Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q amp_1q21.2 253 (52%) 237 0.039337 1 0.042084 1 1.2802e-11 1.21e-08 7.1056e-07 0.000627 0.18581 1 0.02022 1 5.5119e-08 5.01e-05 2.1385e-08 1.96e-05 0.0013992 0.991 0.00012187 0.0977 0.013607 1 0.014627 1 amp_2p16.1 271 (55%) 219 0.0013247 0.944 0.00016277 0.129 5.708e-15 5.45e-12 1.6792e-06 0.00146 0.94107 1 0.41001 1 2.0075e-11 1.89e-08 2.2786e-08 2.08e-05 2.2105e-05 0.0184 0.0007138 0.526 0.0019015 1 0.00022569 0.176 amp_2q31.2 168 (34%) 322 0.019503 1 0.027298 1 3.0722e-07 0.000275 3.1317e-06 0.00268 0.70612 1 0.49859 1 1.7744e-06 0.00153 3.317e-05 0.0273 0.01536 1 0.69153 1 0.00016523 0.13 0.00041497 0.312 amp_3p11.1 96 (20%) 394 0.10591 1 0.81848 1 0.57708 1 0.82799 1 0.31188 1 0.0008128 0.596 0.21542 1 0.90756 1 0.1404 1 0.71368 1 0.74447 1 0.11715 1 amp_3q26.33 442 (90%) 48 0.00041317 0.312 2.2666e-05 0.0188 2.2258e-14 2.12e-11 5.4159e-09 4.99e-06 0.2723 1 0.040324 1 2.0893e-10 1.96e-07 5.1977e-09 4.8e-06 3.5721e-08 3.26e-05 3.1119e-06 0.00267 0.0038387 1 0.00016051 0.127 amp_4q12 114 (23%) 376 0.87803 1 0.20752 1 0.00025555 0.197 0.06873 1 0.28324 1 0.075491 1 0.083118 1 0.07857 1 0.0023071 1 0.58622 1 0.044726 1 1 1 amp_5p15.33 378 (77%) 112 0.8428 1 0.96397 1 2.7673e-10 2.59e-07 0.033856 1 0.38991 1 0.5009 1 0.54989 1 0.056853 1 0.64502 1 0.029304 1 0.35938 1 0.43167 1 amp_5p12 346 (71%) 144 0.94901 1 1 1 2.0904e-09 1.94e-06 0.010408 1 0.20615 1 0.98689 1 0.30326 1 0.67486 1 0.94449 1 0.14356 1 0.67169 1 0.90457 1 amp_6p12.1 162 (33%) 328 0.64926 1 0.73067 1 3.1513e-05 0.026 0.052659 1 0.93033 1 0.23139 1 0.0020196 1 0.10742 1 0.55625 1 0.23703 1 0.023339 1 0.0032522 1 amp_6q12 147 (30%) 343 0.82101 1 0.65321 1 0.00023495 0.183 0.0010969 0.79 0.50448 1 0.38248 1 0.0015635 1 0.0024868 1 0.27752 1 0.13084 1 0.24808 1 0.0077669 1 amp_7p11.2 249 (51%) 241 0.1147 1 0.066132 1 1.8503e-06 0.00159 0.0019506 1 0.69231 1 0.86024 1 0.0022318 1 0.00024745 0.191 0.035997 1 0.070899 1 0.011278 1 0.046773 1 amp_7q21.2 258 (53%) 232 0.10102 1 0.10821 1 8.2842e-15 7.89e-12 1.0203e-06 0.000893 0.073076 1 0.333 1 4.4082e-07 0.000391 1.6794e-06 0.00146 0.00072831 0.536 0.0049641 1 0.0042865 1 0.0012722 0.91 amp_8p11.23 232 (47%) 258 0.013795 1 0.46024 1 0.00062381 0.462 0.018978 1 0.18923 1 0.1001 1 0.038442 1 0.94939 1 0.69493 1 0.16281 1 0.78015 1 