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 Amp Peak 1(1p22.3) 203 (23%) 688 1.4925e-06 0.000475 6.5771e-12 2.99e-09 3.4264e-16 1.8e-13 7.1281e-14 3.49e-11 0.00015144 0.0345 1.7418e-07 6.06e-05 2.3003e-15 1.18e-12 8.6974e-17 4.64e-14 2.7155e-14 1.34e-11 3.2443e-18 1.78e-15 Amp Peak 2(1q21.3) 645 (72%) 246 0.019874 1 0.00012201 0.0282 1.0241e-10 4.46e-08 0.00019414 0.0435 0.071702 1 0.0081676 1 0.00029231 0.0634 0.0010408 0.2 3.9484e-05 0.0101 0.0043 0.671 Amp Peak 3(1q44) 642 (72%) 249 0.38691 1 0.06703 1 2.1655e-08 8.12e-06 0.00052668 0.11 0.92763 1 0.34515 1 0.33487 1 0.5326 1 0.4169 1 0.64049 1 Amp Peak 4(3p26.1) 182 (20%) 709 0.0005336 0.11 3.4471e-05 0.00902 5.0987e-13 2.43e-10 3.2759e-07 0.00011 0.0062989 0.926 0.0063799 0.931 5.0341e-10 2.09e-07 3.4533e-05 0.00902 1.0067e-08 3.86e-06 2.9517e-06 0.000894 Amp Peak 5(3q26.32) 286 (32%) 605 4.5392e-11 2.02e-08 1.5096e-10 6.48e-08 2.5782e-37 1.58e-34 3.9194e-15 1.98e-12 1.2088e-06 0.000389 5.8992e-06 0.0017 1.9467e-23 1.13e-20 1.7099e-20 9.68e-18 2.7964e-16 1.48e-13 6.2433e-21 3.55e-18 Amp Peak 6(4q13.3) 141 (16%) 750 0.00084957 0.17 0.00055521 0.114 3.3436e-16 1.76e-13 8.7172e-07 0.000282 0.083821 1 0.5615 1 1.0074e-05 0.00286 0.00052268 0.109 0.00064945 0.132 2.8003e-07 9.52e-05 Amp Peak 7(6p23) 235 (26%) 656 5.8471e-11 2.57e-08 6.0496e-09 2.36e-06 8.384e-33 5.07e-30 2.5808e-15 1.32e-12 9.9953e-07 0.000323 7.4104e-05 0.0181 1.8729e-14 9.36e-12 6.8325e-11 2.99e-08 9.532e-19 5.27e-16 2.914e-16 1.54e-13 Amp Peak 8(6q21) 165 (19%) 726 2.7991e-15 1.43e-12 6.1523e-10 2.55e-07 1.009e-39 6.21e-37 1.0942e-11 4.95e-09 1.0359e-08 3.95e-06 4.9081e-07 0.000162 6.6413e-24 3.87e-21 2.2194e-18 1.22e-15 3.1284e-21 1.78e-18 2.8569e-26 1.69e-23 Amp Peak 9(8p11.23) 335 (38%) 556 0.041036 1 0.0082593 1 3.123e-26 1.84e-23 2.4711e-10 1.05e-07 0.048572 1 0.0092515 1 1.757e-05 0.0048 0.0026551 0.438 0.15965 1 0.037376 1 Amp Peak 10(8p11.21) 345 (39%) 546 0.2593 1 0.15255 1 2.997e-25 1.76e-22 3.7747e-05 0.0097 0.78006 1 0.68044 1 5.2174e-05 0.013 0.00013441 0.0309 0.037218 1 0.20749 1 Amp Peak 11(8q24.21) 573 (64%) 318 3.6091e-10 1.52e-07 2.0292e-10 8.62e-08 1.7661e-45 1.1e-42 5.5749e-23 3.22e-20 3.676e-08 1.34e-05 5.2744e-07 0.000174 2.336e-20 1.31e-17 6.8831e-13 3.27e-10 3.182e-24 1.86e-21 1.553e-19 8.65e-17 Amp Peak 12(10p15.1) 253 (28%) 638 7.9722e-17 4.26e-14 4.1821e-19 2.32e-16 4.5796e-35 2.79e-32 9.0186e-24 5.24e-21 1.4282e-10 6.14e-08 1.4603e-12 6.88e-10 2.518e-29 1.51e-26 3.1024e-28 1.85e-25 1.725e-27 1.03e-24 6.4508e-35 3.93e-32 Amp Peak 13(10q22.3) 129 (14%) 762 5.4479e-05 0.0135 0.053608 