Table 3.

Methylation data of the studied markers on the panel of breast cancer cell lines. Cell lines were ranked in the epithelial–mesenchymal spectrum from the epithelial luminal (top), intermediate (middle), to mesenchymal basal (bottom) groups according to Tan et al. [11] unless indicated otherwise. The levels of homogeneous methylation were stated numerically as percentages of methylation. The estimated levels of heterogeneous methylation were described as ‘very high’, ‘high’, ‘moderate’, ‘low’, and ‘very low’. Zero means no methylation. ‘n.a.’ means no amplification. The methylation result is colour-coded to aid visualisation: red for 100% or very high methylation; orange for 50%, 50–100%, or high methylation; yellow for 10%, 10–50%, or moderate methylation; light yellow for 3%, 3–10%, or low methylation; no highlighting for 0%, very low methylation, or no amplification.

Breast Cancer Cell Lines	EMP-Unassigned Group							Mesenchymal Group					Epithelial Group
	AKR1B1	APC	RASSF1A	RARβ	SFRP2	GFRA1	CDKN2A	TWIST1	CRABP1	DKK3	EGFR	VIM	GRHL2	MIR200C	CDH1
MFM-223	very high	100%	100%	100%	10–50%	100%	moderate	high	100%	100%	low	very low	0	0	0
MDA-MB-453	very high	100%	moderate	100%	50–100%	high	0	high	moderate	100%	10–50%	100%	0	0	0
BT-474	100%	10–50%	100%	100%	50–100%	0	0	very low	high	moderate	very low	0	0	0	0
ZR-75-1	moderate	100%	100%	high	moderate	very low	low	moderate	low	low	very low	moderate	0	0	0
HCC1419	very high	0	100%	very low	high	0	0	very low	high	moderate	very low	moderate	0	0	0
UACC-893	very high	50%	100%	high	high	moderate	0	high	low	moderate	0	low	0	0	0
SK-BR-3	moderate	low	50%	high	moderate	0	0	very low	0	0	very low	moderate	0	0	n.a.
T-47D	moderate	0	100%	very low	moderate	0	100%	high	moderate	moderate	moderate	100%	0	0	0
CAL-148	very high	100%	100%	high	moderate	0	0	100%	high	low	very low	moderate	0	0	0
MCF-7	very high	10–50%	100%	100%	high	0	n.a.	high	moderate	moderate	low	100%	0	0	0
UACC-732	high	50%	100%	high	moderate	0	0	high	low	moderate	very high	100%	0	0	0
MDA-MB-468	0	3%	100%	50–100%	moderate	moderate	0	high	low	moderate	0	0	0	0	0
HCC1954	100%	100%	100%	high	high	low	100%	moderate	moderate	high	very low	0	0	0	0
HCC70	0	0	0	50%	very low	low	0	moderate	0	moderate	very low	0	0	0	0
BT-20	0	100%	50%	100%	100%	100%	n.a.	100%	high	100%	0	100%	0	0	0
HCC1806	0	0	0	very low	0	0	n.a.	0	very low	0	very low	very low	0	0	0
HCC1569	10–50%	50–100%	10–50%	very low	100%	100%	low	100%	0	moderate	very low	0	0	0	0
SUM-149PT	0	0	0	moderate	low	0	n.a.	very low	very low	very low	very low	0	0	0	0
CAL-120	0	0	0	50%	moderate	0	0	very low	low	0	very low	0	very low	very low	very low
MCF 10A	0	0	moderate	high	low	low	n.a.	very low	very low	low	0	0	high	0	0
PMC42-LA	0	0	moderate	100%	low	0	n.a.	low	very low	0	0	0	10%	low	0
PMC42-ET	0	0	moderate	50–100%	moderate	0	n.a.	moderate	low	0	0	0	50–100%	high	very low
MDA-MB-231	0	0	50%	very low	high	moderate	n.a.	100%	low	high	very low	10%	moderate	moderate	moderate
BT-549	0	0	very low	very low	0	0	0	low	low	very low	very low	0	high	moderate	very low
SUM-159PT	0	0	50%	moderate	high	low	very low	high	0	0	very low	0	high	high	moderate
Hs578T	0	0	10–50%	0	very low	n.a.	n.a.	high	0	0	0	0	moderate	high	moderate