0.22078 1 amp_8q24.21 342 (70%) 148 0.91827 1 0.78513 1 0.0063584 1 0.32954 1 0.82552 1 0.75421 1 0.8285 1 0.93626 1 0.51116 1 0.67183 1 0.34771 1 1 1 amp_9p13.3 134 (27%) 356 0.124 1 0.82407 1 0.0025257 1 0.0022079 1 0.071177 1 0.0096005 1 0.00063607 0.47 0.00016024 0.127 0.032905 1 0.32297 1 0.10287 1 0.081063 1 amp_11q13.3 181 (37%) 309 0.048396 1 0.067186 1 9.4885e-07 0.000833 0.00023958 0.186 0.25521 1 0.039019 1 0.014715 1 0.024354 1 0.0016498 1 0.10442 1 0.024972 1 0.42478 1 amp_12p13.33 249 (51%) 241 0.0076593 1 0.044129 1 1.829e-07 0.000164 0.00095019 0.69 0.35622 1 0.79411 1 1.6738e-07 0.000151 5.142e-05 0.042 0.025853 1 0.022655 1 0.20446 1 0.058797 1 amp_12q15 178 (36%) 312 0.13572 1 0.19888 1 7.449e-05 0.0602 0.014356 1 0.75988 1 0.5214 1 0.010916 1 0.0055463 1 0.64539 1 0.36979 1 0.083078 1 0.1681 1 amp_13q34 88 (18%) 402 0.97743 1 0.022866 1 0.34987 1 0.71254 1 0.83546 1 0.08641 1 0.83641 1 0.70324 1 0.38282 1 0.14866 1 0.63848 1 0.56675 1 amp_14q13.3 154 (31%) 336 0.31292 1 0.19369 1 0.14539 1 0.13717 1 0.69791 1 0.0081772 1 0.15551 1 0.032332 1 0.0091929 1 0.17143 1 0.28738 1 0.71873 1 amp_15q26.3 176 (36%) 314 0.35809 1 0.064746 1 8.011e-06 0.00681 0.00040706 0.308 0.43944 1 0.036995 1 1.5673e-05 0.0131 0.00079131 0.581 0.0086515 1 0.0019762 1 0.0076098 1 0.014407 1 amp_17q25.1 233 (48%) 257 0.0087194 1 0.021019 1 9.1916e-14 8.72e-11 4.7654e-08 4.34e-05 0.38271 1 0.31433 1 5.4169e-06 0.00462 9.2676e-08 8.37e-05 0.00014823 0.118 0.022324 1 1.0383e-05 0.00879 3.0891e-06 0.00265 amp_18p11.32 175 (36%) 315 0.042881 1 0.0107 1 7.6192e-08 6.9e-05 2.5712e-05 0.0213 0.49494 1 0.48431 1 0.030998 1 0.00046839 0.351 0.0022262 1 0.045463 1 0.0058766 1 0.020024 1 amp_18q11.2 148 (30%) 342 0.00035999 0.274 0.02841 1 7.7159e-09 7.11e-06 2.3091e-05 0.0192 0.25103 1 0.35889 1 1.675e-06 0.00145 2.2147e-09 2.06e-06 0.00082097 0.6 0.0052954 1 0.00016674 0.131 0.0001881 0.148 amp_19q12 218 (44%) 272 0.36988 1 0.56521 1 1.712e-11 1.61e-08 0.0016895 1 0.22456 1 0.052154 1 0.0019946 1 0.0025906 1 0.1408 1 0.43951 1 0.021991 1 0.034297 1 amp_19q13.2 229 (47%) 261 0.33935 1 0.42102 1 2.3472e-09 2.18e-06 0.0030608 1 0.36844 1 0.27937 1 0.0027647 1 0.0011721 0.843 0.34489 1 0.49803 1 0.061117 1 0.076625 1 amp_20p12.2 273 (56%) 217 0.0010449 0.755 0.0096931 1 5.8086e-10 5.41e-07 0.0002485 0.192 0.91413 1 0.37818 