1 1.0105e-09 4.12e-07 0.00022593 0.0499 0.0027915 0.458 0.014602 1 9.9264e-08 3.51e-05 0.0017097 0.304 5.1712e-06 0.00149 0.00014718 0.0337 Amp Peak 14(11p13) 186 (21%) 705 0.001696 0.304 0.11164 1 3.2974e-08 1.21e-05 0.00075057 0.152 0.096909 1 0.14023 1 8.0291e-05 0.0194 0.028177 1 3.5049e-05 0.00904 1.3947e-05 0.00391 Amp Peak 15(11q13.3) 340 (38%) 551 0.23083 1 0.025315 1 6.2008e-34 3.77e-31 1.8285e-08 6.89e-06 0.95737 1 0.17376 1 0.04243 1 0.31959 1 0.0021283 0.368 0.11929 1 Amp Peak 16(11q14.1) 220 (25%) 671 0.014339 1 0.078337 1 4.5848e-13 2.19e-10 3.1428e-05 0.0083 0.070315 1 0.18875 1 0.00011169 0.0261 0.0012125 0.23 4.6398e-07 0.000155 7.0124e-05 0.0172 Amp Peak 17(12p13.33) 232 (26%) 659 1.7403e-10 7.43e-08 1.3528e-13 6.57e-11 3.3214e-28 1.98e-25 4.3965e-15 2.22e-12 6.7855e-08 2.42e-05 3.0795e-07 0.000104 1.7932e-17 9.7e-15 2.0923e-15 1.08e-12 4.1582e-22 2.39e-19 3.451e-19 1.92e-16 Amp Peak 18(12q15) 228 (26%) 663 1.7547e-06 0.000551 6.2929e-08 2.26e-05 1.5951e-25 9.36e-23 1.6394e-13 7.95e-11 0.18715 1 0.072382 1 1.1747e-05 0.00331 0.010493 1 6.1364e-09 2.39e-06 0.17547 1 Amp Peak 19(13q12.3) 125 (14%) 766 0.0088459 1 0.028166 1 9.3451e-06 0.00266 0.019472 1 0.0090675 1 0.10639 1 2.1802e-06 0.000674 0.015127 1 3.5297e-06 0.00106 0.005046 0.777 Amp Peak 20(13q34) 157 (18%) 734 0.0011047 0.211 8.5736e-10 3.53e-07 1.9008e-20 1.07e-17 2.3702e-12 1.1e-09 4.1038e-06 0.0012 2.8825e-08 1.06e-05 3.5403e-16 1.86e-13 3.0451e-15 1.55e-12 2.3592e-15 1.21e-12 1.2619e-19 7.04e-17 Amp Peak 21(14q21.1) 179 (20%) 712 0.012308 1 0.00042976 0.0911 1.0341e-13 5.04e-11 3.9147e-06 0.00116 0.12705 1 0.045887 1 1.6526e-05 0.00453 0.0012288 0.232 0.00011313 0.0264 0.026092 1 Amp Peak 22(15q26.3) 162 (18%) 729 3.1592e-07 0.000107 0.00028641 0.0624 2.3575e-14 1.17e-11 0.00091017 0.18 0.00016762 0.038 0.026328 1 5.2469e-08 1.91e-05 3.2892e-05 0.00865 1.3701e-07 4.8e-05 4.1751e-10 1.74e-07 Amp Peak 23(17p11.2) 124 (14%) 767 0.15133 1 0.030527 1 7.6042e-07 0.000248 0.002992 0.482 0.35776 1 0.61303 1 0.0023647 0.397 0.07069 1 0.18297 1 0.34203 1 Amp Peak 24(17q12) 289 (32%) 602 0.00010835 0.0256 1.5148e-05 0.00418 9.137e-37 5.6e-34 8.7175e-08 3.09e-05 0.047649 1 0.005472 0.826 6.5874e-05 0.0162 0.025312 1 0.0016274 0.295 0.00041554 0.0885 Amp Peak 25(17q23.1) 367 (41%) 524 0.00036742 0.0788 5.1075e-05 0.0128 4.1161e-40 2.54e-37 4.7326e-09 1.86e-06 0.1894 1 0.46222 1 0.00019857 0.0443 0.32738 1 1.7187e-06 0.000541 0.04448 1 Amp Peak 26(19q12) 231 (26%) 660 5.6131e-08 2.03e-05 5.5543e-12 2.53e-09 1.8142e-24 1.06e-21 1.3736e-08 5.21e-06 6.5623e-07 0.000216 1.507e-06 