ATTED-II:: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

被引:301
作者
Obayashi, Takeshi
Kinoshita, Kengo
Nakai, Kenta
Shibaoka, Masayuki
Hayashi, Shinpei
Saeki, Motoshi
Shibata, Daisuke
Saito, Kazuki
Ohta, Hiroyuki
机构
[1] Univ Tokyo, Inst Med Sci, Human Genome Ctr, Minato Ku, Tokyo 1088639, Japan
[2] Tokyo Inst Technol, Grad Sch Biosci & Biotechnol, Midori Ku, Yokohama, Kanagawa 2268501, Japan
[3] Chiba Univ, Grad Sch Pharmaceut Sci, Chiba 2638522, Japan
[4] SORST, JST, Struct & Funct Biomol, Kawaguchi, Saitama 3320012, Japan
[5] Tokyo Inst Technol, Grad Sch Informat Sci & Engn, Meguro Ku, Tokyo 1528550, Japan
[6] Kazusa DNA Res Inst, Chiba 2920812, Japan
[7] RIKEN, Plant Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan
[8] Res Ctr Evolving Earth & Planets, Midori Ku, Yokohama, Kanagawa 2268501, Japan
基金
日本科学技术振兴机构;
关键词
D O I
10.1093/nar/gkl783
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 coregulated 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.
引用
收藏
页码:D863 / D869
页数:7
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