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 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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Amp Peak 1(1q31.1) 134 (23%) 441 0.46848 1 0.55953 1 0.00020463 0.125 0.72236 1 0.31062 1 0.82655 1 0.035772 1 0.59765 1 0.76478 1 0.94434 1 Amp Peak 2(2q33.1) 123 (21%) 452 0.042299 1 0.018839 1 1.5207e-06 0.000982 0.0050196 1 0.5325 1 0.29825 1 0.083012 1 0.0051763 1 0.18061 1 0.0012944 0.753 Amp Peak 3(5p12) 107 (19%) 468 0.10927 1 0.97471 1 6.5452e-06 0.00417 0.7939 1 0.042324 1 0.70151 1 0.10839 1 0.057672 1 0.88927 1 0.34721 1 Amp Peak 4(5q22.3) 59 (10%) 516 0.9046 1 0.41019 1 0.0037006 1 0.3195 1 0.35083 1 0.59065 1 0.18869 1 0.030709 1 0.46039 1 0.89428 1 Amp Peak 5(6p21.1) 146 (25%) 429 0.024692 1 0.0014495 0.842 3.9711e-14 2.79e-11 0.16938 1 0.48212 1 0.6576 1 0.00094035 0.555 0.00030314 0.183 0.53094 1 0.0067783 1 Amp Peak 6(7p21.3) 337 (59%) 238 0.00043479 0.26 0.0049714 1 7.9137e-22 5.75e-19 7.1064e-06 0.00451 0.022271 1 0.0020641 1 4.4469e-06 0.00285 6.0679e-06 0.00387 0.022382 1 0.0025921 1 Amp Peak 7(8p11.23) 196 (34%) 379 0.49951 1 0.33946 1 2.8317e-23 2.07e-20 0.30365 1 0.98119 1 0.64668 1 0.13548 1 0.3605 1 0.015361 1 0.077226 1 Amp Peak 8(8p11.21) 238 (41%) 337 0.25487 1 0.19058 1 3.3334e-31 2.45e-28 0.23711 1 0.49748 1 0.68152 1 0.015657 1 0.19942 1 0.081506 1 0.20055 1 Amp Peak 9(8q12.1) 309 (54%) 266 0.065106 1 0.084239 1 1.9068e-36 1.41e-33 0.015312 1 0.025169 1 0.14723 1 0.0011485 0.674 0.01408 1 0.10208 1 0.1461 1 Amp Peak 10(8q24.21) 345 (60%) 230 0.21136 1 0.089174 1 3.1776e-35 2.35e-32 0.0042881 1 0.034874 1 0.29211 1 0.0037086 1 0.041636 1 0.25116 1 0.17643 1 Amp Peak 11(10q22.3) 35 (6%) 540 0.90278 1 0.22385 1 0.65461 1 0.56037 1 0.63426 1 0.50643 1 0.79803 1 0.17974 1 0.58747 1 0.28086 1 Amp Peak 12(11p15.5) 129 (22%) 446 3.6048e-05 0.0224 0.0010011 0.59 1.8397e-06 0.00118 0.0034433 1 0.38932 1 0.36891 1 2.0728e-05 0.013 8.5631e-06 0.00541 0.35173 1 0.0090568 1 Amp Peak 13(12p13.32) 144 (25%) 431 0.17402 1 0.91102 1 0.25212 1 0.13658 1 0.42615 1 0.99748 1 0.23306 1 0.46864 1 0.67615 1 0.88617 1 Amp Peak 14(13q12.13) 371 (65%) 204 2.0857e-08 1.39e-05 5.8826e-07 0.000383 6.4175e-44 4.79e-41 8.9135e-11 6.1e-08 0.010542 1 0.19854 1 8.725e-11 5.98e-08 2.2476e-11 1.55e-08 0.013611 1 0.23666 1 Amp Peak 15(13q12.2) 366 (64%) 209 6.5088e-07 0.000423 3.3665e-06 