Molecular subtypes 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 0 (0%) 464 0.57587 1 0.58086 1 0.026366 1 0.13789 1 0.59505 1 0.11168 1 0.17722 1 0.0077864 1 0.43808 1 0.87726 1 0.25337 1 0.17921 1 1q gain 0 (0%) 385 0.4999 1 0.45913 1 4.6903e-07 0.000421 1.1755e-05 0.0102 0.59714 1 0.59038 1 1.1989e-05 0.0104 2.7096e-06 0.00239 0.00053947 0.415 0.00018409 0.149 0.0090144 1 0.002643 1 2p gain 0 (0%) 369 0.023806 1 0.027417 1 1.1486e-15 1.08e-12 1.4703e-08 1.34e-05 0.065662 1 0.21632 1 1.2822e-09 1.18e-06 3.6403e-06 0.0032 7.6827e-05 0.064 0.0028003 1 2.6371e-05 0.0224 3.7539e-06 0.0033 2q gain 0 (0%) 441 0.30462 1 0.17761 1 2.3888e-06 0.00211 0.00079086 0.599 0.21385 1 0.32996 1 2.1172e-05 0.018 0.00045845 0.357 0.09896 1 0.068321 1 0.00054373 0.418 0.0031431 1 3p gain 0 (0%) 435 0.35284 1 0.54961 1 0.0012847 0.955 0.0087404 1 0.65032 1 0.24947 1 0.063978 1 0.029411 1 0.93851 1 0.95802 1 0.41825 1 0.5906 1 3q gain 0 (0%) 272 0.093071 1 0.72194 1 3.1298e-06 0.00276 0.01556 1 0.28538 1 0.40945 1 0.013582 1 0.0025933 1 0.0089496 1 0.60186 1 0.29066 1 1 1 4p gain 0 (0%) 473 0.10116 1 0.33866 1 0.012422 1 0.066341 1 0.13225 1 0.46423 1 0.0040881 1 0.022189 1 0.89626 1 0.61098 1 0.74227 1 0.074409 1 4q gain 0 (0%) 482 1 1 0.68337 1 0.38634 1 NA NA NA NA NA NA 0.58866 1 0.0094941 1 0.41087 1 0.54408 1 NA NA 0.20966 1 5p gain 0 (0%) 264 0.94773 1 0.27014 1 1.4743e-07 0.000133 0.1223 1 0.44896 1 0.46119 1 0.069909 1 0.36494 1 0.43392 1 0.239 1 0.020841 1 0.82484 1 5q gain 0 (0%) 438 0.11377 1 0.23889 1 0.0019579 1 0.20406 1 0.81956 1 0.85331 1 0.090221 1 0.51046 1 0.82727 1 0.48423 1 0.57352 1 0.85783 1 6p gain 0 (0%) 448 0.0061744 1 0.3245 1 2.6577e-05 0.0225 0.21927 1 0.81311 1 0.28139 1 0.0086526 1 0.27591 1 0.83423 1 0.76351 1 0.53324 1 1 1 6q gain 0 (0%) 459 0.046208 1 0.33866 1 4.5118e-06 0.00395 0.024742 1 0.60601 1 0.7335 1 0.024931 1 0.090646 1 0.6437 1 0.83955 1 0.059179 1 0.11951 1 7p gain 0 (0%) 350 0.42079 1 0.32317 1 5.7425e-07 0.000514 2.4854e-05 0.0211 0.73142 1 0.9882 1 0.0043003 1 0.001168 0.87 0.012658 1 0.23476 1 4.2371e-05 0.0355 0.00088705 0.669 7q gain 0 (0%) 368 0.12389 1 0.075155 1 2.1675e-13 2.03e-10 1.2128e-06 0.00108 0.67861 1 0.76792 1 1.3086e-05 0.0113 1.1761e-05 0.0102 0.00051153 0.395 0.077598 1 7.7716e-05 0.0647 0.00014141 0.116 8p gain 0 (0%) 427 0.04238 1 0.071511 1 0.0070883 1 0.1641 1 0.55099 1 0.36294 1 0.041041 1 0.00083498 0.631 0.33618 1 0.26795 1 0.87118 1 0.40359 1 8q gain 0 (0%) 346 0.012 1 0.038605 1 1.5618e-05 0.0134 0.00017512 0.142 0.90397 1 0.82586 1 0.0005006 0.387 0.00024255 0.194 0.13755 1 0.13675 