Table 3 Validation of genes with differential DNA methylation as predictors of hormone status from the Illumina BCCC (training dataset) using TCGA (validation dataset)
From: DNA methylation and hormone receptor status in breast cancer
Training dataset | Validation dataset | Correlation with expression | ||||
|---|---|---|---|---|---|---|
Gene | Associationa | SAM d scoreb | Associationa | SAM d scorec | ρ d | P valued |
FZD9 | Positive | 3.94 | Positive | 8.65 | −0.44 | 1.4E−15 |
MME | Positive | 2.95 | Positive | 2.14 | −0.13 | 2.1E−02 |
RAB32 | Positive | 2.70 | Positivee | 1.11 | −0.27 | 1.4E−06 |
BCAP31 | Positive | 2.66 | Positive | 5.61 | −0.28 | 4.9E−07 |
HDAC9 | Positive | 2.64 | Positive | 7.60 | −0.15 | 8.5E−03 |
PAX6 | Positive | 2.64 | Positive | 4.56 | −0.27 | 2.0E−06 |
SCGB3A1 | Positive | 2.53 | Positive | 9.51 | −0.29 | 3.8E−07 |
PDGFRA | Positive | 2.52 | Positive | 2.09 | −0.30 | 1.1E−07 |
IGFBP3 | Positive | 2.51 | Positive | 6.37 | −0.22 | 1.1E−04 |
PTGS2 | Positive | 2.50 | Positive | 5.69 | −0.30 | 5.2E−08 |
SRC | Positive | 2.50 | Not-associated | 0.00 | NA | NA |
CHI3L2 | Positive | 2.45 | Positive | 2.65 | −0.69 | 2.2E−44 |
PGR | Positive | 2.44 | Positive | 5.39 | 0.34 | 1.3E−09 |
TMPRSS4 | Positive | 2.43 | NA | NA | NA | NA |
RASSF1 | Positive | 2.43 | Positive | 7.78 | −0.05 | 4.2E−01 |
TBX1 | Positive | 2.43 | Positive | 4.62 | −0.05 | 4.2E−01 |
PARP1 | Positive | 2.38 | Positive | 2.48 | −0.12 | 2.0E−02 |
COL1A1 | Positive | 2.32 | Positive | 4.15 | 0.08 | 1.7E−01 |
SOX17 | Positive | 2.32 | Positive | 2.22 | −0.13 | 5.7E−05 |
RUNX3 | Positive | 2.29 | Positive | 7.06 | −0.13 | 2.0E−02 |
TES | Positive | 2.23 | Positive | 2.15 | −0.45 | 2.6E−16 |
GPATC3 | Positive | 2.21 | Positivee | 0.17 | NA | NA |
S100A2 | Positive | 2.21 | Positive | 9.32 | −0.52 | 2.6E−22 |
MYH11 | Positive | 2.20 | Positive | 3.61 | −0.10 | 8.0E−02 |
BMP2 | Positive | 2.19 | Positive | 4.66 | −0.37 | 1.3E−11 |