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

Table 3 Differentially methylated loci (p < 5 × 10⁻⁶): females vs. males (BE, HGD/EAC combined)

Probe ID	Gene	Average β females	Average β males (overall change)	p value	Probe location	Relative expression BE vs. normal^	Relative expression EAC vs. normal^	Relation to island
cg17272795	ZNF37A	0.34	0.10 (↓)	1.76E-09	TSS1500	1.06*	−1.05*	Shore
cg07753967	FRG1B	0.44	0.10 (↓)	2.13E-09	TSS1500	NS	NS	Island
cg25791279	PISD	0.26	0.15 (↓)	8.77E-09	TSS200	NS	2.17–3.20*	Shore
cg25489030	FRG1B	0.46	0.30 (↓)	3.63E-08	Body	NS	NS	Island
cg02531214	ZNF37A	0.34	0.13 (↓)	1.76E-07	TSS1500	1.06*	−1.05*	Shore
cg20811988	FRG1B	0.33	0.11 (↓)	7.17E-07	Body	NS	NS	Island
cg03395511	DUSP22	0.11	0.42 (↑)	8.15E-07	TSS200	NS	NS	Shore
cg14815891	FRG1B	0.33	0.08 (↓)	1.03E-06	Body	NS	NS	Island
cg01516881	DUSP22	0.07	0.23 (↑)	1.23E-06	Body	NS	NS	Island
cg21508714	RBM20	0.31	0.12 (↓)	1.42E-06	Body	NS	NS	Island
cg11386792	RBM20	0.44	0.13 (↓)	1.74E-06	Body	NS	NS	Island
cg16004008	NRGN	0.35	0.20 (↓)	1.91E-06	TSS1500	1.45–1.46*	1.57–3.23*	Shore
cg03066577	C3orf55	0.26	0.11 (↓)	2.17E-06	5′UTR; 1st exon; body	NS	4.95*	Island
cg21548813	DUSP22	0.08	0.36 (↑)	2.25E-06	TSS1500	NS	NS	Shore
cg14819088	SLC34A1	0.67	0.78 (↑)	2.52E-06	TSS200	NS	NS	Open sea
cg15383120	DUSP22	0.08	0.38 (↑)	2.52E-06	TSS200	NS	NS	Shore
cg18110333	DUSP22	0.09	0.39 (↑)	3.92E-06	1st exon; 5′UTR	NS	NS	Island
cg16602806	MTRR	0.19	0.09 (↓)	4.59E-06	Body; TSS1500; 5′UTR	1.65*	1.77*	Shore
cg25959506	RASD2	0.27	0.11 (↓)	4.91E-06	TSS1500	NS	NS	Island

5′UTR = 5′ untranslated region; TSS200/TSS1500 = 200 or 1500 bp’s upstream from transcription start site; Shore = DNA sequence up to 2 kb from CpG island; Open sea = DNA sequence >4 kb from CpG island; NS = not significant; ^ = relative gene expression data obtained from www.oncomine.org; *p ≤ 0.05; (↑)/(↓) = increase/decrease in methylation in male vs. females

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