1 0.0039421 1 5.1831e-05 0.0423 0.0096035 1 0.34436 1 0.03821 1 0.43471 1 amp_20q11.21 298 (61%) 192 0.81086 1 0.87166 1 3.5779e-07 0.000319 0.0052227 1 0.78766 1 0.71539 1 0.57034 1 0.34618 1 0.12619 1 0.061014 1 0.050744 1 0.73357 1 amp_22q11.21 253 (52%) 237 0.11363 1 0.30827 1 0.00013483 0.108 0.0010533 0.76 0.83001 1 0.58907 1 8.839e-05 0.0712 0.028524 1 0.041312 1 0.26455 1 0.0048037 1 0.37566 1 amp_xq28 122 (25%) 368 0.87318 1 0.76733 1 0.020081 1 0.047983 1 0.037745 1 0.086268 1 0.085748 1 0.21566 1 0.0060414 1 0.031395 1 0.079957 1 0.014329 1 del_1p36.32 213 (43%) 277 4.9516e-07 0.000439 4.0835e-08 3.72e-05 1.7241e-35 1.66e-32 1.977e-19 1.89e-16 0.36739 1 0.012804 1 6.3127e-21 6.05e-18 1.0455e-25 1e-22 1.1761e-06 0.00102 2.9395e-06 0.00253 0.0019922 1 3.6784e-07 0.000328 del_1p13.1 212 (43%) 278 0.00016432 0.13 1.2161e-05 0.0103 1.2319e-20 1.18e-17 5.4928e-12 5.2e-09 0.039934 1 0.068581 1 5.28e-12 5e-09 3.454e-14 3.28e-11 3.1254e-08 2.86e-05 9.5278e-07 0.000836 0.0098716 1 1.0595e-05 0.00896 del_2p25.3 50 (10%) 440 0.12345 1 0.02934 1 0.13322 1 0.39154 1 0.27399 1 0.81118 1 0.44292 1 0.079033 1 0.022749 1 0.42819 1 0.06845 1 0.17293 1 del_2q22.1 124 (25%) 366 0.313 1 0.36315 1 2.5945e-07 0.000232 0.00028791 0.22 0.39113 1 0.084343 1 0.0021077 1 0.0014447 1 0.00012617 0.101 0.030759 1 0.00020936 0.164 0.019883 1 del_2q37.1 155 (32%) 335 0.0032884 1 0.0020625 1 5.6464e-10 5.27e-07 6.3148e-07 0.000558 0.38046 1 0.3685 1 1.2826e-06 0.00112 1.9597e-05 0.0163 1.3281e-05 0.0112 0.64957 1 1.093e-05 0.00924 0.00050712 0.379 del_3p25.3 389 (79%) 101 0.384 1 0.25312 1 0.0093349 1 0.00093698 0.681 0.86759 1 0.18115 1 0.0089776 1 0.000554 0.413 0.00085708 0.626 0.014193 1 0.10186 1 0.021228 1 del_3p13 424 (87%) 66 0.26122 1 0.79957 1 1.3293e-07 0.00012 0.00027295 0.209 0.76382 1 0.02164 1 0.0024459 1 8.9941e-05 0.0724 4.8265e-05 0.0395 0.01685 1 0.0013574 0.964 0.0002839 0.217 del_3p12.3 413 (84%) 77 0.1595 1 0.88966 1 1.1688e-06 0.00102 0.00022577 0.176 1 1 0.037749 1 0.0049695 1 0.00018759 0.147 0.00025901 0.199 0.065031 1 0.012099 1 0.0095199 1 del_3q11.1 77 (16%) 413 0.76001 1 0.62576 1 0.2123 1 0.93704 1 0.76356 1 0.29066 1 0.70309 1 0.055077 1 0.76397 1 0.48945 1 0.42886 1 0.22606 1 del_4p15.2 307 (63%) 183 0.00019585 0.153 0.004116 1 8.0628e-10 7.51e-07 1.7483e-06 0.00151 0.76455 1 0.026773 