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Plant Promoter Database (PPDB)

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Plant Genomics Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

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.

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Acknowledgment

We thank Hushna Ara Naznin at Gifu University for critical reading of the manuscript. This work was in part supported by Grant-in-Aids for Scientific Research on Priority Areas “Comparative Genomics” and Publication of Scientific Research Results from Ministry of Education, Culture, Sports, Science and Technology (MEXT), Grant-in-Aids for Scientific Research for Publication of Scientific Research Results (Databases, #238049) from MEXT, a grant-in-aids from Sumitomo Foundation, and a grant-in-aids from Gifu University.

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Authors and Affiliations

  1. United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan

    Kazutaka Kusunoki & Yoshiharu Y. Yamamoto

  2. Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan

    Yoshiharu Y. Yamamoto

  3. RIKEN CSRS, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Yoshiharu Y. Yamamoto

  4. JST ALCA, Tokyo, Japan

    Yoshiharu Y. Yamamoto

Authors
  1. Kazutaka Kusunoki
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  2. Yoshiharu Y. Yamamoto
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Correspondence to Yoshiharu Y. Yamamoto .

Editor information

Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

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Kusunoki, K., Yamamoto, Y.Y. (2017). Plant Promoter Database (PPDB). In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_18

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  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

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