Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL MIR_CNMF MIR_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_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_1p36.21 92 (16%) 479 0.58925 1 0.5715 1 0.40255 1 0.062839 1 1.3791e-09 9.45e-07 0.61188 1 0.026639 1 0.052563 1 0.011223 1 0.015193 1 amp_1q32.1 159 (28%) 412 0.8146 1 0.47908 1 0.33434 1 0.1622 1 4.0277e-09 2.74e-06 0.77757 1 0.90948 1 0.37342 1 0.53979 1 0.1233 1 amp_1q44 99 (17%) 472 0.14306 1 0.57699 1 0.59883 1 0.42591 1 4.1158e-11 2.84e-08 0.51702 1 0.31848 1 0.12418 1 0.93457 1 0.43307 1 amp_2p24.3 49 (9%) 522 0.10107 1 0.065137 1 0.42923 1 0.606 1 0.0012576 0.727 0.14837 1 0.42015 1 0.20616 1 0.88404 1 0.63204 1 amp_3q26.33 111 (19%) 460 0.0079391 1 0.035879 1 0.44511 1 0.10485 1 7.037e-10 4.83e-07 0.00094989 0.553 0.088712 1 0.30145 1 0.28598 1 0.56245 1 amp_4p16.3 48 (8%) 523 0.30922 1 0.1978 1 0.85112 1 0.35346 1 0.3017 1 0.53065 1 0.70905 1 0.2214 1 1 1 0.73408 1 amp_4q12 107 (19%) 464 0.00070719 0.415 2.8147e-05 0.0177 0.53453 1 0.02687 1 1.6534e-07 0.00011 0.44578 1 0.4646 1 0.32227 1 0.1594 1 0.40805 1 amp_7p11.2 502 (88%) 69 1.1399e-10 7.85e-08 1.9027e-09 1.3e-06 3.7942e-06 0.00247 2.8413e-10 1.95e-07 3.027e-21 2.13e-18 4.7315e-08 3.2e-05 1.7678e-05 0.0112 7.5706e-05 0.0469 1.3809e-05 0.00884 0.000346 0.208 amp_7q11.21 459 (80%) 112 1.6273e-05 0.0104 4.9694e-06 0.00323 3.2987e-05 0.0206 7.9339e-05 0.049 3.0182e-08 2.04e-05 0.0013549 0.779 0.0045328 1 0.32227 1 0.00403 1 0.0016671 0.954 amp_7q21.2 475 (83%) 96 2.9242e-05 0.0183 0.00032451 0.195 0.050658 1 0.0010635 0.618 4.8525e-08 3.28e-05 0.00044056 0.263 0.018987 1 0.091217 1 0.065335 1 0.0045782 1 amp_7q31.2 468 (82%) 103 0.001998 1 0.00043536 0.26 0.01086 1 0.032841 1 5.157e-05 0.032 0.00044056 0.263 0.1106 1 0.13609 1 0.40145 1 0.0058777 1 amp_8q24.21 70 (12%) 501 2.3915e-07 0.000159 0.00014149 0.0865 0.026293 1 0.0045263 1 2.3229e-07 0.000154 0.039217 1 0.33573 1 0.0087026 1 0.08876 1 0.13995 1 amp_11p13 31 (5%) 540 0.77087 1 1 1 0.55067 1 0.89156 1 0.3851 1 0.55135 1 0.71382 1 0.51996 1 1 1 0.89274 1 amp_12p13.32 82 (14%) 489 0.66481 1 0.80884 1 0.34402 1 0.88514 1 3.0533e-05 0.0191 0.14011 1 0.38679 1 0.55602 1 0.3045 1 0.27275 1 amp_12q14.1 133 (23%) 438 0.067764 1 0.11428 1 0.098105 1 0.11208 1 6.5569e-08 4.41e-05 0.65938 1 0.093369 1 0.34547 1 0.042393 1 0.10001 1 amp_12q15 92 (16%) 479 0.72725 1 0.63255 1 0.70446 1 0.81334 1 4.2679e-07 0.000282 0.61332 1 0.2961 1 0.63314 1 0.31242 1 0.69368 1 amp_13q34 32 (6%) 539 0.26171 1 0.52179 1 0.031072 1 0.37619 1 0.056831 1 0.77567 