Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice[C][W][OPEN]

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Plant Physiology

• Publication date

  2013-11-14

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1104/pp.113.225862PMID 24235132PMCID PMC3875824
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• OsTZF1, a CCCH-Tandem Zinc Finger Protein, Confers Delayed Senescence and Stress Tolerance in Rice by Regulating Stress-Related Genes1[W][OA]

  2013cited by this paper
• Recent advances in dissecting stress-regulatory crosstalk in rice.

  2013cited by this paper
• STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice

  2013influential reference
• Jasmonate and ethylene signaling mediate whitefly-induced interference with indirect plant defense in Arabidopsis thaliana.

  2013influential reference
• Learning from nature: new approaches to the metabolic engineering of plant defense pathways.

  2013cited by this paper
• Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

  2013cited by this paper
• Random forests-based differential analysis of gene sets for gene expression data.

  2013cited by this paper
• Three Meta-Analyses Define a Set of Commonly Overexpressed Genes from Microarray Datasets on Astrocytomas

  2013cited by this paper
• MetaboAnalyst 2.0—a comprehensive server for metabolomic data analysis

  2012cited by this paper
• Abscisic Acid Deficiency Antagonizes High-Temperature Inhibition of Disease Resistance through Enhancing Nuclear Accumulation of Resistance Proteins SNC1 and RPS4 in Arabidopsis[C][W]

  2012cited by this paper
• Reuse of public genome-wide gene expression data

  2012cited by this paper
• Stable feature selection and classification algorithms for multiclass microarray data

  2012cited by this paper
• Disruption of Abscisic Acid Signaling Constitutively Activates Arabidopsis Resistance to the Necrotrophic Fungus Plectosphaerella cucumerina1[W]

  2012cited by this paper
• The interaction of plant biotic and abiotic stresses: from genes to the field.

  2012influential reference
• Functional disruption of the pentatricopeptide protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis.

  2012cited by this paper
• Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors1[W][OA]

  2012cited by this paper
• Rice MPR25 encodes a pentatricopeptide repeat protein and is essential for RNA editing of nad5 transcripts in mitochondria.

  2012cited by this paper
• A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

  2012cited by this paper
• The cell wall-associated kinases, WAKs, as pectin receptors

  2012cited by this paper
• ABA signal transduction at the crossroad of biotic and abiotic stress responses.

  2012cited by this paper
• The roles of ABA in plant–pathogen interactions

  2011cited by this paper
• Inhibitors of proteolytic enzymes under abiotic stresses in plants (review)

  2011cited by this paper
• Prediction of Drought-Resistant Genes in Arabidopsis thaliana Using SVM-RFE

  2011cited by this paper
• Functions and application of the AP2/ERF transcription factor family in crop improvement.

  2011cited by this paper
• Chemical genetics reveals negative regulation of abscisic acid signaling by a plant immune response pathway.

  2011cited by this paper
• Sekiguchi Lesion Gene Encodes a Cytochrome P450 Monooxygenase That Catalyzes Conversion of Tryptamine to Serotonin in Rice*

  2010cited by this paper
• Root-Specific Expression of OsNAC10 Improves Drought Tolerance and Grain Yield in Rice under Field Drought Conditions1[W][OA]

  2010cited by this paper
• Dimensions of global population projections: what do we know about future population trends and structures?

  2010cited by this paper
• Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.)

  2010cited by this paper
• AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies

  2010influential reference
• Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses

  2010cited by this paper
• A global map of human gene expression

  2010cited by this paper
• OsWRKY IIa Transcription Factors Modulate Rice Innate Immunity

  2010cited by this paper
• Food Security: The Challenge of Feeding 9 Billion People

  2010cited by this paper
• agriGO: a GO analysis toolkit for the agricultural community

  2010cited by this paper
• GreenPhylDB v2.0: comparative and functional genomics in plants

  2010influential reference
• Manipulating Broad-Spectrum Disease Resistance by Suppressing Pathogen-Induced Auxin Accumulation in Rice1[C][W][OA]

  2010cited by this paper
• GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis[W][OA]

  2009cited by this paper
• PMRD: plant microRNA database

  2009cited by this paper
• PlnTFDB: updated content and new features of the plant transcription factor database

  2009cited by this paper
• Networking by small-molecule hormones in plant immunity.

