ArticleNucleic acids research2013
RiceFREND: a platform for retrieving coexpressed gene networks in rice.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-QTL s and haplotypes for efficient zinc biofortification of rice.The plant genome · 2023Pooled it
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
- The rice BRITTLE CULM 4 gene encodes a membrane protein affecting cellulose synthesis in the secondary cell wall.Plant & cell physiology · 2025Article
- Identification of Novel Quantitative Trait Loci and Candidate Genes Associated with Grain Yield and Related Traits Under Low-Light Stress Conditions in Rice.Biomolecules · 2025Article
- Comprehensive Identification of Key Genes Responsible for Leaf Senescence of Rice (Plants (Basel, Switzerland) · 2025Article
- OsFON879, an orphan gene, regulates floral organ homeostasis in rice.Plant biotechnology journal · 2025Article
- Identification and Expression Analysis of Rice MYB Family Members in Response to Heat Stress.Plants (Basel, Switzerland) · 2025Article
- Comprehensive study of tRNA-derived fragments in plants for biotic stress responses.Functional & integrative genomics · 2025Article
- Development of an infiltration-based RNA preservation method for cryogen-free storage of leaves for gene expression analyses in field-grown plants.Plant methods · 2024Article
- OsbHLH5 Synergically Regulates Phenolamide and Diterpenoid Phytoalexins Involved in the Defense of Rice Against Pathogens.International journal of molecular sciences · 2024Article
- Sequence-based analysis of the rice CAMTA family: haplotype and network analyses.Scientific reports · 2024Article
- RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice.Database : the journal of biological databases and curation · 2024Article
- Recent Advances in Metagenomic Approaches, Applications, and Challenge.Current microbiology · 2023Review
- RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice.BMC plant biology · 2023Article
- Genome-wide dissection of AT-hook motif nuclear-localized gene family and their expression profiling for drought and salt stress in rice (Frontiers in plant science · 2023Article
- Article
- Enhanced expression of OsNAC5 leads to up-regulation of OsNAC6 and changes rice (Oryza sativa L.) ionome.Genetics and molecular biology · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass.The Plant journal : for cell and molecular biology · 2022Article
- Gene Co-Expression Network Tools and Databases for Crop Improvement.Plants (Basel, Switzerland) · 2022Review
23 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, 'single guide gene search' and 'multiple guide gene search' to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.
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