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

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

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

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