1 0.0002105 0.164 7.3027e-07 0.000644 0.0015278 1 0.7774 1 0.0010287 0.745 0.00085702 0.626 del_4q22.1 278 (57%) 212 0.0032628 1 0.04659 1 1.6777e-07 0.000151 0.0014959 1 0.10963 1 0.40722 1 0.00018182 0.143 0.0040982 1 0.02756 1 0.054165 1 0.10407 1 0.12023 1 del_4q32.3 322 (66%) 168 0.0065768 1 0.021619 1 7.3656e-11 6.92e-08 7.9557e-05 0.0642 0.065861 1 0.57154 1 7.4332e-06 0.00633 0.00024506 0.19 0.0006377 0.471 0.0088631 1 0.0015115 1 0.00012364 0.099 del_4q35.2 323 (66%) 167 0.068421 1 0.38354 1 1.0585e-09 9.84e-07 3.5252e-05 0.029 0.36112 1 0.58431 1 9.4465e-06 0.00802 0.0049451 1 0.0030544 1 0.016558 1 0.040341 1 0.00050999 0.38 del_5q11.2 360 (73%) 130 0.48187 1 0.41639 1 3.6373e-13 3.45e-10 1.9483e-05 0.0162 1 1 0.2986 1 0.0016434 1 0.01273 1 0.020377 1 2.7588e-05 0.0228 0.0013868 0.983 0.0017825 1 del_6p25.3 128 (26%) 362 0.32137 1 0.047239 1 1.3337e-05 0.0112 3.2361e-05 0.0267 0.37398 1 0.013491 1 3.3896e-07 0.000303 1.0182e-08 9.36e-06 0.064355 1 0.0056616 1 0.070518 1 0.0085613 1 del_6q22.31 118 (24%) 372 0.040522 1 0.022554 1 5.7231e-05 0.0465 0.0017109 1 0.46571 1 0.24548 1 0.00058802 0.437 0.0014927 1 0.082745 1 0.049615 1 0.071994 1 0.049794 1 del_6q26 130 (27%) 360 0.042415 1 0.016133 1 1.756e-05 0.0147 0.00014708 0.117 0.90534 1 0.68409 1 0.00038527 0.292 0.00061022 0.453 0.031924 1 0.031597 1 0.028 1 0.016795 1 del_7q11.22 47 (10%) 443 0.80152 1 0.10838 1 0.00042867 0.322 0.77637 1 0.83978 1 0.6133 1 0.0018286 1 0.041767 1 0.64722 1 0.69447 1 0.73102 1 0.72386 1 del_7q36.3 103 (21%) 387 0.17586 1 0.13393 1 0.0011762 0.844 0.28863 1 0.96756 1 0.21802 1 0.00029497 0.225 0.0019769 1 0.3464 1 0.50371 1 0.06436 1 0.89249 1 del_8p23.2 335 (68%) 155 0.5849 1 0.78883 1 3.8881e-05 0.0319 0.013594 1 0.23252 1 0.089962 1 0.11212 1 0.053846 1 0.14486 1 0.17547 1 0.41374 1 0.057711 1 del_9p23 323 (66%) 167 0.010406 1 0.0070636 1 3.5834e-08 3.27e-05 0.020944 1 0.19683 1 0.2528 1 6.4626e-05 0.0523 0.020149 1 0.0011942 0.856 0.0042184 1 0.010591 1 1 1 del_9p21.3 378 (77%) 112 0.19571 1 0.26054 1 1.7644e-06 0.00152 0.29789 1 0.82392 1 0.4272 1 0.00061463 0.456 0.37584 1 0.16463 1 0.26098 1 0.041983 1 1 1 del_9q21.11 248 (51%) 242 0.00024438 0.189 5.9555e-05 0.0483 4.4799e-11 4.22e-08 2.7403e-09 2.54e-06 0.55013 1 0.1548 1 1.1002e-14 1.05e-11 1.0226e-17 9.77e-15 4.0144e-05 0.0329 6.5721e-08 