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

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 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
  1. Here p1 and p2 are the p-values of the individual significance of two identified gene sets, p1,2 represents the p-value of their co-occurrence significance, n1 and n2 denote their respective coverage, and r1,2 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.