title: In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean.
abstract: Sequence-specific DNA-binding transcription factors (TFs) are often termed as 'master regulators' which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB (http://soybeantfdb.psc.riken.jp) containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by comparative analysis with Arabidopsis. With particular interest in abiotic stress signalling, we analysed the promoter regions for all of the TF encoding genes as a means to identify abiotic stress responsive cis-elements as well as all types of cis-motifs provided by the PLACE database. SoybeanTFDB enables scientists to easily access cis-element and GO annotations to aid in the prediction of TF function and selection of TFs with functions of interest. This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean.
authors.affiliation: RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. mochida@psc.riken.jp
authors.forename: Keiichi
authors.initials: K
authors.lastname: Mochida
authors.forename: Takuhiro
authors.initials: T
authors.lastname: Yoshida
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Kazuko
authors.initials: K
authors.lastname: Yamaguchi-Shinozaki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Lam-Son Phan
authors.initials: LS
authors.lastname: Tran
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins; D014157:Transcription Factors