5.95e-05 0.0019679 1 0.046149 1 del_10p15.3 222 (45%) 268 0.32279 1 0.48716 1 8.4677e-08 7.65e-05 1.5896e-10 1.49e-07 0.16773 1 0.37288 1 4.0793e-06 0.00349 1.1556e-05 0.00975 8.1878e-07 0.000721 5.5068e-06 0.00469 0.0045589 1 0.0053334 1 del_10p15.1 210 (43%) 280 0.13289 1 0.51542 1 3.622e-06 0.0031 4.4824e-11 4.22e-08 0.21046 1 0.41371 1 2.2219e-07 0.000199 1.8373e-05 0.0153 1.3862e-07 0.000125 1.0967e-06 0.000959 0.04501 1 0.0034335 1 del_10q23.31 259 (53%) 231 0.0033464 1 0.0033511 1 1.8616e-08 1.71e-05 1.8283e-08 1.68e-05 0.15151 1 0.22857 1 3.7875e-09 3.5e-06 2.25e-10 2.11e-07 0.0003054 0.233 5.8516e-05 0.0475 2.5354e-06 0.00218 0.0026773 1 del_11p15.5 239 (49%) 251 0.00041334 0.312 0.053768 1 6.1355e-08 5.56e-05 0.0048589 1 0.00034771 0.265 1.4764e-06 0.00128 0.010429 1 0.23702 1 0.040194 1 0.40002 1 0.0016834 1 0.04592 1 del_11q22.1 158 (32%) 332 0.55178 1 0.30704 1 0.00021964 0.171 0.00043381 0.326 0.15045 1 0.9345 1 0.024345 1 0.0013512 0.961 0.0014025 0.992 0.5732 1 0.017243 1 0.0050631 1 del_11q25 182 (37%) 308 0.7875 1 0.59625 1 0.0014326 1 0.049746 1 0.17182 1 0.84182 1 0.015438 1 0.0012318 0.882 0.010091 1 0.50425 1 0.052628 1 0.016481 1 del_12q24.31 85 (17%) 405 0.87985 1 0.59385 1 0.36938 1 0.25735 1 0.19685 1 0.26731 1 0.72133 1 0.53607 1 0.44738 1 0.045045 1 0.43643 1 1 1 del_13q12.11 326 (67%) 164 0.10647 1 0.46278 1 0.0022185 1 0.11924 1 0.87549 1 0.17967 1 0.77764 1 0.62028 1 0.76514 1 0.28103 1 0.041615 1 0.098638 1 del_13q14.2 337 (69%) 153 0.11797 1 0.34557 1 0.00081573 0.597 0.020532 1 0.69508 1 0.6766 1 0.52546 1 0.17224 1 0.17375 1 0.23245 1 0.0049414 1 0.012011 1 del_14q11.2 171 (35%) 319 0.038068 1 0.15876 1 0.57651 1 0.99323 1 0.25684 1 0.26329 1 1.58e-05 0.0132 3.9327e-07 0.00035 0.0065088 1 0.066375 1 0.44406 1 0.30097 1 del_15q12 169 (34%) 321 0.69299 1 0.69759 1 0.10025 1 0.16139 1 0.038706 1 0.012325 1 0.1643 1 0.0032129 1 0.0098719 1 0.92198 1 0.28202 1 0.63394 1 del_15q21.1 162 (33%) 328 0.44743 1 0.52426 1 0.023125 1 0.20494 1 0.093159 1 0.0088646 1 0.20239 1 0.0010932 0.788 0.0032544 1 0.63526 1 0.11194 1 0.40343 1 del_16p13.3 181 (37%) 309 0.25336 1 0.33897 1 0.0012798 0.914 0.049615 1 0.21012 1 0.4744 1 0.61526 1 0.096741 1 0.01595 1 0.91792 1 0.10713 1 0.20766 1 del_16q23.1 204 (42%) 286 0.91102 1 0.3109 1 0.0047198 1 0.20973 1 0.36199 1 0.74562 1 0.061389 1 0.10025 1 0.024987 1 0.25789 1 0.00045488 0.341 0.00239 1 del_17q11.2 128 (26%) 362 0.00012966 0.104 0.00048624 0.364 1.0121e-06 0.000887 1.0307e-05 0.00874 0.37009 1 0.29938 1 9.6299e-09 8.86e-06 1.6108e-11 1.52e-08 0.17546 1 0.0027303 1 0.015301 1 0.00089787 0.654 del_17q25.3 100 (20%) 390 0.0050423 1 0.015991 1 0.0020186 1 0.029397 1 0.61116 1 0.98807 1 0.0050666 1 0.00026357 0.202 0.89115 1 0.033129 1 0.38262 1 0.013987 1 del_18q23 227 (46%) 263 0.5874 1 0.32104 1 0.015778 1 0.20106 1 0.89421 1 0.25827 1 0.89945 1 0.2617 1 0.17987 1 0.63258 1 0.06142 1 0.26918 1 del_19p13.3 229 (47%) 261 0.43899 1 0.0089684 1 0.00010334 0.083 0.77726 1 0.090998 1 0.12411 1 0.14678 1 0.0051263 1 0.04746 1 0.0025009 1 0.32583 1 0.82392 1 del_19q13.32 143 (29%) 347 0.82014 1 0.22659 1 5.887e-08 5.35e-05 1.2288e-05 0.0103 0.16478 1 0.72088 1 0.0063981 1 0.0016126 1 0.004835 1 0.82741 1 0.20929 1 0.019608 1 del_21q11.2 241 (49%) 249 0.5578 1 0.47329 1 4.8575e-05 0.0397 0.14651 1 0.98024 1 0.97214 1 0.10367 1 0.020896 1 9.1698e-05 0.0737 0.055844 1 0.015189 1 0.18343 1 del_21q22.3 276 (56%) 214 0.76444 1 0.14202 1 1.8355e-07 0.000165 0.041778 1 0.51356 1 0.12742 1 0.15265 1 0.0031918 1 0.00015895 0.126 0.082626 1 0.21516 1 0.035621 1 del_22q11.21 92 (19%) 398 0.031147 1 0.16383 1 0.31279 1 0.067275 1 0.13078 1 0.12813 1 0.15282 1 0.045827 1 0.40582 1 0.81622 1 0.54738 1 0.88385 1 del_22q13.32 125 (26%) 365 0.00024821 0.192 0.0023727 1 0.11392 1 0.015179 1 0.4041 1 0.076322 1 0.00019119 0.15 3.418e-05 0.0281 0.053923 1 0.00061543 0.456 0.91337 1 0.61251 1 del_xp22.2 151 (31%) 339 0.71959 1 0.77766 1 5.9756e-05 0.0484 0.00015403 0.122 0.42455 1 0.77154 1 0.021011 1 0.076779 1 0.0016784 1 0.040778 1 0.00097277 0.705 4.4124e-07 0.000391 del_xp21.1 149 (30%) 341 0.45787 1 0.6454 1 1.1594e-06 0.00101 8.7745e-07 0.000772 0.26354 1 0.75352 1 0.00039746 0.301 0.0024023 1 2.443e-05 0.0203 0.019866 1 0.00028043 0.215 5.6381e-10 5.27e-07 del_xp11.3 145 (30%) 345 0.098243 1 0.6454 1 3.7853e-07 0.000337 5.9956e-07 0.000531 0.10533 1 0.085973 1 0.00078803 0.579 0.0014387 1 4.9649e-06 0.00424 0.016159 1 5.4844e-05 0.0446 3.0921e-09 2.86e-06 del_xq22.3 110 (22%) 380 0.022429 1 0.0042216 1 1.7605e-05 0.0147 9.305e-07 0.000818 0.87451 1 0.93475 1 0.0013402 0.954 0.060586 1 5.4549e-05 0.0445 0.20551 1 0.00038674 0.293 0.0075935 1