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The Rice Oligonucleotide Array Database: an atlas of rice gene expression
Peijian Cao1, Ki-Hong Jung, Daeseok Choi
1Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China. jzhu@zju.edu.cn.
Rice (New York, N.Y.)
|November 28, 2013
Summary
Researchers developed the Rice Oligonucleotide Array Database (ROAD) to integrate diverse rice gene expression data. This tool aids in analyzing gene profiles, co-expression, and biological patterns for rice and grass species.
Area of Science:
- Plant Biology
- Genomics
- Bioinformatics
Background:
- Microarray technology enables high-throughput gene expression analysis.
- Diverse platforms for rice gene expression analysis complicate data integration and analysis.
- A need exists for tools that broadly integrate microarray data from different platforms.
Purpose of the Study:
- To develop a comprehensive database for rice gene expression analysis.
- To provide a user-friendly platform for exploring and analyzing rice microarray data.
- To facilitate meta-analysis and functional insights from diverse rice gene expression datasets.
Main Methods:
- Development of the Rice Oligonucleotide Array Database (ROAD).
- Integration of 1,867 publicly available rice microarray hybridizations.
- Implementation of web-based tools for data extraction, visualization, meta-analysis, co-expression analysis, and functional annotation (Gene Ontology, KEGG Orthology).
Main Results:
- The ROAD provides a centralized resource for exploring rice gene expression across numerous hybridizations.
- User-friendly interface allows extraction of gene expression profiles and supports meta-analysis across tissues and developmental stages.
- Embedded tools facilitate co-expression analysis under various stress conditions and functional identification of biological patterns.
Conclusions:
- The Rice Oligonucleotide Array Database (ROAD) offers comprehensive gene expression profiles for all rice genes.
- ROAD serves as a valuable resource for researchers studying rice and other grass species.
- Facilitates deeper understanding of gene regulation and biological functions in grasses.
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