OPEN ACCESS ARTICLE

This Article Free via Open Access: OA OA Full Text Full Text (PDF) Supplemental Data OA All Versions of this Article: 149/1/171    most recent pp.108.128579v1 Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (3) Citing Articles via Google Scholar Google Scholar Articles by Yilmaz, A. Articles by Grotewold, E. Search for Related Content PubMed PubMed Citation Articles by Yilmaz, A. Articles by Grotewold, E. Agricola Articles by Yilmaz, A. Articles by Grotewold, E. Related Collections The Grasses

BIOINFORMATICS

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses^1,[W],[OA]

Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center (A.Y., B.G.F., E.G.), and Department of Biomedical Informatics (D.J.), The Ohio State University, Columbus, Ohio 43210; Instituto de Química, Departamento de Bioquímica, Universidade de São Paulo, São Paulo, Brazil (M.Y.N., G.M.S.); and Department of Biology, University of Toledo, Toledo, Ohio 43606 (J.G.)

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

² These authors contributed equally to the article.

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: Erich Grotewold (grotewold.1{at}osu.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.108.128579

^* Corresponding author; e-mail grotewold.1{at}osu.edu.

Received August 29, 2008; accepted October 29, 2008; published November 5, 2008.

This article has been cited by other articles:

				K. Mochida, T. Yoshida, T. Sakurai, K. Yamaguchi-Shinozaki, K. Shinozaki, and L.-S. P. Tran In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean DNA Res, December 1, 2009; 16(6): 353 - 369. [Abstract] [Full Text] [PDF]

				P. Perez-Rodriguez, D. M. Riano-Pachon, L. G. G. Correa, S. A. Rensing, B. Kersten, and B. Mueller-Roeber PlnTFDB: updated content and new features of the plant transcription factor database Nucleic Acids Res., October 25, 2009; (2009) gkp805v1. [Abstract] [Full Text] [PDF]

				E. A. Kellogg and C. R. Buell Splendor in the Grasses Plant Physiology, January 1, 2009; 149(1): 1 - 3. [Full Text] [PDF]