0.000478 3.8722e-14 1.91e-11 4.6703e-17 2.51e-14 2.3561e-12 1.1e-09 1.6857e-17 9.15e-15 Amp Peak 27(19q13.42) 232 (26%) 659 0.00020247 0.0449 0.0013831 0.26 5.8026e-15 2.92e-12 4.7118e-06 0.00137 0.0016064 0.294 0.049464 1 0.0045896 0.711 0.024205 1 1.886e-05 0.00513 9.4408e-05 0.0225 Amp Peak 28(20q13.2) 455 (51%) 436 2.5795e-08 9.54e-06 1.2182e-06 0.000391 3.2298e-49 2.02e-46 2.0685e-20 1.16e-17 0.00049377 0.104 0.0099416 1 1.1728e-09 4.75e-07 0.018545 1 3.0179e-11 1.35e-08 2.2943e-08 8.58e-06 Del Peak 1(1p36.13) 373 (42%) 518 0.006087 0.901 3.1739e-06 0.000959 2.9981e-33 1.82e-30 6.6948e-08 2.39e-05 0.00536 0.815 0.063888 1 4.3304e-06 0.00126 0.0027958 0.458 3.4034e-11 1.51e-08 0.10411 1 Del Peak 2(1p21.2) 301 (34%) 590 0.011436 1 0.00010919 0.0257 4.0406e-23 2.34e-20 8.7654e-05 0.021 0.0016422 0.296 0.011188 1 0.0003663 0.0788 0.0013939 0.261 0.0022106 0.38 0.0038819 0.609 Del Peak 3(2q37.3) 263 (30%) 628 7.6923e-07 0.00025 5.892e-09 2.3e-06 5.2724e-20 2.96e-17 4.738e-10 1.97e-07 1.3169e-08 5e-06 1.5277e-07 5.33e-05 3.1925e-11 1.42e-08 2.1954e-07 7.55e-05 3.3007e-12 1.52e-09 2.5782e-07 8.82e-05 Del Peak 4(3p14.3) 274 (31%) 617 2.2308e-13 1.08e-10 8.4208e-09 3.25e-06 2.2631e-32 1.37e-29 4.6478e-12 2.13e-09 2.2113e-09 8.82e-07 1.1969e-05 0.00336 1.6331e-16 8.67e-14 5.3655e-11 2.37e-08 9.8103e-20 5.49e-17 2.2728e-14 1.13e-11 Del Peak 5(4p16.3) 279 (31%) 612 1.3853e-10 5.97e-08 3.158e-12 1.47e-09 2.4601e-27 1.46e-24 8.8219e-12 4.01e-09 6.6491e-07 0.000218 3.2206e-06 0.000969 2.7209e-22 1.57e-19 5.6009e-18 3.06e-15 1.1163e-14 5.6e-12 3.7105e-15 1.88e-12 Del Peak 6(4q35.2) 280 (31%) 611 7.1227e-10 2.94e-07 1.9187e-07 6.65e-05 7.0351e-36 4.3e-33 5.9641e-14 2.92e-11 3.4706e-08 1.27e-05 2.0922e-06 0.000651 3.0353e-21 1.73e-18 1.181e-15 6.12e-13 1.0044e-15 5.23e-13 2.3409e-17 1.26e-14 Del Peak 7(5q11.2) 231 (26%) 660 8.0735e-22 4.63e-19 5.5837e-26 3.28e-23 3.4162e-62 2.15e-59 3.2708e-36 2e-33 1.986e-15 1.02e-12 1.2745e-18 7.04e-16 3.0997e-41 1.92e-38 8.3555e-44 5.19e-41 6.0245e-41 3.72e-38 2.3546e-49 1.47e-46 Del Peak 8(5q21.3) 223 (25%) 668 5.1807e-25 3.03e-22 1.8339e-27 1.09e-24 2.4035e-74 1.51e-71 1.4061e-50 8.82e-48 5.7612e-15 2.9e-12 2.8184e-15 1.44e-12 2.8871e-48 1.8e-45 5.1004e-49 3.18e-46 2.7409e-40 1.69e-37 2.2858e-53 1.44e-50 Del Peak 9(6p25.3) 167 (19%) 724 0.91769 1 0.54218 1 4.0714e-06 0.0012 5.5607e-05 0.0137 0.46905 1 0.58689 1 0.002207 0.38 0.061649 1 0.040327 1 0.10304 1 Del Peak 10(6q15) 293 (33%) 598 0.079515 1 0.00098519 0.191 1.4484e-26 8.57e-24 1.0724e-07 3.79e-05 0.39551 1 0.10459 1 1.9791e-05 0.00536 8.0002e-05 0.0194 0.05288 1 0.0016091 0.294 Del Peak 11(6q27) 303 (34%) 588 0.14805 1 0.39841 1 3.0436e-13 1.46e-10 0.0023442 0.396 0.052389 1 0.58107 1 0.4864 1 0.52041 1 0.15935 1 0.61146 1 Del Peak 12(7p22.3) 117 (13%) 774 0.00023332 0.0513 0.0005474 0.113 7.0882e-16 3.71e-13 1.5406e-05 0.00424 0.022197 1 0.0055599 0.834 7.9341e-09 3.07e-06 3.7204e-06 0.00111 3.8983e-10 1.63e-07 3.6152e-09 1.43e-06 Del Peak 13(7q36.1) 173 (19%) 718 0.00056244 0.115 0.0077642 1 2.341e-08 8.73e-06 0.069033 1 0.60605 1 0.073538 1 0.00082398 0.166 0.043797 1 7.7538e-09 3.01e-06 1.5698e-06 0.000496 Del Peak 14(8p23.2) 469 (53%) 422 3.4414e-05 0.00902 2.9156e-06 0.000886 1.1481e-30 6.91e-28 2.9202e-10 1.23e-07 0.011184 1 0.029966 1 2.3761e-11 1.07e-08 2.0061e-06 0.000626 5.3538e-08 1.94e-05 1.496e-09 6.03e-07 Del Peak 15(8p11.21) 170 (19%) 721 0.00017509 0.0394 0.00259 0.433 1.1158e-10 4.84e-08 0.018991 1 0.036012 1 0.018441 1 0.00099558 0.192 0.03934 1 0.021254 1 4.9717e-06 0.00144 Del Peak 16(9p21.3) 298 (33%) 593 1.0142e-05 0.00287 3.9616e-06 0.00117 7.6258e-29 4.57e-26 2.7556e-14 1.36e-11 0.0034156 0.543 0.33762 1 1.1419e-07 4.02e-05 0.001827 0.323 9.5758e-10 3.94e-07 5.1893e-05 0.013 Del Peak 17(9q21.11) 239 (27%) 652 0.00091444 0.18 1.9801e-05 0.00536 9.5748e-18 5.22e-15 9.7718e-10 4.01e-07 1.437e-05 0.00399 0.0051535 0.788 2.8174e-06 0.000862 8.6718e-05 0.0209 8.6789e-09 3.34e-06 1.3494e-09 5.45e-07 Del Peak 18(10q23.31) 258 (29%) 633 4.6514e-07 0.000155 9.2336e-05 0.0221 1.3083e-18 7.21e-16 5.1422e-11 2.27e-08 5.6891e-08 2.05e-05 2.1493e-05 0.00578 2.3787e-12 1.11e-09 6.3911e-08 2.29e-05 4.4078e-09 1.73e-06 4.1191e-09 1.63e-06 Del Peak 19(10q26.3) 259 (29%) 632 1.7477e-09 7e-07 3.6834e-07 0.000124 1.0179e-19 5.69e-17 1.2427e-10 5.38e-08 2.1184e-08 7.97e-06 1.9169e-07 6.65e-05 1.562e-15 8.08e-13 2.2598e-10 9.58e-08 1.6619e-13 8.04e-11 1.9113e-12 8.96e-10 Del Peak 20(11p15.5) 259 (29%) 632 5.0388e-11 2.23e-08 6.2198e-08 2.24e-05 3e-30 1.8e-27 1.0072e-09 4.12e-07 2.5146e-09 9.98e-07 3.814e-06 0.00114 1.0473e-16 5.57e-14 3.6423e-12 1.68e-09 7.3339e-17 3.92e-14 7.1317e-17 3.82e-14 Del Peak 21(11q23.2) 442 (50%) 449 0.0081861 1 0.083213 1 3.5868e-26 2.11e-23 3.1675e-10 1.33e-07 0.91854 1 0.50725 1 0.0014126 0.263 0.0026171 0.434 0.010591 1 0.0030656 0.49 Del Peak 22(12p13.1) 156 (18%) 735 0.031613 1 0.066986 1 0.0022615 0.384 0.015358 1 0.24385 1 0.050622 1 0.0014539 0.269 0.017338 1 0.00096174 0.188 9.4476e-05 0.0225 Del Peak 23(12q24.31) 162 (18%) 729 1.7049e-10 7.3e-08 9.2928e-11 4.05e-08 1.9007e-19 1.06e-16 2.8667e-13 1.38e-10 1.4422e-05 0.00399 7.1623e-07 0.000234 