  2009cited by this paper
• A Pair of Allelic WRKY Genes Play Opposite Roles in Rice-Bacteria Interactions1[C][W][OA]

  2009cited by this paper
• Importing ArrayExpress datasets into R/Bioconductor

  2009cited by this paper
• A novel wall-associated receptor-like protein kinase gene, OsWAK1, plays important roles in rice blast disease resistance

  2009cited by this paper
• Plant proteases: from phenotypes to molecular mechanisms.

  2008cited by this paper
• OsWRKY62 is a negative regulator of basal and Xa21-mediated defense against Xanthomonas oryzae pv. oryzae in rice.

  2008cited by this paper
• SOMNUS, a CCCH-Type Zinc Finger Protein in Arabidopsis, Negatively Regulates Light-Dependent Seed Germination Downstream of PIL5[W]

  2008cited by this paper
• Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

  2008cited by this paper
• Transcriptional profiling of the PDR gene family in rice roots in response to plant growth regulators, redox perturbations and weak organic acid stresses

  2008cited by this paper
• Activation of the Indole-3-Acetic Acid–Amido Synthetase GH3-8 Suppresses Expansin Expression and Promotes Salicylate- and Jasmonate-Independent Basal Immunity in Rice[W]

  2008cited by this paper
• Targeting of nucleus-encoded proteins to chloroplasts in plants.

  2008cited by this paper
• OsWRKY71, a rice transcription factor, is involved in rice defense response.

  2007cited by this paper
• The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis.

  2007cited by this paper
• The rice OsLOL2 gene encodes a zinc finger protein involved in rice growth and disease resistance

  2007cited by this paper
• Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data

  2006cited by this paper
• Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice

  2006cited by this paper
• RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

  2006cited by this paper
• EGFR Activation and Ultraviolet Light-Induced Skin Carcinogenesis

  2006cited by this paper
• BMC Bioinformatics BioMed Central Methodology article

  2006cited by this paper
• Centering, scaling, and transformations: improving the biological information content of metabolomics data

  2006cited by this paper
• OsLSD1, a rice zinc finger protein, regulates programmed cell death and callus differentiation.

  2005cited by this paper
• Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family1[w]

  2005cited by this paper
• The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family

  2005cited by this paper
• miRBase: microRNA sequences, targets and gene nomenclature

  2005cited by this paper
• Plant serine proteases: biochemical, physiological and molecular features.

  2005cited by this paper
• Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments

  2004cited by this paper
• Ten rice peroxidases redundantly respond to multiple stresses including infection with rice blast fungus.

  2004cited by this paper
• Data mining in bioinformatics using Weka

  2004cited by this paper
• affy - analysis of Affymetrix GeneChip data at the probe level

  2004influential reference
• Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach

  2003cited by this paper
• Summaries of Affymetrix GeneChip probe level data.

  2003cited by this paper
• The Fasciclin-Like Arabinogalactan Proteins of Arabidopsis. A Multigene Family of Putative Cell Adhesion Molecules1

  2003cited by this paper
• Antagonistic control of oxidative stress-induced cell death in Arabidopsis by two related, plant-specific zinc finger proteins

  2003cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003influential reference
• Molecular Cloning and Functional Analysis of a Novel Type of Bowman-Birk Inhibitor Gene Family in Rice1

  2003cited by this paper
• Gene-expression profiles in hereditary breast cancer.

  2001cited by this paper
• Principal component analysis for clustering gene expression data

  2001influential reference
• Characterization of a rice (Oryza sativa L.) Bowman-Birk proteinase inhibitor: tightly light regulated induction in response to cut, jasmonic acid, ethylene and protein phosphatase 2A inhibitors.

  2001cited by this paper
• The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short‐chain dehydrogenase/reductases

  2001influential reference
• Support vector machine classification and validation of cancer tissue samples using microarray expression data

  2000cited by this paper
• PEI1, an Embryo-Specific Zinc Finger Protein Gene Required for Heart-Stage Embryo Formation in Arabidopsis

  1998cited by this paper
• A novel zinc finger protein is encoded by the Arabidopsis LSD1 gene and functions as a negative regulator of plant cell death.

  1997cited by this paper
• Bioinformatics Applications Note Arrayqualitymetrics—a Bioconductor Package for Quality Assessment of Microarray Data

  year unknowncited by this paper

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  2025cites this paper
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  2025cites this paper
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  2025cites this paper
• Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis

  2025cites this paper
• Decoding the ZmNF-YC1–ZmAPRG pathway for phosphorus efficiency

  2025cites this paper
• Enhancing Tolerance to Combined Heat and Drought Stress in Cool-Season Grain Legumes: Mechanisms, Genetic Insights, and Future Directions.

  2025cites this paper
• Using supervised machine-learning approaches to understand abiotic stress tolerance and design resilient crops

  2025influential citation
• Approaches and challenges in machine learning for monitoring agricultural products and predicting plant physiological responses to biotic and abiotic stresses

  2025cites this paper
• k-Nearest neighbour machine method for predicting resistance gene against Magnaporthe oryzae in rice using proteomic markers

  2024cites this paper
• Application of machine learning in the study of development, behavior, nerve, and genotoxicity of zebrafish.

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• Physio-biochemical and nutritional alterations in faba bean due to bean yellow mosaic virus infection

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• A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions

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• Plant-Derived Smoke Solution: A Stress Alleviator in Crop

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• Deciphering Plant Transcriptomes: Leveraging Machine Learning for Deeper Insights

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• Melatonin-mediated physiological and molecular responses to abiotic stress in horticultural crops

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• Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests

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• Soybean gene co‐expression network analysis identifies two co‐regulated gene modules associated with nodule formation and development

  2023cites this paper
• Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

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• Predicting rice diseases using advanced technologies at different scales: present status and future perspectives

  2023cites this paper
• Deep learning uncovers distinct behavior of rice network to pathogens response

  2022cites this paper
• An integrative computational approach to predict stress-specific candidate and shared genes in multiple plant stresses

  2022cites this paper
• Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.)

  2022cites this paper
• Nutrient elements promote disease resistance in tomato by differentially activating immune pathways.

  2022cites this paper
• Identification of Key Gene Network Modules and Hub Genes Associated with Wheat Response to Biotic Stress Using Combined Microarray Meta-analysis and WGCN Analysis

  2022cites this paper
• Transcriptome meta-analysis of abiotic stresses-responsive genes and identification of candidate transcription factors for broad stress tolerance in wheat

  2022cites this paper
• Comprehensive meta-analysis and machine learning approaches identified the role of novel drought specific genes in Oryza sativa

  2022cites this paper
• A2TEA: Identifying trait-specific evolutionary adaptations

  2022cites this paper
• Variations in OsSPL10 confer drought tolerance by directly regulating OsNAC2 expression and ROS production in rice.

  2022cites this paper
• Microalgal based biostimulants as alleviator of biotic and abiotic stresses in crop plants

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• Optimization of best dose of chitosan to Mitigate stress-induced toxic effects of salinity and Nickel in rose

  2021cites this paper
• Plant Disease Detection Using Machine Learning Tools With an Overview on Dimensionality Reduction

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• Machine learning in plant-pathogen interactions: empowering biological predictions from field scale to genome scale.

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• Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics

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• Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

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