Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks at the genome level. To integrate this information into a Web-based knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS). AGRIS, which contains all Arabidopsis (Arabidopsis thaliana) promoter sequences, TFs, and their target genes and functions, provides the scientific community with a platform to establish regulatory networks. AGRIS currently houses three linked databases: AtcisDB (Arabidopsis thaliana cis-regulatory database), AtTFDB (Arabidopsis thaliana transcription factor database), and AtRegNet (Arabidopsis thaliana regulatory network). AtTFDB contains 1,690 Arabidopsis TFs and their sequences (protein and DNA) grouped into 50 (October 2005) families with information on available mutants in the corresponding genes. AtcisDB consists of 25,806 (September 2005) promoter sequences of annotated Arabidopsis genes with a description of putative cis-regulatory elements. AtRegNet links, in direct interactions, several hundred genes with the TFs that control their expression. The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu.

Background: The gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fundamental to understanding gene expression. The determination of the regulatory circuits controlled by each TF and the identification of the cisregulatory sequences for all genes have been identified as two of the goals of the Multinational Coordinated Arabidopsis thaliana Functional Genomics Project by the Multinational Arabidopsis Steering Committee (June 2002).

The estrogen receptor (ER) plays an important role in several physiologic functions of both the reproductive and non-reproductive systems. Malignancies of the ER have been associated with the development of cancers, including those of the prostate and breast. Hence it has become of significant importance to characterize the transcriptional regulation of ER target genes. We have created ERTargetDB in order to integrate the previously published ER target gene information that is available in various publications and databases. This information resource provides researchers with an easy access to ER target genes and the regulatory mechanisms in the corresponding promoters. The current version contains 40 genes with experimentally verified estrogen response elements (EREs), 32 experimentally verified ERE tethering sites, 40 genes identified by the chromatin immunoprecipitation microarray, 381 genes from gene expression microarray and 2948 genes from computational prediction. ERTargetDB provides an integral information resource for direct target genes of ERs for the endocrinology research community. It should prove useful in the investigation of gene regulation and aid the development of computational tools for the prediction of ER target genes.