Table 4.

Associations between Methylation of a Five-Gene Panel and Grade in BC Patients from TCGA

Gene	EOMES	GP5	PAX6	TCF4	ZSCAN12
Probe ID	cg21473142	cg18780769	cg24701575	cg23482397	cg20271532
Benign vs cancer
Benign	0.261	0.137	0.137	0.022	0.072
Cancer	0.606	0.129	0.281	0.028	0.098
P value	.003	.94	.02	1.9 × 10−4	.31
Benign vs LG vs HG
Benign	0.261	0.137	0.137	0.022	0.072
LG	0.314	0.092	0.156	0.026	0.056
HG	0.753	0.232	0.465	0.046	0.225
P value	2.7 × 10−5	2.9 × 10−4	1.3 × 10−4	1.7 × 10−4	.02
LG vs HG
LG	0.314	0.092	0.156	0.046	0.225
HG	0.753	0.232	0.565	0.026	0.056
P value	.003	.001	.001	.04	.02
Benign vs LG
Benign	0.261	0.137	0.137	0.022	0.072
LG	0.314	0.092	0.156	0.026	0.056
P value	.77	.009	.97	.01	.46
Benign vs HG
Benign	0.246	0.137	0.137	0.022	0.072
HG	0.753	0.232	0.565	0.046	0.225
P value	2.3 × 10−6	.01	5.5 × 10−5	9.3 × 10−5	.01
Stage
T2	0.321	0.125	0.226	0.027	0.079
T3	0.671	0.098	0.280	0.046	0.070
T4	0.732	0.195	0.347	0.027	0.429
P value	.12	.39	.77	.59	.44

The most significant probe within each gene for the comparison of LG to HG was used for each association. Median beta values and Mann-Whitney U test or Kruskal-Wallis test P values are shown.