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 24 (5%) 503 0.82324 1 0.92455 1 9.9999e-06 0.00889 0.00059999 0.391 0.00048 0.317 0.0058999 1 0.0057099 1 0.00082999 0.527 0.00106 0.667 0.019 1 0.00382 1 0.10711 1 1q gain 51 (10%) 476 0.40801 1 0.89993 1 9.9999e-06 0.00889 0.01401 1 0.11969 1 0.088469 1 2e-05 0.0151 0.0087599 1 2e-05 0.0151 0.14644 1 0.00222 1 0.30426 1 2p gain 77 (15%) 450 0.70255 1 0.45968 1 9.9999e-06 0.00889 0.084469 1 0.0093299 1 0.32927 1 0.17743 1 0.03185 1 0.4018 1 0.02054 1 0.1309 1 0.36935 1 2q gain 79 (15%) 448 0.55991 1 0.26656 1 9.9999e-06 0.00889 0.17572 1 0.0094599 1 0.15051 1 0.15213 1 0.04211 1 0.54117 1 0.0058599 1 0.23396 1 0.25811 1 3p gain 19 (4%) 508 0.052139 1 0.4333 1 7.9999e-05 0.0562 0.54179 1 0.01714 1 0.00342 1 0.0084999 1 3e-05 0.022 6.9999e-05 0.0495 0.0059599 1 0.03614 1 0.0098699 1 3q gain 61 (12%) 466 0.0124 1 0.03045 1 9.9999e-06 0.00889 0.0037 1 0.0015 0.936 9.9999e-06 0.00889 3e-05 0.022 2e-05 0.0151 9.9999e-06 0.00889 3e-05 0.022 0.00061999 0.403 0.02094 1 4p gain 13 (2%) 514 NA NA NA NA 0.35447 1 0.37504 1 0.31137 1 0.01789 1 0.00034 0.228 0.00101 0.636 9.9999e-05 0.0696 0.11634 1 0.36733 1 0.42028 1 4q gain 13 (2%) 514 NA NA NA NA 0.35389 1 0.45841 1 0.31154 1 0.14668 1 0.00034 0.228 0.0095199 1 0.00018 0.123 0.23984 1 0.36323 1 0.42319 1 5p gain 193 (37%) 334 0.87933 1 0.92452 1 7.9999e-05 0.0562 0.2705 1 0.090539 1 0.83814 1 0.01313 1 0.070849 1 0.087549 1 0.73135 1 0.10725 1 0.79207 1 5q gain 207 (39%) 320 0.33578 1 0.62536 1 0.0086299 1 0.46207 1 0.39632 1 0.49459 1 0.071679 1 0.20983 1 0.53968 1 0.85391 1 0.22263 1 0.39383 1 6p gain 11 (2%) 516 NA NA NA NA 0.074199 1 0.44508 1 0.04367 1 0.24431 1 0.79332 1 0.79836 1 0.86001 1 0.063799 1 0.7389 1 0.2798 1 6q gain 9 (2%) 518 NA NA NA NA 0.15834 1 0.68312 1 0.0094999 1 0.34822 1 1 1 0.85103 1 1 1 0.15619 1 0.55382 1 0.53394 1 7p gain 171 (32%) 356 0.44993 1 0.85885 1 9.9999e-06 0.00889 0.00167 1 3e-05 0.022 0.01875 1 0.00013 0.0898 0.0088899 1 0.00324 1 0.25903 1 0.02337 1 0.55408 1 7q gain 172 (33%) 355 0.452 1 0.85991 1 9.9999e-06 0.00889 0.00479 1 3e-05 0.022 0.0071799 1 0.00011 0.0763 0.00418 1 0.00228 1 0.10059 1 0.067239 1 0.21313 1 8p gain 31 (6%) 496 NA NA NA NA 9.9999e-06 0.00889 3e-04 0.202 0.01208 1 0.138 1 2e-05 0.0151 3e-05 0.022 9.9999e-06 0.00889 0.03393 1 0.00056999 0.373 0.0093799 1 8q gain 62 (12%) 465 0.22776 1 0.10366 1 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00012 0.0832 0.0099799 1 