Gene Degree Gene-level coding P-value Gene-level coding FDR Neighborhood score (without gene) Neighborhood score (with gene) Log ratio of neighborhood scores PIK3CA 60 5.18E-28 2.07E-24 5.48E-23 1.09E-41 18.702 PBRM1 31 2.16E-21 4.79E-18 6.88E-28 6.91E-44 15.998 CTNNB1 267 9.80E-28 2.79E-24 7.75E-57 2.43E-72 15.504 ARID1A 47 2.24E-20 4.46E-17 1.92E-34 4.65E-49 14.617 KRAS 67 1.08E-28 7.18E-25 5.66E-06 2.03E-20 14.445 CDKN2A 136 2.41E-26 6.02E-23 5.85E-20 1.09E-33 13.730 PTEN 212 8.49E-28 2.79E-24 2.07E-24 8.80E-38 13.370 VHL 291 2.44E-29 2.51E-25 6.06E-13 1.94E-23 10.495 SMAD4 165 3.47E-28 1.73E-24 1.93E-06 1.33E-16 10.162 NFE2L2 56 2.49E-18 3.82E-15 1.48E-10 1.13E-20 10.117 MEN1 53 1.53E-14 1.70E-11 9.57E-38 1.10E-47 9.940 TP53 840 2.51E-29 2.51E-25 1.68E-34 3.71E-44 9.656 KDM6A 25 1.81E-11 1.72E-08 2.20E-27 1.89E-35 8.066 ARID2 24 2.31E-11 2.01E-08 3.67E-18 8.48E-26 7.636 MAP2K4 35 2.81E-13 2.95E-10 4.43E-08 1.74E-15 7.407 CDH1 77 2.32E-11 2.01E-08 1.45E-27 3.76E-34 6.585 RB1 212 8.60E-19 1.43E-15 2.25E-10 5.87E-17 6.584 BRAF 38 1.02E-14 1.20E-11 4.71E-03 1.45E-09 6.512 APC 162 8.19E-20 1.49E-16 4.95E-05 3.89E-11 6.105 RNF43 17 1.12E-08 7.23E-06 1.45E-18 2.41E-24 5.780 FBXW7 162 4.06E-17 5.79E-14 5.79E-07 1.09E-12 5.724 AXIN1 61 8.60E-09 5.72E-06 3.15E-54 6.77E-60 5.667 ACVR2A 22 9.18E-10 7.33E-07 3.83E-06 1.50E-11 5.408 NRAS 14 5.22E-10 4.34E-07 9.40E-02 1.42E-06 4.820 DDX3X 112 1.21E-09 9.29E-07 1.50E-22 2.86E-27 4.721 ARHGAP35 11 2.76E-08 1.45E-05 1.08E-03 2.15E-08 4.702 NOTCH1 175 1.48E-08 8.96E-06 3.05E-56 8.38E-61 4.561 TGFBR2 82 1.89E-08 1.07E-05 1.10E-18 7.49E-23 4.167 CASP8 123 1.45E-08 8.96E-06 5.09E-25 4.05E-29 4.100 MAP3K1 127 3.68E-09 2.72E-06 5.32E-19 4.34E-23 4.089 KMT2D 28 1.38E-06 5.51E-04 7.06E-30 6.65E-34 4.026 SMARCA4 170 9.81E-07 4.08E-04 3.76E-102 5.73E-106 3.817 PIK3R1 136 4.83E-08 2.47E-05 6.01E-22 1.64E-25 3.564 ATM 146 6.02E-08 3.00E-05 7.52E-24 2.26E-27 3.522 B2M 20 1.94E-08 1.07E-05 4.47E-02 1.39E-05 3.507 KMT2C 22 6.13E-07 2.78E-04 4.42E-06 1.46E-09 3.482 NF1 23 9.49E-07 4.03E-04 1.00E-04 7.52E-08 3.125 GATA3 21 5.64E-06 2.21E-03 2.32E-06 2.86E-09 2.910 CBFB 17 7.01E-09 4.82E-06 5.86E-01 7.36E-04 2.901 CDKN1A 255 5.55E-09 3.96E-06 3.81E-13 6.13E-16 2.794 SPOP 38 1.82E-08 1.07E-05 3.34E-02 5.61E-05 2.775 RPL5 67 1.90E-05 6.54E-03 9.48E-28 