1 0.020537 1 0.088899 1 0.48971 1 0.81656 1 amp_13q34 30 (5%) 541 0.14265 1 0.71617 1 0.21553 1 0.57981 1 0.11616 1 0.77567 1 0.053838 1 0.11634 1 0.36772 1 0.64785 1 amp_14q32.33 36 (6%) 535 0.19036 1 0.49191 1 0.090546 1 1 1 0.82377 1 0.2891 1 0.02495 1 0.13784 1 0.038374 1 0.81656 1 amp_17p13.2 51 (9%) 520 0.00069736 0.41 0.0063725 1 0.049093 1 0.10662 1 0.000885 0.517 0.073283 1 0.12983 1 0.5504 1 0.40537 1 0.49576 1 amp_17q25.1 84 (15%) 487 0.014244 1 0.23812 1 0.28144 1 0.60881 1 0.00010546 0.0649 0.87318 1 0.13966 1 0.27371 1 0.83281 1 0.71124 1 amp_19p13.3 242 (42%) 329 3.5514e-09 2.42e-06 3.3534e-06 0.00219 0.037692 1 0.00010738 0.0659 1.9975e-24 1.41e-21 0.0005826 0.345 0.0096727 1 1.1429e-05 0.00734 0.80954 1 0.051044 1 amp_19p13.2 247 (43%) 324 3.0707e-12 2.13e-09 2.9689e-06 0.00194 0.14798 1 0.00024083 0.145 2.0462e-25 1.45e-22 0.00067285 0.397 0.013055 1 2.6077e-05 0.0165 0.16889 1 0.020341 1 amp_19q12 213 (37%) 358 9.6892e-11 6.69e-08 2.5832e-08 1.75e-05 0.28399 1 0.0019236 1 1.2914e-19 9.05e-17 0.053297 1 0.0091569 1 0.0001306 0.0799 0.066555 1 0.014261 1 amp_21q21.1 69 (12%) 502 0.0054126 1 0.0099792 1 0.01813 1 0.014163 1 0.00041232 0.247 0.673 1 0.66204 1 0.80698 1 0.084582 1 0.060009 1 del_1p36.32 100 (18%) 471 0.91226 1 0.067259 1 0.58251 1 0.14076 1 0.3499 1 0.35118 1 0.59918 1 0.42058 1 0.25014 1 0.046237 1 del_1p36.23 136 (24%) 435 0.070211 1 0.062768 1 0.55791 1 0.50081 1 3.1537e-05 0.0197 0.45236 1 0.27842 1 0.61619 1 0.017437 1 0.10672 1 del_1p32.3 61 (11%) 510 0.24284 1 0.5979 1 0.81708 1 0.17369 1 0.38881 1 0.16745 1 0.70905 1 0.62903 1 0.79033 1 0.16488 1 del_1p22.1 48 (8%) 523 0.96964 1 0.85165 1 0.798 1 0.08422 1 0.13633 1 0.49491 1 0.86522 1 0.33674 1 1 1 0.014951 1 del_1q42.11 51 (9%) 520 0.21892 1 0.78476 1 0.51098 1 0.57041 1 0.66222 1 0.026006 1 0.13998 1 0.014387 1 0.68571 1 0.66392 1 del_1q44 35 (6%) 536 0.78827 1 0.57939 1 0.73406 1 0.48007 1 0.25086 1 0.01893 1 0.66199 1 0.63481 1 0.53861 1 0.90362 1 del_2q22.1 45 (8%) 526 0.0060766 1 0.053969 1 0.38892 1 0.076297 1 5.2825e-06 0.00341 0.048553 1 0.47773 1 0.85985 1 0.18131 1 0.19667 1 del_2q37.1 54 (9%) 517 0.10239 1 0.036677 1 0.31592 1 0.071774 1 0.047136 1 0.085272 1 0.78353 1 0.74093 1 0.18131 1 0.68736 1 del_3p21.1 52 (9%) 519 0.24573 1 0.505 1 0.67075 1 0.97246 1 0.00081163 0.476 0.10007 1 0.13736 1 0.79386 1 0.46101 1 0.088954 1 del_3q13.31 58 (10%) 513 0.51028 1 0.86434 1 0.68934 1 0.93706 1 2.7615e-05 0.0174 0.20672 1 0.96833 1 0.87787 1 1 1 0.054664 1 del_3q22.1 58 (10%) 513 0.78385 1 0.23296 1 0.94419 1 0.82181 1 