This database provides a user interface to the results of Sheffield et al. (2013). The data is from hundreds of DNaseI-hypersensitivity and Affymetrix microarray experiments.
On this web interface you can find:
- Normalized DNaseI-hypersensitivity profiles for 112 human samples for 2.8 million individual regulatory elements.
- Normalized Affymetrix gene expression profiles for 112 human samples for about 30,000 Ensembl genes.
- Clusters of DNaseI hypersensitive sites, grouped by cross-tissue pattern, plus statistics and sites in each cluster
- Motif analysis results for enriched DNA motifs in regulatory clusters.
- Correlation links between regulatory elements and genes.
Please use the web interface to browse the dataset. For computational use, all of the data is also available for download as text files. Please use these text files for any complex analysis on your local computer. Helpful Links:
ExamplesThere are 5 ways to explore the data:
- By CELLTYPE - Select cell-types to include or exclude.
- By CLUSTER - View promoter, CpG-island, and conserved element overlap for all clusters, and select individual clusters.
- Muscle-specific cluster: cluster 1520
- Prostate and hepatocyte cluster: cluster 910
- Prostate-only cluster: cluster 2483
- Hematopoeitic cluster: cluster 25
- Pluripotency cluster: cluster 104
- By GENE - Search by gene of interest
- By COORDINATE: Give chr, start, stop to find all regulatory elements in a region.
- IRF2 regulator: chr4: 185240845-185240995
- MyoD1 regulator: chr11: 17828545-17828695
- Blood regulator: chr3: 128166420-128166570
- By FACTOR: find a specific TF of interest