This track identifies amplicons overlying DNaseI hypersensitive sites (HSs) and provides an empirical P-value for each. The track is one of a set of tracks that annotate continuous DNaseI sensitivity measurements and DNaseI hypersensitive sites (HSs) over ENCODE regions. DNaseI has long been used to map general chromatin accessibility and the DNaseI "hyperaccessibility" or "hypersensitivity" that is a universal feature of active cis-regulatory sequences. The data were produced using quantitative chromatin profiling (QCP) (Dorschner et al., 2004).
See the UW/Reg Amplicon track for a list of the cell lines/phenotypes studied in these experiments.
Data values are represented on a vertical axis as a score between 0 and 3, corresponding to -log10(P-value) (i.e., a score of 3 indicates a P-value of less than 0.001). Note that these are empirically determined P-values, not binomial/Gaussian P-values. Also, the HSs are called only in the context of plates with an acceptable (though conservative) plate quality score (see the Regulome Quality track).
The subtracks within this composite annotation track may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.
Color differences among the subtracks are arbitrary; they provide a visual cue for distinguishing the different cell lines/phenotypes.
QCP was performed as described in Dorschner et al. See the UW/Reg Amplicon track description for more information.
See the UW/Reg Amplicon track description for verification information.
Data generation, analysis, and validation were performed jointly by groups at Regulome Corporation and the University of Washington (UW) in Seattle.
Regulome Corp.: Michael O. Dorschner, Richard Humbert, Peter J. Sabo, Anthony Shafer, Jeff Goldy, Molly Weaver, Kristin Lee, Fidencio Neri, Brendan Henry, Mike Hawrylycz, Paul Tittel, Jim Wallace, Josh Mack, Janelle Kawamoto, John A. Stamatoyannopoulos.
UW Medical Genetics: Patrick Navas, Man Yu, Hua Cao, Brent Johnson, Ericka Johnson, George Stamatoyannopoulos.
UW Genome Sciences: Scott Kuehn, Robert Thurman, William S. Noble.
Dorschner, M.O., Hawrylycz, M., Humbert, R., Wallace, J.C., Shafer, A., Kawamoto, J., Mack, J., Hall, R., Goldy, J., Sabo, P.J. et al. High-throughput localization of functional elements by quantitative chromatin profiling. Nat Methods 1(3), 219-25 (2004).