Table 1 Targeted bis-seq data for methylation in 20 candidate genes (29 amplicons) in 24 paired HCC tumor and adjacent non-tumor tissues
From: Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas
Gene symbol | Amplicons name | No. of covered CpG sites | Non-tumor | Tumor | Difference | Adjusted P value * |
|---|---|---|---|---|---|---|
Mean, SD | Mean, SD | |||||
CDKL2 | CDKL2.a | 11 | 6.49 (8.35) | 33.52 (18.80) | 27.03 | 2.50E-04 |
CDKL2 | CDKL2.b | 15 | 7.59 (11.57) | 41.29 (21.98) | 33.70 | 1.94E-04 |
CDKL2 | CDKL2.c | 27 | 13.20 (13.50) | 37.15 (20.68) | 23.95 | 2.83E-02 |
CLCN1 | CLCN1 | 28 | 16.31 (10.83) | 47.84 (21.93) | 31.53 | 3.01E-04 |
DUOX1 | DUOX1 | 36 | 16.93 (16.93) | 36.98 (24.43) | 20.05 | 2.77E-01 |
GRASP | GRASP.a | 24 | 12.66 (8.70) | 42.45 (23.56) | 29.79 | 3.92E-04 |
ILDR2 | ILDR2.a | 23 | 7.66 (4.22) | 43.18 (27.32) | 35.52 | 4.21E-05 |
MAST1 | MAST1.a | 16 | 16.40 (20.56) | 59.15 (33.23) | 42.75 | 4.99E-04 |
MAST1 | MAST1.b | 2 | 10.42 (10.98) | 34.74 (21.02) | 24.32 | 4.33E-03 |
MAST1 | MAST1.c | 19 | 15.25 (8.44) | 38.92 (14.03) | 23.67 | 5.15E-05 |
NKX6-2 | NKX6-2.b | 24 | 26.17 (9.56) | 54.97 (17.70) | 28.80 | 4.25E-05 |
OTX1 | OTX1.a | 8 | 22.53 (9.14) | 52.15 (24.09) | 29.62 | 2.63E-03 |
OTX1 | OTX1.b | 28 | 17.68 (12.10) | 49.60 (17.44) | 31.92 | 1.85E-04 |
SERHL | SERHL.a | 16 | 11.94 (4.38) | 35.71 (13.19) | 23.77 | 3.82E-07 |
SERHL | SERHL.b | 11 | 4.86 (2.26) | 17.15 (12.24) | 12.29 | 1.08E-03 |
SPAG6 | SPAG6.b | 53 | 16.07 (5.05) | 34.12 (15.67) | 18.04 | 1.59E-03 |
SPDYA | SPDYA.b | 11 | 46.93 (17.40) | 73.91 (18.14) | 26.98 | 1.29E-02 |
TRIL | TRIL.a | 16 | 18.13 (6.02) | 53.25 (20.58) | 35.12 | 1.01E-05 |
TRIL | TRIL.b | 22 | 13.88 (8.85) | 36.95 (17.75) | 23.07 | 2.22E-03 |
TRIL | TRIL.c | 17 | 9.73 (6.70) | 41.44 (17.52) | 31.71 | 6.62E-06 |
TRIL | TRIL.e | 44 | 12.10 (10.22) | 38.52 (19.07) | 26.42 | 1.55E-03 |
TSPYL5 | TSPYL5 | 57 | 13.83 (12.12) | 41.21 (18.79) | 27.38 | 8.09E-04 |
USP44 | USP44.c | 9 | 61.31 (10.17) | 73.45 (10.01) | 12.14 | 6.81E-03 |
ZNF397OS | ZNF397OS.a | 32 | 13.76 (11.59) | 38.94 (18.21) | 25.18 | 3.10E-04 |
FAM66B | FAM66B | 13 | 91.18 (3.59) | 71.89 (17.30) | −19.29 | 9.49E-04 |
KCNQ2 | KCNQ2 | 44 | 74.06 (14.65) | 45.21 (22.68) | −28.85 | 3.99E-03 |
PROKR2 | PROKR2 | 14 | 83.57 (14.68) | 65.11 (12.97) | −18.46 | 1.11E-02 |
PTPRN2 | PTPRN2 | 8 | 74.68 (11.71) | 53.60 (17.39) | −21.08 | 6.50E-03 |
REXO1L2P | REXO1L2P | 12 | 84.14 (14.58) | 53.98 (22.99) | −30.16 | 1.75E-03 |