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Published on November 5, 2008; 10.1104/pp.108.128579

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Received August 29, 2008
Accepted October 29, 2008

GRASSIUS: A Platform for Comparative Regulatory Genomics Across the Grasses

Alper Yilmaz , Milton Y Nishiyama Jr , Bernardo Garcia-Fuentes , Glaucia Mendes Souza , Daniel Janies , John Gray , and Erich Grotewold *

Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center; Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210; Dept. of Biology, University of Toledo, Toledo OH 43606; Instituto de Quimica, Departamento de Bioquimica, Universidade de Sao Paulo, Brazil

* Corresponding author; email: grotewold.1{at}osu.edu.

Transcription factors (TFs) are major players in gene regulatory networks, and interactions between TFs and their target genes furnish spatio-temporal 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 knowledgebase 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, sorghum, sugarcane and rice. 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 grasses TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames (ORFs) 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 is available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet, as a first step in representing the architecture of grasses regulatory networks. GRASSIUS can be accessed from www.grassius.org.




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