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Table 4 Adjusted differences in mean % methylation comparing adjacent (referent) to cancer tissue, overall and stratified by ER/PR status

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

  All samples   ER/PR Positive   ER/PR Negative  
Na Diff.b 95 % CIc P-Valued Na Diff.b 95 % CIc P-Valued Na Diff.b 95 % CIc P-Valued
Promoter regions             
  BRCA1 198 1.7 (0, 4) NS 136 1 (-1, 4) NS 62 3 (0, 8) 0.09
  CD44e 54 0.5 (0, 1) NS 32 0 (-0.4, 1) NS 22 0 (0,2) NS
  ESR1e 54 -1.5 (-3, 0) 0.099 32 -1 (-4, 1) NS 22 -2 (-4, 1) NS
  GSTM2 212 16.8 (13, 21) < 0.0001 146 10 (6, 16) < 0.0001 66 32 (24, 38) < 0.0001
  GSTP1 227 8.3 (6, 12) < 0.0001 159 9 (6, 14) < 0.0001 68 6 (2, 12) 0.016
  MAGEA1e 54 -14.5 (-22, -9) < 0.0001 32 -22 (-30, -14) < 0.0001 22 -4 (-12, 3) NS
  MSI1e 54 4.7 (2, 8) 0.005 32 4 (1, 10) 0.057 22 5 (1, 9) 0.01
  NFE2L3e 54 5.6 (-4, 16) NS 32 19 (9, 31) 0.001 22 -15 (-26, -4) 0.01
  RASSF1A 234 23.5 (19, 28) < 0.0001 160 26 (21, 31) < 0.0001 74 18 (12, 25) < 0.0001
  RUNX3 227 6.6 (4, 9) < 0.0001 156 9 (6, 11) < 0.0001 71 2 (-1, 7) NS
  SIX3 221 10.9 (9, 14) < 0.0001 151 10 (7, 14) < 0.0001 70 13 (8, 19) < 0.0001
  TFF1 230 -21.6 (-26, -17) < 0.0001 159 -25 (-30, -19) < 0.0001 71 -14 (-23, -5) 0.002
Upstream of promoter             
  EN1 230 13.1 (10, 17) < 0.0001 158 12 (8, 16) < 0.0001 72 16 (9, 24) < 0.0001
  PAX3 230 7.3 (5, 10) < 0.0001 159 6 (4, 9) < 0.0001 71 10 (6, 15) < 0.0001
  PITX2e 54 7.8 (4, 11) < 0.0001 32 7 (3, 10) < 0.0001 22 10 (1, 16) 0.026
  SGK1 233 9.8 (8, 12) < 0.0001 160 9 (7, 12) < 0.0001 73 11 (7, 16) < 0.0001
Introns             
  APC 221 12.3 (9, 16) < 0.0001 153 12 (8, 16) < 0.0001 68 15 (9, 22) < 0.0001
  EGFR 235 12 (9, 15) < 0.0001 161 15 (11, 18) < 0.0001 74 6 (2, 11) 0.009
  LHX2e 54 8.1 (2, 15) 0.017 32 8 (3, 13) 0.006 22 9 (-5, 22) NS
  RFX1 235 19.8 (17, 23) < 0.0001 161 20 (16, 23) < 0.0001 74 21 (16, 26) < 0.0001
  SOX9 231 6.2 (3, 9) < 0.0001 158 6 (3, 10) < 0.0001 73 6 (1, 13) 0.031
DNA Repeats             
  LINE-1 238 -1.5 (-2, -1) < 0.0001 162 -2 (-3, -1) < 0.0001 76 -1 (-3, 0) 0.074
  Sat2 237 -5.4 (-9, -2) 0.001 161 -6 (-10, -2) 0.003 76 -5 (-10, 1) 0.109
  1. aNumber of samples analyzed; the small differences in numbers of samples in this table compared to Table 3 are due to missing data on ER/PR status
  2. bDifference in mean percent methylation (cancer and adjacent) was estimated via linear regression model with generalized estimating equations to account for within-patient covariance
  3. cBias corrected, bootstrapped 95 % confidence intervals (CI) were estimated via 1000 bootstrap replications to account for skewed methylation distributions
  4. dApproximate p-value estimated from a Wald test of the normal-based bootstrapped estimate over its standard error. P-values > 0.1 are suppressed
  5. eThese seven assays were not pursued beyond the pilot phase and therefore have considerably fewer cancer and adjacent tissue samples analyzed
  6. All estimates of mean percent methylation are adjusted for age, race/ethnicity, stage at diagnosis, tumor grade, and either adjusted for or stratified by ER/PR status