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 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 1p gain 22 (4%) 482 1 1 1 1 9.4737e-07 0.000737 0.001635 1 0.0018281 1 0.010553 1 0.03158 1 0.0054073 1 0.00056009 0.38 0.63182 1 0.11698 1 0.0072822 1 1q gain 50 (10%) 454 0.41028 1 0.41105 1 1.2074e-14 1.05e-11 0.036895 1 0.087509 1 0.031246 1 5.6952e-05 0.0411 0.00076077 0.502 2.4588e-05 0.0182 0.65925 1 0.094511 1 0.025775 1 2p gain 75 (15%) 429 0.56067 1 0.40029 1 2.1666e-09 1.79e-06 0.20097 1 0.011792 1 0.87127 1 0.216 1 0.053703 1 0.74224 1 0.39804 1 0.034232 1 0.52066 1 2q gain 76 (15%) 428 0.56067 1 0.40029 1 1.7583e-07 0.00014 0.29955 1 0.011511 1 0.93353 1 0.1906 1 0.048823 1 0.82231 1 0.39804 1 0.087124 1 0.33448 1 3p gain 18 (4%) 486 0.053628 1 0.062305 1 0.0015512 0.982 0.58508 1 0.0073443 1 0.0033196 1 0.016282 1 0.0026705 1 3.7386e-05 0.0273 1.0753e-05 0.00808 0.0025021 1 0.15481 1 3q gain 57 (11%) 447 0.012193 1 0.018801 1 3.7039e-09 3.04e-06 0.012511 1 0.00087165 0.571 1.0317e-06 0.000801 9.9699e-05 0.071 4.4608e-05 0.0325 3.4813e-08 2.82e-05 6.1385e-07 0.000481 0.0014843 0.943 0.15984 1 4p gain 13 (3%) 491 NA NA NA NA 0.067043 1 0.377 1 0.25321 1 0.0017483 1 0.00041752 0.286 0.0007913 0.521 0.0001451 0.103 0.019513 1 0.016245 1 0.19884 1 4q gain 13 (3%) 491 NA NA NA NA 0.26741 1 0.4491 1 0.25321 1 0.020053 1 0.00041752 0.286 0.0076877 1 0.0001451 0.103 0.031207 1 0.016245 1 0.19884 1 5p gain 185 (37%) 319 0.83527 1 0.77796 1 0.0001611 0.114 0.23021 1 0.11822 1 0.096432 1 0.03616 1 0.0049547 1 0.16029 1 0.83645 1 0.19808 1 0.95117 1 5q gain 199 (39%) 305 0.29223 1 0.21196 1 0.012316 1 0.38892 1 0.40404 1 0.074721 1 0.16307 1 0.021387 1 0.7 1 0.40788 1 0.53983 1 0.79897 1 6p gain 10 (2%) 494 NA NA NA NA 0.32172 1 0.34049 1 0.050507 1 0.25206 1 0.49408 1 0.68685 1 0.71617 1 0.45696 1 0.21995 1 0.037414 1 6q gain 8 (2%) 496 NA NA NA NA 0.10135 1 0.56926 1 0.0051485 1 0.42668 1 0.72709 1 1 1 0.90431 1 0.53259 1 0.17799 1 0.11161 1 7p gain 167 (33%) 337 0.41594 1 0.57703 1 3.9934e-13 3.41e-10 0.006273 1 1.608e-05 0.012 0.001785 1 0.00057211 0.387 0.0028602 1 0.0087671 1 0.1528 1 0.038154 1 0.39329 1 7q gain 168 (33%) 336 0.41594 1 0.57703 1 2.1739e-12 1.85e-09 0.015616 1 2.7813e-05 0.0205 0.00069173 0.459 0.00065342 0.436 0.0028032 1 0.0058758 1 0.074202 1 0.1081 1 0.30774 1 8p gain 30 (6%) 474 NA NA NA NA 1.1574e-08 9.46e-06 0.00096443 0.627 0.0045312 1 0.27136 1 7.8953e-06 0.00597 2.7348e-05 0.0202 3.3127e-06 0.00253 0.0059521 1 0.0027212 1 0.0014448 0.92 8q gain 59 (12%) 445 0.22618 1 0.32459 1 7.5562e-18 6.62e-15 2.9352e-06 0.00225 6.9975e-05 0.0502 0.015471 1 3.8039e-11 3.2e-08 5.4213e-10 4.51e-07 1.9582e-09 1.62e-06 