Table 2.

Significance of differentially methylated genes in prostate cancer tissues, analyzed using Infinium Methylation27 BeadChips

GeneSensitivity (95% CI)(95% CI)AUCt Test (P)Transcription start siteStrandCpG island location
A, Genes that are significantly methylated in prostate cancer tissues (n = 158) compared with normal prostate (n = 34)a
 A0X196.2 (91.9–98.5)100 (89.7–100)0.992<0.000141+2: 201,158,654–201,159,798
 CYBA95.5 (91.1–98.2)97.1 (84.7–99.9)0.988<0.00018316: 87,244,422–87,245,165
 EDG393.0 (87.9–96.4)97.1 (84.7 to 99.9)0.97<0.0001363+9: 90,794,956–90,796,827
 ELF488.6 (82.6–93.1)100 (89.7–100)0.994<0.0001600X: 129,071,186–129,073,330
 EPB41L393.7 (88.7–96.9)100 (89.7–100)0.978<0.000118518: 5,532,741–5,534,303
 FLJ1205694.3 (89.5–97.4)100 (89.7–100)0.978<0.0001316+2: 71,058,922–71,060,108
 FLJ9065096.2 (91.9–98.6)100 (89.7–100)0.994<0.0001449+5: 115,324,903–115,327,577
 FLT499.4 (96.5–99.9)100 (89.7–100)0.999<0.00016915: 180,008,152–180,010,059
 GAS696.2 (91.9–98.6)100 (89.7–100)0.99<0.0001964+13: 113,546,578–113,548,278
 GRASP96.2 (91.9–98.6)100 (89.7–100)0.993<0.0001159+12: 50,686,496–50,688,060
 GSTP191.8 (86.3–95.6)100 (89.7–100)0.995<0.0001755+11: 67,106,980–67,108,634
 HAAO93.0 (87.9–96.5)100 (89.7–100)0.979<0.00014542: 42,873,041–42,874,496
 HIF3A95.6 (91.1–98.2)100 (89.7–100)0.989<0.0001153+19: 51,491,754–51,492,473
 HOXC1189.2 (83.3–93.6)97.1 (84.7–99.9)0.985<0.000120+12: 52,652,893–52,656,105
 LEP98.1 (94.6–99.6)97.1 (84.7–99.9)0.997<0.000151+7: 127,667,928–127,668,724
 MGC3960695.6 (91.1–98.2)100 (89.7–100)0.992<0.0001634+X: 134,383,127–134,384,321
 MOBKL2B92.4 (87.1–96.0)100 (89.7–100)0.97<0.00018519: 27,517,915–27,520,017
 RAB3491.8 (86.3–95.6)94.1 (80.3–99.3)0.976<0.000115717: 24,068,248–24,069,280
 RARβ93.0 (87.9–96.5)100 (89.7–100)0.986<0.0001352+3: 25,444,208–25,445,101
 RHCG95.6 (91.1–98.2)100 (89.7–100)0.993<0.000111015: 87,840,274–87,841,084
 RND293.0 (87.9–96.5)100 (89.7–100)0.996<0.0001180+17: 38,429,704–38,431,262
 SLC34A291.1 (85.6–95.1)94.1 (80.3–99.3)0.966<0.000144+4: 25,266,077–25,266,795
 SPATA695.6 (91.1–98.2)100 (89.7–100)0.991<0.00015951: 48,709,694–48,710,842
 TPM494.9 (90.3–97.8)100 (89.7–100)0.977<0.0001306+19: 16,047,744–16,049,758
 ZNF15497.5 (93.6–99.3)94.1 (80.3–99.3)0.99<0.000110019: 62,911,404–62,912,681
B, Hypermethylated genes in tissues of patients with recurrent prostate cancer (n = 98) compared with nonrecurrent cancer (n = 60)b
 ACTL6B65.3 (55.1–74.6)66.7 (53.3–78.3)0.702<0.00011367: 100,091,590–100,092,362
 AEBP163.3 (52.9–72.8)60.0 (46.5–72.4)0.646<0.002138+7: 44,110,152–44,111,361
 AMID77.5 (68.0–85.4)76.7 (64.0–86.6)0.843<0.00012510: 71,562,005–71,562,897
 CD8A75.5 (65.8–83.6)71.7 (58.6–82.5)0.829<0.00011142: 86,869,360–86,871,837
 CRIP161.2 (50.8–70.9)60.0 (46.5–72.4)0.638<0.003793+14: 105,023,580–105,025,363
 FLJ3093480.6 (71.4–87.9)78.3 (65.8–87.9)0.862<0.000182+11: 65,357,151–65,358,255
 FLNC79.6 (70.3–87.1)81.7 (69.6–90.5)0.864<0.0001131+7: 128,257,322–128,258,463
 FMOD76.5 (66.9–84.5)68.3 (55.0–79.7)0.748<0.0001971: 201,586,895–201,587,112
 FOXE365.3 (55.0–74.6)63.3 (49.9–75.4)0.697<0.0001570+1: 47,654,351–47,655,785
 GAS766.3 (56.1–75.6)66.7 (53.3–78.3)0.744<0.000139517: 10,041,659–10,043,517
 GDPD570.4 (60.3–79.2)65.4 (51.6–76.8)0.713<0.000140811: 74,913,525–74,915,608
 HS3ST265.3 (55.0–74.6)75.0 (62.1–85.3)0.798<0.0001257+16: 22,732,005–22,734,135
 LOC34913667.3 (57.1–76.5)65.0 (51.6–76.9)0.742<0.00014797: 150,736,827–150,739,238
 NEUROG166.3 (56.1–75.6)70.0 (56.8–81.2)0.731<0.0001195: 134,898,284–134,900,130
 PLTP68.4 (58.2–77.4)75.1 (62.1–85.3)0.709<0.000116520: 43,972,342–43,974,350
 PTGER266.3 (56.1–75.6)66.7 (53.3–78.3)0.739<0.0001199+14: 51,850,265–51,852,038
 RASGRF269.4 (59.3–78.3)71.7 (58.6–82.5)0.763<0.0001106+5: 80,291,476–80,292,927
 RUNX367.4 (57.1–76.5)71.7 (58.6–82.6)0.746<0.00015281: 25,127,692–25,131,906
 SIX665.3 (55.0–74.6)68.3 (55.0–79.7)0.745<0.0001185+14: 60,045,112–60,046,647
 SLC9A369.4 (59.3–78.3)70.0 (56.8–81.2)0.713<0.00011785: 576,269–577,990
 SPSB462.2 (51.9–71.8)61.7 (48.2–73.9)0.658<0.000891+3: 142,252,136–142,254,676
 SRD5A270.4 (60.3–79.2)71.7 (58.6–82.5)0.748<0.00011252: 31,658,633–31,660,643
 SUSD364.3 (54.0–73.7)63.3 (49.9–75.4)0.652<0.0014560+9: 94,860,370–94,861,840
 SYT1066.3 (56.1–75.6)65.4 (51.6–76.8)0.714<0.000125412: 33,482,438–33,484,467
 TMEM7466.3 (56.1–75.6)68.3 (55.0–79.7)0.664<0.0005148: 109,868,266–109,869,213
C, Significance of genes methylated in prostate cancer tissues of patients with clinical recurrence (n = 59) compared with patients with only biochemical recurrence (n = 39)c
 CHST769.5 (56.1–80.8)64.1 (47.2–78.8)0.668<0.0050255+X: 46,317,905–46,319,911
 LMX1B71.2 (57.9–82.2)64.1 (47.2–78.8)0.684<0.0021106+9: 128,412,539–128,418,074
 PHLDA 361.0 (47.4–73.4)59.0 (42.1–74.4)0.606<0.07723481: 199,704,096–199,705,294
 RAFTLIN62.7 (49.1–75.0)64.1 (47.2–78.8)0.668<0.0050893: 16,529,156–16,530,542
 RASGRF266.1 (52.6–77.9)69.2 (52.4–82.9)0.690<0.0015106+5: 80,291,476–80,292,927
 TNFRSF10D62.7 (49.2–74.9)66.6 (49.7–80.9)0.700<0.0008258: 23,076,422–23,077,641
 ZNF13559.3 (45.7–71.9)61.5 (44.6–76.6)0.664<0.0061144+19: 63,262,091–63,264,376
D, Genes that are methylated in tissues of patients with systemic recurrence (n = 23) compared with local recurrence (n = 36)d
 ALPL65.2 (42.7–83.6)63.8 (46.2–79.1)0.683<0.0182269+1: 21,707,968–21,709,033
 AMPH65.2 (42.7–83.6)75.0 (57.8–87.8)0.77<0.0005357: 38,636,784–38,637,861
 BCDIN378.2 (56.3–92.5)83.3 (67.1–93.6)0.861<0.0001873+7: 99,863,663–99,866,414