1 0.091034 1 0.27001 1 9p gain 0 (0%) 463 0.53407 1 0.62447 1 0.080249 1 0.32964 1 0.17173 1 0.00021605 0.174 0.14008 1 0.0082304 1 0.029362 1 0.1589 1 0.066589 1 0.29703 1 9q gain 0 (0%) 448 0.28582 1 0.26404 1 0.00010455 0.0862 0.00010823 0.0891 0.074636 1 0.0021231 1 2.7787e-05 0.0235 1.4268e-05 0.0123 0.00087522 0.661 0.046367 1 0.19752 1 0.080646 1 10p gain 0 (0%) 462 0.63583 1 1 1 0.014871 1 0.38181 1 0.5302 1 0.3894 1 0.83574 1 0.75005 1 0.24552 1 0.14048 1 0.79009 1 0.82531 1 10q gain 0 (0%) 481 NA NA NA NA 0.22678 1 0.49682 1 0.16228 1 0.68423 1 0.89073 1 0.89975 1 0.25625 1 0.79055 1 0.2486 1 1 1 11p gain 0 (0%) 463 0.92854 1 0.79042 1 0.17542 1 0.072487 1 0.23004 1 0.14861 1 0.056265 1 0.19495 1 0.0079827 1 0.28242 1 0.3311 1 0.17921 1 11q gain 0 (0%) 461 0.081184 1 0.69111 1 0.0015416 1 0.10229 1 0.55121 1 0.48584 1 0.33254 1 0.30099 1 0.21298 1 0.30649 1 0.15234 1 0.088479 1 12p gain 0 (0%) 347 0.034819 1 0.32317 1 5.117e-09 4.7e-06 0.0046564 1 0.27235 1 0.72316 1 0.00031025 0.245 0.0059507 1 0.076753 1 0.17325 1 0.15398 1 0.14231 1 12q gain 0 (0%) 428 0.021188 1 0.27803 1 1.4679e-05 0.0126 0.24686 1 0.15138 1 0.73043 1 0.16434 1 0.01969 1 0.26284 1 0.04988 1 4.3086e-05 0.0361 0.012188 1 13q gain 0 (0%) 476 0.70128 1 0.66406 1 0.48986 1 1 1 0.28874 1 0.34943 1 0.55028 1 0.5314 1 0.74381 1 0.61559 1 0.58407 1 0.18716 1 14q gain 0 (0%) 431 0.1862 1 0.49815 1 0.18988 1 0.08342 1 0.86153 1 0.65618 1 0.26386 1 0.092376 1 0.28713 1 0.0092937 1 0.058828 1 0.47948 1 15q gain 0 (0%) 444 0.39911 1 0.10684 1 0.00091518 0.688 0.019971 1 0.18418 1 0.072692 1 2.0643e-06 0.00183 0.00015093 0.123 0.00034692 0.274 0.0044502 1 0.00070274 0.535 0.010855 1 16p gain 0 (0%) 465 0.45849 1 0.85325 1 0.00021637 0.174 0.25414 1 0.72331 1 0.34116 1 0.10789 1 0.27162 1 0.10255 1 0.54143 1 0.10048 1 0.29703 1 16q gain 0 (0%) 463 0.16206 1 0.23378 1 9.444e-07 0.000841 0.25414 1 0.4554 1 0.15359 1 0.3713 1 0.14289 1 0.047889 1 0.59193 1 0.71242 1 0.60318 1 17p gain 0 (0%) 470 0.26158 1 0.24107 1 1.5243e-06 0.00135 0.00020405 0.164 0.27702 1 0.754 1 4.1429e-05 0.0348 2.693e-06 0.00238 0.069587 1 0.0004913 0.381 0.012018 1 0.11587 1 17q gain 0 (0%) 424 0.006305 1 0.00093451 0.702 5.9199e-14 5.56e-11 4.6957e-08 4.27e-05 0.32414 1 0.39354 1 6.9253e-08 6.27e-05 1.0867e-06 0.000966 0.00041114 0.321 0.0014321 1 0.00049997 0.387 0.00019372 0.157 18p gain 0 (0%) 406 0.00026609 0.212 4.7918e-06 0.00419 2.1502e-09 1.98e-06 4.4849e-05 0.0375 0.13635 1 0.14799 1 3.1244e-05 0.0263 9.0807e-05 0.0752 0.0015485 1 0.010796 1 0.00018907 0.153 1.1805e-05 0.0102 18q gain 0 (0%) 442 