Table 4.

Performance of the different methods on the SAP-NEW dataset

Method	Qtot	P[D]	S[D]	P[N]	S[N]	MCC	AUC
PhD-SNP	0.70	0.77	0.75	0.57	0.61	0.35	0.74
S3D-PROF	0.80	0.80	0.84	0.80	0.76	0.60	0.87
SNPs&GO	0.79	0.84	0.83	0.71	0.71	0.54	0.85
SNPs&GO3d	0.83	0.84	0.86	0.84	0.80	0.67	0.91

D=disease related, N=neutral. For index definition see "Measures of performance