title: GRASSIUS: a platform for comparative regulatory genomics across the grasses.
abstract: 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.
authors.affiliation: Department of Plant Cellular and Molecular Biology, The Ohio State University, Columbus, Ohio 43210, USA.
authors.forename: Alper
authors.initials: A
authors.lastname: Yilmaz
authors.forename: Milton Y
authors.initials: MY
authors.lastname: Nishiyama
authors.forename: Bernardo Garcia
authors.initials: BG
authors.lastname: Fuentes
authors.forename: Glaucia Mendes
authors.initials: GM
authors.lastname: Souza
authors.forename: Daniel
authors.initials: D
authors.lastname: Janies
authors.forename: John
authors.initials: J
authors.lastname: Gray
authors.forename: Erich
authors.initials: E
authors.lastname: Grotewold
mesh_terms: D003628:Database Management Systems; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors