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. Author manuscript; available in PMC: 2020 Aug 1.

Published in final edited form as: Arch Toxicol. 2019 Jul 5;93(8):2219–2235. doi: 10.1007/s00204-019-02505-7

Figure 2. — Differential methylation and differential gene expression profiling of spontaneous and GBE-exposed HCC. A. GBE-HCC vs. CNTL: RefSeq Genes with differential expression profile (N=2037) and their corresponding promoter methylation profile. Differential methylation criteria: Absolute foldchange >= 1.2 and p-value <= 0.05. Differential expression criteria Absolute foldchange >= 2.0 and p-value<=0.05. Genes with at least one promoter overlapping NimbleGen® methylation probe and at least one Affymetrix® probe set were considered. The p-value for comparison of two cohorts is derived by performing paired t-test of mean log2 expression values across all genes with gained (lost) methylation.

B. GBE-HCC vs. CNTL: Mean expression of hypo(hyper) methylated genes. Gained(lost)=1 if promoter methylation fold change >= 1.2 and p-value <= 0.05. Genes with at least one promoter overlapping NimbleGen® methylation probe and at least one Affymetrix® probe set were considered. The p-value for comparison of two cohorts is derived by performing paired t-test of mean log2 expression values across all genes with gained (lost) methylation.

C. SPNT-HCC vs. CNTL: RefSeq Genes with differential expression profile (N=1632) and their corresponding promoter methylation profile. Differential expression criteria: Absolute fold change >= 2.0 and p-value <=0.05. Differential methylation criteria: Absolute fold change >= 1.2 and p-value <= 0.05.

D. SPNT-HCC vs. CNTL: Mean expression of hypo(hyper) methylated refseq genes. Gained (Lost)=1 if promoter methylation fold change >= 1.2 and p-value <= 0.05. Genes with at least one promoter overlapping NimbleGen® methylation probe and at least one Affymetrix® probe set were considered. The p-value for comparison of two cohorts is derived by performing paired t-test of mean log2 expression values across all genes with gained (lost) methylation.

Figure 2. — Differential methylation and differential gene expression profiling of spontaneous and GBE-exposed HCC. A. GBE-HCC vs. CNTL: RefSeq Genes with differential expression profile (N=2037) and their corresponding promoter methylation profile. Differential methylation criteria: Absolute foldchange >= 1.2 and p-value <= 0.05. Differential expression criteria Absolute foldchange >= 2.0 and p-value<=0.05. Genes with at least one promoter overlapping NimbleGen® methylation probe and at least one Affymetrix® probe set were considered. The p-value for comparison of two cohorts is derived by performing paired t-test of mean log2 expression values across all genes with gained (lost) methylation.

B. GBE-HCC vs. CNTL: Mean expression of hypo(hyper) methylated genes. Gained(lost)=1 if promoter methylation fold change >= 1.2 and p-value <= 0.05. Genes with at least one promoter overlapping NimbleGen® methylation probe and at least one Affymetrix® probe set were considered. The p-value for comparison of two cohorts is derived by performing paired t-test of mean log2 expression values across all genes with gained (lost) methylation.

C. SPNT-HCC vs. CNTL: RefSeq Genes with differential expression profile (N=1632) and their corresponding promoter methylation profile. Differential expression criteria: Absolute fold change >= 2.0 and p-value <=0.05. Differential methylation criteria: Absolute fold change >= 1.2 and p-value <= 0.05.

D. SPNT-HCC vs. CNTL: Mean expression of hypo(hyper) methylated refseq genes. Gained (Lost)=1 if promoter methylation fold change >= 1.2 and p-value <= 0.05. Genes with at least one promoter overlapping NimbleGen® methylation probe and at least one Affymetrix® probe set were considered. The p-value for comparison of two cohorts is derived by performing paired t-test of mean log2 expression values across all genes with gained (lost) methylation.