title: bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes.
abstract: Barley (Hordeum vulgare) is one of the world's most important cereal crops. Although its large and complex genome has held back barley genomics for quite a while, the whole genome sequence was released in 2012 by the International Barley Genome Sequencing Consortium (IBSC). Moreover, more than 30,000 barley full-length cDNAs (FLcDNAs) are now available in the public domain. Here we present the Barley Gene Expression Database (bex-db: http://barleyflc.dna.affrc.go.jp/bexdb/index.html) as a repository of transcriptome data including the sequences and the expression profiles of barley genes resulting from microarray analysis. In addition to FLcDNA sequences, bex-db also contains partial sequences of more than 309,000 novel expressed sequence tags (ESTs). Users can browse the data via keyword, sequence homology and expression profile search options. A genome browser was also developed to display the chromosomal locations of barley FLcDNAs and wheat (Triticum aestivum) transcripts as well as Aegilops tauschii gene models on the IBSC genome sequence for future comparative analysis of orthologs among Triticeae species. The bex-db should provide a useful resource for further genomics studies and development of genome-based tools to enhance the progress of the genetic improvement of cereal crops.
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.affiliation: Bioinformatics Solution Group, Hitachi Government & Public Corporation System Engineering, Ltd. , 2-4-18 Toyo, Koto, Tokyo 135-8633 , Japan.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Fujii
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Fuminori
authors.initials: F
authors.lastname: Kobayashi
authors.affiliation: Wheat and Barley Research Division, National Institute of Crop Science , 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518 , Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Nakamura
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
keywords: EST; barley; full-length cDNA; gene expression; genome viewer; microarray