Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_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 11 (3%) 402 NA NA NA NA 0.57626 1 0.90907 1 0.036544 1 0.23445 1 1 1 0.078307 1 0.46021 1 1 1 1q gain 47 (11%) 366 0.052661 1 0.60421 1 0.078786 1 0.30743 1 0.56747 1 0.18103 1 0.094316 1 0.93101 1 0.4366 1 0.83658 1 2p gain 40 (10%) 373 0.097532 1 0.056629 1 0.0040928 1 0.046011 1 0.14097 1 0.48836 1 0.0058999 1 0.004329 1 0.50846 1 0.35508 1 2q gain 39 (9%) 374 0.057657 1 0.051225 1 0.00017278 0.112 0.0023481 1 0.12056 1 0.58893 1 0.0029376 1 0.0026079 1 0.52888 1 0.40458 1 3p gain 20 (5%) 393 0.37803 1 0.42959 1 0.071044 1 0.36719 1 0.71452 1 0.17462 1 0.46373 1 0.85973 1 0.62591 1 0.18436 1 3q gain 30 (7%) 383 0.45805 1 0.055068 1 0.00096864 0.607 0.22011 1 0.39276 1 0.4438 1 0.17821 1 0.58538 1 0.35718 1 0.82412 1 4p gain 3 (1%) 410 NA NA NA NA 0.74635 1 0.47306 1 0.22537 1 0.21377 1 NA NA NA NA 0.20776 1 0.033383 1 4q gain 5 (1%) 408 NA NA NA NA 0.84236 1 1 1 1 1 0.8316 1 NA NA NA NA 0.5788 1 0.33452 1 5p gain 39 (9%) 374 0.28556 1 0.047911 1 0.002235 1 0.023566 1 0.51263 1 0.98717 1 0.34051 1 0.33796 1 0.68528 1 0.53047 1 5q gain 21 (5%) 392 0.65619 1 0.31874 1 0.039106 1 0.18815 1 0.3688 1 0.34548 1 1 1 0.42704 1 1 1 0.94763 1 6p gain 50 (12%) 363 0.51572 1 0.010749 1 0.026735 1 0.67498 1 0.61856 1 0.95465 1 0.29911 1 0.73156 1 0.51347 1 0.24624 1 6q gain 45 (11%) 368 0.33408 1 0.026664 1 0.031676 1 0.35198 1 0.87734 1 0.84738 1 0.4433 1 0.94325 1 0.44104 1 0.30861 1 7p gain 200 (48%) 213 0.0011955 0.745 0.0014094 0.877 1.9164e-15 1.35e-12 9.1419e-05 0.0599 0.31648 1 0.019937 1 1.221e-06 0.000829 7.1941e-05 0.0473 0.42473 1 0.95791 1 7q gain 175 (42%) 238 0.004193 1 0.014622 1 7.0474e-11 4.88e-08 0.0027808 1 0.66662 1 0.075137 1 0.0001633 0.106 0.00045347 0.291 0.47424 1 0.75189 1 8p gain 80 (19%) 333 1 1 0.98822 1 9.2183e-06 0.00616 0.056224 1 0.2496 1 0.16168 1 0.47019 1 0.84908 1 0.615 1 0.57107 1 8q gain 162 (39%) 251 0.79277 1 0.15105 1 9.3911e-12 6.55e-09 0.00066584 0.421 0.65042 1 0.056547 1 0.15048 1 0.13618 1 0.098557 1 0.1543 1 9p gain 46 (11%) 367 0.03165 1 0.26151 1 0.28043 1 0.43276 1 0.08168 1 0.12969 1 0.078335 1 0.34981 1 0.76674 1 0.76256 1 9q gain 39 (9%) 374 0.056767 1 0.3046 1 0.064111 1 0.11304 1 0.01704 1 0.025352 1 0.59499 1 0.8746 1 0.058924 1 0.63487 1 10p gain 18 (4%) 395 0.66898 1 0.55036 1 0.10421 1 0.047659 1 0.95066 1 0.69641 1 0.82579 1 0.45037 1 0.76067 1 0.94138 1 10q gain 7 (2%) 406 NA NA NA NA 0.11363 1 0.042029 1 0.877 1 0.61513 1 NA NA NA NA 0.20178 1 0.15076 1 11p gain 18 (4%) 395 0.14977 1 0.0018981 1 0.00031424 0.203 0.00057549 0.367 1 1 0.60504 1 0.0055855 1 0.042103 1 0.63382 1 0.88213 1 11q gain 22 (5%) 391 0.029722 1 0.0039665 1 3.7234e-06 0.00251 0.0014127 0.877 0.29898 1 0.67656 1 0.00061975 0.394 0.0098033 1 0.38613 1 0.69294 1 12p gain 66 (16%) 347 0.36141 1 0.091238 1 0.0044169 1 0.014562 1 0.53678 1 0.57397 1 0.14612 1 0.56123 1 0.068987 1 0.21035 1 12q gain 60 (15%) 353 0.24467 1 0.18956 1 0.0018101 1 0.0029065 1 0.41709 1 0.54594 1 0.20803 1 0.8739 1 0.012051 1 0.26775 1 13q gain 211 (51%) 202 1.076e-05 0.00717 4.1393e-05 0.0274 2.9518e-33 2.11e-30 0.00026706 0.173 0.10109 1 0.021236 1 8.394e-07 0.000572 8.4619e-06 0.00567 0.044991 1 0.46564 1 14q gain 15 (4%) 398 0.48354 1 0.44965 1 0.056649 1 0.27636 1 0.049926 1 0.367 1 0.30633 1 0.50251 1 1 1 0.80535 1 15q gain 5 (1%) 408 NA NA NA NA 0.073166 1 0.68257 1 0.037418 1 0.063649 1 NA NA NA NA 0.47307 1 0.42668 1 16p gain 67 (16%) 346 0.012748 1 0.011082 1 1.0833e-14 7.62e-12 0.13846 1 0.25803 1 0.048753 1 0.0098556 1 9.9365e-05 0.065 0.12636 1 0.047449 1 16q gain 66 (16%) 347 0.013846 1 0.018495 1 1.4436e-16 1.02e-13 0.13607 1 0.18116 1 0.048753 1 0.0028546 1 0.00040845 0.263 0.31435 1 0.23221 1 17p gain 9 (2%) 404 NA NA NA NA 0.61782 1 0.89252 1 0.62638 1 0.099646 1 NA NA NA NA 0.73695 1 0.89132 1 17q gain 48 (12%) 365 0.089782 1 0.021785 1 0.00091327 0.574 0.0073931 1 0.24997 1 0.18533 1 0.00047514 0.304 0.0060503 1 0.058064 1 0.75324 1 18p gain 15 (4%) 398 0.11676 1 0.82845 1 0.0054775 1 0.013908 1 0.33447 1 0.60323 1 0.21552 1 0.023418 1 0.14412 1 0.3884 1 18q gain 9 (2%) 404 NA NA NA NA 0.023231 1 0.030293 1 0.074678 1 0.066625 1 NA NA NA NA 0.27437 1 0.32669 1 19p gain 34 (8%) 379 0.074386 1 0.22249 1 0.0055403 1 0.051177 1 0.22917 1 0.23327 1 0.75047 1 0.10412 1 0.58806 1 0.57289 1 19q gain 41 (10%) 372 0.067592 1 0.093476 1 0.43743 1 0.066588 1 0.026239 1 0.072086 1 0.0050557 1 0.41898 1 0.92434 1 0.94219 1 20p gain 188 (46%) 225 0.0022252 1 5.9198e-06 0.00398 4.2881e-20 3.05e-17 0.012719 1 0.022913 1 0.064848 1 8.669e-06 0.0058 3.5462e-07 0.000242 0.17412 1 0.075786 1 20q gain 267 (65%) 146 1.1841e-11 8.21e-09 9.6884e-15 6.82e-12 9.4158e-47 6.77e-44 1.0617e-09 7.32e-07 0.0010368 0.649 1.2438e-05 0.00826 3.9537e-16 2.8e-13 5.9833e-18 4.25e-15 0.10269 1 0.42883 1 21q gain 11 (3%) 402 0.1916 1 0.29494 1 0.085831 1 0.33915 1 0.19318 1 0.48036 1 0.59137 1 1 1 0.70412 1 0.68448 1 Xq gain 12 (3%) 401 0.068912 1 0.7347 1 0.033071 1 0.63094 1 0.13267 1 0.35201 1 0.89179 1 0.22526 1 0.35201 1 0.40967 1 1p loss 51 (12%) 362 0.0024918 1 0.00092707 0.582 7.0876e-08 4.87e-05 0.0032853 1 0.71035 1 0.59716 1 0.0043209 1 0.001443 0.895 0.18025 1 0.27379 1 1q loss 18 (4%) 395 0.27063 1 0.11239 1 0.01032 1 0.26876 1 0.40053 1 0.59388 1 0.34513 1 0.029812 1 0.94083 1 0.44046 1 2p loss 4 (1%) 409 0.56945 1 0.14186 1 0.43319 1 NA NA NA NA NA NA 0.15974 1 1 1 0.66171 1 0.13188 1 2q loss 6 (1%) 407 1 1 0.06611 1 0.60146 1 NA NA 0.070954 1 0.2687 1 0.081605 1 1 1 0.17503 1 0.0588 1 3p loss 27 (7%) 386 0.52785 1 0.19969 1 0.0025064 1 0.25233 1 0.42718 1 0.97191 1 0.77166 1 0.19506 1 0.21162 1 0.14292 1 3q loss 12 (3%) 401 0.81607 1 0.69182 1 0.22379 1 1 1 0.12364 1 0.30616 1 1 1 0.18315 1 0.42323 1 0.82207 1 4p loss 84 (20%) 329 0.0019927 1 0.036897 1 1.0515e-11 7.31e-09 0.0029908 1 0.15706 1 0.25508 1 0.0087489 1 0.023375 1 0.08301 1 0.29045 1 4q loss 68 (16%) 345 0.0046998 1 0.016105 1 2.2559e-10 1.56e-07 0.0022265 1 0.10969 1 0.23051 1 0.038839 1 0.21707 1 0.0026607 1 0.035856 1 5p loss 25 (6%) 388 0.65913 1 0.17195 1 0.0017575 1 0.10207 1 0.72509 1 0.69984 1 0.43384 1 0.47736 1 0.84064 1 0.90748 1 5q loss 38 (9%) 375 0.092594 1 0.12247 1 1.1142e-05 0.00741 0.29312 1 0.38129 1 0.28369 1 0.029736 1 0.074251 1 0.55089 1 0.47951 1 6p loss 12 (3%) 401 0.53811 1 0.050029 1 0.0028528 1 1 1 0.75455 1 1 1 0.17551 1 0.34006 1 0.64237 1 0.62386 1 6q loss 21 (5%) 392 0.94266 1 0.5294 1 0.074255 1 0.69654 1 0.16536 1 0.71098 1 0.57506 1 0.31397 1 0.86383 1 1 1 8p loss 93 (23%) 320 0.0002927 0.189 0.0082312 1 7.7588e-17 5.51e-14 0.0010382 0.649 0.22938 1 0.033727 1 0.00021835 0.142 0.0024981 1 0.19995 1 0.35649 1 8q loss 8 (2%) 405 0.40248 1 0.7347 1 0.0096561 1 0.85153 1 0.27311 1 0.72636 1 0.051432 1 0.038103 1 0.19663 1 0.43569 1 9p loss 27 (7%) 386 0.87438 1 0.19679 1 4.3967e-05 0.0291 0.074568 1 0.24082 1 0.17721 1 0.30078 1 0.80652 1 0.5304 1 0.74427 1 9q loss 26 (6%) 387 0.35849 1 0.17139 1 2.5495e-06 0.00172 0.00061883 0.394 0.24082 1 0.17721 1 0.0587 1 0.37149 1 0.11437 1 0.6754 1 10p loss 22 (5%) 391 0.63045 1 0.69182 1 0.00082829 0.522 0.28523 1 0.10864 1 0.63752 1 0.25538 1 0.084192 1 0.23963 1 0.68136 1 10q loss 24 (6%) 389 0.37283 1 0.5689 1 0.00052594 0.336 0.15234 1 0.13532 1 0.94907 1 0.30346 1 0.029714 1 0.69659 1 0.39298 1 11p loss 22 (5%) 391 0.49363 1 0.10558 1 8.336e-05 0.0547 0.00028101 0.182 0.72668 1 0.51436 1 0.92902 1 0.64029 1 0.040081 1 0.16178 1 11q loss 27 (7%) 386 0.36458 1 0.06658 1 7.9223e-06 0.00532 9.6071e-06 0.00641 0.65207 1 0.59388 1 0.66348 1 1 1 0.35754 1 0.20161 1 12p loss 21 (5%) 392 0.096973 1 0.12566 1 7.1022e-05 0.0468 0.20684 1 0.52971 1 0.97191 1 0.28183 1 0.76211 1 0.71974 1 0.20758 1 12q loss 20 (5%) 393 0.18953 1 0.15428 1 0.00010141 0.0662 0.15257 1 0.70572 1 0.93933 1 0.44563 1 0.8183 1 0.41103 1 0.36188 1 13q loss 6 (1%) 407 NA NA NA NA 0.020925 1 0.23224 1 0.037998 1 0.021419 1 NA NA NA NA 0.86925 1 0.7227 1 14q loss 94 (23%) 319 9.7545e-08 6.68e-05 2.1017e-06 0.00142 1.5793e-22 1.13e-19 1.1969e-06 0.000814 0.00025118 0.163 0.0030768 1 1.5378e-07 0.000105 1.7591e-06 0.00119 0.53245 1 0.19414 1 15q loss 99 (24%) 314 0.007525 1 0.0087304 1 9.291e-22 6.62e-19 0.0045786 1 0.054069 1 0.59654 1 0.043741 1 0.00045086 0.289 0.48797 1 0.043531 1 16p loss 9 (2%) 404 0.24922 1 0.57054 1 0.30453 1 0.029781 1 0.52758 1 1 1 0.3831 1 0.31721 1 0.71093 1 1 1 16q loss 7 (2%) 406 0.46196 1 0.91698 1 0.22757 1 NA NA NA NA NA NA 0.64877 1 0.55777 1 0.17503 1 0.16959 1 17p loss 164 (40%) 249 4.4375e-06 0.00299 5.8826e-05 0.0388 4.4431e-23 3.18e-20 2.3112e-07 0.000158 0.027963 1 0.033637 1 0.00041042 0.264 5.09e-05 0.0336 0.14682 1 0.04636 1 17q loss 32 (8%) 381 0.11563 1 0.13434 1 0.0021573 1 0.21993 1 0.6218 1 0.41148 1 0.90299 1 0.36721 1 0.32156 1 0.29072 1 18p loss 209 (51%) 204 2.0412e-14 1.43e-11 6.4706e-10 4.46e-07 2.4423e-46 1.75e-43 5.149e-13 3.6e-10 0.00081037 0.511 8.2397e-05 0.0541 5.9168e-13 4.13e-10 4.6025e-14 3.23e-11 0.25052 1 0.49723 1 18q loss 225 (54%) 188 1.4041e-13 9.83e-11 1.6231e-09 1.12e-06 8.8765e-46 6.36e-43 3.6165e-15 2.55e-12 0.0097463 1 0.00066206 0.419 1.0128e-11 7.05e-09 1.7366e-15 1.23e-12 0.061165 1 0.49873 1 19p loss 14 (3%) 399 1 1 0.3385 1 0.0027471 1 0.095687 1 0.12747 1 0.12335 1 0.46373 1 0.34006 1 0.69276 1 0.087585 1 19q loss 13 (3%) 400 0.92198 1 0.43529 1 0.011541 1 0.095687 1 0.58354 1 0.19581 1 0.42825 1 0.55777 1 0.56958 1 0.061113 1 20p loss 33 (8%) 380 0.013465 1 0.0081801 1 8.8788e-08 6.09e-05 0.051364 1 0.75633 1 0.64487 1 0.063138 1 0.039273 1 0.90557 1 0.52983 1 21q loss 71 (17%) 342 0.010314 1 0.006929 1 2.5982e-06 0.00175 0.25825 1 0.60461 1 0.82672 1 0.10341 1 0.024492 1 0.073098 1 0.60765 1 22q loss 81 (20%) 332 0.0004731 0.303 0.0006228 0.395 1.0613e-11 7.37e-09 0.089431 1 0.062327 1 0.015201 1 0.06208 1 0.0011002 0.687 0.62418 1 0.12297 1 Xq loss 5 (1%) 408 NA NA NA NA 0.84236 1 1 1 0.38896 1 0.67311 1 NA NA NA NA 0.85062 1 0.14029 1