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 1p gain 48 (8%) 552 0.24016 1 0.37322 1 0.02847 1 0.68503 1 0.00499 1 0.00352 1 0.99637 1 0.56531 1 0.31463 1 0.1916 1 0.03284 1 0.51143 1 1q gain 116 (19%) 484 0.77421 1 0.55524 1 0.00307 1 0.48579 1 0.12472 1 0.01763 1 0.9294 1 0.30943 1 0.17285 1 0.13912 1 0.01555 1 0.23525 1 2p gain 117 (20%) 483 0.04093 1 0.01558 1 3e-05 0.0252 0.00353 1 0.62329 1 0.56441 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.04318 1 0.00221 1 0.24166 1 0.00022 0.177 2q gain 115 (19%) 485 0.02597 1 0.00449 1 9.9999e-06 0.0094 0.00135 1 0.6477 1 0.85435 1 0.00109 0.835 9.9999e-06 0.0094 0.10975 1 0.01314 1 0.41395 1 0.00423 1 3p gain 69 (12%) 531 0.01304 1 0.076849 1 9.9999e-06 0.0094 0.13204 1 0.12674 1 0.04249 1 0.36134 1 0.19979 1 0.15125 1 0.50672 1 0.065169 1 0.073459 1 3q gain 95 (16%) 505 0.03194 1 0.00194 1 9.9999e-06 0.0094 0.01169 1 0.12403 1 0.0196 1 0.01773 1 0.0064299 1 0.04427 1 0.5478 1 0.00479 1 0.02385 1 4p gain 19 (3%) 581 0.81277 1 0.56886 1 0.02964 1 0.18345 1 0.15558 1 0.17619 1 0.093259 1 0.35465 1 0.58237 1 0.50514 1 0.25426 1 0.1127 1 4q gain 20 (3%) 580 0.22797 1 0.21387 1 0.00318 1 0.60392 1 0.11278 1 0.51635 1 0.28073 1 0.39112 1 0.3345 1 0.3639 1 0.056829 1 0.96085 1 5p gain 100 (17%) 500 0.49909 1 0.12916 1 0.00080999 0.627 0.92169 1 0.19766 1 0.13955 1 0.02514 1 0.04814 1 0.81379 1 0.40835 1 0.01513 1 0.04478 1 5q gain 63 (10%) 537 0.78353 1 0.59667 1 0.0071099 1 0.97489 1 0.72369 1 0.58876 1 0.19898 1 0.30479 1 0.74228 1 0.00304 1 0.29785 1 0.0072899 1 6p gain 121 (20%) 479 0.01457 1 0.00048 0.378 9.9999e-06 0.0094 0.2969 1 0.85288 1 0.96623 1 0.17859 1 0.03419 1 0.457 1 0.70961 1 0.01307 1 0.00218 1 6q gain 108 (18%) 492 0.15903 1 0.00099999 0.771 9.9999e-06 0.0094 0.34988 1 0.82757 1 0.74184 1 0.18668 1 0.072429 1 0.35639 1 0.89197 1 0.00273 1 0.01692 1 7p gain 339 (56%) 261 0.00047 0.37 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 0.0088099 1 0.0084299 1 2e-05 0.017 9.9999e-06 0.0094 0.0062499 1 0.17704 1 3e-05 0.0252 9.9999e-06 0.0094 7q gain 302 (50%) 298 2e-04 0.161 9.9999e-06 0.0094 9.9999e-06 0.0094 5.9999e-05 0.0497 0.13562 1 0.02578 1 2e-05 0.017 9.9999e-06 0.0094 0.01292 1 0.23769 1 4e-05 0.0334 9.9999e-06 0.0094 8p gain 164 (27%) 436 0.9235 1 0.53086 1 9.9999e-06 0.0094 0.96925 1 0.44315 1 0.28815 1 0.004 1 0.00469 1 0.28877 1 0.37543 1 0.79954 1 0.38276 1 8q gain 306 (51%) 294 0.35063 1 0.16616 1 9.9999e-06 0.0094 0.01717 1 0.096719 1 0.074489 1 0.00016 