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  1. ATTED-II
    Full Name of the Resource : Coexpressed gene sets and gene regulators in Arabidopsis
    Resource Category : Databases -> Plant Databases -> Arabidopsis thaliana

    Brief Description : Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A. thaliana, (ii) prediction of cis regulatory elements in the 200-bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes, and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks.

    Institute/s :
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Japan
    Address of Institute/s :
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
    Country : Japan

    Associated Institutes :

    • Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
    • Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
    • Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8, Saitama 332-0012, Japan
    • Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
    • Structure and Function of Biomolecules, SORST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
    • Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
    • Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan.8 RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
    • Research Center for the Evolving Earth and Planets, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan

    Associated Country : Japan


    Authors/Contributors : Takeshi Obayashi; Shinpei Hayashi
    Contact Email : takeshi.obayashi@atted.jp
    Year : 2009