 BCL11B82.6 (61.2–95.0)80.5 (63.9–91.8)0.797<0.000127414: 98,806,507–98,807,587
 BRD473.9 (51.6–89.7)69.4 (51.8–83.6)0.724<0.003866519: 15,252,811–15,253,031
 C18orf3478.2 (56.3–92.5)77.7 (60.8–89.8)0.806<0.000117418: 29,274,320–29,275,128
 DCAMKL182.6 (61.2–95.5)91.6 (77.5–98.2)0.874<0.000173413: 35,602,437–35,603,802
 FGF591.3 (71.9–98.9)83.3 (67.1–93.6)0.911<0.0001544+4: 81,405,716–81,407,598
 FLJ4248682.6 (61.2–95.0)77.7 (60.8–89.8)0.834<0.00019914: 104,141,516–104,142,673
 JAM286.9 (66.4–97.2)86.1 (70.5–95.3)0.936<0.0001587+21: 25,933,195–25,934,679
 LHX982.6 (61.2–95.0)69.4 (51.8–83.6)0.822<0.0001106+1: 196,146,152–196,148,467
 LOC28353778.2 (56.3–92.5)75.0 (57.8–87.8)0.811<0.000136313: 28,190,499–28,191,650
 LRAT65.2 (42.7–83.6)72.2 (54.8–85.8)0.727<0.0034462+4: 155,882,485–155,885,476
 PDE4B91.3 (71.9–98.9)77.7 (60.8–89.8)0.856<0.0001423+1: 66,030,397–66,031,906
 POU3F391.3 (71.9–98.9)75.2 (57.8–87.8)0.865<0.0001248+2: 104,835,039–104,840,521
 PTGS260.8 (38.5–80.2)80.5 (63.9–91.8)0.688<0.0153371: 184,915,751–184,916,808
 RASGRF273.9 (51.6–89.7)75.4 (57.8–87.8)0.788<0.0002106+5: 80,291,476–80,292,927
 SLC27A678.2 (56.3–92.5)69.4 (51.8–83.6)0.742<0.001722+5: 128,328,505–128,329,501
 SLC03A173.9 (51.6–89.7)83.3 (67.1–93.3)0.797<0.0001333+15: 90,196,981–90,198,831
 SPSB482.6 (61.2–95.0)80.6 (63.9–91.8)0.824<0.000191+3: 142,252,136–142,254,676
 STAT369.5 (47.0–86.7)69.4 (51.8–83.6)0.744<0.001775717: 37,794,547–37,794,828
 SYN273.9 (51.6–89.7)80.5 (63.9–91.8)0.809<0.0001406+3: 12,020,118–12,021,768
 TACR369.5 (47.0–86.7)72.2 (54.8–85.8)0.704<0.00863464: 104,860,449–104,860,859
 TIRAP73.9 (51.6–89.7)69.4 (51.9–83.6)0.779<0.0003645+11: 125,657,511–125,658,777
 WNT1165.22 (42.7–83.6)63.9 (46.2–79.2)0.753<0.001122111: 75,594,610–75,600,053

NOTE: Performance of the genes was analyzed by AUC of the genes for the 2 contrast groups. Sensitivity and specificity are reported for the threshold that minimized sensitivity–specificity. The P value indicates the statistical significance. Location of the CpG site used for analysis is given with respect to the distance from the transcription start site. The CpG island location on the respective chromosome is shown.

Abbreviation: CI, confidence interval.

  • at test P value is obtained by comparing tumor (n = 158) and benign tissues (n = 34).

  • bt test P value is obtained by comparing prostate cancer tissues of patients with recurrence (n = 98) and without recurrence (n = 60).

  • ct test P value is obtained by comparing prostate cancer tissues of patients with clinical recurrence (n = 59) and biochemical recurrence (n = 39).

  • dt test P value is obtained by comparing prostate cancer tissues of patients with systemic recurrence (n = 23) and local recurrence (n = 36).