Discovery of co-occurring driver pathways in cancer

BMC Bioinformatics

Table 1 Co-occurring gene sets identified by applying CoMDP to GBM1

k	Gene set 1	Gene set 2	p ₁	p ₂	n ₁	n ₂	r _1,2	p _1,2
4	CDKN2A, M G₁	MTAP, CYP27B1	0.0207	0.0058	50	49	0.9412	<0.0001
	CDKN2A, TP53,
5	M G ₁	CDKN2B, CYP27B1	0.0003	0.0018	68	57	0.7606	<0.0001
	CDKN2A, PTEN,	CDKN2B, TP53,
6	CYP27B1	M G ₁	0.0002	0.0003	69	71	0.8182	<0.0001
	CDKN2A, PTEN,	CDKN2B, RB1,
7	CYP27B1	TP53, M G₁	0.0002	0.0001	69	74	0.8571	<0.0001
	CDKN2A, PTEN,	CDKN2B, RB1,
8	NF1, CYP27B1	M G₁, ERBB2	0.0015	<0.0001	72	70	0.8933	<0.0001
	CDKN2A, PTEN, NF1,	CDKN2B, RB1,
9	CYP27B1, KDR	M G₁, ERBB2	0.0006	<0.0001	74	70	0.9200	<0.0001
	CDKN2A, PTEN, CYP27B1,	CDKN2B, NF1, RB1,
10	KDR, M G₂	M G₁, ERBB2	<0.0001	<0.0001	72	73	0.9333	<0.0001

Here p₁ and p₂ are the p-values of the individual significance of two identified gene sets, p_1,2 represents the p-value of their co-occurrence significance, n₁ and n₂ denote their respective coverage, and r_1,2 is the ratio of the common coverage to their union coverage (i.e., co-occurrence ratio). There are same meanings in the following tables. MG₁ is a metagene including seven genes: CDK4, FAM119B, MARCH9, TSFM, CENTG1, METTL1, TSPAN31. MG₂ is a metagene including four genes: WT1, SLC1A2, PAX6, ABCC4.

ISSN: 1471-2105