ArticleNucleic acids research2015
GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis.The Plant journal : for cell and molecular biology · 2016Pooled it
- High-Throughput Protein-Protein Interactions Screening Using Pool-Based Liquid Yeast Two-Hybrid Pipeline.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis.Plants (Basel, Switzerland) · 2020Article
- MODEL ASSISTED VARIABLE CLUSTERING: MINIMAX-OPTIMAL RECOVERY AND ALGORITHMS.Annals of statistics · 2020Article
- DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models.Plant methods · 2020Article
- Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development.Cells · 2019Article
- The SCOOP12 peptide regulates defense response and root elongation in Arabidopsis thaliana.Journal of experimental botany · 2019Article
- PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System.Genomics, proteomics & bioinformatics · 2018Article
- Multilevel Regulation of Abiotic Stress Responses in Plants.Frontiers in plant science · 2017Review
- Venus flytrap carnivorous lifestyle builds on herbivore defense strategies.Genome research · 2016Article
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Authors and funding
12 authors.
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Abstract
CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein-protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.
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