0.13 0.0060499 1 0.37159 1 0.01606 1 0.051919 1 0.02022 1 9p gain 118 (20%) 482 0.5382 1 0.58979 1 0.1737 1 0.56816 1 0.12748 1 0.25599 1 0.81039 1 0.57638 1 0.97866 1 0.92106 1 0.084329 1 0.27605 1 9q gain 99 (16%) 501 0.65717 1 0.83281 1 0.50837 1 0.88266 1 0.092759 1 0.27406 1 0.93479 1 0.79382 1 0.57654 1 0.39976 1 0.71726 1 0.75497 1 10p gain 44 (7%) 556 0.10894 1 0.11046 1 0.0066099 1 0.83776 1 0.10672 1 0.04929 1 0.47676 1 0.85729 1 0.50584 1 0.3011 1 0.04131 1 0.12278 1 10q gain 24 (4%) 576 0.91094 1 0.25756 1 0.052279 1 0.1441 1 0.16727 1 0.70514 1 0.97323 1 0.6361 1 0.51708 1 0.66052 1 0.13146 1 0.83668 1 11p gain 82 (14%) 518 0.0126 1 0.0054299 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.65731 1 0.63372 1 0.0017 1 0.0056699 1 0.3296 1 0.40523 1 0.01791 1 0.082739 1 11q gain 74 (12%) 526 0.01621 1 0.00103 0.792 9.9999e-06 0.0094 2e-05 0.017 0.19416 1 0.37426 1 9.9999e-06 0.0094 3e-05 0.0252 0.3013 1 0.060799 1 0.00019 0.154 0.00062999 0.492 12p gain 126 (21%) 474 0.35863 1 0.36115 1 0.11416 1 0.00422 1 0.53187 1 0.3166 1 0.77996 1 0.31034 1 0.50519 1 0.80727 1 0.19071 1 0.29348 1 12q gain 110 (18%) 490 0.25043 1 0.34869 1 0.04382 1 0.00242 1 0.57213 1 0.49382 1 0.56901 1 0.35804 1 0.33969 1 0.48151 1 0.074879 1 0.1309 1 13q gain 359 (60%) 241 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 0.24349 1 0.34597 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.00063999 0.499 0.50107 1 9.9999e-06 0.0094 9.9999e-06 0.0094 14q gain 42 (7%) 558 0.73552 1 0.3975 1 0.01543 1 0.84949 1 0.78991 1 0.82988 1 0.55852 1 0.32585 1 0.88236 1 0.88922 1 0.61707 1 0.737 1 15q gain 15 (2%) 585 0.29774 1 0.152 1 0.15962 1 0.58812 1 0.17173 1 0.20863 1 0.94824 1 0.30286 1 1 1 0.72397 1 0.7139 1 0.74707 1 16p gain 141 (24%) 459 0.0060999 1 0.00405 1 9.9999e-06 0.0094 0.01543 1 0.14229 1 0.66706 1 0.00025 0.199 0.00024 0.192 0.49104 1 0.43866 1 0.01719 1 6.9999e-05 0.0578 16q gain 139 (23%) 461 0.0083499 1 0.00365 1 9.9999e-06 0.0094 0.02908 1 0.23157 1 0.47249 1 0.00046 0.363 0.00019 0.154 0.78593 1 0.47683 1 0.00284 1 5e-05 0.0415 17p gain 37 (6%) 563 0.44277 1 0.16282 1 0.26759 1 0.90001 1 0.19716 1 1 1 0.50618 1 0.067619 1 0.16745 1 0.72038 1 0.6174 1 0.51432 1 17q gain 107 (18%) 493 0.01259 1 0.0050999 1 9.9999e-06 0.0094 0.00256 1 0.27443 1 0.67411 1 0.00016 0.13 2e-05 0.017 0.00212 1 0.01967 1 0.60592 1 0.03882 1 18p gain 33 (6%) 567 0.30904 1 0.37062 1 0.00107 0.821 0.00073999 0.574 0.60755 1 0.059529 1 0.03386 1 0.0052099 1 0.3983 