Table 3.

Variance component-based total effect test p-values for gene sets associated with lung cancer after Bonferroni correction

			Approximated P-Values				Empirical P-Values				Omnibus P-Values
	N0	N T	Q MGC	Q MG	Q M	Q G	Q MGC	Q MG	Q M	Q G	iNOTE chi	iNOTE uni	GSAA
BRUECKNER TARGETS OF MIRLET7A3 DN	78	71	1.1E-05	1.7E-06	5.5E-04	2.4E-04	<1E-04	<1E-04	8E-04	3E-04	8E-04	<1E-04	0.325
BRUECKNER TARGETS OF MIRLET7A3 UP	111	106	1.3E-06	4.1E-07	2.5E-04	1.3E-04	<1E-04	<1E-04	4E-04	1E-04	2E-04	<1E-04	0.230
COLDREN GEFITINIB RESISTANCE DN	230	216	8.0E-09	3.2E-10	1.2E-09	8.9E-04	<1E-04	<1E-04	<1E-04	9E-04	<1E-04	<1E-04	0.095
DAUER STAT3 TARGETS UP	49	49	1.6E-04	4.6E-05	0.002	0.003	7E-04	2E-04	0.003	0.002	4E-04	3E-04	<1E-04
DCA UP.V1 DN	193	163	6.1E-06	4.9E-06	0.003	1.3E-04	<1E-04	<1E-04	0.004	<1E-04	<1E-04	<1E-04	0.920
DCA UP.V1 UP	191	162	7.3E-05	4.7E-05	0.002	0.003	1E-04	1E-04	0.002	0.004	<1E-04	<1E-04	0.065
HALMOS CEBPA TARGETS DN	46	44	2.4E-04	9.5E-05	0.018	5.4E-04	8E-04	<1E-04	0.021	4E-04	0.001	<1E-04	0.645
HATADA METHYLATED IN LUNG CANCER UP	390	356	9.3E-07	2.6E-07	2.8E-06	0.003	<1E-04	<1E-04	<1E-04	0.003	<1E-04	<1E-04	0.900
KIM MYC AMPLIFICATION TARGETS UP	201	169	2.2E-06	1.3E-06	0.004	2.9E-05	<1E-04	<1E-04	0.005	<1E-04	<1E-04	<1E-04	0.605
KOBAYASHI EGFR SIGNALING 24HR DN	251	228	7.3E-04	1.7E-05	9.6E-07	0.109	9E-04	<1E-04	<1E-04	0.110	0.015	<1E-04	0.920
KOBAYASHI EGFR SIGNALING 24HR UP	101	91	1.7E-09	1.9E-08	9.0E-04	3.2E-06	<1E-04	<1E-04	0.001	<1E-04	<1E-04	<1E-04	0.035
KOBAYASHI EGFR SIGNALING 6HR DN	18	18	5.4E-05	9.5E-06	2.5E-04	0.003	<1E-04	<1E-04	9E-04	0.004	<1E-04	<1E-04	0.110
KRAS.600.LUNG.BREAST UP.V1 DN	289	261	3.4E-04	3.4E-04	0.020	0.003	7E-04	2E-04	0.023	0.004	<1E-04	4E-04	0.125
KRAS.600.LUNG.BREAST UP.V1 UP	288	247	8.8E-07	2.3E-06	0.100	7.9E-07	<1E-04	<1E-04	0.105	<1E-04	<1E-04	<1E-04	0.060
KRAS.AMP.LUNG UP.V1 UP	144	121	9.0E-05	1.7E-04	0.288	1.6E-05	5E-04	4E-04	0.284	1E-04	<1E-04	<1E-04	0.045
KRAS.DF.V1 UP	193	175	3.3E-08	1.4E-08	3.1E-04	5.1E-06	<1E-04	<1E-04	4E-04	<1E-04	1E-04	<1E-04	0.160
KRAS.LUNG UP.V1 UP	141	126	5.3E-10	5.1E-09	0.025	1.1E-08	<1E-04	<1E-04	0.026	<1E-04	<1E-04	<1E-04	0.575
LI AMPLIFIED IN LUNG CANCER	178	165	1.6E-04	6.1E-05	9.5E-05	0.031	3E-04	1E-04	1E-04	0.032	0.009	<1E-04	0.180
LOCKWOOD AMPLIFIED IN LUNG CANCER	214	205	1.6E-04	6.7E-06	6.7E-07	0.081	2E-04	<1E-04	<1E-04	0.081	0.014	<1E-04	0.230
SHEDDEN LUNG CANCER GOOD SURVIVAL A12	317	269	7.9E-10	9.7E-09	0.003	1.4E-07	<1E-04	<1E-04	0.002	<1E-04	<1E-04	<1E-04	0.385
SHEDDEN LUNG CANCER GOOD SURVIVAL A4	196	186	6.0E-06	5.7E-06	5.7E-05	0.006	<1E-04	<1E-04	2E-04	0.007	<1E-04	<1E-04	0.470
SHEDDEN LUNG CANCER POOR SURVIVAL A6	456	411	2.2E-08	1.4E-11	8.1E-11	7.6E-04	<1E-04	<1E-04	<1E-04	0.001	1E-04	<1E-04	0.900
SWEET KRAS ONCOGENIC SIGNATURE	89	81	0.010	3.8E-04	3.1E-05	0.157	0.011	4E-04	<1E-04	0.158	0.019	<1E-04	0.180
SWEET KRAS TARGETS DN	66	59	3.1E-08	2.3E-09	5.0E-04	6.5E-07	<1E-04	<1E-04	0.001	<1E-04	<1E-04	<1E-04	0.655
TBK1.DF DN	287	266	2.9E-08	3.9E-09	1.3E-05	2.3E-05	<1E-04	<1E-04	<1E-04	<1E-04	5E-04	<1E-04	0.570
TBK1.DF UP	290	275	0.006	0.001	2.4E-04	0.174	0.008	0.002	2E-04	0.172	0.051	2E-04	0.265
TOOKER GEMCITABINE RESISTANCE DN	122	115	4.1E-05	1.1E-05	8.8E-05	0.006	<1E-04	<1E-04	2E-04	0.007	0.004	<1E-04	0.710
ZHONG RESPONSE TO AZACITIDINE AND TSA UP	183	158	1.1E-05	9.8E-07	3.0E-07	0.024	1E-04	<1E-04	<1E-04	0.025	1E-04	<1E-04	0.935

Satterthwaite-approximated and empirical p-values for all significant gene sets after Bonferroni correction by at least one of the iTEGS and at least one of the iNOTE tests. Empirical p-values and approximated p-values are very similar, irrespective of the sizes of the gene sets tested. N₀: total no. of genes in the gene set; N _T: total no. of genes with methylation and gene expression data available (i.e. tested); Q: the iTEGS Q-statistic test specifying M, G, MG, or MGC; Bonferroni adjusted p-value threshold was calculated as α/M=5×10⁻⁰⁴, where α=0.05 and M is the total number of gene sets tested