Plant Physiology 140:818-829 (2006)
© 2006 American Society of Plant Biologists
OPEN ACCESS ARTICLE
BIOINFORMATICS
AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks1,[W],[OA]
Saranyan K. Palaniswamy,
Stephen James,
Hao Sun,
Rebecca S. Lamb,
Ramana V. Davuluri* and
Erich Grotewold
Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics (S.K.P., H.S., R.V.D.), Department of Plant Cellular and Molecular Biology (S.J., R.S.L., E.G.), and Plant Biotechnology Center (S.J.), The Ohio State University, Columbus, Ohio 43210
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.
1 This work was supported by the National Science Foundation (grant no. MCB–0418891).
The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Ramana V. Davuluri (ramana.davuluri{at}osumc.edu).
[W] The online version of this article contains Web-only data.
[OA] Open Access articles can be viewed online without a subscription.
www.plantphysiol.org/cgi/doi/10.1104/pp.105.072280.
* Corresponding author; e-mail ramana.davuluri{at}osumc.edu; fax 614–688–4006.
Received October 3, 2005;
returned for revision November 4, 2005;
accepted January 6, 2006.
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