9.2364e-05 0.0763 0.00037298 0.293 3.7754e-06 0.00331 0.00071994 0.548 0.11281 1 0.046321 1 2.0354e-05 0.0174 1.218e-05 0.0105 0.011516 1 0.0041024 1 0.0066143 1 0.00030794 0.244 19p gain 0 (0%) 438 0.59087 1 0.84041 1 6.6726e-09 6.12e-06 0.00047349 0.368 0.00067246 0.514 0.0029868 1 0.00055161 0.423 4.2804e-05 0.0359 0.00017315 0.141 0.0041702 1 6.7654e-06 0.00589 0.00061563 0.472 19q gain 0 (0%) 417 0.5478 1 1 1 2.1965e-05 0.0187 0.026389 1 0.066834 1 0.019266 1 0.0027433 1 0.0030574 1 0.2438 1 0.27998 1 0.0013258 0.982 0.065961 1 20p gain 0 (0%) 348 0.15034 1 0.069782 1 2.1526e-11 2e-08 0.00073714 0.56 0.68384 1 0.19449 1 0.0018899 1 0.00014782 0.121 0.0075493 1 0.045816 1 0.015585 1 0.027553 1 20q gain 0 (0%) 359 0.40783 1 0.41279 1 3.4192e-11 3.18e-08 0.0064332 1 0.64823 1 0.35697 1 0.095195 1 0.0054585 1 0.023195 1 0.0058613 1 0.030732 1 0.13356 1 21q gain 0 (0%) 467 0.96899 1 0.30607 1 0.31735 1 0.0001544 0.126 0.52434 1 0.93666 1 0.67823 1 0.58078 1 0.37448 1 0.14878 1 0.8616 1 0.35674 1 22q gain 0 (0%) 370 0.0073913 1 0.0044999 1 7.5894e-10 7.03e-07 9.7742e-05 0.0806 0.22719 1 0.016673 1 0.00026032 0.207 0.0010118 0.758 3.0316e-05 0.0256 0.0065805 1 0.0044995 1 0.0018788 1 Xq gain 0 (0%) 472 0.70128 1 0.58871 1 0.14058 1 0.019726 1 0.45078 1 0.58167 1 0.87608 1 0.52254 1 0.10368 1 0.090903 1 0.4892 1 0.26997 1 1p loss 0 (0%) 412 0.001492 1 0.00035663 0.281 2.947e-19 2.78e-16 4.3658e-10 4.05e-07 0.2652 1 0.013137 1 3.7553e-13 3.52e-10 1.2301e-12 1.15e-09 1.7425e-05 0.0149 0.036866 1 0.010568 1 1.2109e-07 0.000109 1q loss 0 (0%) 471 0.88292 1 0.61962 1 0.0025966 1 0.12338 1 0.73524 1 0.17683 1 0.13091 1 0.066428 1 0.037178 1 0.94832 1 0.22092 1 0.0076515 1 2p loss 0 (0%) 483 NA NA NA NA 0.026679 1 0.014176 1 NA NA NA NA 0.60481 1 0.56561 1 0.14427 1 1 1 0.27086 1 0.01958 1 2q loss 0 (0%) 473 0.81279 1 0.19208 1 0.0048145 1 0.051109 1 0.73676 1 0.58167 1 0.20651 1 0.016771 1 0.035828 1 0.45376 1 0.50238 1 0.12029 1 3p loss 0 (0%) 288 0.020861 1 0.25799 1 1.4865e-05 0.0128 1.6052e-06 0.00142 0.36727 1 0.16622 1 0.060049 1 0.0064512 1 0.00096353 0.723 0.15356 1 0.028657 1 0.00066557 0.509 3q loss 0 (0%) 455 0.30167 1 0.59977 1 0.00019991 0.161 0.13381 1 0.65392 1 0.9124 1 0.45734 1 0.48536 1 0.50081 1 0.90868 1 0.0018926 1 0.0019939 1 4p loss 0 (0%) 289 0.10476 1 0.032923 1 3.0339e-14 2.85e-11 1.5792e-12 1.47e-09 0.053333 1 0.32731 1 0.00026705 0.212 8.5705e-05 0.071 1.2681e-08 1.16e-05 0.28026 1 6.2708e-06 0.00547 4.8899e-07 0.000439 4q loss 0 (0%) 315 0.02449 1 0.01029 1 6.5943e-14 6.19e-11 7.7579e-10 7.18e-07 0.0093424 1 0.081532 1 8.8844e-06 