ArticleBMC genomics2015
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice.Frontiers in plant science · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Ecosystem-specific microbiota and microbiome databases in the era of big data.Environmental microbiome · 2022Review
- Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates.Frontiers in plant science · 2022Article
- Iron insufficiency in floral buds impairs pollen development by disrupting tapetum function.The Plant journal : for cell and molecular biology · 2021Article
- Article
- Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid inInternational journal of molecular sciences · 2021Article
- Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores.Journal of integrative plant biology · 2021Article
- Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice.Frontiers in plant science · 2021Article
- Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management.Frontiers in plant science · 2021Review
- Article
- Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice.Rice (New York, N.Y.) · 2019Article
- Genome-Wide Association Analysis of the Genetic Basis for Sheath Blight Resistance in Rice.Rice (New York, N.Y.) · 2019Article
- Proteomic Changes in the Sound Vibration-TreatedThe plant pathology journal · 2019Article
- Stress-Activated Protein Kinase OsSAPK9 Regulates Tolerance to Salt Stress and Resistance to Bacterial Blight in Rice.Rice (New York, N.Y.) · 2019Article
- Infrastructures of systems biology that facilitate functional genomic study in rice.Rice (New York, N.Y.) · 2019Review
- PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System.Genomics, proteomics & bioinformatics · 2018Article
- The Application of Multi-Locus GWAS for the Detection of Salt-Tolerance Loci in Rice.Frontiers in plant science · 2018Article
- Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22.Scientific reports · 2017Article
- EXPath tool-a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn general, the expression of gene alters conditionally to catalyze a specific metabolic pathway. Microarray-based datasets have been massively produced to monitor gene expression levels in parallel with numerous experimental treatments. Although several studies facilitated the linkage of gene expression data and metabolic pathways, none of them are amassed for plants. Moreover, advanced analysis such as pathways enrichment or how genes express under different conditions is not rendered. DESCRIPTION: Therefore, EXPath was developed to not only comprehensively congregate the public microarray expression data from over 1000 samples in biotic stress, abiotic stress, and hormone secretion but also allow the usage of this abundant resource for coexpression analysis and differentially expression genes (DEGs) identification, finally inferring the enriched KEGG pathways and gene ontology (GO) terms of three model plants: Arabidopsis thaliana, Oryza sativa, and Zea mays. Users can access the gene expression patterns of interest under various conditions via five main functions (Gene Search, Pathway Search, DEGs Search, Pathways/GO Enrichment, and Coexpression analysis) in EXPath, which are presented by a user-friendly interface and valuable for further research.
conclusionsIn conclusion, EXPath, freely available at http://expath.itps.ncku.edu.tw, is a database resource that collects and utilizes gene expression profiles derived from microarray platforms under various conditions to infer metabolic pathways for plants.
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