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.

Figure 1

Screenshots of ATTED-II pages relevant to the search for wounding-responsive gene groups. (A) Top page. (B) Search results. (C) Functional category page. Four co-expressed gene groups were found for wounding response. (D) Results of the co-expressed gene search. ‘Target’ in tables in (C) or (D) indicates predicted subcellular localization. For example, ‘C,C’ indicates both TargetP and WoLF PSORT predict that the gene product is localized in chloroplasts. Yellow-colored AGI codes in the table in (C) indicate genes in the co-expressed gene network. Pink-colored AGI codes in the table in (D) indicate query genes used to search for co-expressed genes.

Figure 2

Screenshots of ATTED-II pages relevant to the search for a predicted regulatory scheme of At5g62490. (A) Top page. (B) Search results. (C) Locus page. The co-expressed gene list and predicted cis elements for At5g62490. (D) Co-expressed genes page. Results of a statistical test for the presence of a cis element in the 50 co-expressed genes. (E) Cis elements page and detailed information for ACACGTG. For simplicity, some graphs are omitted in (C) and (E).