Table 1.

Predicting In Vitro Binding

Method/criterion	AUC	TP1FP	Spearman
RAP	0.880	0.435	0.293
BEEML-PBM	0.873	0.418	0.283
Seed-and-Wobble	0.858	0.332	0.239
RankMotif++	0.869	0.292	0.245

The table shows average results in three different criteria for each method over 316 PBM pairs. In each experiment, a PWM was learned using one array and then used to rank probes of its paired array. This ranking was compared to the original probe ranking using AUC, sensitivity at 1% false positive (TP1FP), and Spearman rank coefficient. AUC, area under the curve; PWM, position weight matrix; RAP, rank, align, PWM; PBM, protein-binding microarray.