6.9058e-17 3.71e-14 2.1557e-16 1.14e-13 3.2805e-12 1.52e-09 3.2352e-12 1.5e-09 Del Peak 24(13q14.2) 407 (46%) 484 0.010184 1 3.07e-05 0.00814 2.4345e-28 1.46e-25 2.5093e-06 0.000773 0.55938 1 0.10385 1 1.3352e-07 4.69e-05 3.4521e-05 0.00902 1.5518e-08 5.87e-06 2.6164e-05 0.00701 Del Peak 25(14q24.3) 286 (32%) 605 2.5826e-07 8.82e-05 1.054e-09 4.29e-07 6.7492e-33 4.09e-30 4.5811e-13 2.19e-10 2.5132e-07 8.62e-05 2.886e-06 0.00088 1.986e-14 9.91e-12 1.1005e-12 5.22e-10 8.2532e-18 4.51e-15 1.2316e-20 6.98e-18 Del Peak 26(15q13.1) 310 (35%) 581 2.1198e-06 0.000657 3.2612e-08 1.2e-05 9.2898e-31 5.6e-28 5.25e-12 2.4e-09 0.00031636 0.0683 4.7814e-05 0.012 3.2689e-15 1.66e-12 1.4288e-12 6.74e-10 1.0239e-15 5.32e-13 2.6696e-21 1.53e-18 Del Peak 27(16q24.3) 575 (65%) 316 1.7616e-12 8.28e-10 5.6752e-13 2.7e-10 6.5647e-11 2.88e-08 4.1644e-10 1.74e-07 1.7129e-09 6.89e-07 2.079e-11 9.36e-09 3.3411e-18 1.83e-15 1.1923e-17 6.49e-15 5.6742e-14 2.79e-11 1.9939e-20 1.12e-17 Del Peak 28(17p12) 537 (60%) 354 4.0088e-06 0.00118 0.054032 1 1.3529e-21 7.75e-19 2.1549e-07 7.43e-05 0.00011351 0.0264 0.0081833 1 0.0028466 0.461 0.098642 1 1.4865e-06 0.000474 1.811e-06 0.000567 Del Peak 29(17q21.31) 312 (35%) 579 2.3455e-12 1.1e-09 3.8221e-07 0.000128 9.3122e-23 5.37e-20 4.985e-14 2.45e-11 1.5526e-11 7e-09 5.8755e-11 2.58e-08 1.2089e-20 6.87e-18 1.1744e-15 6.1e-13 1.7768e-14 8.9e-12 2.7721e-16 1.47e-13 Del Peak 30(18q23) 290 (33%) 601 6.0392e-06 0.00173 0.027168 1 3.8679e-12 1.78e-09 1.016e-08 3.88e-06 0.0060122 0.896 0.59579 1 2.7374e-05 0.00731 0.039642 1 4.3119e-05 0.011 0.00016864 0.0381 Del Peak 31(19p13.3) 301 (34%) 590 1.0806e-09 4.39e-07 9.679e-09 3.72e-06 3.9698e-43 2.46e-40 4.0492e-17 2.18e-14 2.6747e-06 0.000821 4.3128e-05 0.011 3.1094e-13 1.49e-10 2.3007e-09 9.16e-07 9.0702e-16 4.73e-13 2.1398e-14 1.07e-11 Del Peak 32(19q13.32) 180 (20%) 711 3.0318e-05 0.00806 8.2869e-06 0.00237 1.7712e-17 9.6e-15 3.0674e-11 1.37e-08 0.00046867 0.0989 4.5177e-05 0.0114 4.3958e-09 1.73e-06 1.3876e-06 0.000444 1.3741e-10 5.94e-08 2.4617e-08 9.16e-06 Del Peak 33(20p13) 132 (15%) 759 0.0020553 0.36 1.4187e-05 0.00396 9.517e-14 4.64e-11 3.975e-07 0.000133 0.00085031 0.17 0.0068303 0.99 1.8017e-10 7.68e-08 2.5676e-08 9.53e-06 1.0576e-11 4.79e-09 1.7448e-09 7e-07 Del Peak 34(21q11.2) 181 (20%) 710 0.0020931 0.364 0.059264 1 1.3799e-12 6.53e-10 0.00027502 0.0602 0.3089 1 0.5039 1 0.010527 1 0.23488 1 0.017198 1 0.073493 1 Del Peak 35(22q13.32) 399 (45%) 492 0.070286 1 0.10948 1 0.00093558 0.183 0.0014644 0.269 0.11059 1 0.018766 1 0.0020093 0.354 0.020837 1 0.0034235 0.543 0.16948 1