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 7.9999e-05 0.0562 9.9999e-06 0.00889 0.00039 0.26 9p gain 13 (2%) 514 NA NA NA NA 0.30808 1 0.90315 1 0.82579 1 0.70962 1 0.25159 1 0.02243 1 0.93903 1 0.34998 1 0.37783 1 1 1 9q gain 12 (2%) 515 NA NA NA NA 0.093129 1 0.91054 1 0.62603 1 0.4549 1 0.2416 1 0.03597 1 0.81585 1 0.25307 1 0.89777 1 0.61502 1 10p gain 17 (3%) 510 NA NA NA NA 5e-05 0.0359 0.25436 1 0.35987 1 0.054979 1 0.00077999 0.497 0.00056999 0.373 0.059519 1 0.02629 1 0.5308 1 0.02257 1 10q gain 12 (2%) 515 NA NA NA NA 0.00064999 0.421 0.11449 1 0.0484 1 0.13147 1 0.01192 1 0.0070599 1 0.065609 1 0.26903 1 0.57991 1 0.04079 1 11p gain 31 (6%) 496 0.2323 1 0.67155 1 6.9999e-05 0.0495 0.28647 1 0.11159 1 0.35513 1 0.28959 1 0.1305 1 0.21 1 0.34852 1 0.56808 1 0.04189 1 11q gain 29 (6%) 498 0.34141 1 0.90664 1 0.00018 0.123 0.5261 1 0.36425 1 0.88828 1 0.56594 1 0.35568 1 0.53931 1 0.55619 1 0.58193 1 0.28558 1 12p gain 121 (23%) 406 0.01336 1 0.0309 1 9.9999e-06 0.00889 3e-05 0.022 9.9999e-06 0.00889 5.9999e-05 0.0428 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00015 0.103 9.9999e-06 0.00889 0.00038 0.253 12q gain 122 (23%) 405 0.01336 1 0.03291 1 9.9999e-06 0.00889 5e-05 0.0359 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 4e-05 0.0289 9.9999e-06 0.00889 0.00027 0.183 13q gain 22 (4%) 505 NA NA NA NA 0.39058 1 0.03895 1 0.72461 1 0.68602 1 0.073319 1 0.29614 1 0.34879 1 0.45237 1 0.64779 1 0.50554 1 14q gain 16 (3%) 511 0.76875 1 0.57314 1 0.04437 1 0.34768 1 0.02828 1 0.04562 1 0.0202 1 0.00058999 0.385 0.00229 1 0.0067899 1 0.76696 1 0.25828 1 15q gain 26 (5%) 501 1 1 0.11726 1 0.00499 1 0.72385 1 0.48871 1 0.6105 1 0.64502 1 0.15496 1 0.87062 1 0.18822 1 0.91805 1 1 1 16p gain 107 (20%) 420 0.27388 1 0.37948 1 0.00065999 0.426 0.16771 1 0.00194 1 0.17998 1 0.01428 1 0.00469 1 0.04673 1 0.03856 1 0.18351 1 0.083129 1 16q gain 99 (19%) 428 0.23371 1 0.34905 1 0.00052999 0.349 0.082259 1 0.00233 1 0.04194 1 0.01245 1 0.02053 1 0.01218 1 0.14737 1 0.068909 1 0.18918 1 17p gain 26 (5%) 501 0.01918 1 0.0052399 1 9.9999e-06 0.00889 0.77569 1 0.29493 1 0.081119 1 0.22907 1 0.050119 1 0.18371 1 0.42438 1 0.43212 1 0.03557 1 17q gain 33 (6%) 494 0.067809 1 0.02611 1 5.9999e-05 0.0428 0.2237 1 0.47623 1 0.074389 1 0.13858 1 0.02243 1 0.10767 1 0.23747 1 0.17409 1 0.01133 1 18p gain 25 (5%) 502 0.3138 1 0.075459 1 0.68418 1 0.47685 1 0.8488 1 0.02277 1 0.080609 1 0.58839 1 0.83241 1 0.6284 1 0.60125 1 0.065539 1 18q gain 25 (5%) 502 0.31296 1 0.074889 1 0.55406 1 0.55778 1 0.70253 1 0.087739 1 0.079639 1 0.58686 1 0.93113 1 0.62928 1 0.60297 1 0.065389 1 19p gain 51 (10%) 476 0.22681 1 0.48224 1 9.9999e-06 0.00889 6.9999e-05 0.0495 0.0085099 1 0.064199 1 0.00457 1 0.00042 0.279 9.9999e-05 0.0696 0.52259 1 0.11639 1 0.67518 1 19q gain 57 (11%) 470 0.10246 1 0.22448 1 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00061999 0.403 0.01044 1 0.00242 1 9.9999e-06 0.00889 2e-05 0.0151 0.28834 1 0.04606 1 0.37982 1 20p gain 112 (21%) 415 0.11739 1 0.1136 1 9.9999e-06 0.00889 2e-05 0.0151 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 2e-05 0.0151 2e-05 0.0151 0.00015 0.103 20q gain 115 (22%) 412 0.04159 1 0.074239 1 9.9999e-06 0.00889 2e-05 0.0151 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 2e-05 0.0151 21q gain 50 (9%) 477 0.26841 1 0.20759 1 9.9999e-06 0.00889 0.00143 0.894 0.00077999 0.497 0.30992 1 0.00069999 0.45 0.0080999 1 0.0098599 1 0.34021 1 0.064639 1 0.080719 1 22q gain 40 (8%) 487 0.32618 1 0.21752 1 0.00042 0.279 0.20783 1 0.36257 1 0.94863 1 0.10741 1 0.057389 1 0.0391 1 0.81704 1 0.44884 1 0.24969 1 xq gain 31 (6%) 496 0.39037 1 0.70295 1 0.03367 1 0.29206 1 0.0232 1 0.01861 1 0.18415 1 0.141 1 0.33951 1 0.62327 1 0.12919 1 0.067789 1 1p loss 57 (11%) 470 0.00083999 0.533 0.00283 1 9.9999e-06 0.00889 0.69811 1 0.00045 0.298 0.11718 1 0.13181 1 0.00016 0.11 0.0072499 1 0.00051999 0.343 0.195 1 0.070739 1 1q loss 36 (7%) 491 0.01093 1 0.01093 1 4e-05 0.0289 0.36854 1 0.01121 1 0.050069 1 0.0041 1 9.9999e-06 0.00889 0.01039 1 0.00073999 0.474 0.34471 1 0.10638 1 2p loss 14 (3%) 513 5.9999e-05 0.0428 0.00060999 0.397 0.00021 0.143 0.66208 1 5.9999e-05 0.0428 4e-05 0.0289 9.9999e-06 0.00889 9.9999e-06 0.00889 3e-05 0.022 9.9999e-06 0.00889 0.64229 1 0.01363 1 2q loss 14 (3%) 513 0.00021 0.143 0.00066999 0.431 0.0015 0.936 1 1 0.00012 0.0832 5e-05 0.0359 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 0.64377 1 0.01382 1 3p loss 380 (72%) 147 0.00319 1 0.01012 1 9.9999e-06 0.00889 0.00073999 0.474 0.02383 1 0.01697 1 9.9999e-06 0.00889 9.9999e-06 0.00889 0.085719 1 0.0068099 1 0.16547 1 0.01053 1 3q loss 99 (19%) 428 0.9231 1 0.51452 1 9.9999e-06 0.00889 0.43964 1 0.15318 1 0.28028 1 0.20182 1 0.02496 1 0.4961 1 0.75134 1 0.31592 1 0.97449 1 4p loss 72 (14%) 455 0.53129 1 0.81503 1 9.9999e-06 0.00889 0.00019 0.13 0.12346 1 0.67532 1 0.0015 0.936 0.00086999 0.551 0.83968 1 0.060779 1 0.11651 1 0.12953 1 4q