title: ppdb: plant promoter database version 3.0.
abstract: ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27,000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
authors.affiliation: The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193 Japan, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193 Japan, Center for Sustainable Resource Science, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan, Advanced Science Research Center, Kanazawa University, Takaramachi 13-1. Kanazawa City, Ishikawa 920-0934, Japan, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki City, Aichi 444-8585 Japan, Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D79104 Freiburg, Germany, Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 9, 35043 Marburg, Germany and Graduate School of Environmental Life Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522 Japan.
authors.forename: Ayaka
authors.initials: A
authors.lastname: Hieno
authors.forename: Hushna Ara
authors.initials: HA
authors.lastname: Naznin
authors.forename: Mitsuro
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authors.lastname: Hyakumachi
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Mututomo
authors.initials: M
authors.lastname: Tokizawa
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Koyama
authors.forename: Naoki
authors.initials: N
authors.lastname: Sato
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Nishiyama
authors.forename: Mitsuyasu
authors.initials: M
authors.lastname: Hasebe
authors.forename: Andreas D
authors.initials: AD
authors.lastname: Zimmer
authors.forename: Daniel
authors.initials: D
authors.lastname: Lang
authors.forename: Ralf
authors.initials: R
authors.lastname: Reski
authors.forename: Stefan A
authors.initials: SA
authors.lastname: Rensing
authors.forename: Junichi
authors.initials: J
authors.lastname: Obokata
authors.forename: Yoshiharu Y
authors.initials: YY
authors.lastname: Yamamoto
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019068:Bryopsida / Q000235:genetics; D030561:Databases, Nucleic Acid; D017343:Genes, Plant; D018745:Genome, Plant; D020407:Internet; D012275:Oryza / Q000235:genetics; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D024363:Transcription Initiation Site