bex-db: Bioinformatics Workbench for Comprehensive Study of Barley Expressed Genes

As the same as rice, maize and wheat, barley (Hordeum vulugare) is one of the major cereals in the world. The progresses of comprehensive genomics in this crop, however, have been greatly restricted so far mainly due to its large genome size (5.1 Gb) and high ratio of repetitive elements (80%). In 2012, the International Barley Genome Sequencing Consortium released a physical, genetic and functional assemble of the barley genome, indicating that the barley genomics enters a new phase. Here we present our barley expression database (bex-db: http://barleyflc.dna.affrc.go.jp/hvdb/index.html) to provide the transcriptome data composing barley cDNA sequences and expression profiles. In addition to Full-length cDNAs (FlcDNAs) with the completed sequences, data of novel ESTs from more than 160,000 FlcDNA clones are also available in the bex-db (172,595 clones in total). On the basis of our microarray analysis (30,653 FlcDNA-based probes), moreover, expression profiles obtained under 42 conditions are included as well. Our database also contains information of pairs of coexpressed genes based on Pearson’s correlation coefficient. Three different search systems, keyword search, homology search and expression profile search, are provided for the access to related FlcDNA clones that can be easily requested by users on our browser. Use of the above database thereafter should be able to facilitate our future studies on the genomics and functions of barley genome.