Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL nCNV (%) nWild-Type Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Chi-square test_P Chi-square test_Q Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 89 (10%) 802 0.00041183 0.192 1.6001e-06 0.000997 2.8331e-07 0.000184 0.019094 1 5.4527e-05 0.0292 0.00029752 0.144 7.7807e-07 0.000494 3.1045e-05 0.0171 2.8048e-05 0.0156 2.212e-05 0.0124 1q gain 473 (53%) 418 0.16279 1 0.70397 1 1.1187e-09 7.89e-07 4.0163e-14 3.04e-11 0.11973 1 0.15747 1 0.10475 1 0.017219 1 0.024847 1 0.026122 1 2p gain 48 (5%) 843 7.7602e-12 5.74e-09 2.8807e-11 2.1e-08 2.4676e-10 1.76e-07 4.9675e-05 0.0267 2.709e-08 1.84e-05 4.8889e-08 3.28e-05 1.0645e-11 7.86e-09 6.5987e-13 4.92e-10 1.3615e-11 1e-08 5.4518e-10 3.87e-07 2q gain 25 (3%) 866 2.6595e-07 0.000173 1.8498e-05 0.0105 0.00033435 0.159 0.0061211 1 1.6454e-07 0.000108 0.00052147 0.237 3.1477e-06 0.00191 7.9932e-06 0.00474 0.00029555 0.143 0.00016323 0.0816 3p gain 52 (6%) 839 0.83485 1 0.038142 1 1.3674e-06 0.000856 0.18135 1 0.52754 1 0.2161 1 0.043186 1 0.046571 1 0.025029 1 0.16994 1 3q gain 98 (11%) 793 0.015343 1 0.0025018 0.991 1.9081e-09 1.34e-06 0.00054011 0.245 0.026598 1 0.17145 1 0.00016047 0.0806 0.00040896 0.191 3.1332e-05 0.0172 0.00105 0.455 4p gain 29 (3%) 862 0.11607 1 4.2543e-05 0.0231 1.6722e-07 0.00011 0.0015606 0.662 0.044743 1 0.039867 1 0.015957 1 0.0017774 0.736 0.00029727 0.144 0.25765 1 4q gain 27 (3%) 864 0.23598 1 0.00043835 0.203 3.7799e-09 2.64e-06 0.00517 1 0.055083 1 0.010507 1 0.010657 1 0.0057554 1 0.003197 1 0.11261 1 5p gain 166 (19%) 725 0.51355 1 0.38612 1 2.3974e-09 1.68e-06 0.18102 1 0.54074 1 0.3146 1 0.70701 1 0.31485 1 0.02131 1 0.63199 1 5q gain 102 (11%) 789 0.025127 1 0.0045266 1 1.362e-15 1.05e-12 0.0034935 1 0.0013424 0.573 0.0022623 0.905 0.00057674 0.26 1.1465e-05 0.00666 0.0048763 1 2.1781e-05 0.0123 6p gain 101 (11%) 790 2.8697e-05 0.016 2.0027e-05 0.0113 1.0304e-14 7.89e-12 4.2649e-07 0.000274 0.0041532 1 0.050851 1 7.8559e-09 5.44e-06 2.6682e-08 1.82e-05 1.5057e-11 1.11e-08 1.1299e-08 7.79e-06 6q gain 59 (7%) 832 0.00013505 0.0687 0.0051332 1 2.2325e-15 1.73e-12 0.0043839 1 0.00036343 0.171 0.027849 1 6.4341e-06 0.00383 2.1519e-06 0.00133 3.2157e-07 0.000208 1.4816e-06 0.000925 7p gain 153 (17%) 738 0.39196 1 0.38813 1 0.00030163 0.145 0.0045603 1 0.98598 1 0.51259 1 0.030205 1 0.11517 1 0.19577 1 0.039334 1 7q gain 111 (12%) 780 0.15923 1 0.015985 1 1.52e-05 0.00871 0.00043697 0.203 0.31248 1 0.19889 1 0.0057434 1 0.00043837 0.203 0.077275 1 0.00029511 0.143 8p gain 169 (19%) 722 0.13442 1 0.013389 1 5.5999e-13 4.19e-10 0.0027677 1 0.14258 1 0.39121 1 0.00019214 0.0951 0.00011276 0.0583 0.0031716 1 0.89318 1 8q gain 366 (41%) 