| |
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
|
---
|
---
| |
---
| | |
-
aPyrosequencing (Pyroseq) assay coordinates are given in Table 1
-
bNon-cancer tissue adjacent to paired breast cancer from 96 patients in the TCGA Illumina Methylation450 database for genome-wide DNA methylation [14]
-
cSamples from the invasive component of the breast cancer from patients in the TCGA Methylation450 and expression (expr.; RNA-seq) databases [16, 17]
-
dDifference in mean % methylation for cancer minus that for the paired adjacent tissue for the 96 patients with both in the TCGA database
-
eFrom a dependent sample Wilcoxon Sign Rank test; P-values > 0.10 are suppressed
-
fSpearman correlation coefficient for methylation levels vs expression levels among all the invasive breast cancer samples in the TCGA database
-
gThe four underlined genes were the only ones that had a positive association of cancer methylation in non-promoter regions with expression levels of the associated gene