0.00067966 0.4 0.27242 1 0.96429 1 0.80821 1 1 1 0.103 1 del_3q29 65 (11%) 506 0.092341 1 0.22493 1 0.53476 1 0.62253 1 0.044879 1 0.60055 1 0.44607 1 0.52358 1 0.92808 1 0.75587 1 del_4p16.3 77 (13%) 494 0.048593 1 0.0059146 1 0.32637 1 0.4998 1 0.006618 1 0.92322 1 0.8189 1 0.69221 1 0.84853 1 0.81928 1 del_4q34.3 91 (16%) 480 0.0057388 1 0.0063958 1 0.075052 1 0.12652 1 1.1403e-06 0.000749 0.0013453 0.775 0.0988 1 0.28252 1 0.11833 1 0.94416 1 del_5q35.3 53 (9%) 518 2.5216e-05 0.016 0.0020292 1 0.00034023 0.204 0.0024981 1 7.0885e-06 0.00457 0.005376 1 0.84022 1 0.38811 1 0.20816 1 0.79885 1 del_6q22.31 157 (27%) 414 0.63121 1 0.78076 1 0.29532 1 0.14201 1 5.5166e-08 3.72e-05 0.28898 1 0.34486 1 0.10164 1 0.77635 1 0.4079 1 del_6q26 178 (31%) 393 0.73929 1 0.064077 1 0.47623 1 0.15745 1 0.00021538 0.13 0.55664 1 0.035348 1 0.0075376 1 0.7637 1 0.29571 1 del_8p23.2 65 (11%) 506 0.37675 1 0.45976 1 0.18026 1 0.80034 1 0.12196 1 1 1 0.94352 1 0.83449 1 0.72143 1 0.38433 1 del_9p21.3 416 (73%) 155 5.8022e-06 0.00374 1.1194e-07 7.5e-05 0.69418 1 0.0041602 1 4.1955e-13 2.92e-10 0.082306 1 0.13735 1 0.008538 1 0.029289 1 0.0032295 1 del_9q34.2 78 (14%) 493 0.21501 1 0.062427 1 0.51648 1 0.14613 1 0.33826 1 0.12671 1 0.22241 1 0.14221 1 0.43629 1 0.059279 1 del_10p15.3 465 (81%) 106 4.3155e-06 0.00281 0.00015176 0.0926 0.0087277 1 2.5886e-05 0.0164 2.3382e-20 1.64e-17 0.094587 1 0.0057106 1 0.02752 1 0.014567 1 0.41138 1 del_10p13 466 (82%) 105 6.7596e-07 0.000446 1.5072e-05 0.00963 0.0025666 1 5.1353e-06 0.00332 5.6146e-22 3.96e-19 0.048875 1 0.0001598 0.0973 0.0044418 1 0.082932 1 0.41138 1 del_10p11.23 471 (82%) 100 1.1415e-09 7.83e-07 1.9034e-07 0.000127 0.00010446 0.0643 1.1613e-06 0.000762 4.0133e-25 2.84e-22 0.02006 1 0.00092362 0.538 0.017708 1 0.046676 1 0.074037 1 del_10q23.31 508 (89%) 63 1.2531e-06 0.000821 3.9326e-05 0.0245 0.012514 1 0.00028706 0.173 1.8119e-18 1.27e-15 0.13263 1 0.011823 1 0.13269 1 0.3692 1 0.16075 1 del_10q26.3 509 (89%) 62 3.2126e-07 0.000213 5.0588e-06 0.00328 0.043315 1 0.0034712 1 1.1282e-15 7.89e-13 0.0073337 1 0.12222 1 0.074381 1 0.25023 1 0.37402 1 del_11p15.5 127 (22%) 444 2.1891e-09 1.5e-06 2.0109e-07 0.000134 0.16225 1 0.00035441 0.212 3.4883e-14 2.43e-11 0.011209 1 0.1669 1 0.096178 1 0.0028735 1 0.12834 1 del_11p11.2 103 (18%) 468 1.1069e-07 7.43e-05 0.00017684 0.108 0.50001 1 0.0088137 1 4.4251e-12 3.07e-09 0.05298 1 0.91019 1 0.56762 1 0.093456 1 0.46635 1 del_11q14.1 95 (17%) 476 7.9726e-07 0.000525 0.015119 1 0.87256 1 0.096118 1 1.1617e-15 8.11e-13 0.41081 1 0.73515 1 0.49818 1 