Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL MIR_CNMF MIR_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_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 1p gain 40 (7%) 523 0.68087 1 0.093426 1 0.93357 1 0.065064 1 1.1016e-05 0.00719 0.38839 1 0.47773 1 0.92453 1 0.4599 1 0.069597 1 1q gain 45 (8%) 518 0.62112 1 0.11628 1 0.43965 1 0.34345 1 2.6408e-08 1.78e-05 0.29525 1 0.71251 1 0.88151 1 1 1 0.15175 1 2p gain 20 (4%) 543 0.10988 1 0.78553 1 0.0019972 1 0.1284 1 0.2516 1 0.46032 1 0.68524 1 0.38479 1 0.57734 1 0.79667 1 2q gain 18 (3%) 545 0.17277 1 0.44651 1 3.903e-05 0.0254 0.074318 1 0.37173 1 0.46032 1 0.53498 1 0.51996 1 0.79538 1 0.3663 1 3p gain 30 (5%) 533 0.0035955 1 0.057296 1 0.55096 1 0.67656 1 0.019313 1 0.15031 1 0.40452 1 0.13699 1 0.80774 1 0.77856 1 3q gain 30 (5%) 533 0.0035955 1 0.057296 1 0.55096 1 0.90721 1 0.047297 1 0.15031 1 0.40452 1 0.13699 1 0.74816 1 0.57974 1 4p gain 15 (3%) 548 0.74677 1 0.65551 1 0.38221 1 0.045643 1 0.28984 1 NA NA 0.4441 1 0.14938 1 NA NA NA NA 4q gain 14 (2%) 549 0.73329 1 0.63255 1 0.20631 1 0.082752 1 0.19264 1 NA NA 0.4441 1 0.14938 1 NA NA NA NA 5p gain 30 (5%) 533 0.11223 1 0.31043 1 0.24106 1 0.3533 1 0.0036962 1 NA NA 0.1693 1 0.65201 1 0.20133 1 0.20182 1 5q gain 23 (4%) 540 0.042686 1 0.18309 1 0.050792 1 0.090482 1 0.01521 1 NA NA NA NA NA NA 0.4425 1 0.36479 1 6p gain 7 (1%) 556 0.78987 1 0.76862 1 0.65661 1 0.39511 1 0.16089 1 NA NA NA NA NA NA NA NA NA NA 6q gain 9 (2%) 554 0.23727 1 0.60124 1 0.59532 1 0.7463 1 0.02951 1 NA NA NA NA NA NA NA NA NA NA 7p gain 434 (77%) 129 4.496e-08 3.02e-05 7.1983e-07 0.000482 0.00071765 0.451 1.8178e-09 1.23e-06 1.9998e-16 1.38e-13 0.0011004 0.687 0.0016235 0.995 0.47149 1 0.041144 1 0.005521 1 7q gain 439 (78%) 124 3.4884e-06 0.00231 1.749e-05 0.0114 0.0010184 0.637 1.5607e-06 0.00104 9.3585e-15 6.46e-12 0.0034775 1 0.019908 1 0.36112 1 0.091588 1 0.011457 1 8p gain 26 (5%) 537 0.0012374 0.767 0.081363 1 0.3346 1 0.0081176 1 0.0015023 0.924 0.15031 1 0.064059 1 0.060006 1 0.80774 1 0.5513 1 8q gain 31 (6%) 532 0.00051068 0.324 0.041582 1 0.28577 1 0.005352 1 0.0036246 1 0.043391 1 0.064059 1 0.060006 1 0.33783 1 0.54716 1 9p gain 17 (3%) 546 0.23381 1 0.039366 1 0.73832 1 0.55983 1 0.042235 1 0.54431 1 0.21472 1 0.30529 1 0.31935 1 0.7656 1 9q gain 34 (6%) 529 0.43124 1 0.031685 1 0.61869 1 0.73907 1 0.16894 1 1 1 0.43331 1 0.11583 1 0.58832 1 0.67007 1 10p gain 12 (2%) 551 0.00052018 0.329 0.0047211 1 0.091096 1 0.0014495 0.893 0.0012274 