OGRO: The Overview of functionally characterized Genes in Rice online database

作者：Eiji Yamamoto, Jun‐ichi Yonemaru, Toshio Yamamoto, Masahiro Yano · 发表于：Rice · 年份：2012 · DOI：10.1186/1939-8433-5-26 · 被引用次数：159 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Genomics and Phylogenetic Studies、Rice Cultivation and Yield Improvement

BACKGROUND: The high-quality sequence information and rich bioinformatics tools available for rice have contributed to remarkable advances in functional genomics. To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes. RESULTS: As of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about 1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized to facilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison of genomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were often co-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters were different genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the O verview of Functionally Characterized G enes in R ice O nline database (OGRO) on the Q-TARO website ( http://qtaro.abr.affrc.go.jp/ogro ). The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterize...