RiceXPro V3.0: A Comprehensive Database for Field Transcriptome and more

Microarray technology has remained as an indispensable tool for monitoring the transcriptome of a given organism under various biological conditions. We have updated our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp/), to provide more comprehensive information on the transcriptome of rice that encompasses the entire growth cycle in the field as well as various experimental conditions. The current version includes microarray data from organs / tissues at various stages of growth and development in the field, rice plants subjected to treatment with various hormones, and specific cells / tissues isolated by laser microdissection. The expression data for each gene can be accessed via 4 types of interfaces that include keyword search, chromosome/region search, analysis tools for retrieving the data statistically, and a BLAST-based search function to explore the gene expression profile with similarity to a query sequence. These options generate gene expression profiles in table, graph, or heatmap formats. In addition to the interface for retrieving expression information of a gene/genes in each data set, we have incorporated an interface for a global approach in searching an overall view of the gene expression profiles from multiple data sets within each category. The RiceXPro can be used as a platform to infer the function of a gene/genes based on specificity of expression and gain insights into the biological processes involved in the expression of many agronomic traits in rice.