0.762 NA NA 0.30734 1 0.38357 1 NA NA NA NA 11p gain 4 (1%) 559 1 1 1 1 0.6817 1 0.49737 1 0.25879 1 NA NA NA NA NA NA NA NA NA NA 11q gain 7 (1%) 556 0.15234 1 0.20907 1 0.26518 1 0.078108 1 0.16089 1 NA NA 1 1 0.42091 1 NA NA NA NA 12p gain 43 (8%) 520 0.41254 1 0.20086 1 1 1 0.26493 1 0.0012597 0.78 0.44579 1 0.35954 1 0.79984 1 0.042701 1 0.25906 1 12q gain 33 (6%) 530 0.31979 1 0.066373 1 0.99342 1 0.20921 1 0.0056682 1 0.63417 1 0.54957 1 0.69468 1 0.10947 1 0.69967 1 13q gain 3 (1%) 560 0.77651 1 0.79227 1 0.15622 1 0.49737 1 0.28937 1 NA NA NA NA NA NA 1 1 0.52663 1 14q gain 7 (1%) 556 0.70562 1 0.67434 1 0.056688 1 0.56424 1 0.63794 1 NA NA NA NA NA NA NA NA NA NA 15q gain 6 (1%) 557 0.37943 1 0.53571 1 0.51228 1 0.58797 1 0.012615 1 NA NA NA NA NA NA NA NA NA NA 16p gain 18 (3%) 545 0.031801 1 0.29738 1 0.60037 1 0.26252 1 0.01546 1 NA NA 0.33206 1 0.44161 1 NA NA NA NA 16q gain 18 (3%) 545 0.047996 1 0.25275 1 0.4388 1 0.032451 1 0.01546 1 NA NA 0.43331 1 0.44161 1 NA NA NA NA 17p gain 11 (2%) 552 0.018837 1 0.38893 1 0.72128 1 0.34903 1 0.10809 1 NA NA 1 1 0.28433 1 NA NA NA NA 17q gain 19 (3%) 544 0.21995 1 1 1 0.80602 1 0.60914 1 0.058389 1 NA NA 0.78567 1 0.38357 1 0.20817 1 0.56157 1 18p gain 28 (5%) 535 0.50098 1 0.18804 1 0.50908 1 0.36419 1 0.00032644 0.208 0.31253 1 0.40836 1 0.54773 1 0.065603 1 0.25906 1 18q gain 30 (5%) 533 0.1095 1 0.186 1 0.35609 1 0.59709 1 0.00015903 0.102 0.31253 1 0.72162 1 0.40714 1 0.020882 1 0.103 1 19p gain 176 (31%) 387 2.1502e-14 1.48e-11 3.1164e-10 2.12e-07 0.23626 1 0.00011721 0.0755 1.0224e-23 7.09e-21 0.00045117 0.286 0.017521 1 3.0851e-06 0.00205 0.10158 1 0.0082126 1 19q gain 151 (27%) 412 7.2243e-16 4.99e-13 3.7547e-12 2.57e-09 0.06713 1 2.3083e-05 0.015 1.6393e-28 1.14e-25 0.011177 1 0.052846 1 4.3117e-06 0.00285 0.025026 1 0.012356 1 20p gain 180 (32%) 383 2.1678e-13 1.49e-10 3.7172e-12 2.55e-09 0.20059 1 6.2058e-05 0.0402 1.5381e-09 1.04e-06 0.064489 1 0.09463 1 0.0022784 1 0.91408 1 0.00071253 0.448 20q gain 178 (32%) 385 3.2454e-13 2.23e-10 4.3762e-11 2.98e-08 0.15703 1 6.8018e-06 0.00446 2.9794e-09 2.01e-06 0.011022 1 0.059476 1 0.0011577 0.72 0.83414 1 0.0004034 0.257 21q gain 36 (6%) 527 0.0026753 1 0.031762 1 0.0081585 1 0.0019135 1 0.046905 1 NA NA 0.41081 1 0.9117 1 0.017132 1 0.032917 1 22q gain 11 (2%) 552 0.037825 1 0.14315 1 0.1269 1 0.47972 1 0.076683 1 NA NA 1 1 0.28433 1 NA NA NA NA Xq gain 4 (1%) 559 0.3308 1 0.46842 1 0.75657 1 0.2588 1 0.070179 1 NA NA NA NA NA NA NA NA NA NA 1p loss 5 (1%) 558 0.84895 1 0.82265 1 1 1 0.099622 1 0.53161 1 NA NA NA NA NA NA NA NA NA NA 1q loss 4 (1%) 559 0.2177 1 1 1 0.6817 1 1 1 1 1 NA NA NA NA NA NA NA NA NA NA 2p loss 10 (2%) 553 0.027368 1 0.070517 1 0.65554 1 0.11199 1 0.16334 1 0.13489 1 0.72416 1 1 1 0.039301 1 0.11956 1 2q loss 9 (2%) 554 0.035033 1 0.071016 1 0.23618 1 0.056192 1 0.18334 1 0.13489 1 0.72416 1 1 1 0.039301 1 0.11956 1 3p loss 22 (4%) 541 0.85448 1 0.5126 1 0.58219 1 0.50162 1 0.0076254 1 0.15031 1 0.083521 1 0.65346 1 0.36977 1 0.43586 1 3q loss 16 (3%) 547 0.64281 1 0.47259 1 0.027112 1 0.38333 1 0.0002967 0.19 NA NA 0.80732 1 1 1 0.45435 1 0.27807 1 4p loss 26 (5%) 537 0.019939 1 0.66862 1 0.17472 1 0.021059 1 0.87616 1 0.76135 1 0.090276 1 0.43045 1 0.14019 1 0.43586 1 4q loss 25 (4%) 538 0.04257 1 0.64428 1 0.16244 1 0.14536 1 0.10113 1 0.7007 1 0.098474 1 0.55099 1 0.51727 1 0.56157 1 5p loss 21 (4%) 542 0.0042313 1 0.094713 1 0.18584 1 0.096646 1 0.10997 1 0.08582 1 0.46938 1 1 1 0.78531 1 0.49478 1 5q loss 20 (4%) 543 0.074287 1 0.87215 1 0.30362 1 0.12203 1 0.051235 1 0.08582 1 0.87271 1 1 1 0.46511 1 0.48265 1 6p loss 47 (8%) 516 0.97995 1 0.55299 1 0.37527 1 0.53796 1 2.8402e-09 1.92e-06 0.62167 1 0.91389 1 0.59227 1 0.89628 1 0.60397 1 6q loss 80 (14%) 483 0.67175 1 0.57986 1 0.46152 1 0.11223 1 1.8677e-08 1.26e-05 0.085252 1 0.89585 1 0.6777 1 0.82443 1 0.38273 1 7p loss 5 (1%) 558 0.54206 1 0.45331 1 0.8104 1 0.034114 1 0.53161 1 NA NA NA NA NA NA NA NA NA NA 7q loss 4 (1%) 559 0.84895 1 0.82265 1 1 1 0.099622 1 0.83344 1 NA NA NA NA NA NA NA NA NA NA 8p loss 34 (6%) 529 0.89438 1 0.59278 1 0.78347 1 0.23936 1 0.27205 1 0.13415 1 0.65148 1 0.9117 1 0.72571 1 0.69967 1 8q loss 21 (4%) 542 0.71695 1 0.14364 1 0.38399 1 0.18485 1 0.015407 1 NA NA 0.21181 1 0.82341 1 1 1 0.36479 1 9p loss 164 (29%) 399 0.013659 1 0.0013308 0.822 0.83219 1 0.14675 1 0.22653 1 0.92065 1 0.28153 1 0.058514 1 0.034762 1 0.026047 1 9q loss 63 (11%) 500 0.046121 1 0.025175 1 0.5635 1 0.2616 1 0.058693 1 0.55243 1 0.036699 1 0.052832 1 0.63558 1 0.18437 1 10p loss 437 (78%) 126 1.1958e-06 0.000799 8.3746e-06 0.00548 0.035758 1 1.5818e-08 1.07e-05 1.7964e-28 1.25e-25 0.0034774 1 0.00056666 0.358 0.00065568 0.413 0.53073 1 0.06028 1 10q loss 450 (80%) 113 2.1639e-06 0.00144 4.4995e-06 0.00297 0.024215 1 7.6534e-06 0.00501 3.0902e-31 2.15e-28 0.0020187 1 6.963e-05 0.045 0.0016438 1 0.72949 1 0.090801 1 11p loss 64 (11%) 499 1.1977e-07 8.04e-05 6.6108e-06 0.00434 0.094557 1 2.4322e-06 0.00162 7.7704e-12 