ArticlePlant & cell physiology2011
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice.
Article in Plant & cell physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- Article
- A gene network-driven approach to infer novel pathogenicity-associated genes: application tomSystems · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing.Plants (Basel, Switzerland) · 2022Article
- Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Original Form of CFrontiers in plant science · 2022Article
- Genomics and transcriptomics to protect rice (Frontiers in plant science · 2022Review
- Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production.Breeding science · 2021Article
- Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.Frontiers in genetics · 2021Article
- Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management.Frontiers in plant science · 2021Review
- Cell wall Glycine-rich Protein2 is involved in tapetal differentiation and pollen maturation.Journal of plant research · 2020Article
- Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice.International journal of molecular sciences · 2020Article
- Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots.Plant physiology · 2020Article
- HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis.BMC bioinformatics · 2019Article
- Infrastructures of systems biology that facilitate functional genomic study in rice.Rice (New York, N.Y.) · 2019Review
- Pathway Editing Targets for Thiamine Biofortification in Rice Grains.Frontiers in plant science · 2018Review
- Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice.Rice (New York, N.Y.) · 2017Article
- RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.BMC bioinformatics · 2017Article
- Gene coexpression network forPlant biotechnology (Tokyo, Japan) · 2017Article
- RapaNet: A Web Tool for the Co-Expression Analysis ofEvolutionary bioinformatics online · 2017Article
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20 authors.
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Abstract
Similarity of gene expression profiles provides important clues for understanding the biological functions of genes, biological processes and metabolic pathways related to genes. A gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. For GEN construction, the Pearson correlation coefficient (PCC) has been widely used as an index to evaluate the similarities of expression profiles for gene pairs. However, calculation of PCCs for all gene pairs requires large amounts of both time and computer resources. Based on correspondence analysis, we developed a new method for GEN construction, which takes minimal time even for large-scale expression data with general computational circumstances. Moreover, our method requires no prior parameters to remove sample redundancies in the data set. Using the new method, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology.
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