Table 3.

Co-occurring gene sets identified by applying CoMDP to GBM2 with somatic mutations and CNAs

k	Gene set 1	Gene set 2	p 1	p 2	n 1	n 2	r 1,2	p 1,2
4	CDKN2A, M G 3	CDKN2B, CYP27B1	0.0045	0.0056	60	63	0.9219	<0.0001
	CDKN2A,
5	CYP27B1, COL1A2	CDKN2B, M G 3	0.0072	0.0018	62	63	0.9531	<0.0001
	CDKN2A,	CDKN2B,
6	CYP27B1, COL1A2	M G 3, ERBB2	0.0073	0.0003	62	65	0.9538	<0.0001
	CDKN2A, TP53,	CDKN2B, RB1,
7	M G 3 , TAF1	CYP27B1	0.0001	0.0001	77	70	0.8375	<0.0001
	CDKN2A, TP53,	CDKN2B, RB1,
8	M G 3 , TAF1	CYP27B1, PRNP	0.0002	<0.0001	77	71	0.8500	<0.0001
	CDKN2A, TP53, TAF1,	CDKN2B, RB1,
9	M G 3 , PIK3R1	CYP27B1, SYNE1	0.0002	<0.0001	79	72	0.8642	<0.0001
	CDKN2A, TP53, TAF1,	CDKN2B, RB1, SYNE1,
10	M G 3 , PIK3R1	CYP27B1, M G 4	0.0001	<0.0001	79	73	0.8765	<0.0001

MG ₃ is a metagene including three genes: CDK4, MARCH9, TSPAN31. MG ₄ is a metagene including 168 genes.