MOTIVATION: There is accumulating evidence that the chromatin environment of transcription factor (TF) binding sites in promoter regions has a critical influence on their regulatory potential. Recent studies have mapped TF binding sites and nucleosome positions throughout the yeast genome; however, there is a lack of computation tools to integrate these data types. RESULTS: We have developed the Ceres software to facilitate the integrated analysis of TF binding sites and nucleosome positions in the model eukaryote S. cerevisiae. Ceres enables users to dynamically display the spatial organization of TF binding sites and nucleosome positions of individual genes, or the average profiles for large gene sets. Ceres provides novel statistical tools to test for the enrichment of TF binding sites and chromatin environments for user-selected gene sets. Ceres also enables users to search the genome for combinations of TF binding sites that are associated with specific chromatin environments. Preliminary analysis using the Ceres software indicates that functional and conserved TF binding sites are often associated with specific chromatin environments. AVAILABILITY: http://bioinformatics1.smb.wsu.edu/Ceres. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database containing promoter sequences, predicted transcription factor (TF) binding sites, gene ontology annotation and microarray expression data for 24 209 genes in the rice genome. These tools are seamlessly integrated in the Osiris web site, allowing the user to visualize TF binding sites in multiple promoters; analyze the statistical significance of enriched TF binding sites; query for genes containing similar promoter regulatory logic or gene function and visualize the microarray expression patterns of queried or selected gene sets. AVAILABILITY: http://www.bioinformatics2.wsu.edu/Osiris

UNLABELLED: Covalent modifications to histone proteins play a critical role in regulating gene transcription. Previous studies have used chromatin immunoprecipitation (ChIP) based microarray assays to profile genomic regions that are enriched or depleted for a particular histone modification. Such studies have been conducted extensively in the yeast Saccharomyces cerevisiae, but currently no comprehensive data repositories or analysis tools are available for these data sets. For this reason, we have developed the ChromatinDB database, which contains genome-wide ChIP data for 22 different histones or histone modifications in S. cerevisiae. ChromatinDB provides novel tools to facilitate the visualization and statistical analysis of chromatin features for user-selected gene sets. AVAILABILITY: http://www.bioinformatics2.wsu.edu/ChromatinDB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: To better understand the regulatory networks that control plant gene expression, tools are needed to systematically analyze and visualize promoter regulatory sequences in Arabidopsis thaliana. We have developed the Athena database, which contains 30,067 predicted Arabidopsis promoter sequences and consensus sequences for 105 previously characterized transcription factor (TF) binding sites. Athena provides four novel tools to facilitate the analysis of promoter sequences: a promoter visualization tool to enable the rapid inspection of key regulatory sequences in multiple promoters; a TF binding site enrichment tool to identify statistically over-represented TF sites occurring in a user-selected subset of promoters; a data-mining tool to rapidly select promoter sequences containing the specified combination of TF binding sites; and a tool to display the distribution of TF binding site positions in a selected set of promoter sequences.