1 0.078449 1 0.11192 1 0.03496 1 18q gain 20 (3%) 580 0.04517 1 0.4371 1 0.0077699 1 0.0089699 1 0.61318 1 0.01414 1 0.0063099 1 0.00022 0.177 0.12879 1 0.02193 1 0.03964 1 0.01516 1 19p gain 100 (17%) 500 0.41164 1 0.02798 1 9.9999e-06 0.0094 0.063129 1 0.15839 1 0.77126 1 0.22311 1 0.00122 0.927 0.079469 1 0.73348 1 0.073239 1 0.01294 1 19q gain 110 (18%) 490 0.077529 1 0.0089099 1 3e-05 0.0252 0.086739 1 0.03089 1 0.46063 1 0.61088 1 0.00214 1 0.29855 1 0.97882 1 0.11175 1 0.02093 1 20p gain 343 (57%) 257 0.00025 0.199 2e-05 0.017 9.9999e-06 0.0094 0.00129 0.979 0.01882 1 0.10392 1 8.9999e-05 0.0738 9.9999e-06 0.0094 0.34881 1 0.064049 1 0.00068999 0.537 4e-05 0.0334 20q gain 454 (76%) 146 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 0.0050599 1 0.00491 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.02007 1 0.00053999 0.423 9.9999e-06 0.0094 9.9999e-06 0.0094 21q gain 32 (5%) 568 0.31263 1 0.26335 1 0.00052999 0.416 0.76326 1 0.48438 1 0.2558 1 0.86351 1 0.481 1 0.41108 1 0.96903 1 0.26017 1 0.84461 1 22q gain 23 (4%) 577 0.11515 1 0.13407 1 0.02014 1 0.31099 1 0.86011 1 0.69263 1 0.14811 1 0.65791 1 0.69099 1 0.91681 1 0.12951 1 0.44611 1 xq gain 101 (17%) 499 0.2579 1 0.28508 1 0.00014 0.114 0.12411 1 0.10815 1 0.067599 1 0.61977 1 0.91506 1 0.41851 1 1 1 0.58969 1 0.27971 1 1p loss 135 (22%) 465 0.065749 1 0.02992 1 9.9999e-06 0.0094 0.00238 1 0.99012 1 0.86762 1 0.00105 0.806 0.00027 0.215 0.29849 1 0.04549 1 0.0447 1 0.00341 1 1q loss 76 (13%) 524 0.23275 1 0.21137 1 9.9999e-06 0.0094 0.29986 1 0.86848 1 0.81276 1 0.00021 0.169 0.0012 0.913 0.76891 1 0.0098599 1 0.12641 1 0.0072999 1 2p loss 17 (3%) 583 1 1 0.61569 1 0.00049 0.385 0.03334 1 0.34594 1 0.81097 1 0.16456 1 0.057329 1 0.093889 1 0.22766 1 0.73956 1 0.61625 1 2q loss 13 (2%) 587 0.80487 1 0.21471 1 0.0303 1 0.18696 1 0.53333 1 0.38867 1 0.35523 1 0.090389 1 0.16199 1 0.04621 1 0.19692 1 0.92146 1 3p loss 68 (11%) 532 0.35875 1 0.83531 1 0.33497 1 0.49256 1 0.53468 1 0.62874 1 0.61218 1 0.68654 1 0.77532 1 0.39561 1 0.056009 1 0.17478 1 3q loss 44 (7%) 556 0.24713 1 0.24718 1 0.52598 1 0.5694 1 0.3191 1 0.95734 1 0.61585 1 0.47697 1 0.57586 1 0.33871 1 0.36538 1 0.39605 1 4p loss 190 (32%) 410 0.02908 1 0.01544 1 9.9999e-06 0.0094 0.00132 1 0.47749 1 0.29898 1 0.00046 0.363 0.00013 0.106 0.081279 1 0.46532 1 6.9999e-05 0.0578 0.00221 1 4q loss 184 (31%) 416 0.04227 1 0.075099 1 9.9999e-06 0.0094 5e-05 0.0415 0.75948 1 0.58879 1 0.00077999 0.604 0.00015 0.122 0.10592 1 0.13454 1 0.00101 0.778 0.00023 0.184 5p loss 81 (14%) 519 0.37676 1 0.69549 1 3e-05 0.0252 0.03085 1 0.68665 1 0.76042 1 0.78029 1 0.29336 1 1 1 0.20743 1 0.10856 1 0.00112 0.856 5q loss 115 (19%) 485 0.0086599 1 0.02895 1 9.9999e-06 0.0094 0.03252 1 0.11123 1 0.10056 1 0.0098999 1 0.03912 1 0.62426 1 0.63573 1 0.00054999 0.431 6.9999e-05 0.0578 6p loss 45 (8%) 555 0.56027 1 0.0218 1 0.02628 1 0.84308 1 0.068169 1 0.076789 1 0.90949 1 0.25363 1 0.45567 1 0.93628 1 0.068139 1 0.44391 1 6q loss 68 (11%) 532 0.44543 1 0.31271 1 0.02323 1 0.69441 1 0.22799 1 0.15689 1 0.10724 1 0.26891 1 0.51387 1 0.51907 1 0.80489 1 0.71429 1 7q loss 4 (1%) 596 NA NA NA NA 0.32974 1 1 1 1 1 0.74187 1 0.53218 1 0.95863 1 1 1 0.22268 1 NA NA NA NA 8p loss 212 (35%) 388 0.0091199 1 0.0061399 1 9.9999e-06 0.0094 7.9999e-05 0.0658 0.32774 1 0.03985 1 0.00066999 0.522 4e-05 0.0334 0.5123 1 0.20717 1 0.00068999 0.537 2e-05 0.017 8q loss 33 (6%) 567 0.68409 1 0.67911 1 0.00116 0.885 0.80535 1 0.96615 1 0.27001 1 0.59993 1 0.56527 1 0.43272 1 0.44938 1 0.52196 1 0.13919 1 9p loss 73 (12%) 527 0.49078 1 0.20157 1 9.9999e-06 0.0094 0.01151 1 0.84364 1 0.47226 1 8.9999e-05 0.0738 0.0098699 1 0.20632 1 0.11065 1 0.00137 1 0.02768 1 9q loss 72 (12%) 528 0.04855 1 0.01388 1 9.9999e-06 0.0094 0.00274 1 0.92991 1 0.25121 1 8.9999e-05 0.0738 0.00061999 0.485 0.46702 1 0.01622 1 0.00022 0.177 0.02681 1 10p loss 98 (16%) 502 0.01103 1 0.18584 1 9.9999e-06 0.0094 0.01363 1 0.01754 1 0.40794 1 0.00080999 0.627 0.00032 0.254 0.2087 1 0.36252 1 0.02148 1 0.00449 1 10q loss 106 (18%) 494 0.02246 1 0.25406 1 9.9999e-06 0.0094 0.0076999 1 0.01322 1 0.40006 1 3e-05 0.0252 2e-05 0.017 0.70366 1 0.38269 1 0.00036 0.285 0.00014 0.114 11p loss 73 (12%) 527 0.95283 1 1 1 0.04627 1 0.17647 1 0.49919 1 0.60262 1 0.5203 1 0.22517 1 0.91261 1 0.23668 1 0.04483 1 0.2286 1 11q loss 91 (15%) 509 0.84633 1 0.68253 1 0.04074 1 0.03955 1 0.95646 1 0.70029 1 0.99393 1 0.76357 1 0.80621 1 0.41607 1 0.14949 1 0.39224 1 12p loss 70 (12%) 530 0.066799 1 0.01382 1 9.9999e-06 0.0094 0.04757 1 0.8768 1 0.58239 1 0.052179 1 0.03662 1 0.82257 1 0.82032 1 0.0062999 1 0.00221 1 12q loss 70 (12%) 530 0.12413 1 0.02668 1 9.9999e-06 0.0094 0.059789 1 0.64329 1 0.97464 1 0.0094299 1 0.00478 1 0.26166 1 0.88367 1 0.0087299 1 0.00187 1 13q loss 20 (3%) 580 0.29564 1 0.01606 1 0.098079 1 0.32646 1 0.29374 1 0.0067399 1 0.73208 1 0.14862 1 0.73446 1 0.78874 1 0.01919 1 0.62494 1 14q loss 199 (33%) 401 0.00021 0.169 7.9999e-05 0.0658 9.9999e-06 0.0094 9.9999e-06 0.0094 0.00277 1 0.18091 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.13332 1 0.11917 1 9.9999e-06 0.0094 9.9999e-06 0.0094 15q loss 222 (37%) 378 9.9999e-05 0.0816 0.00174 1 9.9999e-06 0.0094 0.00032 0.254 0.23768 1 0.77887 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.82147 1 0.68496 1 9.9999e-06 0.0094 9.9999e-06 0.0094 16p loss 41 (7%) 559 0.072529 1 0.371 1 0.15546 1 0.96954 1 0.34237 1 0.23906 1 0.87457 1 0.71316 1 0.8337 1 0.23803 1 0.8401 1 0.96843 1 16q loss 43 (7%) 557 0.02587 1 0.58512 1 0.0075999 1 0.91092 1 0.24068 1 0.23876 1 0.98693 1 0.95155 1 0.57293 1 0.55216 1 1 1 0.94818 1 17p loss 330 (55%) 270 3e-05 0.0252 5.9999e-05 0.0497 9.9999e-06 0.0094 9.9999e-06 0.0094 0.12169 1 0.0084199 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.0363 1 0.02448 1 9.9999e-06 0.0094 9.9999e-06 0.0094 17q loss 89 (15%) 511 0.99268 1 0.78315 1 0.00119 0.907 0.67284 1 0.88278 1 0.076089 1 0.54818 1 0.03635 1 0.94618 1 0.41704 1 0.064829 1 0.1037 1 18p loss 367 (61%) 233 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 0.03218 1 0.04817 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.0073999 1 0.0095999 1 9.9999e-06 0.0094 9.9999e-06 0.0094 18q loss 396 (66%) 204 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 9.9999e-06 0.0094 0.051499 1 0.10144 1 9.9999e-06 0.0094 9.9999e-06 0.0094 0.00109 0.835 0.00461 1 9.9999e-06 0.0094 9.9999e-06 0.0094 19p loss 64 (11%) 536 0.37732 1 0.47648 1 8.9999e-05 0.0738 0.25697 1 0.69633 1 0.24669 1 0.01531 1 0.057609 1 0.15711 1 0.0066499 1 0.5044 1 0.066899 1 19q loss 54 (9%) 546 0.66756 1 0.14728 1 0.00021 0.169 0.78964 1 0.088879 1 0.40702 1 0.10813 1 0.32508 1 0.27187 1 0.04688 1 0.36711 1 0.17383 1 20p loss 64 (11%) 536 0.11264 1 0.01938 1 4e-05 0.0334 0.00402 1 0.78505 1 0.94745 1 0.42361 1 0.0085699 1 0.74498 1 0.51143 1 0.1099 1 0.051779 1 20q loss 5 (1%) 595 NA NA NA NA 0.88623 1 0.26881 1 0.094869 1 0.70023 1 0.40052 1 0.65116 1 0.82824 1 0.68902 1 NA NA NA NA 21q loss 187 (31%) 413 0.02582 1 0.04144 1 9.9999e-06 0.0094 0.02852 1 0.70196 1 0.53589 1 6.9999e-05 0.0578 0.04503 1 0.12281 1 0.13002 1 0.00269 1 0.01783 1 22q loss 197 (33%) 403 0.00471 1 0.00031 0.246 9.9999e-06 0.0094 0.064089 1 0.77692 1 0.79938 1 0.005 1 0.00024 0.192 0.97696 1 0.070029 1 0.00084999 0.656 0.00434 1 xq loss 78 (13%) 522 0.98671 1 0.68904 1 0.0483 1 0.40738 1 0.052589 1 0.43648 1 0.49972 1 0.15331 1 0.04389 1 0.71968 1 0.46443 1 0.078959 1