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PMID: 17130150 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D863-9

Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H

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.

MeSH Terms
Arabidopsis/genetics Binding Sites Databases, Genetic Gene Expression Profiling Gene Expression Regulation, Plant Internet Regulatory Elements, Transcriptional Transcription Factors/metabolism User-Computer Interface
Chemicals
Transcription Factors
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Obayashi Takeshi
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
Kinoshita Kengo
Nakai Kenta
Shibaoka Masayuki
Hayashi Shinpei
Saeki Motoshi
Shibata Daisuke
Saito Kazuki
Ohta Hiroyuki
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl783
Published
2007-01-00
Epub
2006-00-27
Pages
D863-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1716726
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl783 PMC Full Text View journal details
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