525 0.0064552 1 4.3715e-05 0.0236 3.1459e-23 2.49e-20 4.6562e-09 3.25e-06 0.66766 1 0.55936 1 8.4036e-08 5.57e-05 4.6276e-06 0.00278 1.1942e-10 8.6e-08 0.003086 1 9p gain 67 (8%) 824 0.00031738 0.152 6.9971e-08 4.67e-05 1.1496e-09 8.09e-07 0.00055777 0.252 0.011288 1 0.00013812 0.0702 1.2997e-07 8.58e-05 2.6335e-08 1.8e-05 3.2337e-06 0.00196 3.8982e-07 0.000251 9q gain 54 (6%) 837 0.33599 1 0.042779 1 9.788e-05 0.0514 0.33813 1 0.96765 1 0.5434 1 0.043389 1 0.0068317 1 0.049146 1 0.24324 1 10p gain 109 (12%) 782 6.6062e-09 4.58e-06 7.1906e-08 4.79e-05 2.6216e-18 2.04e-15 1.2132e-13 9.12e-11 1.3235e-05 0.00764 1.1027e-06 0.000696 3.5934e-15 2.77e-12 1.138e-14 8.71e-12 1.4057e-14 1.07e-11 4.471e-14 3.38e-11 10q gain 44 (5%) 847 0.0017412 0.724 0.012595 1 1.225e-05 0.00709 0.021889 1 0.082237 1 0.051488 1 0.0039073 1 0.0026556 1 0.0011418 0.492 0.0080131 1 11p gain 64 (7%) 827 0.61314 1 0.61078 1 0.011606 1 0.23222 1 0.38412 1 0.16348 1 0.63686 1 0.81876 1 0.42822 1 0.30411 1 11q gain 45 (5%) 846 0.17445 1 0.80905 1 0.00058211 0.261 0.28581 1 0.93543 1 0.68705 1 0.32969 1 0.43331 1 0.23128 1 0.09402 1 12p gain 110 (12%) 781 0.0024015 0.958 0.00056345 0.254 1.712e-14 1.3e-11 0.00014189 0.0717 0.37444 1 0.09137 1 7.3752e-05 0.0389 0.00039696 0.186 5.5292e-06 0.00331 0.00053221 0.242 12q gain 83 (9%) 808 0.020805 1 0.0047963 1 1.2083e-14 9.23e-12 0.00035673 0.169 0.25556 1 0.5139 1 0.0016465 0.69 0.039445 1 0.007561 1 0.42127 1 13q gain 45 (5%) 846 0.047319 1 0.086497 1 0.051872 1 0.045766 1 0.019638 1 0.13422 1 0.00042436 0.198 0.0405 1 0.0069335 1 0.0081042 1 14q gain 77 (9%) 814 0.076363 1 0.021394 1 0.00012149 0.0624 0.0059435 1 0.94883 1 0.28235 1 1.9379e-05 0.011 0.0011139 0.481 0.00079108 0.35 0.11029 1 15q gain 46 (5%) 845 0.60422 1 0.33882 1 0.29003 1 0.34458 1 0.91828 1 0.48039 1 0.21552 1 0.18094 1 0.2447 1 0.096373 1 16p gain 239 (27%) 652 0.0014652 0.623 0.0016191 0.682 0.0075427 1 8.8043e-06 0.0052 0.0006973 0.312 0.00060828 0.273 0.00015648 0.0787 3.6364e-06 0.0022 0.00071349 0.318 0.02698 1 16q gain 53 (6%) 838 0.5052 1 0.34428 1 0.0018371 0.757 0.16822 1 0.14259 1 0.77542 1 0.11138 1 0.1088 1 0.0079273 1 0.0035147 1 17p gain 46 (5%) 845 0.090621 1 0.30851 1 0.00076596 0.34 0.83153 1 0.17785 1 0.23448 1 0.57491 1 0.72055 1 0.4741 1 0.52846 1 17q gain 122 (14%) 769 0.036811 1 0.0074553 1 2.3038e-22 1.82e-19 6.1651e-05 0.0329 0.36961 1 0.0094374 1 3.5701e-05 0.0195 4.6193e-06 0.00278 0.091405 1 0.018495 1 18p gain 86 (10%) 805 0.0071903 1 0.00017244 0.0859 1.7738e-07 0.000116 2.5571e-06 0.00157 0.0037556 1 0.0032577 1 3.0526e-06 0.00186 3.8145e-08 2.57e-05 2.1937e-06 0.00135 9.6543e-06 0.00566 18q gain 74 (8%) 817 0.17571 1 0.0020606 0.832 8.8307e-06 0.00521 