0.11895 1 0.58371 1 del_12p13.1 72 (13%) 499 0.050929 1 0.0046778 1 0.25393 1 0.17543 1 0.063406 1 0.51702 1 0.66453 1 0.4783 1 1 1 0.61087 1 del_12q12 76 (13%) 495 0.013875 1 0.00062129 0.367 0.26657 1 0.097857 1 9.1501e-05 0.0565 0.071383 1 0.099884 1 0.4167 1 1 1 0.62588 1 del_12q15 77 (13%) 494 0.00018677 0.113 6.1251e-05 0.038 0.48489 1 0.28531 1 1.4444e-06 0.000945 0.018179 1 0.55351 1 0.50916 1 0.72838 1 0.61196 1 del_13q14.2 237 (42%) 334 1.5998e-07 0.000107 3.8243e-05 0.0238 0.35065 1 0.036605 1 4.7879e-23 3.38e-20 0.0046804 1 0.85317 1 0.12567 1 0.080946 1 0.2796 1 del_14q13.1 176 (31%) 395 1.2949e-05 0.0083 0.010435 1 0.61097 1 0.54801 1 8.7998e-21 6.19e-18 0.3121 1 0.61619 1 0.27253 1 0.42926 1 0.50958 1 del_14q24.2 172 (30%) 399 1.2928e-07 8.65e-05 0.00057738 0.342 0.057782 1 0.54398 1 1.0502e-27 7.46e-25 0.044832 1 0.54102 1 0.1763 1 0.087641 1 0.051525 1 del_15q14 150 (26%) 421 2.2651e-05 0.0144 6.607e-08 4.44e-05 0.001241 0.72 0.00011581 0.071 7.9057e-07 0.000521 0.0012446 0.721 0.058365 1 0.010768 1 0.00083256 0.487 0.055136 1 del_16p12.2 92 (16%) 479 0.40201 1 0.4993 1 0.28429 1 0.90638 1 0.21588 1 0.14281 1 0.40429 1 0.53662 1 0.43109 1 0.41583 1 del_16q23.3 97 (17%) 474 0.022378 1 0.56476 1 0.86228 1 0.8167 1 0.0059695 1 0.53667 1 0.03876 1 0.084752 1 0.51342 1 0.47385 1 del_17p13.2 86 (15%) 485 0.0031774 1 0.7057 1 0.94345 1 0.1807 1 1.4738e-08 1e-05 0.029929 1 0.62382 1 0.45461 1 0.5461 1 0.26619 1 del_17p13.1 95 (17%) 476 0.00045571 0.271 0.33602 1 0.68337 1 0.2506 1 7.7921e-13 5.42e-10 0.0024528 1 0.68922 1 0.44441 1 0.61445 1 0.28234 1 del_17q11.2 71 (12%) 500 8.5121e-06 0.00547 0.00136 0.781 0.0025736 1 0.10114 1 1.6036e-05 0.0102 0.33925 1 0.0068233 1 0.0051011 1 0.52024 1 0.10495 1 del_18q22.3 81 (14%) 490 0.12722 1 0.031161 1 0.77908 1 0.067451 1 2.1958e-05 0.0139 0.040275 1 0.011227 1 0.0012761 0.736 0.19472 1 0.53956 1 del_19q13.41 99 (17%) 472 0.0033052 1 0.00021108 0.128 0.040706 1 0.019443 1 0.0017094 0.976 0.17603 1 0.055213 1 0.5079 1 0.035216 1 0.1392 1 del_21q22.11 46 (8%) 525 0.0015848 0.908 0.0035134 1 0.0058094 1 0.11106 1 0.0020462 1 0.34239 1 0.15428 1 0.35976 1 0.68124 1 0.15989 1 del_22q13.32 211 (37%) 360 0.7142 1 0.22354 1 0.039622 1 0.32592 1 2.6713e-05 0.0168 0.196 1 0.78406 1 0.91653 1 0.051087 1 0.95441 1 del_xp22.2 116 (20%) 455 0.0059225 1 0.029491 1 0.11293 1 0.32342 1 3.0128e-08 2.04e-05 0.013805 1 0.67778 1 0.16935 1 0.28019 1 0.75457 1 del_xq23 107 (19%) 464 0.019251 1 0.022348 1 0.098745 1 0.23681 1 3.3693e-11 2.33e-08 0.041731 1 0.90872 1 0.58186 1 0.16147 1 0.54883 1