Table 2.

Thresholds and effectiveness of scores derived from human–mouse–rat genome alignments for finding CRMs in the reference set for the HBB complex

Binary discrimination by position
Discrimination of intervalsb
Method
Threshold
Sn, Spa
Threshold
Snint
True discovery rate
MCS 1.55 0.55 3.3 0.44 0.54
PhastCons 0.031 0.50 0.13 0.50 0.54
Regulatory potential -0.006 0.61 0 0.78 0.63
Regulatory potential, no HBBc
-0.007
0.60
0
0.78
0.59

a Sn indicates sensitivity; Sp, specificity. Optimal Sn and Sp are determined at the crossover point and thus are equal.

b The intervals are evaluated by the maximum score within each interval.

c RP scores computed using a training set that excludes CRMs from the HBB complex.