Table 4.

Differentially methylated regions in prostate cancer compared to adjacent benign tissue^a

DMR No.	Chromosome	Gene	DMR start (bp)	DMR end (bp)	DMR size (bp)	No. CpGsb	Mean β cancer	Mean β benign	Mean β difference	P-value
1	6	HLA-J	29974174	29975231	1058	35	0.55	0.26	0.28	1.11E-76
2	6	–	30094969	30095358	390	19	0.67	0.45	0.21	2.01E-33
3	6	HLA-H	29855329	29855567	239	9 (2)	0.62	0.35	0.27	2.60E-20
4	6	HLA-G	29796293	29796516	224	11	0.51	0.34	0.17	9.36E-20
5	17	SEPT9	75315256	75315897	642	8 (8)	0.49	0.19	0.29	1.59E-19
6	3	RARB	25469684	25470221	538	9 (9)	0.59	0.30	0.29	3.05E-19
7	6	SLC44A4; NEU1	31831160	31831553	394	9 (8)	0.51	0.23	0.29	1.41E-17
8	6	IER3	30711510	30711712	203	8	0.61	0.32	0.29	1.54E-17
9	17	RARA	38465280	38465740	461	7 (7)	0.57	0.30	0.27	1.51E-16
10	10	PRAP1	135160660	135161434	775	8 (7)	0.56	0.33	0.23	2.13E-16
11	11	SHANK2	70672595	70672885	291	6	0.57	0.34	0.24	6.49E-14
12	6	–	44528201	44529749	1549	6	0.59	0.36	0.23	5.04E-13
13	20	LOC284798	25129479	25129570	92	5 (5)	0.50	0.23	0.27	1.96E-12
14	2	CLIP4	29338072	29338128	57	5 (5)	0.56	0.24	0.32	2.08E-12
15	6	HCG4	29759872	29760100	229	7	0.47	0.29	0.18	3.03E-12
16	2	–	123418130	123419685	1556	5	0.64	0.35	0.29	4.80E-12
17	11	DGKZ	46382644	46383528	885	5 (1)	0.57	0.31	0.26	5.04E-12
18	22	NFAM1	42827738	42828512	775	6 (5)	0.66	0.42	0.24	5.28E-12
19	2	NRXN1	50574924	50575243	320	5	0.44	0.22	0.22	6.93E-09
20	6	HLA-E	30458022	30458224	203	10	0.39	0.26	0.13	1.66E-05

Abbreviations: DMR, differentially methylated region; bp, base pairs

^aAll significant DMRs (Q-value <0.001) were hypermethylated in PCa, and no hypomethylated regions were identified.

^bThe number in parenthesis is the number of promoter region CpGs.