Table 3. Eighteen top-ranked CpG sites for classifying prostate tumors with any PTEN loss versus intact PTEN.

CpG ID	Chr.	Gene name	Genetic location	Epigenetic location	Mean β PTEN intact	Mean β PTEN deleted	Mean β difference	Elastic Net coefficient
cg05877648	6			Island	0.09	0.12	0.03	2.30
cg12150066	1	GNB1	TSS1500	S_Shore	0.09	0.14	0.05	1.16
cg17422460	6	BAT4;CSNK2B	Body;TSS1500	N_Shore	0.23	0.32	0.08	0.90
cg04121624	10	RHOBTB1	Body;TSS200	N_Shore	0.27	0.36	0.08	0.32
cg12444684	1	JAK1	5’UTR	N_Shore	0.17	0.27	0.10	0.13
cg27106909	16	YPEL3	1stExon;5’UTR	N_Shore	0.18	0.27	0.09	0.06
cg16166160	6			Island	0.18	0.26	0.08	0.05
cg03640071	11	JAM3	3’UTR		0.69	0.76	0.07	0.01
cg12930882	5	GDNF	Body		0.69	0.62	0.08	-0.10
cg20554353	7			S_Shore	0.79	0.72	0.07	-0.14
cg02072532	14				0.87	0.79	0.07	-0.31
cg13657981	7	CALD1	Body		0.79	0.73	0.06	-0.31
cg16937410	3				0.60	0.51	0.09	-0.73
cg20670923	18	VAPA	Body	S_Shore	0.41	0.34	0.07	-0.85
cg10162251	2	RNF144A	5’UTR		0.89	0.84	0.04	-0.90
cg04838191	2				0.87	0.81	0.06	-0.90
cg20708856	13	ATP11A	Body	S_Shore	0.84	0.77	0.07	-0.92
cg24742298	17	SEZ6	Body	N_Shelf	0.80	0.72	0.08	-1.47