@article{fef7133dafe34c4590c1301a4f481a0a,
title = "ATTED-II: A database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis",
abstract = "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.",
author = "Takeshi Obayashi and Kengo Kinoshita and Kenta Nakai and Masayuki Shibaoka and Shinpei Hayashi and Motoshi Saeki and Daisuke Shibata and Kazuki Saito and Hiroyuki Ohta",
note = "Funding Information: We thank Dr Takayuki Tohge, Mr Tetsuya Sakurai and Mr Keiji Akiyama for valuable discussions about utilization of the co-expressed gene lists. We also thank Dr Nicolas Sierro for his comments on the manuscript. This work was supported in part by the project {\textquoteleft}Development of Fundamental Technologies for Controlling the Production of Industrial Materials by Plants{\textquoteright} 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. Computation time was provided by the Super Computer System, Human Genome Center, Institute of Medical Science, The University of Tokyo. Funding to pay the Open Access publication charges for this article was provided by Tokyo Institute of Technology.",
year = "2007",
month = jan,
doi = "10.1093/nar/gkl783",
language = "English",
volume = "35",
pages = "D863--D869",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 1",
}