BU ORChID Track Settings
 
ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab)   (All Mapping and Sequencing tracks)

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 Signal  OH Radical Cleavage Intensity Database (ORChID) V1 from ENCODE/Boston Univ    Schema   2010-10-24 
 
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 Signal  OH Radical Cleavage Intensity Database (ORChID) V2 from ENCODE/Boston Univ    Schema   2010-10-24 
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Description

This set of tracks displays the predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the genome. Because the hydroxyl radical cleavage intensity is proportional to the solvent accessible surface area of the deoxyribose hydrogen atoms (Balasubramanian et al., 1998), these tracks represent a structural profile of the DNA in the genome.

For additional details, please visit the Tullius lab website.

Display Conventions and Configuration

These tracks 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. For more information, click the Graph configuration help link.

In the full and pack display modes, positive intensity values are shown in red and negative intensity values are shown in tan. In the squish and dense display modes, intensity is represented in grayscale (the darker the shading, the higher the intensity). To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide.

Recommended Track Settings

Because the ORChID tracks are single nucleotide resolution and different viewing scales result in different levels of smoothing, the default data view scale parameter (auto-scale to data view) is not always ideal for visualizing the variability in the data. As a result, we recommend the following data view scale parameters for different scales:

Viewing scale Data view scaling Vertical viewing range: min Vertical viewing range: max
less than 10 Kb auto-scale to data view NA NA
10 Kb use vertical viewing range setting 0 0.75
100 Kb use vertical viewing range setting 0.1 0.5
1 Mb or larger use vertical viewing range setting 0.2 0.4

Note that these settings are only recommendations and may not be ideal for all viewing circumstances.

Methods

Hydroxyl radical cleavage intensity predictions were performed using an in-house sliding tetramer window (STW) algorithm on the hg19 version of the human genome. This algorithm draws data from the ·OH Radical Cleavage Intensity Database (ORChID), which contains more than 150 experimentally determined cleavage patterns. The ORChID Version 1 predictions are performed on the + strand of the DNA sequence. These predictions are fairly accurate, with a Pearson coefficient of 0.88 between the predicted and experimentally determined cleavage intensities. For ORChID Version 2, two predictions are performed, one on the + strand and the other on the - strand, and then the average of the predicted cleavage intensity for nucleotides in close proximity across the minor groove is presented. For more details on the hydroxyl radical cleavage method, see below for reference (Greenbaum et al. 2007).

The hydroxyl radical cleavage pattern for any DNA sequence can be predicted, either using a web-based server or via a Perl script. For details please see the ORChID website.

Verification

The STW algorithm has been cross-validated by removing each test sequence from the training set and performing a prediction. The mean correlation coefficient (between predicted and experimental cleavage patterns) from this study was 0.88.

Credits

These data were generated at Boston University and NHGRI.

Contact: Tom Tullius

These data are the result of the combined efforts of Bo Pang (now at MIT), Jason Greenbaum (now at The La Jolla Institute for Allergy and Immunology), Steve Parker and Elliott Margulies at The National Human Genome Research Institute, National Institutes of Health, and Eric Bishop and Tom Tullius at Boston University.

References

Balasubramanian B, Pogozelski WK, and Tullius TD. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA. 1998 Aug 18;95(17):9738-43.

Greenbaum JA, Pang B, and Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 2007 Jun;17(6):947-53.

Price MA, and Tullius TD. Using the Hydroxyl Radical to Probe DNA Structure. Meth. Enzymol. 1992;212:194-219.

Tullius TD. Probing DNA Structure with Hydroxyl Radicals. Curr Protoc Nucleic Acid Chem. 2002 Feb;Chapter 6:Unit 6.7. Review.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.