0.032099 1 0.20784 1 0.20009 1 0.00024136 0.119 9.7985e-05 0.0514 8.5626e-05 0.045 0.0060251 1 19p gain 67 (8%) 824 0.095288 1 0.014741 1 0.00010206 0.0532 0.15344 1 0.07517 1 0.10261 1 0.013878 1 0.00044371 0.204 0.020514 1 0.00087662 0.383 19q gain 83 (9%) 808 0.46741 1 0.038377 1 0.00011368 0.0587 0.072239 1 0.19949 1 0.1603 1 0.045849 1 0.0012733 0.545 0.0504 1 0.0084167 1 20p gain 236 (26%) 655 1.4129e-05 0.00811 0.0018439 0.758 5.704e-26 4.53e-23 2.6075e-05 0.0146 0.03103 1 0.10839 1 0.0015927 0.674 0.065 1 1.9841e-06 0.00123 0.27025 1 20q gain 272 (31%) 619 0.00031069 0.149 0.00084315 0.371 1.2169e-33 9.72e-31 2.7663e-10 1.97e-07 0.23809 1 0.75205 1 1.2395e-05 0.00716 0.0067279 1 3.7779e-07 0.000244 0.13901 1 21q gain 101 (11%) 790 0.001992 0.811 6.9421e-05 0.0369 5.0024e-09 3.48e-06 2.1184e-06 0.00131 0.11295 1 0.012655 1 1.6526e-10 1.18e-07 6.6345e-10 4.7e-07 1.0763e-05 0.00627 1.9661e-05 0.0112 22q gain 42 (5%) 849 0.012766 1 0.0047833 1 5.2679e-11 3.81e-08 0.015341 1 0.133 1 0.14754 1 3.0234e-06 0.00185 1.4095e-05 0.0081 0.00030084 0.145 6.3219e-06 0.00377 Xq gain 20 (2%) 871 3.9005e-05 0.0212 0.00088887 0.387 7.0047e-05 0.0371 0.013918 1 0.08052 1 0.0084987 1 0.00050777 0.232 7.9708e-05 0.042 9.2541e-06 0.00543 9.9262e-05 0.0518 1p loss 123 (14%) 768 0.00047163 0.216 3.778e-10 2.68e-07 6.7727e-22 5.32e-19 2.3463e-06 0.00144 0.53055 1 0.28159 1 1.5402e-11 1.13e-08 2.2688e-07 0.000148 0.00016687 0.0833 0.00025942 0.127 1q loss 21 (2%) 870 0.25688 1 0.066969 1 0.042083 1 0.16188 1 0.40635 1 0.85225 1 0.018849 1 0.4614 1 0.022517 1 0.47953 1 2p loss 71 (8%) 820 0.0022224 0.891 0.00030953 0.149 5.1585e-12 3.83e-09 2.1984e-05 0.0124 0.060025 1 0.017223 1 1.2284e-06 0.000773 1.3695e-06 0.000856 2.219e-05 0.0124 0.0057124 1 2q loss 87 (10%) 804 0.076111 1 0.0032556 1 3.9277e-11 2.86e-08 1.9986e-05 0.0113 0.13675 1 0.084499 1 0.0016202 0.682 0.0021509 0.865 3.6148e-05 0.0197 0.4861 1 3p loss 90 (10%) 801 1.6334e-07 0.000107 0.0003375 0.16 1.1944e-08 8.22e-06 0.00013214 0.0675 0.0027497 1 6.6174e-05 0.0352 1.8309e-05 0.0105 0.0016684 0.696 1.8166e-07 0.000119 0.00013113 0.0671 3q loss 45 (5%) 846 2.8925e-05 0.0161 0.0041248 1 2.7099e-05 0.0151 0.032729 1 0.20628 1 0.079775 1 0.011985 1 0.12597 1 0.0011418 0.492 0.086565 1 4p loss 184 (21%) 707 2.6935e-08 1.83e-05 6.3619e-13 4.76e-10 8.6324e-26 6.84e-23 2e-14 1.52e-11 0.00018127 0.0901 1.3378e-05 0.00771 5.0797e-15 3.9e-12 6.3815e-15 4.89e-12 1.9904e-14 1.51e-11 1.7114e-10 1.23e-07 4q loss 154 (17%) 737 4.267e-05 0.0231 5.7122e-09 3.97e-06 6.3166e-22 4.97e-19 7.7831e-12 5.75e-09 0.015738 1 0.0019284 0.787 5.2511e-11 3.8e-08 4.6961e-11 3.41e-08 3.5513e-08 2.4e-05 7.552e-08 5.02e-05 5p loss 72 (8%) 819 4.4935e-05 