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Table 4 Differentially methylated loci (p < 1 × 10−4): ever smokers vs. never smokers (BE, LGD, HGD/EAC combined)

From: Global DNA methylation patterns in Barrett’s esophagus, dysplastic Barrett’s, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use

Probe ID Gene Average β ever smoker Average β never smoker (overall change) p value Probe location Relation to island Relative expression BE vs. normal^ Relative expression EAC vs. normal^ Cancer associated?
cg05951860 CTTNBP2 0.49 0.15 (↓) 5.80E-07 Body Island NS NS Y
cg15310873 C20orf85 0.74 0.60 (↓) 5.06E-06 Body Island NS 3.34* N
cg23039279 PROK2 0.48 0.21 (↓) 1.92E-05 5′UTR; 1st exon Island NS 1.90* Y
cg16024318 SLC6A7 0.39 0.20 (↓) 2.68E-05 5′UTR; 1st exon Island 1.31* 1.17* Y
cg20285514 GNG4 0.52 0.19 (↓) 2.82E-05 TSS200; 5′UTR Island NS NS Y
cg07657743 WNT7A 0.56 0.22 (↓) 3.93E-05 Body Island NS NS N
cg19169023 TYRO3 0.74 0.57 (↓) 4.24E-05 Body Shore NS NS N
cg25757598 RALYL 0.51 0.25 (↓) 4.59E-05 5′UTR; 1st exon Island 1.16* 2.30* N
cg14196840 CTTNBP2 0.37 0.11 (↓) 5.08E-05 Body Island NS NS Y
cg04842146 RALYL 0.46 0.15 (↓) 5.55E-05 TSS1500 Shore 1.16* 2.30* Y
cg20620272 C3orf50 0.42 0.16 (↓) 5.77E-05 Body Island NS NS N
cg09374774 FAM78A 0.19 0.43 (↑) 5.80E-05 TSS200 Island NS 1.04* N
cg18016194 RALYL 0.50 0.29 (↓) 7.17E-05 5′UTR; 1st exon Island 1.16* 2.30* N
cg27603796 CTTNBP2 0.47 0.21 (↓) 7.21E-05 Body Shore NS NS Y
cg00818822 RFX2 0.90 0.80 (↓) 8.05E-05 Body Island 1.24* 6.23* N
cg10879116 LPAR3 0.51 0.26 (↓) 8.54E-05 5′UTR Island NS NS Y
cg11981631 ABCC8 0.59 0.30 (↓) 9.36E-05 Body Island 1.38* 1.11–1.70* Y
cg06600429 GABRB2 0.32 0.55 (↑) 9.75E-05 TSS1500 Shore NS NS Y
  1. 5′UTR = 5′ untranslated region; TSS200/TSS1500 = 200/1500 bp’s upstream from transcription start site; Shore = DNA sequence up to 2 kb from CpG island; NS = not significant; ^ = relative gene expression data obtained from www.oncomine.org; *p ≤ 0.05; (↑)/(↓) = increase/decrease in methylation never smokers vs. smokers