0.0047915 1 3.7376e-06 0.00285 5.2663e-06 0.004 9p gain 14 (3%) 490 NA NA NA NA 0.10782 1 1 1 0.80136 1 0.86106 1 0.43705 1 0.57875 1 1 1 0.017538 1 0.83205 1 0.91504 1 9q gain 12 (2%) 492 NA NA NA NA 0.0046797 1 0.8353 1 0.56846 1 0.29075 1 0.24693 1 0.55899 1 0.75941 1 0.022721 1 0.69897 1 0.89032 1 10p gain 16 (3%) 488 NA NA NA NA 0.00082307 0.54 0.11259 1 0.15913 1 0.36647 1 0.0024316 1 0.0005814 0.392 0.094246 1 0.47112 1 0.47137 1 0.27646 1 10q gain 12 (2%) 492 NA NA NA NA 0.00028704 0.199 0.082229 1 0.067334 1 0.54603 1 0.016396 1 0.0091918 1 0.05843 1 0.37822 1 0.43913 1 0.097142 1 11p gain 30 (6%) 474 0.23165 1 0.25217 1 3.3032e-06 0.00253 0.30823 1 0.19528 1 0.24639 1 0.21729 1 0.27947 1 0.28244 1 0.041962 1 0.26844 1 0.55514 1 11q gain 28 (6%) 476 0.34099 1 0.53903 1 0.00012478 0.0886 0.18751 1 0.4232 1 0.51319 1 0.46321 1 0.54229 1 0.61197 1 0.030823 1 0.60284 1 0.91876 1 12p gain 118 (23%) 386 0.012874 1 0.014228 1 6.2131e-14 5.36e-11 0.00017395 0.122 1.3367e-12 1.14e-09 0.0010333 0.669 6.5293e-12 5.55e-09 1.759e-11 1.49e-08 1.0048e-09 8.33e-07 0.023981 1 4.884e-07 0.000383 0.00057518 0.388 12q gain 119 (24%) 385 0.012874 1 0.014228 1 5.4687e-14 4.72e-11 0.00011834 0.0841 3.7799e-14 3.27e-11 0.00028836 0.2 8.8975e-12 7.54e-09 7.9098e-12 6.71e-09 1.4276e-10 1.19e-07 0.030785 1 1.8077e-07 0.000144 0.00027986 0.195 13q gain 22 (4%) 482 NA NA NA NA 0.30942 1 0.010383 1 0.64797 1 0.56881 1 0.072388 1 0.3016 1 0.34968 1 1 1 0.64474 1 0.18906 1 14q gain 16 (3%) 488 0.76851 1 0.78254 1 0.0005687 0.385 0.32823 1 0.012121 1 0.0069981 1 0.0083662 1 0.059607 1 0.0019572 1 5.453e-05 0.0396 0.43913 1 0.28998 1 15q gain 26 (5%) 478 1 1 1 1 0.001238 0.792 0.59897 1 0.45203 1 0.15002 1 0.66145 1 0.90187 1 0.77311 1 0.23706 1 0.65491 1 0.78759 1 16p gain 106 (21%) 398 0.28203 1 0.33712 1 0.00060105 0.404 0.39878 1 0.0014674 0.933 0.04981 1 0.030398 1 0.0010953 0.705 0.030014 1 0.095698 1 0.2116 1 0.22119 1 16q gain 98 (19%) 406 0.23296 1 0.21777 1 0.00027499 0.191 0.22724 1 0.0023038 1 0.063492 1 0.027589 1 0.0033498 1 0.0084671 1 0.12916 1 0.049185 1 0.30549 1 17p gain 24 (5%) 480 0.018559 1 0.034912 1 3.5237e-06 0.00269 0.72735 1 0.32918 1 0.073361 1 0.2434 1 0.081727 1 0.27223 1 0.0033119 1 0.25888 1 0.066561 1 17q gain 30 (6%) 474 0.069157 1 0.098773 1 2.5777e-05 0.0191 0.39423 1 0.49259 1 0.076145 1 0.18356 1 0.025393 1 0.11124 1 0.00094701 0.617 0.13149 1 0.021235 1 18p gain 25 (5%) 479 0.31209 1 0.25229 1 0.085635 1 0.40519 1 0.83155 1 0.19135 1 0.18402 1 0.82237 1 0.83002 1 0.60463 1 0.33105 1 0.13991 1 18q gain 25 (5%) 479 0.31209 1 0.25229 1 0.1245 1 0.41315 1 0.73299 1 0.51027 1 0.18402 1 0.82237 1 0.87382 1 0.60463 1 0.33105 1 0.13991 1 19p gain 50 (10%) 454 0.22618 1 0.32459 1 5.7314e-10 4.76e-07 0.0049435 1 0.0092424 1 0.079396 1 0.003764 1 0.011472 1 0.00016722 0.118 0.0040931 1 0.0064803 1 0.77908 1 19q gain 56 (11%) 448 0.10193 1 0.14864 1 7.3318e-12 6.22e-09 0.0006543 0.436 0.001838 1 0.010066 1 0.0017255 1 0.0051516 1 6.4294e-05 0.0463 0.00049104 0.335 0.001763 1 0.618 1 20p gain 110 (22%) 394 0.11564 1 0.16346 1 1.0909e-21 9.61e-19 5.6154e-05 0.0407 1.0713e-07 8.59e-05 0.0017354 1 3.9631e-13 3.39e-10 2.0056e-11 1.69e-08 2.0269e-10 1.69e-07 0.00025336 0.177 7.7965e-07 0.00061 0.0032897 1 20q gain 113 (22%) 391 0.045714 1 0.06749 1 4.6378e-23 4.1e-20 5.6154e-05 0.0407 6.7616e-09 5.54e-06 0.00089632 0.586 7.9661e-15 6.91e-12 2.0812e-12 1.77e-09 1.9619e-11 1.66e-08 0.00014455 0.102 3.2346e-07 0.000255 0.0019667 1 21q gain 50 (10%) 454 0.26897 1 0.27964 1 3.086e-07 0.000243 0.0086674 1 0.0011012 0.707 0.50897 1 0.00048323 0.33 9.7807e-05 0.0697 0.014447 1 1 1 0.029006 1 0.0321 1 22q gain 40 (8%) 464 0.32729 1 0.028901 1 1.732e-05 0.0129 0.67931 1 0.37794 1 0.5812 1 0.068023 1 0.18565 1 0.03258 1 0.23003 1 0.018795 1 0.27393 1 xq gain 27 (5%) 477 0.41403 1 0.42477 1 0.14654 1 0.7232 1 0.0047758 1 0.0044641 1 0.22879 1 0.34228 1 0.26368 1 1 1 0.18499 1 0.23348 1 1p loss 58 (12%) 446 0.0017522 1 0.00063021 0.421 1.3057e-09 1.08e-06 0.46941 1 0.00060551 0.406 0.18666 1 0.13792 1 0.00096605 0.627 0.18896 1 8.6312e-11 7.22e-08 0.091131 1 0.008453 1 1q loss 37 (7%) 467 0.021718 1 0.029804 1 1.0543e-09 8.72e-07 0.28899 1 0.012964 1 0.078698 1 0.0048811 1 0.00049978 0.34 0.20793 1 1.2314e-10 1.03e-07 0.085553 1 0.050892 1 2p loss 14 (3%) 490 3.5787e-05 0.0262 6.2984e-05 0.0454 8.8449e-07 0.000691 0.66785 1 4.5828e-05 0.0333 2.3548e-06 0.00181 2.107e-07 0.000167 4.802e-09 3.94e-06 5.5411e-05 0.0402 2.123e-14 1.84e-11 0.059273 1 0.039903 1 2q loss 14 (3%) 490 0.00024867 0.174 0.00038936 0.267 8.8449e-07 0.000691 1 1 0.00031624 0.219 2.3548e-06 0.00181 2.107e-07 0.000167 6.6769e-08 5.38e-05 8.1589e-06 0.00616 1.2328e-12 1.05e-09 0.059273 1 0.039903 1 3p loss 364 (72%) 140 0.0034866 1 0.00066344 0.441 4.7233e-22 4.17e-19 0.020668 1 0.028395 1 0.013867 1 9.0855e-07 0.000708 1.8404e-11 1.56e-08 0.12734 1 1.8069e-05 0.0134 0.13119 1 0.00071281 0.473 3q loss 101 (20%) 403 0.92264 1 0.85231 1 0.0010128 0.656 0.47319 1 0.3475 1 0.084712 1 0.048093 1 0.073637 1 0.60608 1 0.38802 1 0.075916 1 0.13867 1 4p loss 71 (14%) 433 0.53135 1 0.38886 1 1.0242e-09 8.48e-07 0.0013598 0.869 0.084529 1 0.33647 1 0.0020292 1 0.053551 1 0.86197 1 0.3232 1 0.1536 1 0.29872 1 4q loss 65 (13%) 439 0.38705 1 0.34568 1 3.3825e-13 2.9e-10 0.00052903 0.36 0.051013 1 0.19873 1 0.00081048 0.532 0.0021123 1 0.41785 1 0.16476 1 0.065362 1 0.12427 1 5p loss 7 (1%) 497 NA NA NA NA 0.019476 1 0.29091 1 0.65716 1 0.2869 1 0.027023 1 0.030768 1 0.030136 1 0.0087386 1 NA NA NA NA 5q loss 6 (1%) 498 NA NA NA NA 0.041524 1 0.53395 1 0.47139 1 0.62591 1 0.046108 1 0.049578 1 0.065045 1 0.0010782 0.695 NA NA NA NA 6p loss 100 (20%) 404 0.011254 1 0.0028151 1 1.1436e-17 9.99e-15 0.00072253 0.478 1.012e-06 0.000786 0.00023397 0.164 7.6223e-08 6.14e-05 1.66e-07 0.000133 2.3288e-11 1.96e-08 4.6115e-06 0.00351 3.0366e-08 2.47e-05 3.0782e-05 0.0226 6q loss 127 (25%) 377 0.047526 1 0.021165 1 3.5312e-17 3.08e-14 0.043405 1 9.8169e-06 0.00739 0.0027724 1 0.00033239 0.229 0.0017339 1 1.0834e-07 8.68e-05 0.00033608 0.231 1.7504e-05 0.013 0.0050607 1 7p loss 3 (1%) 501 NA NA NA NA 0.34001 1 NA NA NA NA NA NA 0.16616 1 0.13396 1 0.052701 1 0.27955 1 0.052414 1 0.19935 1 7q loss 4 (1%) 500 NA NA NA NA 0.12575 1 0.36257 1 0.097958 1 1 1 0.050491 1 0.092462 1 0.29411 1 0.39697 1 0.052414 1 0.19935 1 8p loss 135 (27%) 369 0.35372 1 0.42649 1 2.6983e-05 0.0199 0.21585 1 0.23296 1 0.2765 1 0.11704 1 0.24344 1 0.072607 1 0.39388 1 0.05935 1 0.24304 1 8q loss 65 (13%) 439 0.64737 1 0.74664 1 0.044623 1 0.14364 1 0.29923 1 0.63009 1 0.78193 1 0.67291 1 0.54365 1 0.88293 1 0.076773 1 0.17146 1 9p loss 144 (29%) 360 0.004171 1 0.00053301 0.362 8.2256e-44 7.3e-41 5.7458e-19 5.05e-16 1.496e-05 0.0112 0.001095 0.705 1.3966e-22 1.23e-19 2.7006e-23 2.39e-20 2.1312e-13 1.83e-10 7.6453e-05 0.0548 2.0737e-08 1.69e-05 2.9621e-05 0.0218 9q loss 147 (29%) 357 0.010069 1 0.0014349 0.915 5.7102e-44 5.08e-41 1.8014e-18 1.58e-15 1.0599e-06 0.00082 0.0015911 1 4.9797e-24 4.42e-21 9.2988e-24 8.24e-21 1.6406e-15 1.42e-12 0.00016536 0.116 2.6318e-08 2.14e-05 3.107e-06 0.00238 10p loss 66 (13%) 438 0.17348 1 0.23862 1 2.2756e-09 1.87e-06 0.055321 1 0.76399 1 0.3493 1 0.082696 1 0.21532 1 0.030115 1 0.0011487 0.736 0.032442 1 0.47058 1 10q loss 86 (17%) 418 0.31524 1 0.36049 1 5.2031e-09 4.27e-06 0.0071475 1 0.99022 1 0.14926 1 0.069817 1 0.21315 1 0.072232 1 0.01746 1 0.052421 1 0.28741 1 11p loss 18 (4%) 486 NA NA NA NA 7.7932e-05 0.0558 0.047325 1 0.13967 1 0.55314 1 0.19771 1 0.15659 1 0.17512 1 0.04552 1 0.1058 1 0.015088 1 11q loss 23 (5%) 481 0.18897 1 0.20731 1 1.8141e-06 0.0014 0.014251 1 0.10125 1 0.41768 1 0.019271 1 0.014138 1 0.037276 1 0.10897 1 0.028428 1 0.052863 1 12p loss 3 (1%) 501 NA NA NA NA 0.18328 1 NA NA NA NA NA NA 0.43191 1 0.37983 1 0.46976 1 0.43901 1 NA NA NA NA 12q loss 4 (1%) 500 NA NA NA NA 0.46231 1 NA NA 0.52479 1 0.18488 1 1 1 0.80815 1 0.22911 1 0.75095 1 NA NA NA NA 13q loss 69 (14%) 435 0.0030403 1 0.0045545 1 3.8062e-10 3.17e-07 0.00073734 0.487 7.6632e-06 0.0058 0.0030671 1 