0.0242 5.9757e-07 0.000382 7.5943e-21 5.95e-18 7.3006e-10 5.16e-07 0.00014137 0.0715 4.1934e-06 0.00253 9.1169e-09 6.3e-06 2.391e-08 1.64e-05 3.7384e-15 2.88e-12 1.7752e-12 1.32e-09 5q loss 123 (14%) 768 1.8211e-14 1.39e-11 4.8426e-15 3.72e-12 5.8457e-49 4.68e-46 1.0186e-31 8.13e-29 2.7511e-08 1.87e-05 1.4481e-10 1.04e-07 3.3066e-22 2.61e-19 7.8339e-24 6.2e-21 1.3106e-27 1.04e-24 1.2911e-30 1.03e-27 6p loss 105 (12%) 786 0.0083883 1 0.00024201 0.119 2.1878e-08 1.5e-05 3.0819e-05 0.017 0.016806 1 0.0050614 1 1.3604e-06 0.000853 6.9791e-06 0.00415 0.00014679 0.074 0.0030418 1 6q loss 164 (18%) 727 0.0016151 0.682 3.0393e-06 0.00186 1.5812e-13 1.19e-10 2.9037e-07 0.000188 0.00071134 0.317 0.0076028 1 7.5095e-09 5.2e-06 7.6592e-08 5.09e-05 0.00023601 0.116 3.0636e-06 0.00187 7p loss 47 (5%) 844 0.092594 1 0.031007 1 4.0682e-06 0.00246 0.004151 1 0.42364 1 0.44254 1 0.0017441 0.724 0.0095521 1 0.0084835 1 0.0080766 1 7q loss 63 (7%) 828 0.038155 1 0.15841 1 0.0058446 1 0.12502 1 0.23418 1 0.42096 1 0.043399 1 0.33309 1 0.019963 1 0.27639 1 8p loss 274 (31%) 617 0.009888 1 0.14156 1 1.9759e-16 1.53e-13 1.9266e-06 0.0012 0.61977 1 0.93589 1 0.00080907 0.357 0.14221 1 0.00046411 0.213 0.040201 1 8q loss 45 (5%) 846 0.57334 1 0.54889 1 0.16332 1 0.14802 1 0.82266 1 0.85639 1 0.025508 1 0.6523 1 0.073137 1 1 1 9p loss 184 (21%) 707 0.0086559 1 0.00043694 0.203 3.9931e-21 3.13e-18 3.3653e-11 2.45e-08 0.032834 1 0.74696 1 1.7595e-06 0.00109 0.088433 1 8.4319e-07 0.000535 0.0066855 1 9q loss 142 (16%) 749 0.0048587 1 0.00013816 0.0702 6.5689e-17 5.1e-14 1.103e-08 7.61e-06 0.010475 1 0.17035 1 1.3607e-08 9.35e-06 0.00038939 0.183 7.8388e-11 5.66e-08 0.00016199 0.0812 10p loss 71 (8%) 820 0.054651 1 0.032543 1 1.5214e-05 0.00871 0.010764 1 0.60506 1 0.39885 1 0.00029049 0.141 0.17247 1 0.0020105 0.814 0.20014 1 10q loss 110 (12%) 781 0.0055815 1 0.0024429 0.97 3.6907e-11 2.69e-08 3.7221e-06 0.00225 0.0034536 1 0.055923 1 7.5687e-06 0.0045 0.029949 1 0.0019991 0.812 0.013761 1 11p loss 148 (17%) 743 0.87393 1 0.21839 1 6.7038e-12 4.97e-09 2.7799e-08 1.88e-05 0.13274 1 0.022531 1 0.0035007 1 0.031121 1 9.8973e-05 0.0518 0.31888 1 11q loss 228 (26%) 663 3.8505e-05 0.021 0.0018533 0.76 6.2555e-26 4.96e-23 2.1216e-10 1.51e-07 0.17293 1 0.19832 1 3.0021e-06 0.00184 0.00034561 0.164 0.0024034 0.958 0.0047212 1 12p loss 67 (8%) 824 0.05201 1 0.19384 1 0.0018207 0.752 9.2139e-06 0.00542 0.15692 1 0.33272 1 0.00011246 0.0583 0.0037088 1 0.0074869 1 0.02552 1 12q loss 52 (6%) 839 0.003138 1 0.00018697 0.0927 4.0772e-07 0.000262 3.1711e-08 2.15e-05 0.0060035 1 0.003455 1 5.4024e-08 3.61e-05 1.3068e-07 8.61e-05 1.0816e-05 0.00629 1.9813e-05 0.0112 13q loss 264 (30%) 627 0.022469 1 0.00033248 0.159 