Description

This track displays the 3-way regulatory potential (RP) score computed from alignments of human (hg16, Jul. '03), mouse (mm3, Feb. '03) and rat (rn3, Jun. '03). RP scores compare frequencies of short alignment patterns between regulatory elements and neutral DNA.

The default display range for the track is 0 to 0.1. Score values at or below 0 indicate resemblance to alignment patterns typical of neutral DNA and are truncated and displayed at 0. Score values at or above 0.1 indicate very marked resemblance to alignment patterns typical of regulatory elemenents and are truncated and displayed at 0.1. Absence of a score value at a given location indicates lack of alignment.

Preliminary results from a calibration study investigating sensitivity and specificity of the 3-way RP score on the hemoglobin beta gene cluster suggest the use of a threshold ~ 0.0002 for identifying new putative regulatory elements.

(A 3-way RP score computed from alignments of human, mouse and rat is also available on this browser).

Methods

The comparison employs log-ratios of transitions probabilities from two Markov models. Training the score entails selecting appropriate alphabet (alignment column symbols) and order (length of the patterns=order+1) for the Markov models, and estimating their transition probabilities, based on alignment data from known regulatory elements and ancestral repeats. The 3-way RP score uses a 10-symbol alphabet and order 2.

In the track, score values are displayed using a system of overlapping windows of size 100bp along aligned portions of the human sequence. Log-ratios are added over positions in a window, and the sum is normalized for length.

Using the Filter

The track filter can be used to configure display attributes of the track's graph.

When you have finished configuring the filter, click the Submit button.

Credits

Work on RP scores is performed by members of the Comparative Genomics and Bioinformatics Center at Penn State University. More information on this research and the collection of known regulatory elements used in training the score can be found at this site.

Mouse and rat sequence data were provided by the Mouse and Rat Sequencing Consortia. The alignment data were created in collaboration with the UCSC Genome Bioinformatics group.

References

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. (2004). Aligning Multiple Genomic Sequences with the Threaded Blockset Aligner. Genome Res. 14(4):708-15.

Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison RC and Chiaromonte F. (2004) Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. 14(4):700-707.