loss 65 (12%) 462 0.38529 1 0.7825 1 9.9999e-06 0.00889 3e-05 0.022 0.090789 1 0.21459 1 0.00061999 0.403 9.9999e-06 0.00889 0.43751 1 0.02399 1 0.0484 1 0.11181 1 5p loss 7 (1%) 520 NA NA NA NA 0.38603 1 0.28961 1 0.63656 1 0.063219 1 0.02668 1 0.01142 1 0.0316 1 0.01486 1 NA NA NA NA 5q loss 6 (1%) 521 NA NA NA NA 0.44754 1 0.54439 1 0.49787 1 0.15094 1 0.04496 1 0.01563 1 0.068819 1 0.02679 1 NA NA NA NA 6p loss 100 (19%) 427 0.01092 1 0.01449 1 9.9999e-06 0.00889 5.9999e-05 0.0428 3e-05 0.022 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00034 0.228 6q loss 128 (24%) 399 0.04983 1 0.051119 1 9.9999e-06 0.00889 0.0058999 1 2e-05 0.0151 0.00128 0.803 6.9999e-05 0.0495 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00095999 0.606 2e-04 0.136 0.0069499 1 7p loss 3 (1%) 524 NA NA NA NA 0.28022 1 NA NA NA NA NA NA 0.058919 1 0.16541 1 0.054929 1 0.081719 1 0.062949 1 0.31847 1 7q loss 4 (1%) 523 NA NA NA NA 0.10405 1 0.34218 1 0.075329 1 0.23225 1 0.04821 1 0.085919 1 0.29787 1 0.3366 1 0.062129 1 0.31286 1 8p loss 137 (26%) 390 0.37749 1 0.16699 1 2e-05 0.0151 0.27658 1 0.19718 1 0.24996 1 0.069029 1 0.00070999 0.456 0.03511 1 0.071119 1 0.20647 1 0.03081 1 8q loss 64 (12%) 463 0.64492 1 0.12687 1 0.44747 1 0.050089 1 0.28791 1 0.8832 1 0.5017 1 0.25241 1 0.41378 1 0.70399 1 0.1311 1 0.15758 1 9p loss 149 (28%) 378 0.00375 1 0.03669 1 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00016 0.11 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 7.9999e-05 0.0562 9q loss 150 (28%) 377 0.01026 1 0.058109 1 9.9999e-06 0.00889 9.9999e-06 0.00889 2e-05 0.0151 0.00052999 0.349 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 7.9999e-05 0.0562 10p loss 67 (13%) 460 0.1734 1 0.4046 1 9.9999e-06 0.00889 0.081199 1 0.77404 1 0.03255 1 0.17495 1 0.00054999 0.361 0.02731 1 0.0098999 1 0.19338 1 0.17786 1 10q loss 89 (17%) 438 0.32909 1 0.39618 1 9.9999e-06 0.00889 0.00478 1 0.99052 1 0.01126 1 0.11056 1 0.00086999 0.551 0.051309 1 0.0073799 1 0.2948 1 0.04949 1 11p loss 18 (3%) 509 NA NA NA NA 3e-05 0.022 0.0247 1 0.25654 1 0.02138 1 0.15475 1 0.02706 1 0.13667 1 0.01076 1 0.12602 1 0.0096399 1 11q loss 23 (4%) 504 0.18918 1 0.37456 1 9.9999e-06 0.00889 0.0052799 1 0.16223 1 0.02079 1 0.01393 1 0.00053999 0.355 0.01663 1 0.00122 0.766 0.051849 1 0.0057599 1 12p loss 4 (1%) 523 NA NA NA NA 0.47585 1 NA NA NA NA NA NA 0.43471 1 0.79043 1 0.4677 1 0.31193 1 NA NA NA NA 12q loss 4 (1%) 523 NA NA NA NA 1 1 NA NA 0.36563 1 0.31932 1 1 1 1 1 0.23083 1 0.68591 1 NA NA NA NA 13q loss 71 (13%) 456 0.00336 1 0.04659 1 9.9999e-06 0.00889 3e-04 0.202 2e-05 0.0151 0.00029 0.196 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 0.073309 1 3e-04 0.202 14q loss 216 (41%) 311 2e-05 0.0151 7.9999e-05 0.0562 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 0.0019 1 15q loss 36 (7%) 491 0.11753 1 0.33238 1 9.9999e-06 0.00889 0.00075999 0.485 0.02671 1 0.23019 1 9.9999e-06 0.00889 9.9999e-06 0.00889 0.00064999 0.421 0.0079899 1 0.0023 1 0.10533 1 16p loss 10 (2%) 517 NA NA NA NA 0.077239 1 0.87648 1 0.02709 1 0.096329 1 0.29464 1 0.055809 1 0.072019 1 0.01671 1 0.57928 1 0.86727 1 16q loss 16 (3%) 511 NA NA NA NA 0.01547 1 0.90886 1 0.03071 1 0.38136 1 0.21832 1 0.02992 1 0.0429 1 0.01001 1 0.26297 1 0.70337 1 17p loss 46 (9%) 481 0.00014 0.0966 0.00023 0.156 9.9999e-06 0.00889 0.087389 1 0.0090099 1 0.0079599 1 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 2e-05 0.0151 0.24404 1 0.02192 1 17q loss 28 (5%) 499 0.00071999 0.462 0.00043 0.285 0.00034 0.228 0.53693 1 0.2203 1 0.02693 1 0.00029 0.196 9.9999e-06 0.00889 9.9999e-06 0.00889 2e-04 0.136 0.49744 1 0.12354 1 18p loss 93 (18%) 434 0.056809 1 0.45745 1 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 5e-05 0.0359 9.9999e-06 0.00889 18q loss 95 (18%) 432 0.04532 1 0.21737 1 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 3e-05 0.022 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 9.9999e-06 0.00889 2e-05 0.0151 9.9999e-06 0.00889 19p loss 11 (2%) 516 NA NA NA NA 5e-05 0.0359 0.03117 1 0.00317 1 0.00209 1 0.15645 1 0.0097799 1 0.2182 1 0.056559 1 0.12822 1 0.04685 1 19q loss 4 (1%) 523 NA NA NA NA 0.0155 1 NA NA 0.96601 1 0.078039 1 0.35132 1 0.51127 1 0.82678 1 0.54733 1 NA NA NA NA 20p loss 8 (2%) 519 NA NA NA NA 0.22772 1 1 1 0.02841 1 0.78779 1 0.091289 1 0.21727 1 0.01211 1 0.088439 1 NA NA NA NA 20q loss 3 (1%) 524 NA NA NA NA 0.27736 1 NA NA NA NA NA NA 0.057849 1 0.13783 1 0.055099 1 0.081019 1 NA NA NA NA 21q loss 55 (10%) 472 0.02587 1 0.089929 1 5.9999e-05 0.0428 0.01277 1 0.03027 1 0.0080899 1 0.0053299 1 6.9999e-05 0.0495 0.00351 1 0.00381 1 0.229 1 0.03443 1 22q loss 39 (7%) 488 0.01023 1 0.00142 0.889 9.9999e-06 0.00889 0.00348 1 0.00426 1 0.088139 1 9.9999e-06 0.00889 4e-05 0.0289 2e-05 0.0151 0.02226 1 0.0088199 1 0.22712 1 xq loss 47 (9%) 480 0.02397 1 0.064339 1 2e-05 0.0151 0.01683 1 0.17606 1 0.0088199 1 0.054579 1 0.00336 1 0.01003 1 0.00396 1 0.18647 1 0.02901 1