Discovery of co-occurring driver pathways in cancer

BMC Bioinformatics

Table 4 Co-occurring gene sets identified by applying CoMDP to the ovarian carcinoma dadaset

k	Gene set 1	Gene set 2	p ₁	p ₂	n ₁	n ₂	r _1,2	p _1,2
4	TP53	MYC, CCNE1, NINJ2	1.0000	<0.0001	251	155	0.4397	0.0410
		MYC, CCNE1,
5	TP53	NINJ2, M G ₅	1.0000	0.0100	251	169	0.4894	0.0250
		MYC, CCNE1,
6	TP53	NINJ2, ZNF596, USH2A	1.0000	<0.0001	251	183	0.5228	0.0120
		MYC, CCNE1,
7	TP53, LYRM5	NINJ2, ZNF596, USH2A	0.0270	0.0030	264	183	0.5629	<0.0001
		MYC, CCNE1, NINJ2,
8	TP53, LYRM5	BRD4, ZNF596, USH2A	0.0230	0.0210	264	197	0.6007	0.001
		MYC, CCNE1, NINJ2,
9	TP53, LYRM5	BRD4, ZNF596,	0.0340	0.0160	264	206	0.6263	<0.0001
		USH2A, HMCN1
		MYC, CCNE1, NINJ2,
10	TP53, LYRM5	NF1, ZNF596,	0.0390	0.001	264	211	0.6493	<0.0001
		USH2A, HMCN1, TPD52L2

MG₅ is a metagene including two genes: CHKB, KLHDC7B. For k = 4 ∼ 6 because of only one gene contained in the gene set 1, the corresponding p-value equals 1.0000.

ISSN: 1471-2105