RiceXPro 2012: Update on the Comprehensive Rice Gene Expression Database

The complete genome sequence of Oryza sativa ssp. japonica cv. Nipponbare has elucidated the genome structure of a major cereal crop that provides food for almost half the world population. Deciphering the function of all predicted genes in rice remains as the ultimate goal in order to ensure the development of improved varieties that will sustain an expanding world population. Although a comprehensive annotation of the high-quality genome sequence identified approximately 32,000 genes that define the rice plant, more than half of which does not have known biological functions. With the aim of elucidating the function of all predicted rice genes, we have been performing high-resolution transcriptome analysis of rice grown under the natural field conditions and developing a gene expression database (RiceXPro, URL: http://RiceXPro.dna.affrc.go.jp/) to provide an overview of the transcriptional changes throughout the life cycle of the rice plant. Current version of RiceXPro contains three data sets corresponding to spatiotemporal gene expression of various organs and tissues, continuous gene expression profiles of leaf from transplanting to harvesting, and root system gene expression profiles covering various developmental stages and tissue-types. An intuitive web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of gene expression. Together with other analysis tools such as t-test, calculation of fold change, and degree of correlation, RiceXPro provides baseline methods for gene expression profiling of various agronomically important traits in rice.