Table 3.

Results of comparison of three site model methods applied to the TRANSFAC PWMs on respective ChIP-seq data sets. Three measures of site recognition methods were applied—full AUC and two partial-AUCs. We computed the number of PWMs that gives maximal value of the measure (full AUC or partial-AUC) for the given site model. The last row gives the number of PWMs when all three methods produced equal values for the respective measure. In bold we indicate a method that gives the highest number of PWMs with maximal AUC_FP0.1 criteria.

A) MACS
Site model method.	Number of PWMs with maximal AUC	Number of PWMs with maximal partial AUC_TP0.8	Number of PWMs with maximal partial AUC_FP0.1
Additive	152	154	40
Multiplicative	61	58	92
MATCH	42	43	113
All three methods give the same AUC value	10	10	20

B) SISSRs
Method name	Number of PWMs with maximal AUC	Number of PWMs with maximal partial AUC_TP0.8	Number of PWMs with maximal partial AUC_FP0.1
Additive	138	134	45
Multiplicative	62	65	85
MATCH	52	53	107
All three methods give the same AUC value	11	11	26