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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

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

doi

10.1093/nar/gkl783

subject

Has Abstract

pub_date

2007-01-01 00:00:00

pages

D863-9

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gkl783

journal_volume

35

pub_type

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