5.31e-09 0.0010687 0.668 0.67888 1 0.065924 1 0.044323 1 0.42633 1 11q loss 55 (10%) 508 9.716e-05 0.0627 0.0042704 1 0.51227 1 0.0050141 1 2.0983e-10 1.43e-07 0.25352 1 0.5772 1 0.093295 1 0.64757 1 0.8683 1 12p loss 38 (7%) 525 0.011562 1 0.017206 1 0.15074 1 0.030631 1 0.75622 1 0.42488 1 0.10009 1 0.47409 1 1 1 1 1 12q loss 35 (6%) 528 0.0088162 1 0.018454 1 0.61033 1 0.053631 1 0.12705 1 0.13959 1 0.10189 1 0.69468 1 0.8388 1 0.54716 1 13q loss 138 (25%) 425 0.00080072 0.502 4.4193e-05 0.0287 0.56854 1 0.64706 1 4.2999e-13 2.95e-10 0.0011431 0.712 0.60059 1 0.018195 1 0.21993 1 0.30902 1 14q loss 121 (21%) 442 4.4911e-07 0.000301 0.025015 1 0.59547 1 0.71406 1 8.6332e-34 6.02e-31 0.015872 1 0.75255 1 0.06036 1 0.035904 1 0.004944 1 15q loss 62 (11%) 501 5.4289e-05 0.0352 0.0003151 0.201 0.00062222 0.393 4.0575e-06 0.00269 6.2567e-06 0.00412 0.00025796 0.165 0.10831 1 0.022362 1 0.015296 1 0.45219 1 16p loss 23 (4%) 540 0.20025 1 0.68421 1 0.46021 1 0.79298 1 0.12681 1 0.39679 1 0.64396 1 0.88983 1 0.50141 1 0.18455 1 16q loss 41 (7%) 522 0.11169 1 0.020949 1 0.12157 1 0.51995 1 0.28729 1 0.22791 1 0.075369 1 0.94503 1 0.70619 1 0.56879 1 17p loss 36 (6%) 527 0.42912 1 0.62014 1 0.83476 1 0.63284 1 5.9367e-06 0.00391 0.17989 1 0.05555 1 0.82603 1 0.50251 1 1 1 17q loss 19 (3%) 544 0.39029 1 0.13631 1 0.40222 1 0.34677 1 0.0016983 1 NA NA 0.21433 1 0.27726 1 0.1677 1 0.093343 1 18p loss 44 (8%) 519 0.024424 1 0.087057 1 0.50372 1 0.71238 1 0.0015637 0.96 0.074704 1 0.2461 1 0.038732 1 0.059642 1 0.52075 1 18q loss 39 (7%) 524 0.28026 1 0.38096 1 0.33713 1 0.92284 1 0.079532 1 0.05994 1 0.15398 1 0.006512 1 0.56663 1 0.68736 1 19p loss 13 (2%) 550 0.0028351 1 0.023992 1 0.00041824 0.266 0.007381 1 0.15821 1 0.59226 1 0.37089 1 0.57388 1 0.57734 1 0.15653 1 19q loss 18 (3%) 545 0.0090173 1 0.047047 1 0.0096366 1 0.0014393 0.888 0.073818 1 0.59226 1 0.37089 1 0.57388 1 0.8579 1 0.36479 1 20p loss 11 (2%) 552 0.054022 1 0.12912 1 0.11565 1 0.062145 1 0.0037726 1 NA NA 0.41365 1 0.38357 1 NA NA NA NA 20q loss 10 (2%) 553 0.078923 1 0.17139 1 0.65554 1 0.39895 1 0.019047 1 NA NA 0.41365 1 0.38357 1 NA NA NA NA 21q loss 25 (4%) 538 0.013321 1 0.01525 1 0.090285 1 0.012074 1 0.028397 1 0.21912 1 0.027916 1 0.32615 1 0.60213 1 0.84833 1 22q loss 140 (25%) 423 0.80852 1 1 1 0.51073 1 0.8861 1 0.00014802 0.0952 0.27507 1 0.73138 1 0.95544 1 0.1561 1 0.88475 1 Xq loss 11 (2%) 552 0.44326 1 0.46795 1 0.11565 1 0.36973 1 0.15293 1 NA NA 0.63573 1 0.31618 1 0.51727 1 0.45361 1