CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer

Table 1 Comparison of CoMEt, Multi-Dendrix, and mutex on the TCGA GBM dataset from the TCGA Pan-Cancer project [5] with and without mutation filtering. The consensus modules output by each algorithm are shown for the dataset with and without mutation filtering. The (A) and (D) following the gene names indicate amplifications and deletions, respectively

Algorithm	Without filtering	With filtering
CoMEt
	1. IDH1, PIK3CA, PTEN, *KSR2*	1. IDH1, PIK3CA, PTEN, *DNAH11*
	2. MDM2(A), RPL5, STAG2, TP53	2. MDM2(A), RPL5, STAG2, TP53, *SEMA3E*
	3. EGFR, NF1, *CALCR, PCDHA3, PPP1R3A*	3. EGFR, NF1, *PKHD1, THSD7B*
	4. CDK4(A), CDKN2A(D), PTPN11, RB1, ZNF407	4. CDK4(A), CDKN2A(D), PTPN11, RB1, ZNF407
Multi-Dendrix
	1. CNTNAP2, CDKN2A(D), CDK4(A), EGFR, IDH1, MDM2(A), MDM4(A), NF1, PIK3CA, PTEN, RB1, *COL6A3, MAST4, PCDHA3, PCLO, PDGFRA* (A), *PIK3R1*	1. CNTNAP2, EGFR, IDH1, MDM2(A), MDM4(A), PTEN, TP53, *ATRX, CHD9, HRNR, MUC4, MUC16, TTN*
		2. CDKN2A(D), CDK4(A), NF1, RB1, *FRG1B*
mutex	1. CDK4(A), CDKN2A(D), EHD3, MAST4, NF1, PTPN11, RB1	1. CDK4(A), CDKN2A(D), EHD3, MAST4, MDM2(A), NF1, PTPN11, RB1, STAG2, TP53, *CACNA1S, CALCR, DGKD, EGFR, FRG1B, PKHD1, THSD7B, ZNF407*
	2. MDM2(A), STAG2, TP53