0.00216 2.2045e-45 1.65e-42 2.3112e-11 1.59e-08 0.025639 1 0.36311 1 6.4939e-10 4.41e-07 7.1054e-11 4.87e-08 0.026046 1 0.28461 1 Amp Peak 16(13q22.1) 371 (65%) 204 5.1363e-06 0.00328 2.278e-05 0.0143 7.6851e-42 5.7e-39 2.9909e-09 2.02e-06 0.052981 1 0.16208 1 4.3351e-09 2.91e-06 6.6708e-11 4.58e-08 0.03008 1 0.04712 1 Amp Peak 17(15q26.1) 43 (7%) 532 0.85836 1 0.47865 1 0.24946 1 0.84162 1 0.1731 1 0.62275 1 0.8488 1 0.71952 1 0.92601 1 1 1 Amp Peak 18(16p11.2) 161 (28%) 414 0.016608 1 0.0095853 1 1.3311e-20 9.64e-18 0.0015397 0.891 0.023521 1 0.016375 1 0.010231 1 0.0002203 0.134 0.81077 1 0.11023 1 Amp Peak 19(17q12) 144 (25%) 431 0.010941 1 0.02859 1 3.4581e-09 2.33e-06 0.0072631 1 0.24984 1 0.10322 1 6.1523e-05 0.038 0.00036729 0.221 0.038998 1 0.23162 1 Amp Peak 20(17q24.1) 128 (22%) 447 0.011564 1 0.0010668 0.627 1.5413e-08 1.03e-05 0.00034993 0.211 0.093794 1 0.0076274 1 7.9837e-05 0.0492 0.0023711 1 0.0012716 0.743 0.041926 1 Amp Peak 21(19p13.2) 97 (17%) 478 0.048769 1 0.61167 1 8.872e-08 5.85e-05 0.031724 1 0.58719 1 0.64762 1 0.0315 1 0.010154 1 0.27415 1 0.13138 1 Amp Peak 22(19q12) 122 (21%) 453 0.019148 1 0.021801 1 6.2256e-08 4.11e-05 0.25113 1 0.072262 1 0.51708 1 0.010787 1 0.00028544 0.173 0.70958 1 0.49006 1 Amp Peak 23(20p11.23) 301 (52%) 274 0.0086402 1 0.0007773 0.461 5.5572e-17 4e-14 0.014078 1 0.017095 1 0.72049 1 0.010624 1 1.5041e-06 0.000973 0.35274 1 0.42547 1 Amp Peak 24(20p11.21) 339 (59%) 236 0.00016679 0.102 5.1112e-06 0.00327 8.5661e-23 6.24e-20 6.9846e-06 0.00444 0.015376 1 0.43129 1 3.2316e-05 0.0201 7.752e-10 5.25e-07 0.10712 1 0.18811 1 Amp Peak 25(20q11.21) 439 (76%) 136 2.5654e-15 1.83e-12 5.2538e-13 3.67e-10 1.5402e-42 1.14e-39 2.1295e-16 1.53e-13 0.0052758 1 0.028382 1 4.7734e-17 3.44e-14 4.3776e-22 3.19e-19 0.12378 1 0.018878 1 Amp Peak 26(20q12) 441 (77%) 134 2.0388e-16 1.46e-13 2.7776e-14 1.96e-11 5.8367e-43 4.34e-40 3.5601e-15 2.53e-12 0.0027205 1 0.013857 1 2.3358e-17 1.68e-14 5.058e-23 3.69e-20 0.065014 1 0.0077889 1 Amp Peak 27(20q13.32) 444 (77%) 131 1.7529e-15 1.25e-12 9.9082e-13 6.91e-10 5.6648e-43 4.22e-40 3.2142e-14 2.27e-11 0.0046907 1 0.013158 1 7.6055e-18 5.5e-15 4.9259e-22 3.58e-19 0.11691 1 0.032951 1 Amp Peak 28(Xq28) 121 (21%) 454 0.52638 1 0.36301 1 1.7197e-06 0.00111 0.10043 1 0.0033673 1 0.038687 1 0.24145 1 0.59193 1 0.98952 1 0.78345 1 Del Peak 1(1p36.11) 222 (39%) 353 3.2244e-05 