This study | TCGA database, within study region +/- 100 bp | TCGA database, within study region | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Pyroseqa | Illum. 450 k: Mean % methylation | Assn. with expr. | Illum. 450 k: Mean % Methylation | Assn. with expr. | |||||||||||
Gene | # CpG | # CpG | Adjacentb (N = 96) | Cancerc (N = 96) | Diffd | P-valuee | ρf | P-value | # CpG | Adjacentb (N = 96) | Cancerc (N = 96) | Diffd | P-valuee | ρf | P-value |
Promoter region | |||||||||||||||
BRCA1 | 11 | 13 | 4 | 4 | 0 | NS | -0.19 | 0.0000 | 9 | 3 | 4 | 0 | NS | -0.20 | 0.0000 |
CD44 | 8 | 5 | 4 | 9 | 5 | 0.0001 | -0.18 | 0.0000 | 1 | 6 | 10 | 5 | 0.004 | -0.18 | 0.0000 |
ESR1 | 5 | 2 | 67 | 40 | -28 | 0.0000 | -0.52 | 0.0000 | 2 | 67 | 40 | -28 | 0.0000 | -0.52 | 0.0000 |
GSTM2 | 8 | 3 | 4 | 16 | 13 | 0.0000 | -0.13 | 0.0003 | 1 | 2 | 2 | -1 | 0.0000 | -0.13 | 0.0002 |
GSTP1 | 4 | 2 | 7 | 24 | 17 | 0.0000 | -0.43 | 0.0000 | 0 | --- | --- | --- | --- | --- | |
MAGEA1 | 6 | 2 | 97 | 77 | -21 | 0.0000 | -0.23 | 0.0000 | 2 | 97 | 77 | -20 | 0.0000 | -0.23 | 0.0000 |
MSI1 | 5 | 2 | 3 | 6 | 3 | 0.0000 | -0.20 | 0.0000 | 0 | --- | --- | --- | --- | --- | |
NFE2L3 | 14 | 1 | 39 | 48 | 9 | 0.0001 | -0.55 | 0.0000 | 0 | --- | --- | --- | --- | --- | |
RASSF1 | 9 | 2 | 12 | 47 | 35 | 0.0000 | -0.18 | 0.0000 | 1 | 9 | 49 | 41 | 0.0000 | -0.16 | 0.0000 |
RUNX3 | 28 | 1 | 2 | 23 | 21 | 0.0000 | -0.28 | 0.0000 | 0 | --- | --- | --- | --- | --- | |
SIX3 | 12 | 4 | 6 | 24 | 18 | 0.0000 | -0.21 | 0.0000 | 2 | 4 | 26 | 22 | 0.0000 | -0.20 | 0.0000 |
TFF1 | 5 | 4 | 77 | 46 | -31 | 0.0000 | -0.20 | 0.0000 | 1 | 74 | 47 | -27 | 0.0000 | -0.19 | 0.0000 |
Upstream of promoter | |||||||||||||||
EN1 g | 6 | 2 | 23 | 32 | 8 | 0.0000 | 0.12 | 0.001 | 0 | --- | --- | --- | --- | --- | |
PAX3 | 5 | 2 | 6 | 30 | 24 | 0.0000 | -0.12 | 0.004 | 1 | 9 | 29 | 19 | 0.0000 | -0.10 | 0.003 |
PITX2 g | 10 | 2 | 23 | 38 | 15 | 0.0000 | 0.22 | 0.0000 | 0 | --- | --- | --- | --- | --- | |
SGK1 | 6 | 4 | 9 | 21 | 12 | 0.0000 | -0.10 | 0.003 | 2 | 5 | 17 | 12 | 0.0000 | -0.11 | 0.003 |
Introns | |||||||||||||||
APC g | 4 | 11 | 6 | 28 | 22 | 0.0000 | 0.13 | 0.002 | 3 | 5 | 28 | 23 | 0.0000 | 0.12 | 0.004 |
EGFR | 4 | 1 | 9 | 37 | 29 | 0.0000 | -0.15 | 0.0000 | 1 | 9 | 37 | 29 | 0.0000 | -0.15 | 0.0000 |
LHX2 g | 11 | 1 | 17 | 32 | 15 | 0.0000 | 0.24 | 0.0000 | 0 | --- | --- | --- | --- | --- | |
RFX1 | 4 | 0 | --- | --- | --- | --- | --- | 0 | --- | --- | --- | --- | --- | ||
SOX9 | 4 | 1 | 5 | 15 | 11 | 0.0000 | -0.34 | 0.0000 | 0 | --- | --- | --- |