Protein expression based multimarker analysis of breast cancer samples

BMC Cancer

Table 6 Validation results for WGCNA* mortality groups in three Affymetrix data sets

#	Data Set	Marker Probeset			Hazard Ratio		P-values			Validates at 0.1
		ATP1B1	TP53	TGFBR2	Mod.	High	Mod.	High	Model
1	Miller 2005	1	1	1	0.88	2.35	0.693	0.053	0.173	yes
2	Miller 2005	1	1	2	0.94	2.39	0.853	0.049	0.184	yes
3	Miller 2005	1	2	1	1.10	0.93	0.777	0.884	0.944	no
4	Miller 2005	1	2	2	1.17	0.94	0.611	0.914	0.865	no
5	Miller 2005	2	1	1	0.82	1.18	0.538	0.750	0.754	no
6	Miller 2005	2	1	2	0.88	1.20	0.676	0.727	0.840	no
7	Miller 2005	2	2	1	1.05	0.32	0.873	0.258	0.371	no
8	Miller 2005	2	2	2	1.12	0.32	0.709	0.265	0.351	no
9	Pawitan 2005	1	1	1	0.64	3.17	0.429	0.024	0.062	yes
10	Pawitan 2005	1	1	2	0.41	2.91	0.158	0.036	0.026	yes
11	Pawitan 2005	1	2	1	0.93	4.89	0.894	0.001	0.014	yes
12	Pawitan 2005	1	2	2	0.41	4.05	0.156	0.004	0.004	yes
13	Pawitan 2005	2	1	1	0.64	3.22	0.430	0.023	0.060	yes
14	Pawitan 2005	2	1	2	0.41	2.95	0.159	0.034	0.025	yes
15	Pawitan 2005	2	2	1	0.92	4.37	0.880	0.002	0.022	yes
16	Pawitan 2005	2	2	2	0.41	3.62	0.152	0.008	0.007	yes

The Pawitan 2005 data set validated at the 0.1 level for all eight probe set combinations for the high mortality group. The Miller 2005 data set validated for two probe set combinations. The WGCNA* moderate mortality group did not validate. None of the probe set combinations validated for the Sotiriou 2006 data set (not shown). The rows highlighted bold indicate probe set combinations with Kaplan-Meier plots in Figure 5. Probe set abbreviations are as follows ATP1B1: 1 = 201242_s_at, 2 = 201243_s_at; TP53: 1 = 201746_at, 2 = 211300_s_at; TGFBR2: 1 = 207334_s_at, 2 = 208944_at.

ISSN: 1471-2407