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.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Obayashi
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
authors.forename: Masayuki
authors.initials: M
authors.lastname: Shibaoka
authors.forename: Shinpei
authors.initials: S
authors.lastname: Hayashi
authors.forename: Motoshi
authors.initials: M
authors.lastname: Saeki
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shibata
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ohta
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors