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Table 2 Frequency and median PMR values of AD, Adj NTL and NTL tissues for 28 loci

From: Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma

HUGOa Frequencyb Medianf p-valueg   
  ADc
n = 51
Adj NTLd
n = 38
NTLe
n = 11
AD
n = 51
Adj NTL
n = 38
NTL
n = 11
AD vs All NTL AD vs AdjNTL AD vs matched NTL BH-MC Thresholdh Importance Measurei
OPCML 98 79 36 107.15 8.93 10.02 9E-15 8E-13 2E-10 0.0025 7.38
CDX2 100j 66 9 43.97 3.40 0.12 4E-13 2E-10 8E-10 0.0050 3.49
HOXA1 94 71 36 160.00 4.90 0.12 2E-12 2E-10 2E-10 N/A 8.52
CDKN2A EX2 100 100 82 191.07 46.17 27.39 6E-12 4E-10 1E-10 N/A 5.80
SFRP1 94k 87 36 132.93 10.01 4.78 1E-10 2E-08 1E-09 0.0075 2.62
CDH13 78 45 0 39.65 4.95 78.05 4E-08 9E-07 2E-08 N/A 2.14
TWIST1 82 66 9 392.16 6.87 8.03 1E-07 8E-06 1E-07 0.0100 2.77
LZTS1 100 100 100 107.75 170.95 210.95 5E-06 0.0003 0.0262 0.0125 1.52
RASSF1 69k 58 9 92.53 0.86 5.45 6E-05 0.0010 1E-07 N/A 1.83
SFRP4 67k 42 9 3.25 1.03 8.71 0.0005 0.0052 0.0086 0.0150 0.39
SFRP5 90k 92 45 14.38 5.78 4.59 0.0005 0.0095 0.0010 0.0175 0.72
ESR1 49k 32 9 5.72 1.29 0.63 0.0049 0.0283 0.0007 N/A 0.33
CDH1 94 89 55 17.62 12.74 10.22 0.0092 0.0686 0.0151 N/A 0.51
SLC6A20 25 11 9 7.81 0.38 154.45 0.0426 0.0569 0.0244 0.0200 0.10
PGR 14 5 0 59.92 6.95 N/A 0.0850 0.1753 0.4375 0.0225 0.08
MT1A 100 100 100 104.45 108.58 112.44 0.2276 0.4283 0.7422 0.0250 0.84
MT2A 88 76 55 12.31 12.22 15.48 0.2650 0.4568 0.4622 0.0275 0.37
ATM 75 68 27 0.16 0.19 0.03 0.2954 0.9498 0.5131 0.0300 0.07
PTEN 29 26 0 1.21 0.85 N/A 0.3319 0.7976 0.8077 0.0325 0.07
SYK 29 24 18 0.42 0.15 3.34 0.4314 0.5002 0.8904 0.0350 0.07
CDKN2B 98 97 91 8.29 10.05 8.48 0.4400 0.2422 0.5335 0.0375 0.44
CYP1B1 29 26 18 1.80 1.26 0.13 0.4481 0.6565 0.1454 0.0400 0.11
CHFR 8 5 0 0.49 1.65 N/A 0.4560 0.6677 1.0000 0.0425 0.04
APC 80 97 82 15.10 4.60 10.81 0.5999 0.5923 0.0394 N/A 1.89
SOCS4 12j 13 18 0.25 1.70 85.45 0.6040 0.7637 0.3125 0.0450 0.13
MGMT 16 18 0 224.53 9.22 N/A 0.7141 0.8988 0.2031 N/A 0.07
HMGA1 20j 18 27 0.19 0.02 0.12 0.9642 0.7645 0.6221 0.0475 0.00001
VHL 0 0 0 N/A N/A N/A 1.0000 1.0000 1.0000 0.0500 0
  1. a HUGO, Human Genome Organization nomenclature sorted by AD vs All NTL p-value with the most significant at the top.
  2. bPercentage of samples with positive methylation value.
  3. cAD, Adenocarcinoma
  4. dAdj NTL, Adjacent non-tumor lung from adenocarcinoma patients
  5. eNTL, Non-tumor lung from non-cancer patients
  6. fMedian percent methylated reference calculated from positive methylation values
  7. gStatistically significant numbers are highlighted in bold; AD vs. all NTL and AD vs. AdjNTL: Wilcoxon rank sum test; AD vs. matched NTL: Wilcoxon signed rank test
  8. hBH-MC threshold, Benjamini- Hochberg multiple comparison threshold p-value
  9. iImportance Measure based on random forest analysis
  10. jn = 50
  11. kn = 49