Nucleic Acids Research Advance Access originally published online on November 27, 2006
Nucleic Acids Research 2007 35(Database issue):D863-D869; doi:10.1093/nar/gkl783
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Nucleic Acids Research, 2007, Vol. 35, Database issue D863-D869
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
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
*To whom correspondence should be addressed at Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan. Tel: +81 45 924 5736; Fax: +81 45 924 5823; Email: atted{at}bio.titech.ac.jp
Received August 15, 2006. Revised September 25, 2006. Accepted September 29, 2006.
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 (http://www.atted.bio.titech.ac.jp) 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.
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