Obayashi Takeshi, Kinoshita Kengo, Nakai Kenta, Shibaoka Masayuki, Hayashi Shinpei, Saeki Motoshi, Shibata Daisuke, Saito Kazuki, Ohta Hiroyuki
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
Nucleic Acids Res. 2007 Jan;35(Database issue):D863-9. doi: 10.1093/nar/gkl783. Epub 2006 Nov 27.
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.
公开可用的共表达基因集数据库对于各种实验设计而言将是一个有价值的工具，包括针对基因进行功能鉴定或调控研究。在此，我们报告了拟南芥反式作用因子和顺式元件预测数据库（ATTED-II）的构建，该数据库基于从微阵列数据推导的共表达基因以及预测的顺式元件提供共调控基因关系。ATTED-II（http://www.atted.bio.titech.ac.jp）具有以下特点：（i）根据58个公开可用的实验系列计算得出的共表达基因列表和网络，这些实验系列由1388个拟南芥基因芯片数据组成；（ii）对转录起始位点上游200 bp区域内的顺式调控元件进行预测，以在共表达基因中预测共调控基因；以及（iii）单个基因表达模式的可视化展示。因此，ATTED-II可以帮助研究人员阐明特定基因和基因网络的功能与调控。
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