OryzaExpress: An Integration Database for Functional Annotations and Gene Expression Networks in Rice

Abstract

Similarity of gene expression profiles provides important clues for understanding biological functions of genes, biological processes and metabolic pathways related with genes. Gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. Based on correspondence analysis, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome, and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology.