Fig. 2

Number of genes differentially methylated and expressed in the GGH-modulated HCT116 and MDA-MB-435 cells. Sixty-one hyper- and 54 hypomethylated genes were common between the HCT116 and MDA-MB-435 cell lines in response to GGH overexpression, whereas 117 hyper- and 129 hypomethylated genes were common between these cell lines in response to GGH inhibition (a). DNA hyper- or hypomethylation was calculated by subtracting the β-value of corresponding control from the β-value of Sense or siRNA. We determined the β-value difference of 0.2 as having 99 % confidence based on intra- and inter-assay variations (a). Nine down- and 10 upregulated genes were common between two cell lines after GGH overexpression, whereas 11 down- and 12 upregulated genes were common in these cell lines in response to GGH inhibition (b). We determined the number of genes with a fold change >1.3 or <−1.3 using an unpaired t-test with the FDR corrected P-value ≤0.05 (b)