2.4513e-26 1.95e-23 9.0633e-08 6e-05 0.83767 1 0.56749 1 0.00024182 0.119 0.003709 1 3.0853e-09 2.16e-06 0.15832 1 14q loss 131 (15%) 760 2.489e-07 0.000162 4.2258e-08 2.84e-05 1.0211e-21 8.02e-19 2.8904e-15 2.23e-12 0.00010274 0.0534 4.0634e-05 0.0221 1.2121e-10 8.71e-08 5.5902e-12 4.15e-09 6.4463e-13 4.82e-10 8.2486e-14 6.23e-11 15q loss 159 (18%) 732 0.0089415 1 0.00012602 0.0646 2.7288e-18 2.12e-15 2.0309e-06 0.00126 0.13423 1 0.0076182 1 3.1259e-05 0.0172 0.000971 0.421 1.9228e-07 0.000125 6.5848e-07 0.00042 16p loss 56 (6%) 835 0.069949 1 0.022374 1 6.4543e-05 0.0344 0.00010895 0.0565 0.088008 1 0.18584 1 0.001664 0.696 0.0039432 1 0.00086377 0.378 0.0018842 0.771 16q loss 392 (44%) 499 2.0648e-11 1.51e-08 1.5978e-13 1.2e-10 1.4062e-11 1.03e-08 2.7888e-14 2.11e-11 7.0305e-07 0.000447 5.2411e-11 3.8e-08 7.208e-19 5.62e-16 2.1146e-20 1.65e-17 1.9558e-19 1.53e-16 5.8682e-20 4.58e-17 17p loss 367 (41%) 524 0.037618 1 0.67782 1 2.0398e-12 1.52e-09 1.3967e-07 9.19e-05 0.0012091 0.519 0.15162 1 0.20966 1 0.91401 1 2.9401e-05 0.0163 0.027558 1 17q loss 141 (16%) 750 4.0151e-08 2.7e-05 1.0339e-06 0.000654 9.2734e-14 6.98e-11 1.1184e-06 0.000705 3.3791e-10 2.4e-07 5.8436e-07 0.000374 1.731e-10 1.24e-07 1.0572e-05 0.00617 3.6698e-09 2.57e-06 1.0935e-06 0.000691 18p loss 172 (19%) 719 0.062464 1 0.077894 1 3.2002e-08 2.16e-05 4.3221e-06 0.0026 0.98719 1 0.97434 1 0.036883 1 0.55878 1 0.045219 1 0.027529 1 18q loss 175 (20%) 716 0.0092465 1 0.12151 1 9.7614e-11 7.04e-08 4.0439e-08 2.72e-05 0.54752 1 0.79453 1 0.0035725 1 0.13641 1 0.055409 1 0.18796 1 19p loss 65 (7%) 826 0.14285 1 0.00027333 0.133 8.8289e-14 6.66e-11 1.8961e-09 1.33e-06 0.53801 1 0.11757 1 0.00084491 0.371 0.0021035 0.848 0.00080779 0.357 0.16504 1 19q loss 51 (6%) 840 0.11641 1 3.1205e-05 0.0172 1.4268e-11 1.05e-08 1.1502e-05 0.00667 0.14976 1 0.12495 1 0.0001328 0.0677 0.00088018 0.384 0.013739 1 0.25838 1 20p loss 54 (6%) 837 0.55448 1 0.015671 1 9.3784e-08 6.2e-05 0.00043131 0.201 0.36197 1 0.49766 1 0.0036639 1 0.00047878 0.219 5.0868e-05 0.0273 0.0032533 1 20q loss 29 (3%) 862 0.84842 1 0.10221 1 4.7509e-06 0.00285 8.4293e-06 0.00499 0.52909 1 0.16217 1 0.0041759 1 0.00021663 0.107 5.0627e-05 0.0272 2.7609e-05 0.0154 21q loss 87 (10%) 804 0.23477 1 0.29842 1 1.3137e-06 0.000825 0.35383 1 0.97797 1 0.87361 1 0.32439 1 0.401 1 0.034605 1 0.14465 1 22q loss 298 (33%) 593 3.0778e-05 0.017 5.4191e-07 0.000347 4.9693e-08 3.32e-05 9.121e-06 0.00537 0.00035787 0.169 1.0169e-05 0.00595 1.5413e-11 1.13e-08 8.2786e-10 5.84e-07 1.6457e-08 1.13e-05 6.5805e-07 0.00042 Xq loss 30 (3%) 861 0.0041487 1 0.12236 1 0.00011878 0.0612 0.0014259 0.607 0.035578 1 0.31662 1 0.0096351 1 0.069236 1 7.2127e-05 0.0382 0.027751 1