1.87E-30 2.704 HRAS 63 4.95E-05 1.62E-02 2.12E-43 5.02E-46 2.626 MAP2K7 39 6.58E-06 2.53E-03 1.73E-07 4.97E-10 2.542 SMARCB1 79 1.08E-04 3.28E-02 5.94E-56 2.49E-58 2.377 HLA-A 59 6.70E-07 2.97E-04 8.09E-04 5.27E-06 2.186 ACVR1B 37 2.95E-05 9.98E-03 2.55E-07 1.67E-09 2.184 USP9X 74 8.06E-05 2.51E-02 1.15E-24 7.56E-27 2.182 DAXX 134 1.29E-04 3.85E-02 1.10E-55 8.02E-58 2.137 AKT1 268 1.03E-04 3.18E-02 1.64E-71 1.59E-73 2.014 SOX9 14 2.11E-04 5.86E-02 1.55E-03 2.41E-05 1.809 RPL22 58 1.99E-08 1.07E-05 2.00E-01 3.26E-03 1.788 KEAP1 102 2.29E-07 1.06E-04 6.31E-03 1.31E-04 1.683 BRD7 38 9.60E-04 2.37E-01 2.12E-22 4.95E-24 1.632 EPHA2 53 1.76E-05 6.16E-03 6.37E-03 2.09E-04 1.484 CDKN1B 74 1.32E-05 4.80E-03 1.56E-03 5.48E-05 1.455 EPHA6 1 6.64E-03 1.00E+00 8.36E-01 3.44E-02 1.386 ARID1B 27 3.90E-03 7.36E-01 9.49E-18 5.93E-19 1.204 BCL9 6 3.50E-03 6.91E-01 1.30E-21 8.12E-23 1.203 KDM5C 36 6.04E-05 1.91E-02 9.08E-02 6.18E-03 1.167 TAF1 62 5.97E-03 1.00E+00 8.86E-45 7.53E-46 1.071 RPS6KA3 31 2.44E-04 6.68E-02 8.84E-02 8.40E-03 1.022 TBL1XR1 41 7.20E-03 1.00E+00 3.22E-14 3.75E-15 0.934 RRAS2 21 3.58E-03 6.94E-01 7.85E-03 1.04E-03 0.877 STK11 74 5.61E-03 9.83E-01 1.19E-08 1.99E-09 0.776 RASA1 49 3.85E-03 7.36E-01 4.53E-04 8.11E-05 0.747 CREBBP 288 9.11E-03 1.00E+00 1.92E-43 3.52E-44 0.737 BRCA2 65 1.14E-02 1.00E+00 6.29E-13 1.18E-13 0.727 BTG2 17 3.91E-03 7.36E-01 1.38E-01 2.68E-02 0.712 FOXA1 38 1.25E-06 5.09E-04 9.24E-01 2.43E-01 0.579 KAT8 33 3.15E-02 1.00E+00 6.01E-26 1.78E-26 0.528 TCF7L2 30 3.08E-02 1.00E+00 1.39E-30 4.19E-31 0.520 HDAC2 287 2.38E-02 1.00E+00 5.64E-37 1.77E-37 0.504 NOTCH2 29 7.70E-03 1.00E+00 1.50E-01 5.18E-02 0.463 AJUBA 23 4.52E-02 1.00E+00 3.83E-17 1.47E-17 0.415 YWHAE 290 1.98E-02 1.00E+00 3.69E-13 1.49E-13 0.392 EGFR 812 1.71E-05 6.09E-03 1.57E-02 6.53E-03 0.381 PRKAR1A 71 3.40E-04 9.06E-02 4.86E-01 2.02E-01 0.380 PTCH1 86 9.50E-07 4.03E-04 8.58E-01 3.62E-01 0.375 KANSL1 36 3.25E-04 8.78E-02 8.38E-01 4.05E-01 0.315 SF3B1 107 9.77E-06 3.61E-03 7.83E-01 4.00E-01 0.292 STAG2 25 2.51E-02 1.00E+00 3.04E-01 1.62E-01 0.273 RHOA 98 1.14E-02 1.00E+00 1.50E-01 8.77E-02 0.233 RAC1 137 2.00E-02 1.00E+00 7.21E-01 6.29E-01 0.059 CDK12 18 2.06E-02 1.00E+00 9.87E-01 8.97E-01 0.042 BAX 52 5.68E-04 1.49E-01 9.98E-01 9.53E-01 0.020 ALB 165 1.25E-07 5.94E-05 1.00E+00 1.00E+00 0.000