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

• DOI

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.

BibTeX

@article{obayashi-nar200701,
    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},
    title = {{ATTED-II}: a database of co-expressed genes and \textit{cis} elements for identifying co-regulated gene groups in \textit{Arabidopsis}},
    journal = {Nucleic Acids Research},
    volume = 35,
    number = {Database},
    pages = {D863--D869},
    doi = {10.1093/nar/gkl783},
    year = 2007,
}