0.00772 6.5366e-07 0.000584 1.065e-07 9.62e-05 0.0050785 1 0.00016262 0.133 3.7042e-06 0.00326 5p loss 0 (0%) 453 0.16831 1 0.83716 1 0.003404 1 0.0057894 1 0.39071 1 0.22045 1 0.47101 1 0.28241 1 0.61524 1 0.88667 1 0.029432 1 0.017583 1 5q loss 0 (0%) 312 0.21398 1 0.54498 1 1.9472e-08 1.78e-05 9.1691e-08 8.29e-05 0.083988 1 0.12524 1 0.13475 1 0.037754 1 2.0439e-05 0.0174 0.080823 1 0.0010324 0.772 0.0017091 1 6p loss 0 (0%) 443 0.091555 1 0.039089 1 7.8145e-06 0.0068 0.0010342 0.773 0.07526 1 0.029667 1 0.00021294 0.171 0.00025418 0.203 0.011848 1 0.7347 1 0.015329 1 0.0014555 1 6q loss 0 (0%) 437 0.18932 1 0.077443 1 0.00040316 0.315 0.0071731 1 0.088271 1 0.15857 1 0.0086444 1 0.019111 1 0.027203 1 0.59099 1 0.012177 1 0.012188 1 7p loss 0 (0%) 459 0.34021 1 0.28929 1 0.0028131 1 0.00039374 0.309 0.75426 1 0.059447 1 0.94352 1 0.77099 1 0.54054 1 0.19436 1 0.95815 1 0.24759 1 7q loss 0 (0%) 474 0.35634 1 0.30239 1 0.078013 1 0.43348 1 1 1 0.69605 1 0.061713 1 0.12833 1 0.092508 1 0.21551 1 0.3676 1 1 1 8p loss 0 (0%) 336 0.54951 1 0.99284 1 1.1503e-07 0.000104 6.2199e-06 0.00543 0.077389 1 0.75272 1 0.022893 1 0.14808 1 7.3545e-05 0.0613 0.56373 1 0.055139 1 0.0024272 1 8q loss 0 (0%) 469 0.13609 1 0.065955 1 0.010349 1 0.031165 1 0.15683 1 0.23041 1 0.54595 1 0.53971 1 0.16113 1 0.4291 1 0.44419 1 0.32195 1 9p loss 0 (0%) 296 0.14245 1 0.2292 1 7.4184e-13 6.94e-10 5.5084e-08 5e-05 0.96575 1 0.39855 1 0.013445 1 0.15587 1 9.191e-05 0.076 0.12457 1 0.2402 1 0.73273 1 9q loss 0 (0%) 359 0.002805 1 0.0023656 1 5.0287e-18 4.74e-15 1.8458e-07 0.000166 1 1 0.3999 1 1.032e-09 9.54e-07 9.2166e-09 8.44e-06 3.8021e-05 0.032 0.00037718 0.296 0.44594 1 0.37963 1 10p loss 0 (0%) 379 0.026056 1 0.12754 1 3.8023e-10 3.53e-07 5.4168e-09 4.97e-06 1 1 0.16046 1 1.9034e-05 0.0163 9.2943e-07 0.000829 5.6383e-08 5.11e-05 0.00027922 0.222 0.00091125 0.686 0.00030425 0.241 10q loss 0 (0%) 374 0.0013 0.965 0.0004167 0.325 2.0379e-12 1.9e-09 1.3732e-08 1.26e-05 0.26581 1 0.011788 1 5.6889e-07 0.00051 2.5823e-08 2.35e-05 7.4435e-08 6.74e-05 0.0032202 1 0.00013785 0.113 1.1102e-05 0.00964 11p loss 0 (0%) 409 0.064357 1 0.071855 1 8.5813e-07 0.000766 0.00051365 0.396 0.033254 1 0.0076038 1 0.0040245 1 0.039523 1 0.0019484 1 0.33619 1 0.020177 1 0.007756 1 11q loss 0 (0%) 430 0.66227 1 1 1 4.277e-08 3.89e-05 0.00032761 0.259 0.080352 1 0.18891 1 0.0055328 1 0.047749 1 0.00024409 0.195 0.18339 1 0.045785 1 0.0034459 1 12p loss 0 (0%) 480 NA NA NA NA 0.53418 1 0.077662 1 NA NA NA NA 1 1 0.14305 1 0.13276 1 0.3759 1 0.44022 1 0.47729 1 12q loss 0 (0%) 475 NA NA NA NA 0.27614 