RiceXPro and RiceFREND: Informatics Resources for Rice Functional Genomics

Functional genomics has become an important research area for exploring useful genes that can be used for crop improvement. We have developed two databases for rice functional genomics, namely, RiceXPro (http://ricexpro.dna.affrc.go.jp/) and RiceFREND (http://ricefrend.dna.affrc.go.jp/), based on the gene expression profiles of the rice plant in the field and various experimental conditions. RiceXPro is a database designed as a repository of gene expression profiles derived from microarray analysis. The current version contains 753 microarray data classified into 26 datasets under field/development, plant hormone and cell/tissue-type data categories. The gene expression of each gene can be characterized from 4 types of interfaces including keyword search, chromosome/region search, analysis tools for retrieving the data statistically, and BLAST-based search for gene expression profile with similarity to a query sequence. The expression data are shown in table, graph, or heatmap formats. RiceFREND is a database of gene coexpression networks in rice. The gene coexpression analysis is performed based on 24 datasets representing 815 microarray data. Coexpression analysis is performed via ‘single guide gene’ and ‘multiple guide genes’ searches in which a pre-selected gene or set of genes is used as ‘guide gene’ to retrieve coexpressed genes. These genes can be viewed in HyperTree, Cytoscape Web or Graphviz formats in addition to tabular format. Additional tools such as ‘GO enrichment test’ and ‘cis-element analysis’ are provided for further assistance in figuring out gene function. These databases could be used as powerful tools for functional genomics and may contribute in understanding many complex agronomic traits in rice.