyzing transcriptional data related to plant defense responses and new insights into the understanding of plant-pathogen interactions.
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