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Table 5 Methylation comparing cancer to paired adjacent samples, and correlation of methylation in invasive breast cancer samples with gene expression

From: Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

  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 --- ---   ---   
  1. aPyrosequencing (Pyroseq) assay coordinates are given in Table 1
  2. bNon-cancer tissue adjacent to paired breast cancer from 96 patients in the TCGA Illumina Methylation450 database for genome-wide DNA methylation [14]
  3. cSamples from the invasive component of the breast cancer from patients in the TCGA Methylation450 and expression (expr.; RNA-seq) databases [16, 17]
  4. dDifference in mean % methylation for cancer minus that for the paired adjacent tissue for the 96 patients with both in the TCGA database
  5. eFrom a dependent sample Wilcoxon Sign Rank test; P-values > 0.10 are suppressed
  6. fSpearman correlation coefficient for methylation levels vs expression levels among all the invasive breast cancer samples in the TCGA database
  7. 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
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