Table 3.

Validated Differentially Methylated and Expressed Genes in FFPE

Gene	CHR	CpG	Methylation	Δβ	P value	Gene location	CpG location
HLA-F	6	cg22298860	Hyper	0.145	2.0 × 10−7	TSS1500	Shore
		cg26751972	Hyper	0.143	4.6 × 10−6	Body	Island
		cg11768167	Hyper	0.101	1.1 × 10−5	TSS1500	Shore
		cg11587584	Hyper	0.101	1.6 × 10−4	Body	Shore
KLF11	2	cg05647197	Hypo	−0.156	2.0 × 10−5	TSS1500	Shore
		cg18424122	Hypo	−0.148	9.2 × 10−5	TSS1500	Shore
		cg01354088	Hypo	−0.123	2.5 × 10−4	TSS1500	Island
		cg12005760	Hypo	−0.113	1.1 × 10−4	TSS1500	Island
		cg15123428	Hypo	−0.110	3.2 × 10−4	Body	Shore
		cg11249298	Hypo	−0.107	1.8 × 10−8	Body	Shore

CHR, chromosome; FFPE, formalin fixed, paraffin embedded; Hyper, hypermethylation; Hypo, hypomethylation; TSS, transcription start site.