Table 3.

Methylation levels and frequencies above cut off values of the extended data sample in normal breast tissue, atypical ductal hyperplasia, ductal carcinoma in situ, and invasive ductal carcinoma in the extended data sample

GenesNBT (n = 32)ADH (n = 26)DCIS (n = 50)IDC (n = 62)P*
Multiple comparisonNBT vs PATHNBAT vs ADHNBT vs DCISNBT vs IDCADH vs DCISADH vs IDCDCIS vs IDCPRE vs IDC
APC0 (0-0)5.09 (0-372.23)4.55 (0-466.0)89.75 (0.09-561.50)0.00001§0.000010.0040.000010.000010.550.090.190.08
3** (9)10** (39)22** (44)34** (55)0.00020.00020.0070.00090.000090.800.20.220.13
CDH10 (0-1.43)0 (0-21.37)0 (0-10.64)4.69 (0-28.44)0.0005§0.00090.20.010.00030.350.030.150.04
4** (12)7** (27)15** (30)26** (42)0.030.010.140.080.0030.80.190.140.06
CTNNB10 (0-0)0 (0-0)0 (0-1.14)0 (0-0.87)0.08§0.050.660.10.020.290.090.450.2
3** (9)4** (15)7** (14)11 (18)0.750.340.720.650.640.290.770.140.55
ESR10 (0-15.48)2.78 (0-11.40)0.68 (0-14.01)1.58 (0-14.21)0.91§0.530.790.660.450.910.700.740.70
8** (25)4** (15)12** (24)15** (25)0.950.810.750.590.790.660.720.720.81
TIMP30 (0-17.69)2.62 (0-41.13)0.23 (0-13.96)1.64 (0-17.48)0.63§0.480.230.860.560.260.460.660.88
8** (25)11** (42)16** (32)20** (33)0.690.390.250.710.520.50.50.820.84
GSTPI0 (0-0)0 (0-0)0 (0-0)0 (0-15.24)0.27§0.180.850.350.070.530.160.330.2
3** (9)3** (11)8** (16)14** (23)0.310.220.680.410.080.730.240.330.23
  • *Upper P values for each gene refer to Kruskal Wallis, Mann Whitney, and Dunn tests as indicated. Lower P values for each gene refer to χ2 square test; all statistics were computed by adopting a permutation approach with 10,000 resamplings (see Materials and Method).

  • Multiple comparison among NBT, ADH, DCIS, and IDC; PATH merges the ADH, DCIS, and IDC groups (n = 138); PRE merges the ADH and DCIS groups (n = 76).

  • Median value (IQR).

  • §Kruskal Wallis.

  • Mann Whitney.

  • Dunn.

  • **No. of samples methylated above cutoff value (% of methylated samples).