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. 2021 Oct 3;43(3):1419–1435. doi: 10.3390/cimb43030100

Table 2.

Comparison of the MSRE-based approach and the qMSP approach. 6 targets from the targeted DNA methylation array have been selected for validation by qMSP. TMEFF2, PITX2, TWIST1 showed high differential methylation (p < 1 × 10−7); TFPI2 and DCC showed intermediate methylation difference and PTGS showed no differential methylation. qMSP confirms the findings for 5 of the 6 targets. The intermediate differential methylation for DCC from MSRE based approach was not confirmed by qMSP.

Gene Symbol p-Value
(Fresh Frozen Tissue)
Fold-Change
(Fresh Frozen Tissue)
p-Value (FFPE) Fold-Change (FFPE)
TMEFF2 <1 × 10−7 16.95 <1 × 10−7 68.39
PITX2 <1 x10−7 17.86 <1 × 10−7 15.14
TWIST1 <1 x10−7 24.39 <1 × 10−7 43.28
TFPI2 2.3 x10−6 66.67 0.0127 1.82
DCC 0.0140 20.00 0.2366 1.47
PTGS2 0.2905 2.33 0.8630 1.09