title: Plant Promoter Database (PPDB).
abstract: ppdb ( http://ppdb.agr.gifu-u.ac.jp ) is a web-based plant promoter database that provides promoter information of each gene in genomes of Arabidopsis, rice, poplar, and Physcomitrella patens. In this database, recognition of a promoter structure is achieved by annotating genome sequences with our sequence lists of bioinformatically identified octamers for core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA Elements) and regulatory element groups (REGs), together with information of transcription start sites (TSSs) that have been experimentally identified. Our promoter elements are octamer sequences that show strongly biased localization profiles in the promoter region, extracted by the local distribution of short sequence (LDSS) analysis. In addition, REGs are linked with the information of the PLACE database and also with their physiological roles that are predicted using large-scale gene expression data.
authors.affiliation: United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Kusunoki
authors.affiliation: United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan. yyy@gifu-u.ac.jp.|Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan. yyy@gifu-u.ac.jp.|RIKEN CSRS, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. yyy@gifu-u.ac.jp.|JST ALCA, Tokyo, Japan. yyy@gifu-u.ac.jp.
authors.forename: Yoshiharu Y
authors.initials: YY
authors.lastname: Yamamoto
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D010944:Plants / Q000235:genetics*; D011401:Promoter Regions, Genetic; D020218:Response Elements; D016385:TATA Box; D024363:Transcription Initiation Site; D064878:Web Browser
keywords: Core element; LDSS; Promoter; REG; Transcription start site (TSS)