Clinical Features 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 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 Fisher's exact test_P Fisher's exact test_Q Chi-square test_P Chi-square test_Q 1p gain 56 (12%) 396 0.00044663 0.311 0.10605 1 1 1 0.85872 1 0.97618 1 0.97271 1 0.43234 1 0.78475 1 0.64461 1 0.61452 1 1q gain 101 (22%) 351 2.8207e-07 0.000216 1.9734e-07 0.000151 0.28948 1 0.65283 1 0.00041434 0.29 0.0010179 0.697 0.00019092 0.137 0.2652 1 0.00032145 0.226 0.002152 1 2p gain 79 (17%) 373 1.3158e-08 1.02e-05 2.1025e-10 1.65e-07 0.081676 1 0.70791 1 0.019781 1 0.027812 1 0.22503 1 0.057359 1 0.1311 1 3.2446e-05 0.0239 2q gain 62 (14%) 390 1.1267e-07 8.66e-05 2.5852e-09 2.02e-06 0.53354 1 0.89847 1 0.084112 1 0.11634 1 0.6478 1 0.0864 1 0.15556 1 0.016023 1 3p gain 68 (15%) 384 0.16594 1 0.00025243 0.179 0.11191 1 0.050456 1 0.0026654 1 0.0059259 1 0.002781 1 0.09734 1 0.19188 1 0.68537 1 3q gain 218 (48%) 234 0.00028029 0.198 4.5273e-05 0.0332 0.68232 1 0.62813 1 0.00042227 0.295 0.0038193 1 0.0031199 1 0.14604 1 0.10104 1 0.58212 1 4p gain 32 (7%) 420 0.031854 1 0.00022762 0.162 0.5761 1 0.8238 1 0.25326 1 0.37284 1 0.058904 1 0.12337 1 0.31002 1 0.26292 1 4q gain 28 (6%) 424 0.43191 1 0.03581 1 1 1 0.89197 1 0.61466 1 0.71122 1 0.82191 1 1 1 0.7654 1 0.37832 1 5p gain 166 (37%) 286 8.2378e-09 6.42e-06 0.001472 0.995 0.93582 1 0.63953 1 0.065449 1 0.76072 1 0.2813 1 1 1 0.22415 1 0.94046 1 5q gain 59 (13%) 393 0.010424 1 0.49842 1 0.5078 1 0.6729 1 0.77839 1 0.51919 1 0.49182 1 0.23475 1 0.90616 1 0.51982 1 6p gain 67 (15%) 385 0.00021757 0.155 0.014467 1 0.49218 1 0.56312 1 0.94929 1 0.67426 1 0.87973 1 0.10326 1 0.62479 1 0.46621 1 6q gain 54 (12%) 398 0.0013364 0.906 0.021199 1 0.19677 1 0.12706 1 0.10141 1 0.10686 1 0.16073 1 0.38867 1 0.25078 1 0.53885 1 7p gain 162 (36%) 290 6.5773e-10 5.16e-07 3.856e-08 2.97e-05 0.62432 1 0.52004 1 0.70081 1 0.66478 1 0.13601 1 0.13791 1 0.37819 1 0.065907 1 7q gain 111 (25%) 341 4.3211e-07 0.00033 8.3223e-09 6.47e-06 0.17555 1 0.91277 1 0.1343 1 0.10656 1 0.0034541 1 0.73947 1 0.17979 1 0.0010754 0.736 8p gain 129 (29%) 323 0.25014 1 0.016939 1 0.42456 1 0.62821 1 0.38483 1 0.11551 1 0.40388 1 0.62004 1 0.54353 1 0.65304 1 8q gain 272 (60%) 180 0.00443 1 0.00040867 0.287 0.093453 1 0.68169 1 0.14861 1 0.10493 1 0.16484 1 0.033937 1 0.38633 1 0.096899 1 9p gain 89 (20%) 363 5.1347e-19 4.1e-16 0.00018941 0.136 0.3542 1 0.021411 1 0.037386 1 0.011139 1 0.023157 1 0.64627 1 0.0050127 1 0.41111 1 9q gain 120 (27%) 332 1.9703e-16 1.57e-13 0.044914 1 0.129 1 0.10276 1 0.52045 1 0.088943 1 0.69113 1 0.45596 1 0.17156 1 0.33175 1 10p gain 34 (8%) 418 0.035615 1 7.7612e-06 0.00581 0.57872 1 0.5291 1 0.14371 1 0.030928 1 0.12953 1 0.18916 1 0.27897 1 0.049341 1 10q gain 32 (7%) 420 0.024276 1 0.42156 1 0.097263 1 0.34104 1 0.48206 1 0.31743 1 0.52904 1 0.21011 1 0.42764 1 0.063511 1 11p gain 56 (12%) 396 0.03296 1 0.00041285 0.289 0.83938 1 0.66498 1 0.37619 1 0.052562 1 0.45241 1 0.52825 1 0.0040592 1 0.83527 1 11q gain 60 (13%) 392 0.13057 1 0.0017515 1 0.42767 1 0.76071 1 0.28907 1 0.05451 1 0.7173 1 0.59377 1 0.16596 1 0.6192 1 12p gain 125 (28%) 327 1.6525e-08 1.28e-05 5.4853e-07 0.000417 0.016096 1 0.31798 1 0.0027874 1 0.0024668 1 0.025608 1 0.33308 1 0.034116 1 0.0024933 1 12q gain 76 (17%) 376 0.00012543 0.0904 0.0011179 0.761 0.079149 1 0.14928 1 0.025864 1 0.077966 1 0.50943 1 0.92574 1 0.067434 1 0.061148 1 13q gain 51 (11%) 401 0.00080941 0.557 0.0050125 1 0.58842 1 0.50238 1 0.0028428 1 0.010658 1 0.13445 1 0.046919 1 0.046194 1 0.61263 1 14q gain 131 (29%) 321 5.5222e-07 0.00042 5.9434e-06 0.00446 0.21676 1 0.47922 1 0.090496 1 0.40622 1 0.089935 1 0.0016855 1 0.11447 1 0.004054 1 15q gain 66 (15%) 386 0.0061807 1 0.071254 1 0.38116 1 0.85143 1 0.24246 1 0.51206 1 0.49772 1 0.6013 1 0.19727 1 0.53334 1 16p gain 93 (21%) 359 2.0944e-05 0.0155 4.4576e-07 0.00034 0.32424 1 0.81329 1 0.47224 1 0.98301 1 0.51185 1 0.41779 1 0.60836 1 0.27191 1 16q gain 94 (21%) 358 1.7453e-05 0.013 8.6949e-05 0.063 0.49887 1 0.82604 1 0.19018 1 0.17873 1 0.35632 1 0.060298 1 0.4951 1 0.25794 1 17p gain 59 (13%) 393 4.4101e-06 0.00332 5.6607e-05 0.0413 0.59659 1 0.31058 1 0.0034836 1 0.04646 1 0.034479 1 0.031794 1 0.70101 1 0.14635 1 17q gain 76 (17%) 376 2.2366e-07 0.000171 0.00019358 0.138 0.52963 1 0.60394 1 0.068972 1 0.074254 1 0.11371 1 0.46164 1 0.24949 1 0.016325 1 18p gain 105 (23%) 347 2.806e-08 2.17e-05 2.7033e-06 0.00205 0.33276 1 0.76945 1 0.062669 1 0.0033151 1 0.67798 1 0.93651 1 0.0022883 1 0.037409 1 18q gain 43 (10%) 409 0.54693 1 7.7286e-05 0.0561 0.016803 1 0.40811 1 0.00071677 0.495 0.0032171 1 0.0010819 0.739 0.35333 1 0.00010714 0.0775 0.19365 1 19p gain 40 (9%) 412 0.092806 1 1.8056e-05 0.0134 0.089235 1 0.068385 1 0.082883 1 0.028113 1 0.073613 1 0.13827 1 0.31531 1 0.31419 1 19q gain 57 (13%) 395 0.26465 1 0.0003383 0.238 0.90588 1 0.3381 1 0.06058 1 0.012875 1 0.04705 1 0.1907 1 0.37682 1 0.18202 1 20p gain 165 (37%) 287 0.0067896 1 3.4757e-05 0.0256 0.89294 1 0.26723 1 0.0060172 1 0.031671 1 0.068313 1 0.011923 1 0.52799 1 0.024707 1 20q gain 175 (39%) 277 8.7507e-05 0.0634 3.192e-06 0.00241 0.87447 1 0.82011 1 0.0015233 1 0.0032825 1 0.079139 1 0.0076475 1 0.11937 1 0.027643 1 21q gain 29 (6%) 423 0.073826 1 0.027366 1 0.015127 1 0.76785 1 0.10355 1 0.12105 1 0.21748 1 0.87295 1 0.0077819 1 0.30392 1 22q gain 95 (21%) 357 0.00019544 0.14 4.6256e-11 3.65e-08 0.1526 1 0.37624 1 0.031351 1 0.075888 1 0.013885 1 0.50134 1 2.1254e-05 0.0157 7.4059e-05 0.0538 xq gain 72 (16%) 380 4.0373e-05 0.0297 0.004261 1 0.25074 1 0.75124 1 0.14235 1 0.032626 1 0.24176 1 0.31678 1 0.6721 1 0.90451 1 1p loss 47 (10%) 405 0.00022179 0.158 9.8472e-09 7.65e-06 0.064982 1 0.53815 1 0.0044235 1 0.028283 1 0.20491 1 0.68458 1 0.57501 1 0.0013182 0.895 1q loss 33 (7%) 419 0.32423 1 0.11161 1 0.77998 1 0.69635 1 0.25468 1 0.19275 1 0.11778 1 0.10959 1 0.04461 1 0.63172 1 2p loss 30 (7%) 422 0.15249 1 0.014138 1 0.15909 1 0.15253 1 0.13387 1 0.41002 1 0.08197 1 0.73606 1 0.28438 1 0.5684 1 2q loss 40 (9%) 412 0.31244 1 0.028028 1 0.83585 1 0.17175 1 0.7769 1 0.52897 1 0.32402 1 0.77578 1 0.43873 1 0.84717 1 3p loss 262 (58%) 190 5.8737e-24 4.69e-21 1.3589e-15 1.08e-12 0.88382 1 0.088644 1 0.033525 1 0.20764 1 0.092905 1 0.11735 1 0.34463 1 0.0029085 1 3q loss 57 (13%) 395 0.012398 1 0.38238 1 0.39331 1 1 1 0.61055 1 0.84745 1 0.54983 1 0.71483 1 0.3531 1 0.46677 1 4p loss 167 (37%) 285 2.2098e-14 1.75e-11 3.0048e-12 2.38e-09 0.039159 1 0.59242 1 0.00085236 0.586 2.8825e-05 0.0213 0.019564 1 0.8852 1 0.021306 1 4.2861e-06 0.00323 4q loss 133 (29%) 319 6.9378e-11 5.46e-08 3.2831e-08 2.53e-05 0.55343 1 0.43352 1 0.017373 1 0.0050779 1 0.012371 1 0.65508 1 0.17852 1 0.006065 1 5p loss 41 (9%) 411 0.0003012 0.213 0.0003105 0.219 0.37521 1 0.59107 1 0.67958 1 0.27746 1 0.57907 1 0.80241 1 0.072721 1 0.46666 1 5q loss 138 (31%) 314 7.7813e-15 6.18e-12 4.1537e-15 3.3e-12 0.2053 1 0.1454 1 0.22246 1 0.00076073 0.525 0.73259 1 0.14518 1 0.33364 1 0.066598 1 6p loss 59 (13%) 393 0.0014161 0.959 0.0038633 1 0.028232 1 0.48061 1 0.17112 1 0.3719 1 0.3483 1 0.95723 1 0.75021 1 0.13255 1 6q loss 56 (12%) 396 0.049747 1 0.0098208 1 0.13387 1 0.2732 1 0.72401 1 0.7229 1 0.62198 1 0.54599 1 0.63948 1 0.74219 1 7p loss 24 (5%) 428 0.07288 1 0.1191 1 0.010206 1 0.20746 1 0.9339 1 0.28978 1 0.28546 1 0.66046 1 0.088831 1 0.29795 1 7q loss 39 (9%) 413 0.39849 1 0.13859 1 0.52519 1 0.27131 1 0.27474 1 0.4977 1 0.12258 1 0.13465 1 0.68663 1 0.20187 1 8p loss 166 (37%) 286 1.842e-05 0.0137 0.00012027 0.0868 0.34785 1 0.31144 1 0.16286 1 0.019185 1 0.28085 1 0.015756 1 0.10683 1 0.0031137 1 8q loss 25 (6%) 427 0.096803 1 0.58844 1 0.67816 1 0.64803 1 1 1 1 1 0.74918 1 0.76247 1 0.61684 1 0.30166 1 9p loss 152 (34%) 300 4.8751e-29 3.9e-26 3.3981e-14 2.69e-11 0.69014 1 0.13604 1 0.38486 1 0.17745 1 0.06019 1 0.50681 1 0.073952 1 0.00054927 0.381 9q loss 70 (15%) 382 1.7474e-10 1.37e-07 8.9631e-06 0.0067 0.97278 1 0.85143 1 0.50219 1 0.394 1 0.87747 1 0.0045008 1 0.30851 1 0.07156 1 10p loss 134 (30%) 318 2.2762e-06 0.00173 0.0024361 1 0.31622 1 0.09801 1 0.45813 1 0.29305 1 0.17322 1 0.27017 1 0.6304 1 0.093847 1 10q loss 91 (20%) 361 1.6411e-05 0.0122 0.00080443 0.554 0.20753 1 0.33021 1 0.0809 1 0.018767 1 0.11129 1 0.77882 1 0.0057858 1 0.45923 1 11p loss 116 (26%) 336 7.9219e-08 6.1e-05 0.00049359 0.344 0.43648 1 0.91683 1 0.002234 1 0.013657 1 0.013848 1 0.73349 1 0.063199 1 0.092994 1 11q loss 139 (31%) 313 0.00014665 0.105 5.4018e-05 0.0395 0.12557 1 0.40883 1 0.0037101 1 0.030409 1 0.56144 1 0.56263 1 0.31171 1 0.9059 1 12p loss 29 (6%) 423 0.5886 1 0.036426 1 0.6461 1 0.60528 1 0.74883 1 1 1 0.28327 1 0.59959 1 0.29971 1 0.094963 1 12q loss 25 (6%) 427 0.067371 1 0.010045 1 0.87131 1 0.26688 1 0.49846 1 0.75985 1 0.54639 1 0.33776 1 0.14012 1 0.23208 1 13q loss 145 (32%) 307 7.6036e-06 0.0057 2.6777e-07 0.000205 0.45409 1 0.90718 1 0.0016309 1 6.5843e-05 0.0479 0.010232 1 0.93111 1 0.010496 1 0.024838 1 14q loss 44 (10%) 408 0.13344 1 0.014943 1 0.037227 1 0.41525 1 0.0085432 1 0.098682 1 0.069106 1 0.36343 1 0.0023553 1 0.0092726 1 15q loss 83 (18%) 369 1.4224e-06 0.00108 0.16799 1 0.62524 1 0.41349 1 0.036832 1 0.10429 1 0.22338 1 0.25669 1 0.1773 1 0.32432 1 16p loss 53 (12%) 399 0.0019326 1 0.0030037 1 0.98718 1 0.65234 1 0.03768 1 0.033391 1 0.75982 1 0.2123 1 0.25073 1 0.42861 1 16q loss 68 (15%) 384 0.56064 1 2.5121e-09 1.96e-06 0.47868 1 0.078006 1 2.6874e-08 2.08e-05 2.3166e-09 1.81e-06 0.0076962 1 0.066069 1 1.0706e-05 0.008 0.060492 1 17p loss 96 (21%) 356 2.0479e-05 0.0152 0.00019077 0.137 0.39291 1 0.27806 1 0.50486 1 0.136 1 0.60778 1 0.73755 1 0.1693 1 0.66488 1 17q loss 30 (7%) 422 0.041678 1 0.43706 1 0.90272 1 0.0047845 1 0.63688 1 0.49278 1 0.78215 1 0.59959 1 0.57182 1 0.83042 1 18p loss 88 (19%) 364 0.0061461 1 0.00089852 0.616 0.64744 1 0.27976 1 0.79562 1 0.6478 1 0.36769 1 0.62774 1 0.24036 1 0.75101 1 18q loss 185 (41%) 267 6.802e-11 5.36e-08 9.2184e-12 7.28e-09 0.2812 1 0.012915 1 0.0027966 1 0.00020595 0.147 0.041592 1 0.002963 1 0.041766 1 0.1043 1 19p loss 87 (19%) 365 0.002525 1 0.00023832 0.169 0.70291 1 0.2041 1 0.016975 1 0.072577 1 0.35977 1 0.038318 1 0.046504 1 0.28695 1 19q loss 77 (17%) 375 5.5971e-05 0.0409 4.3655e-05 0.032 0.13361 1 0.44159 1 0.2186 1 0.43976 1 0.29417 1 0.23481 1 0.93607 1 0.58877 1 20p loss 44 (10%) 408 5.2659e-06 0.00396 0.0011161 0.761 0.48326 1 0.16982 1 0.20143 1 0.36415 1 0.16424 1 0.12521 1 0.51914 1 0.45767 1 20q loss 28 (6%) 424 0.0042131 1 0.0052306 1 0.2116 1 0.057998 1 0.024409 1 0.0012378 0.842 0.012154 1 0.14436 1 0.01481 1 0.21126 1 21q loss 162 (36%) 290 2.6724e-09 2.08e-06 1.5569e-07 0.00012 0.57123 1 0.5117 1 0.30448 1 0.41654 1 0.77216 1 0.40105 1 0.27844 1 0.037846 1 22q loss 67 (15%) 385 0.072678 1 0.00044035 0.307 0.81139 1 0.45891 1 0.00013875 0.0999 0.012588 1 0.00050965 0.354 0.17218 1 0.00052266 0.363 0.094463 1 xq loss 71 (16%) 381 0.00062619 0.433 2.7568e-06 0.00208 0.18051 1 0.072536 1 0.0091234 1 0.01951 1 3.0886e-05 0.0228 0.23002 1 0.023157 1 6.0958e-05 0.0444