Table 3.

Kaplan-Meier logrank test p-values for best principal component (best binarized PC) derived from correlation matrix of DNA repair genes with significant individual KM tests after adjustment of expression for age, stage, and PCNA metagene effects. Cancers listed had both age at diagnosis and stage available in TCGA clinical data.

Cancer	n	Kaplan-Meier Logrank a						Random Genes (B = 1000) b
		A	S	P	A, S	A, S, P	N	A	S	A, S	P	A, S, P	N
Breast	1105	0.0057	0.0049	0.0004	0.0069	0.0015	0.0060	0.0790	0.0450	0.0050	0.0860	0.0350	0.0650
Cervical	309	0.0071	0.0014	0.0015	0.0100	0.0151	0.0088	0.2150	0.0630	0.0120	0.2530	0.0730	0.2810
Colorectal	633	0.0550	0.0255	0.0048	0.0188	0.0106	0.0330	0.2050	0.0700	0.0120	0.0450	0.0340	0.1160
Liver	379	0.0000	0.0002	0.0004	0.0001	0.0027	0.0001	0.1150	0.2220	0.0020	0.2140	0.0130	0.1720
Lung	522	0.0120	0.0008	0.0003	0.0021	0.0036	0.0070	0.4850	0.0560	0.0070	0.1030	0.0400	0.3570
Lung SC	505	0.0057	0.0050	0.0040	0.0050	0.0040	0.0057	0.0400	0.0290	0.0110	0.0290	0.0100	0.0330
Ovarian	603	0.0259	0.0088	0.0184	0.0722	0.0100	0.0183	0.2310	0.1250	0.2010	0.5240	0.0700	0.2060
Melanoma	479	0.0000	0.0001	0.0002	0.0000	0.0001	0.0001	0.0170	0.0710	0.0190	0.0250	0.0040	0.0670
Renal CC	538	0.0000	0.0000	0.0000	0.0000	0.0003	0.0000	0.2570	0.4230	0.0100	0.1340	0.2780	0.4710
Renal Pap.	292	0.0000	0.0001	0.0011	0.0000	0.0012	0.0000	0.0770	0.0100	0.1060	0.0040	0.0190	0.0320
Stomach	478	0.6412	0.0103	0.0180	0.0103	0.0107	0.6412	0.6570	0.0070	0.0300	0.0060	0.0160	0.6780
Uterine	548	0.0013	0.0024	0.0150	0.0010	0.0072	0.0009	0.0250	0.0390	0.3620	0.0070	0.1070	0.0190

A—Expression adjusted for age at diagnosis. S—Expression adjusted for stage. P—Expression adjusted for PCNA metagene expression. A,S—Expression adjusted for age at diagnosis and stage. A,S,P—Expression adjusted for age at diagnosis, stage, and PCNA metagene expression. N—No adjustment to expression. ^a—KM logrank test of binarized principal component scores from correlation matrix of DNA repair genes with significant logrank tests. ^b—p-Values based on number of times KM test χ² (b) based on random genes exceeded χ² based on non-random genes. SC: squamous cell; CC: clear cell. Bold highlighting for p-values denotes cancers for which KM logrank or randomization tests were significant when age, stage, and PCNA adjustments were made.