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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
  1. NA gene was absent in the dataset
  2. aIndicates whether gene hypermethylation was associated with increased likelihood of ER/PR-positive breast cancer versus ER/PR-negative breast cancer (“Positive”)
  3. b d scores from SAM analysis using Δ of 0.7 on the GoldenGate dataset
  4. c d scores from SAM analysis using Δ of 3 on the TCGA dataset. In cases where several probes per gene were present, the data is shown for the probe with the highest SAM d score
  5. dPearson correlation coefficient between methylation and expression from TCGA and the corresponding P value
  6. eNon-significant association