1.2109e-05 0.00907 2.1731e-07 0.000172 1.0415e-06 0.000807 1.6647e-05 0.0124 0.016281 1 0.00029428 0.204 14q loss 211 (42%) 293 3.1171e-05 0.0228 4.3065e-05 0.0314 1.4553e-18 1.28e-15 6.2116e-08 5.02e-05 1.0117e-13 8.71e-11 1.2787e-07 0.000102 1.0241e-19 9.01e-17 1.4895e-15 1.29e-12 6.2732e-11 5.26e-08 0.91072 1 0.0010654 0.688 0.00031657 0.219 15q loss 35 (7%) 469 0.11774 1 0.12687 1 4.0811e-11 3.43e-08 0.0078729 1 0.041965 1 0.4139 1 7.5108e-06 0.00569 1.0817e-05 0.00811 0.0014998 0.951 0.035895 1 0.00091268 0.595 0.1403 1 16p loss 9 (2%) 495 NA NA NA NA 0.12607 1 0.63136 1 0.036005 1 0.83662 1 0.11489 1 0.021851 1 0.10211 1 0.061784 1 0.45276 1 0.073506 1 16q loss 14 (3%) 490 NA NA NA NA 0.0048311 1 0.34392 1 0.05764 1 0.59467 1 0.1486 1 0.0037119 1 0.11522 1 0.014415 1 0.50361 1 0.15481 1 17p loss 46 (9%) 458 0.00013537 0.096 0.00027063 0.189 8.3574e-09 6.84e-06 0.13987 1 0.0051073 1 0.0016327 1 2.0815e-07 0.000165 1.0012e-07 8.05e-05 1.5457e-08 1.26e-05 6.2246e-08 5.02e-05 0.056609 1 0.30662 1 17q loss 28 (6%) 476 0.00061803 0.413 0.00091193 0.595 2.9509e-06 0.00226 0.58508 1 0.15674 1 0.023748 1 8.5827e-05 0.0613 3.1124e-05 0.0228 6.3419e-06 0.00481 4.6254e-07 0.000364 0.11698 1 0.33473 1 18p loss 91 (18%) 413 0.057359 1 0.13502 1 2.15e-13 1.85e-10 2.6816e-07 0.000212 3.0725e-08 2.49e-05 0.0018299 1 8.1767e-18 7.15e-15 4.86e-16 4.23e-13 7.1182e-11 5.97e-08 6.24e-07 0.000489 1.0109e-07 8.12e-05 7.9631e-05 0.0569 18q loss 93 (18%) 411 0.046805 1 0.064915 1 3.8083e-13 3.26e-10 1.9663e-06 0.00152 1.9858e-07 0.000158 0.0067011 1 7.3368e-17 6.4e-14 7.8624e-16 6.84e-13 2.104e-10 1.75e-07 3.5106e-07 0.000276 3.0366e-08 2.47e-05 9.2777e-06 0.007 19p loss 11 (2%) 493 NA NA NA NA 0.00061479 0.412 0.060367 1 0.00058958 0.397 0.00078757 0.519 0.18842 1 0.02217 1 0.23727 1 0.43644 1 0.16181 1 0.10982 1 19q loss 4 (1%) 500 NA NA NA NA 0.016143 1 NA NA 0.88973 1 0.16833 1 0.43575 1 0.39309 1 0.82613 1 1 1 NA NA NA NA 20p loss 8 (2%) 496 NA NA NA NA 0.34247 1 1 1 0.058197 1 1 1 0.10635 1 0.10503 1 0.011089 1 0.075981 1 NA NA NA NA 20q loss 3 (1%) 501 NA NA NA NA 0.34001 1 NA NA NA NA NA NA 0.16616 1 0.13396 1 0.052701 1 0.053466 1 NA NA NA NA 21q loss 55 (11%) 449 0.026008 1 0.030636 1 2.1484e-07 0.00017 0.024137 1 0.027744 1 0.0078775 1 0.0063275 1 0.00041566 0.285 0.024907 1 3.264e-05 0.0239 0.15553 1 0.05749 1 22q loss 39 (8%) 465 0.010053 1 0.015526 1 1.4934e-08 1.22e-05 0.0069517 1 0.0042271 1 0.035821 1 2.1663e-06 0.00167 1.057e-05 0.00795 1.9109e-05 0.0142 0.045024 1 0.030723 1 0.18494 1 xq loss 48 (10%) 456 0.071856 1 0.033098 1 0.000204 0.143 0.026585 1 0.19482 1 0.0076257 1 0.065449 1 0.0047694 1 0.086249 1 6.5192e-05 0.0469 0.018898 1 0.01425 1