Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer

BMC Cancer

Table 3 ROAST test results for the multi-locus signatures

Time point	Direction	P-value	Prop. (down)	Prop. (up)
ER+/HER2- (193 CpG sites)
1	Up	0.3948	0.06	0.07
2	Up	0.6744	0.24	0.24
5	Up	0.3137	0.26	0.28
7	Up	0.0017	0.23	0.35
TAM (32 CpG sites)
1	Down	0.0995	0.06	0.03
2	Down	0.1736	0.16	0.06
5	Down	0.0037	0.28	0.06
7	Down	0.0028	0.22	0.13
AI (164 CpG sites)
1	Up	0.1004	0.05	0.13
2	Up	0.5434	0.15	0.22
5	Down	0.2088	0.24	0.23
7	Up	0.0222	0.15	0.26

Direction indicates the direction of change. Methylation loci were weighted by their direction of change in the survival signature. ‘Up’ therefore corresponds to changes in the same direction in the survival signature and in the T47D RA experiment. That is, if a locus is risk in/decreasing in the survival signature than it is hyper/hypomethylated in the cell line signature for the indicated time point as compared to WT baseline. ‘Down’ corresponds to changes in the opposite direction. Prop., proportion of loci in the signature contributing to the estimated p-value and direction. Significant p-values (< 0.05) for concordant changes (‘Up’) are indicated in bold

ISSN: 1471-2407