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

From: Discovery of co-occurring driver pathways in cancer

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       
  1. 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.