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What is Ceres?
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Ceres is a web-based software for the integrated analysis of transcription factor (TF) binding sites and nucleosome positioning data for yeast promoter sequences.
- Ceres contains predicted, conserved, and experimentally validated binding sites for 104 yeast transcription factors.
- Ceres also contains genome-wide nucleosome positioning data sets in various environmental conditions (e.g. normal, heat-shock).
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What can Ceres do?
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Ceres provides several features to enable the exploration of DNA- and chromatin-mediated gene regulation:
- Visualization
Visualizes the positions of TF binding sites and nucleosome positions for up to 100 user-selected genes. This tool also tests whether TF binding sites are enriched in the user selected gene set.
- Chromatin Viewer
Visualize trends in nucleosome positioning among user-selected sets of genes. This tool also tests for significant correlation between the nucleosome profiles of the user selected genes. The promoter display tool can be used to compare the nucleosome profiles of genes in different experimental conditions.
- Gene Set Analysis
Identify significantly enriched TF binding sites, chromatin environments, or Gene Ontology terms among a user-selected gene set. This tool enables users to analyze large gene sets (e.g. from a gene expression profiling experiment), and allows users to specify the P-value cutoffs for the enrichment analysis.
- Data Mining
The data mining tools in Ceres allow for selection of sets of genes based on two different factors.
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Genes can be selected by specifying a set of binding factors whose putative sites must be present
within all of those genes' promoter regions.
- Importantly, the chromatin environment of the selected binding factor/binding site can be specified (e.g. nucleosome free or nucleosome interior).
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Alternatively, genes can be selected using Gene Ontology
annotations. Both GO (Gene Ontology) Slim terms and Gene Ontology terms are available. One can select a
set of genes by either choosing a union of the genes annotated by a selected set of Slim terms or Gene
Ontology terms.
The selected genes's putative binding factors are listed, including enrichment data. Furthermore, enriched
presence of Gene Ontology terms is given. Genes selected in this tool are exportable to the analysis suite as a genome subset to investigate.
- Analysis Suite
The analysis suite provides both enhaced data mining tools for selecting genes as well as several
data displays.
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Genes are selectable based upon genome subsets, shared sets of binding factor sites (and chromatin environments), or Gene Ontology
annotations, or any combination of the three.
Several data analysis displays are currently available.
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Histograms are available that plot the distribution of binding factor sites for a set of binding factors
and selected promoters. This distribution can also be tested for bias versus a random background model.
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Chromatin analysis tools are available to display the average trend in nucleosome positioning in the selected genes, the distribution and enrichment of chromatin environments for the found TF binding sites, and histogram tool of the cumulative chromatin environments of the selected TFs.
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Text output of nucleosome positions, TF binding site locations, and binding sitefrequencies are also available.
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Referencing and Contacting us
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| Updated: 10:46 AM, 8 Mar 2009 |
© 2008
Robert Morris, Timothy Ryan O'Connor, and John J. Wyrick . All rights reserved |
Contact: John Wyrick |
| 675 Fulmer Hall | |
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Pullman, WA 99164
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