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NAR Molecular Biology Database Collection entry number 934
Obayashi T.1,2,3, Kinoshita K.4,5, Nakai K.4, Shibaoka M.6, Hayashi S.6, Saeki M.6, Shibata D.7, Saito K.2,3,8 and Ohta H.1,9
1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
2 Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.3 Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8, Saitama 332-0012, Japan.
4 Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.
5 Structure and Function of Biomolecules, SORST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
6 Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
7 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.
9 Research Center for the Evolving Earth and Planets, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.

Database 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.


Construction of ATTED-II was supported in part by the project "Development of Fundamental Technologies for Controlling the Production of Industrial Materials by Plants" supported by NEDO (New Energy and Industrial Technology Development Organization, Japan) and by CREST (Core Research for Evolutional Science and Technology) of the Japan Science and Technology Agency.

Category: Plant databases
Subcategory: Arabidopsis thaliana

Go to the abstract in the NAR 2009 Database Issue.
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