A gene co-expression database for understanding biological processes in soybean

Abstract

The sobean genome has been decoded independently in the United States, China, South Korea, and Japan using varieties indigenous to those regions. Using an EST library of the variety indigenous to the United States, a DNA microarray technique was developed and gene expression data in microarray experiments have been accumulated in public databases such as the Gene Expression Omnibus database (GEO). Such data can be used for genome-wide bioinformatics approaches to co-expression analysis for predicting gene function. To extract co-expressed genes in soybean, we analyzed soybean gene expression data based on DNA microarray datasets obtained from GEO and developed a database for soybean gene co-expression analysis. Using the database, we illustrate the steps to retrieve co-expressed genes that may be involved in isoflavonoid biosynthesis and secondary cell wall biosynthesis. Our database is useful for extracting co-expressed genes, which may be involved in a particular biological process, and then for understanding the mechanisms of such processes in legumes.