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Table 1 Statistical analysis of differences in methylation levels between tumor and adjacent non-tumor tissues

From: Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer

  Tumor   Adjacent Non-Tumor    
Gene Name a Methylation
Frequency b
Median
PMR c
Methylation
Frequency b
Median
PMR c
p-value d MC
Corr. e
GDNF 95% 67.11 95% 3.29 5.0E-11 0.0017
MTHFR f 100% 56.51 100% 25.95 2.0E-10 *
OPCML g 95% 19.49 98% 5.80 1.0E-09 *
TNFRSF25 98% 50.52 93% 25.89 2.0E-07 *
TCF21 93% 60.64 88% 11.17 3.0E-07 *
PAX8 f 100% 83.90 100% 69.49 9.0E-06 0.0034
PTPRN2 80% 35.60 58% 4.02 1.0E-05 0.0052
PITX2 93% 19.37 95% 1.50 3.0E-05 0.0069
MT1G 95% 1.89 93% 0.59 0.0001 0.0086
PENK 93% 14.30 95% 6.82 0.0002 0.0103
GP1BB 98% 59.52 100% 42.68 0.0009 *
MGMT f 100% 26.73 98% 33.96 0.0009 *
SLC38A4 f 56% 6.00 31% 0.00 0.0010 0.0121
SFRP2 98% 10.19 91% 2.67 0.0038 *
RARRES1 60% 9.27 47% 0.71 0.0048 0.0138
DIRAS3 100% 57.25 100% 63.92 0.0074 *
NEUROG1 37% 3.03 17% 0.08 0.0079 0.0155
WDR33 31% 0.34 9% 0.20 0.0089 0.0172
TFAP2A 46% 5.68 20% 10.00 0.0092 0.0190
SFRP1 91% 1.63 98% 0.56 0.0124 *
CYP1B1 58% 3.53 40% 0.41 0.0143 *
HOXC9 66% 10.62 60% 0.48 0.0157 0.0207
ABCB1 100% 27.07 100% 24.33 0.0193 0.0224
HRAS f 100% 82.08 100% 90.01 0.0215 0.0241
GRIN2B 44% 28.03 31% 1.26 0.0235 0.0259
CACNA1G 93% 0.74 95% 0.44 0.0282 0.0276
HIC1 98% 33.81 100% 23.52 0.0315 0.0293
CPVL 66% 1.65 53% 0.33 0.0739 0.0310
SEZ6L 89% 5.08 95% 3.51 0.0745 0.0328
NEUROD1 44% 9.97 33% 0.70 0.0748 0.0345
CCND2 98% 1.74 96% 1.18 0.0827 0.0362
MINT1 98% 3.18 98% 2.49 0.0879 0.0379
DLEC 55% 19.39 64% 0.17 0.1169 *
RNR1 100% 43.28 100% 31.91 0.1930 0.0397
BLT1 98% 28.01 100% 25.63 0.2420 0.0414
ONECUT2 98% 17.23 100% 14.29 0.3369 *
PLAGL1 100% 45.72 100% 50.38 0.3747 0.0431
GATM 26% 11.95 69% 0.10 0.4462 0.0448
CDX1 98% 46.96 100% 44.40 0.7469 0.0466
TWIST1 66% 1.98 86% 1.07 0.7578 0.0483
TMEFF2 100% 11.54 100% 11.82 0.7591 *
RPA3 49% 0.24 49% 0.16 0.8863 0.0500
  1. a Human Genome Organization nomenclature. Loci showing a statistically significant difference in methylation between tumor and non-tumor tissue are highlighted in italics. The top eight loci are noted in bold. Loci are ranked in order of ascending p-value. b Percentage of samples with positive methylation value. c Median percent methylated reference calculated from positive methylation values. d p-value calculated by Wilcoxon signed rank test. e To minimize the risk of false discovery, a false-discovery rate threshold using the Benjamini and Hochberg (1995) approach was applied to all loci not previously found to be methylated in squamous cell lung cancer (see methods). f This reaction is not targeted to a CpG Island g This primer/probe set shares homology with the CpG island of the adjacent HNT gene, which appears to have arisen via gene duplication. * Denotes loci previously reported to be methylated in lung cancer tumor samples