Description

For each 12-mer in the human genome a measure of constraint was scored using SiPhy (see reference below), both as a rate-based score (omega), and a measure that includes biased substitution patterns (pi). Those falling in annotated Ancestral Repeats were used as a background. An empirical cutoff score was set corresponding to 10% FDR, and all 12-mers above this score were considered significant. Overlapping significant 12-mers were clustered to yield larger elements.

Detail

There are four tracks in this set:

Constraint Elements pi lods score,
data: mean: 7.214417, min: 1.711200, max: 16.237301, std: 1.364699
Constraint Elements pi branch length score,
data: mean: 4.173642, min: -0.049714, max: 7.351400, std: 0.755658
Constraint Elements omega lods score,
data: mean: 7.667489, min: 1.676100, max: 16.680599, std: 1.378213
Constraint Elements omega branch length score,
data: mean: 4.255876, min: 0.301830, max: 7.376400, std: 0.731477

Credits

Data provided by Or Zuk at broad.mit.edu and Manuel Garber at broadinstitute.org

References

Garber, M. et al. Identifying novel constrained elements by exploiting biased substitution patterns Bioinformatics 25, i54-62, doi:btp190 [pii] 10.1093/bioinformatics/btp190 (2009)