ArticlePlanta2019
Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana.
Article in Planta, 2019. 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, 38 citations in OpenAlex.
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- Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits.G3 (Bethesda, Md.) · 2024Article
- Exploring large-scale gene coexpression networks in peach (Horticulture research · 2024Article
- Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated with pear petal defense responses againstFrontiers in plant science · 2024Article
- Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation.Scientific reports · 2023Article
- Transcriptomic analysis reveals the gene regulatory networks involved in leaf and root response to osmotic stress in tomato.Frontiers in plant science · 2023Article
- Transcriptome and Regional Association Analyses Reveal the Effects of Oleosin Genes on the Accumulation of Oil Content inPlants (Basel, Switzerland) · 2022Article
- Applications of cell- and tissue-specific 'omics to improve plant productivity.Emerging topics in life sciences · 2022Review
- Comprehensive functional analysis of the PYL-PP2C-SnRK2s family inFrontiers in plant science · 2022Article
- Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits.Frontiers in plant science · 2022Article
- Transcriptomics and metabolomics changes triggered by exogenous 6-benzylaminopurine in relieving epicotyl dormancy ofFrontiers in plant science · 2022Article
- Integrated physiological and transcriptomic analyses reveal the molecular mechanism behind the response to cultivation inFrontiers in plant science · 2022Article
- Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum.Biochemical genetics · 2021Article
- Identification of key genes associated with secondary metabolites biosynthesis by system network analysis in Valeriana officinalis.Journal of plant research · 2021Article
- CoCoCoNet: conserved and comparative co-expression across a diverse set of species.Nucleic acids research · 2020Article
- Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships.Frontiers in plant science · 2020Article
- A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization.Frontiers in plant science · 2019Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
MAIN
conclusionA comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. A web tool to explore module information was also provided. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. These data can be reused for research on gene function through a systematic analysis of gene co-expression relationships. We collected microarray data from National Center for Biotechnology Information Gene Expression Omnibus, identified modules of co-expressed genes and annotated module functions. These modules were associated with experiments/traits, which provided potential signature modules for phenotypes. Novel heat shock proteins were implicated according to guilt by association. A higher-order module networks analysis suggested that the Arabidopsis network can be further organized into 15 meta-modules and that a chloroplast meta-module has a distinct gene expression pattern from the other 14 meta-modules. A comparison with the rice transcriptome revealed preserved modules and KEGG pathways. All the module gene information was available from an online tool at http://bioinformatics.fafu.edu.cn/arabi/ . Our findings provide a new source for future gene discovery in Arabidopsis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.