1 0.038489 1 0.29227 1 0.38118 1 0.6576 1 0.44879 1 0.018172 1 0.048273 1 0.9391 1 0.5826 1 13q loss 0 (0%) 307 0.12911 1 0.37643 1 2.894e-09 2.66e-06 1.0307e-06 0.000917 0.14906 1 0.43995 1 0.67409 1 0.17806 1 5.034e-05 0.042 0.071783 1 0.0012612 0.938 8.1727e-05 0.0678 14q loss 0 (0%) 403 0.0022995 1 0.025803 1 0.00047773 0.371 0.05875 1 0.04584 1 0.042167 1 1.4813e-09 1.37e-06 4.9774e-13 4.66e-10 2.8811e-05 0.0243 0.016913 1 0.11543 1 0.080818 1 15q loss 0 (0%) 428 0.80457 1 0.0098422 1 0.001142 0.852 2.9786e-05 0.0251 0.0080068 1 0.0017183 1 0.27231 1 0.010339 1 0.15429 1 0.44659 1 0.44624 1 0.72959 1 16p loss 0 (0%) 416 0.79399 1 0.15334 1 0.00011509 0.0946 0.017884 1 0.41198 1 0.32579 1 0.37504 1 0.030165 1 0.027434 1 0.044915 1 0.46213 1 0.28747 1 16q loss 0 (0%) 394 0.21654 1 0.44945 1 0.00067964 0.519 0.0088793 1 0.17168 1 0.13181 1 0.024726 1 0.00082088 0.621 0.00012725 0.104 0.0036437 1 0.00039687 0.311 0.00017345 0.141 17p loss 0 (0%) 310 0.11305 1 0.43332 1 1.5264e-05 0.0131 0.001454 1 0.010684 1 0.069425 1 0.32692 1 0.34819 1 0.043767 1 0.30493 1 0.64817 1 0.13811 1 17q loss 0 (0%) 457 0.29931 1 0.13491 1 0.17501 1 0.0017545 1 0.3043 1 0.94292 1 0.0041964 1 0.016224 1 0.73596 1 0.93852 1 0.73674 1 0.52476 1 18p loss 0 (0%) 432 0.3179 1 0.97064 1 0.0020586 1 0.62111 1 0.13805 1 0.8681 1 0.65888 1 0.40508 1 0.21596 1 0.69892 1 0.56017 1 0.86122 1 18q loss 0 (0%) 395 0.59042 1 0.7531 1 0.00051599 0.397 0.10051 1 0.20494 1 0.82866 1 0.64607 1 0.1167 1 0.31302 1 0.67222 1 0.53865 1 1 1 19p loss 0 (0%) 413 0.013991 1 0.01333 1 1.8881e-05 0.0161 0.37745 1 0.83237 1 0.8814 1 0.00017607 0.143 0.00022159 0.178 0.041052 1 7.8836e-05 0.0655 0.96293 1 0.76289 1 19q loss 0 (0%) 440 0.31631 1 0.52768 1 0.055998 1 0.12477 1 0.034579 1 0.10349 1 0.97947 1 0.93892 1 0.17867 1 0.70628 1 0.18609 1 0.13492 1 20p loss 0 (0%) 469 0.20824 1 0.10984 1 0.19144 1 0.082093 1 0.077222 1 0.64425 1 0.41717 1 0.68233 1 0.19053 1 0.57736 1 0.78224 1 0.19571 1 20q loss 0 (0%) 465 0.0069786 1 0.014371 1 0.0023376 1 0.28421 1 0.13746 1 0.48631 1 0.00044959 0.35 0.0003612 0.284 0.032354 1 0.14893 1 0.3311 1 0.17921 1 21q loss 0 (0%) 338 0.018957 1 0.064039 1 1.5791e-11 1.47e-08 5.6804e-06 0.00496 0.22723 1 0.18117 1 0.043872 1 0.019437 1 0.00025918 0.207 0.07484 1 0.10795 1 0.0066924 1 22q loss 0 (0%) 441 0.072884 1 0.068677 1 0.30676 1 0.3899 1 0.48505 1 0.20159 1 0.037255 1 0.018018 1 0.22693 1 0.17931 1 0.22288 1 0.1247 1 Xq loss 0 (0%) 463 0.52298 1 0.59764 1 0.031324 1 0.022419 1 0.57715 1 0.0007658 0.581 0.22136 1 0.093406 1 0.005797 1 0.35976 1 0.012506 1 0.34493 1