0.0201 0.0025597 1 2.207e-13 1.54e-10 2.1039e-05 0.0132 0.025938 1 0.22537 1 7.3103e-06 0.00463 5.8883e-05 0.0364 0.15838 1 0.018302 1 Del Peak 2(1p33) 156 (27%) 419 0.0053664 1 0.064623 1 8.9471e-13 6.25e-10 0.00037065 0.223 0.16104 1 0.53027 1 0.030862 1 0.093483 1 0.53241 1 0.015895 1 Del Peak 3(1p13.2) 157 (27%) 418 0.13297 1 0.090829 1 3.379e-09 2.28e-06 0.015335 1 0.29926 1 0.78194 1 0.051289 1 0.092962 1 0.75564 1 0.3515 1 Del Peak 4(2p12) 20 (3%) 555 1 1 0.5615 1 0.0019382 1 0.011104 1 0.035896 1 0.97464 1 0.32466 1 0.22776 1 0.016497 1 0.021531 1 Del Peak 5(2q22.1) 33 (6%) 542 0.92667 1 0.6263 1 0.14635 1 0.83265 1 0.016431 1 0.82587 1 0.16658 1 0.16701 1 0.31564 1 0.27226 1 Del Peak 6(2q37.2) 30 (5%) 545 0.92364 1 0.57641 1 0.28501 1 0.83265 1 0.2341 1 0.59965 1 0.66595 1 0.2859 1 0.24408 1 0.36359 1 Del Peak 7(3p26.3) 84 (15%) 491 0.10553 1 0.77216 1 0.16257 1 0.35748 1 0.85894 1 0.5179 1 0.10099 1 0.28329 1 0.27674 1 0.72808 1 Del Peak 8(3p14.2) 104 (18%) 471 0.45951 1 0.88027 1 0.93155 1 0.59731 1 0.34078 1 0.89544 1 0.24711 1 0.071253 1 0.059527 1 0.91843 1 Del Peak 9(3q26.31) 56 (10%) 519 0.30358 1 0.83681 1 0.4484 1 0.37333 1 0.16321 1 0.26042 1 0.30589 1 0.87998 1 0.093407 1 0.12285 1 Del Peak 10(4p16.1) 182 (32%) 393 0.032415 1 0.27379 1 1.6474e-12 1.15e-09 0.0020286 1 0.34614 1 0.72213 1 0.045893 1 0.013706 1 0.62193 1 0.11684 1 Del Peak 11(4q22.1) 198 (34%) 377 0.018593 1 0.046098 1 1.2505e-14 8.84e-12 7.6585e-05 0.0473 0.35384 1 0.69721 1 0.17572 1 0.0035491 1 0.14791 1 0.4088 1 Del Peak 12(4q35.1) 211 (37%) 364 0.0089243 1 0.17749 1 1.2462e-13 8.75e-11 0.00064166 0.382 0.41054 1 0.47685 1 0.062888 1 0.014218 1 0.52329 1 0.74296 1 Del Peak 13(5q11.2) 140 (24%) 435 0.0015088 0.875 0.15356 1 2.1328e-12 1.48e-09 0.0028212 1 0.11051 1 0.30588 1 0.002261 1 0.0047844 1 1 1 0.75785 1 Del Peak 14(5q22.2) 172 (30%) 403 0.0007635 0.454 0.033253 1 2.2261e-09 1.5e-06 0.11369 1 0.39517 1 0.93398 1 0.00053973 0.322 0.00023768 0.145 0.77075 1 0.85443 1 Del Peak 15(6p25.3) 78 (14%) 497 0.82929 1 0.47471 1 0.08489 1 0.26246 1 0.18406 1 0.45478 1 0.66572 1 0.19589 1 0.60986 1 0.95718 1 Del Peak 16(6q26) 90 (16%) 485 0.89418 1 0.64768 1 0.04006 1 0.76234 1 0.051367 1 0.47981 1 0.31239 1 0.10362 1 0.22283 1 0.50721 1 Del Peak 17(7q31.1) 15 (3%) 560 0.091873 1 0.50151 1 1 1 1 1 0.59232 1 0.41129 1 0.14063 1 0.86915 1 0.23486 1 0.49815 1 Del Peak 18(8p23.2) 272 (47%) 303 0.0008907 0.526 0.029967 1 2.1272e-34 1.57e-31 1.9574e-06 0.00126 0.019188 1 0.014044 1 3.9437e-05 0.0245 0.001242 0.727 0.80158 1 0.39873 1 Del Peak 19(8p22) 285 (50%) 290 0.00173 0.998 0.027541 1 1.581e-37 1.17e-34 1.3157e-06 0.000854 0.012248 1 0.0070586 1 5.2503e-05 0.0326 0.00024313 0.148 0.76329 1 0.64202 1 Del Peak 20(8p11.21) 124 (22%) 451 0.012961 1 0.12546 1 4.8516e-07 0.000317 0.34128 1 0.0055675 1 0.30486 1 0.025063 1 0.10499 1 0.1625 1 0.40038 1 Del Peak 21(8q11.1) 44 (8%) 531 0.2885 1 0.92255 1 0.0026632 1 0.66125 1 0.05145 1 0.49439 1 0.56598 1 0.87863 1 0.081906 1 0.019346 1 Del Peak 22(9p24.2) 78 (14%) 497 0.266 1 0.265 1 0.0017841 1 0.050595 1 0.56196 1 0.51483 1 0.14724 1 0.017437 1 0.29637 1 0.2426 1 Del Peak 23(10p15.3) 102 (18%) 473 0.32308 1 0.39496 1 1.3776e-07 9.05e-05 0.028831 1 0.07997 1 0.27358 1 0.075746 1 0.18852 1 0.71014 1 0.30188 1 Del Peak 24(10q21.1) 118 (21%) 457 0.25872 1 0.070251 1 3.1348e-11 2.16e-08 0.14957 1 0.030401 1 0.055891 1 0.18118 1 0.01098 1 0.69109 1 0.57652 1 Del Peak 25(10q23.31) 145 (25%) 430 0.27414 1 0.24499 1 9.0881e-08 5.98e-05 0.15474 1 0.12712 1 0.51877 1 0.93582 1 0.033009 1 0.76199 1 0.36526 1 Del Peak 26(10q25.2) 140 (24%) 435 0.38224 1 0.066234 1 3.0619e-12 2.12e-09 0.10548 1 0.010775 1 0.50727 1 0.98443 1 0.0082783 1 0.97166 1 0.77949 1 Del Peak 27(11q22.3) 104 (18%) 471 0.58711 1 0.89518 1 0.03853 1 0.12502 1 0.11015 1 0.12343 1 0.14367 1 0.055971 1 0.65677 1 0.36295 1 Del Peak 28(12p13.1) 77 (13%) 498 0.0077768 1 0.018975 1 3.8948e-08 2.58e-05 0.42864 1 0.92075 1 0.85449 1 0.62374 1 0.0057525 1 0.44647 1 0.91879 1 Del Peak 29(12q21.2) 80 (14%) 495 0.12557 1 0.020082 1 5.5178e-07 0.00036 0.34774 1 0.83297 1 0.92388 1 0.68939 1 0.009644 1 0.52063 1 0.97871 1 Del Peak 30(14q22.1) 185 (32%) 390 9.4564e-05 0.0581 0.00011107 0.068 1.9531e-28 1.43e-25 8.1404e-06 0.00515 9.0789e-05 0.0558 0.078663 1 0.00051186 0.306 2.4861e-07 0.000163 0.12679 1 0.43856 1 Del Peak 31(15q11.2) 233 (41%) 342 0.00040277 0.242 0.0028174 1 1.2039e-23 8.82e-21 0.0057215 1 0.02598 1 0.46925 1 0.040473 1 0.0098446 1 0.47751 1 0.11089 1 Del Peak 32(15q21.1) 227 (39%) 348 0.0016117 0.932 0.031236 1 2.4292e-21 1.76e-18 0.0035788 1 0.011785 1 0.33141 1 0.11629 1 0.029654 1 0.74178 1 0.45864 1 Del Peak 33(15q22.33) 217 (38%) 358 0.00040405 0.242 0.0017515 1 4.4907e-23 3.28e-20 0.00084041 0.498 0.092059 1 0.49711 1 0.02199 1 0.0018439 1 0.86536 1 0.1165 1 Del Peak 34(16p13.3) 58 (10%) 517 0.14134 1 0.24152 1 0.21481 1 0.67595 1 0.065371 1 0.76625 1 0.31792 1 0.36867 1 0.63651 1 0.59521 1 Del Peak 35(16q23.1) 72 (13%) 503 0.05863 1 0.002199 1 0.17918 1 0.32666 1 0.28716 1 0.80712 1 0.0073968 1 0.021331 1 0.80518 1 0.63247 1 Del Peak 36(17p12) 343 (60%) 232 2.7601e-08 1.84e-05 2.2999e-05 0.0144 2.0063e-34 1.48e-31 6.04e-09 4.05e-06 0.0055355 1 0.0044117 1 1.4187e-06 0.000919 1.4557e-07 9.55e-05 0.051965 1 0.67329 1 Del Peak 37(17q24.3) 84 (15%) 491 0.91034 1 0.72248 1 0.029627 1 0.52806 1 0.74521 1 0.19596 1 0.66272 1 0.58654 1 0.91947 1 0.42487 1 Del Peak 38(18p11.31) 341 (59%) 234 1.6969e-13 1.19e-10 4.5705e-10 3.11e-07 1.1905e-41 8.82e-39 2.3143e-15 1.65e-12 0.14162 1 0.017301 1 2.2539e-12 1.56e-09 3.6811e-14 2.59e-11 0.018344 1 0.38647 1 Del Peak 39(18q12.2) 386 (67%) 189 3.4078e-10 2.32e-07 1.7113e-08 1.14e-05 1.2945e-49 9.68e-47 8.059e-18 5.82e-15 0.12764 1 0.028572 1 4.8797e-08 3.23e-05 3.4181e-12 2.37e-09 0.0057877 1 0.059024 1 Del Peak 40(18q21.2) 403 (70%) 172 1.3918e-10 9.49e-08 2.4012e-08 1.6e-05 1.2388e-50 9.28e-48 3.4304e-15 2.44e-12 0.028239 1 0.016591 1 2.9693e-08 1.97e-05 1.0354e-11 7.15e-09 0.00065728 0.391 0.12629 1 Del Peak 41(18q22.1) 398 (69%) 177 7.5002e-10 5.09e-07 5.1034e-07 0.000333 9.5463e-53 7.16e-50 1.3687e-15 9.8e-13 0.025896 1 0.020428 1 2.9693e-08 1.97e-05 1.015e-10 6.93e-08 0.0012813 0.747 0.17094 1 Del Peak 42(19p13.3) 92 (16%) 483 0.092294 1 0.7323 1 1.3518e-05 0.0085 0.82504 1 0.77606 1 0.46131 1 0.2538 1 0.3783 1 0.57921 1 0.91111 1 Del Peak 43(19q13.43) 68 (12%) 507 0.9509 1 0.41421 1 0.0001104 0.0677 0.59989 1 0.78233 1 0.91453 1 0.345 1 0.37836 1 0.25511 1 0.50243 1 Del Peak 44(20p12.1) 179 (31%) 396 0.016349 1 0.017955 1 6.5033e-15 4.62e-12 1.0094e-05 0.00637 0.87036 1 0.10544 1 0.0045376 1 0.0059842 1 0.22326 1 0.97624 1 Del Peak 45(20p12.1) 179 (31%) 396 0.016349 1 0.017955 1 6.5033e-15 4.62e-12 1.0094e-05 0.00637 0.87036 1 0.10544 1 0.0045376 1 0.0059842 1 0.22326 1 0.97624 1 Del Peak 46(21q11.2) 195 (34%) 380 0.0012074 0.708 0.11638 1 4.0688e-09 2.73e-06 0.010909 1 0.44016 1 0.3645 1 0.090612 1 0.062626 1 0.23351 1 0.049362 1 Del Peak 47(22q13.32) 204 (35%) 371 0.021477 1 0.0028973 1 9.8306e-15 6.96e-12 0.029932 1 0.39666 1 0.90788 1 0.08272 1 0.001792 1 0.69579 1 0.011544 1