Table 1.

Differentially Methylated Regions (DMRs) and Differentially Expressed Genes (DEGs) Promoter Regions Overlap Summary. This displays odds ratio and corresponding p-value to assess co-occurrence of differential methylation and differential gene expression. The observed overlap between promoter regions (+/− 2kb around transcriptional start site, TSS) of differentially expressed refseq genes and differentially methylated sites was computed and compared with expected overlap using 10000 chromosome bound circular shift permutations.

Comparison				GBE-HCC vs. CNTL		SPNT-HCC vs. CNTL
Type				Repressed	Upregulated	Repressed	Upregulated
Comparison	Methylation	Number of Probes	Stat	6375	13692	9817	13782
GBE-HCC vs. CNTL	Lost	7264	Odds Ratio	0.248	1.177	0.530	0.951
			P-value	0.0105	0.4686	0.0679	0.8550
	Gained	10807	Odds Ratio	3.146	0.518	3.354	0.914
			P-value	<0.0001	0.0057	<0.0001	0.6466
SPNT-HCC vs. CNTL	Lost	4796	Odds Ratio	0.387	1.315	0.411	1.643
			P-value	0.1043	0.3206	.0635	0.0465
	Gained	6509	Odds Ratio	1.563	0.669	3.544	0.623
			P-value	0.1565	0.1513	<0.0001	0.1085

Number of features = 713332

Number of circular shift permutations used = 10000

DMRs were identified using W=500, P=0.05 and nProbes>=4 criteria and false discovery rate of 0.001

DEGs were identified using post-ANOVA adhoc tests using Foldchange>=2 and p-value<=0.005 criteria

Promoter region was defined as 2kb upstream and 2kb downstream of txStart