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 0.065623 1 0.20886 1 0.42521 1 0.68335 1 0.46021 1 1 1 1q gain 47 (11%) 366 0.053097 1 0.73195 1 0.078786 1 0.30743 1 0.61175 1 0.12518 1 0.11959 1 0.29923 1 0.4366 1 0.83658 1 2p gain 40 (10%) 373 0.156 1 0.037771 1 0.0040928 1 0.046011 1 0.1818 1 0.37275 1 0.00038556 0.249 0.019921 1 0.50846 1 0.35508 1 2q gain 39 (9%) 374 0.098461 1 0.035248 1 0.00017278 0.113 0.0023481 1 0.12194 1 0.46618 1 0.0010917 0.686 0.038358 1 0.52888 1 0.40458 1 3p gain 20 (5%) 393 0.39682 1 0.38241 1 0.071044 1 0.36719 1 0.70057 1 0.13684 1 0.97363 1 0.67551 1 0.62591 1 0.18436 1 3q gain 30 (7%) 383 0.48206 1 0.045848 1 0.00096864 0.611 0.22011 1 0.4628 1 0.35385 1 0.41476 1 0.63539 1 0.35718 1 0.82412 1 4p gain 3 (1%) 410 NA NA NA NA 0.74635 1 0.47306 1 0.27053 1 0.34139 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 1 1 NA NA NA NA 0.5788 1 0.33452 1 5p gain 39 (9%) 374 0.28969 1 0.041804 1 0.002235 1 0.023566 1 0.5289 1 0.92241 1 0.61763 1 1 1 0.68528 1 0.53047 1 5q gain 21 (5%) 392 0.65716 1 0.56376 1 0.039106 1 0.18815 1 0.56622 1 0.64958 1 0.74855 1 0.57791 1 1 1 0.94763 1 6p gain 50 (12%) 363 0.17049 1 0.011561 1 0.026735 1 0.67498 1 0.55908 1 0.68372 1 0.036737 1 0.26847 1 0.51347 1 0.24624 1 6q gain 45 (11%) 368 0.31237 1 0.024817 1 0.031676 1 0.35198 1 0.71695 1 0.62265 1 0.15625 1 0.62058 1 0.44104 1 0.30861 1 7p gain 200 (48%) 213 0.0012376 0.775 0.0037522 1 1.9164e-15 1.37e-12 9.1419e-05 0.0599 0.19699 1 0.0047606 1 1.0881e-07 7.5e-05 2.8504e-05 0.019 0.42473 1 0.95791 1 7q gain 175 (42%) 238 0.0047588 1 0.023568 1 7.0474e-11 4.92e-08 0.0027808 1 0.5367 1 0.023278 1 3.0119e-06 0.00204 0.00018602 0.121 0.47424 1 0.75189 1 8p gain 80 (19%) 333 0.92471 1 0.78522 1 9.2183e-06 0.00619 0.056224 1 0.18398 1 0.22276 1 0.17509 1 0.032702 1 0.615 1 0.57107 1 8q gain 162 (39%) 251 0.75056 1 0.6124 1 9.3911e-12 6.6e-09 0.00066584 0.425 0.64798 1 0.21462 1 0.0071979 1 0.12747 1 0.098557 1 0.1543 1 9p gain 46 (11%) 367 0.033453 1 0.21301 1 0.28043 1 0.43276 1 0.23239 1 0.18632 1 0.87901 1 0.76037 1 0.76674 1 0.76256 1 9q gain 39 (9%) 374 0.091518 1 0.07755 1 0.064111 1 0.11304 1 0.018363 1 0.026965 1 0.36187 1 0.65886 1 0.058924 1 0.63487 1 10p gain 18 (4%) 395 0.64997 1 0.62538 1 0.10421 1 0.047659 1 0.84537 1 0.70524 1 0.90416 1 0.46649 1 0.76067 1 0.94138 1 10q gain 7 (2%) 406 NA NA NA NA 0.11363 1 0.042029 1 0.67899 1 0.74596 1 0.93301 1 0.21941 1 0.20178 1 0.15076 1 11p gain 18 (4%) 395 0.15112 1 0.001355 0.847 0.00031424 0.203 0.00057549 0.369 0.49561 1 0.59587 1 0.87143 1 0.88902 1 0.63382 1 0.88213 1 11q gain 22 (5%) 391 0.030148 1 0.0022731 1 3.7234e-06 0.00251 0.0014127 0.881 0.12068 1 0.51658 1 0.1506 1 0.22004 1 0.38613 1 0.69294 1 12p gain 66 (16%) 347 0.24785 1 0.71014 1 0.0044169 1 0.014562 1 0.20485 1 0.80059 1 0.36103 1 0.68168 1 0.068987 1 0.21035 1 12q gain 60 (15%) 353 0.24785 1 0.54186 1 0.0018101 1 0.0029065 1 0.14198 1 0.75117 1 0.26963 1 0.69054 1 0.012051 1 0.26775 1 13q gain 211 (51%) 202 2.9524e-06 0.002 3.3163e-05 0.022 2.9518e-33 2.13e-30 0.00026706 0.173 0.24565 1 0.014638 1 1.7083e-06 0.00117 7.158e-05 0.0472 0.044991 1 0.46564 1 14q gain 15 (4%) 398 0.48458 1 0.4434 1 0.056649 1 0.27636 1 0.18897 1 0.43773 1 0.14473 1 0.12695 1 1 1 0.80535 1 15q gain 5 (1%) 408 NA NA NA NA 0.073166 1 0.68257 1 0.12053 1 0.059239 1 0.78261 1 0.48055 1 0.47307 1 0.42668 1 16p gain 67 (16%) 346 0.012989 1 0.0037979 1 1.0833e-14 7.69e-12 0.13846 1 0.16256 1 0.025635 1 0.050958 1 0.17966 1 0.12636 1 0.047449 1 16q gain 66 (16%) 347 0.013862 1 0.0064365 1 1.4436e-16 1.03e-13 0.13607 1 0.13223 1 0.025635 1 0.050958 1 0.17966 1 0.31435 1 0.23221 1 17p gain 9 (2%) 404 NA NA NA NA 0.61782 1 0.89252 1 0.20204 1 0.085973 1 0.031649 1 0.22465 1 0.73695 1 0.89132 1 17q gain 48 (12%) 365 0.092916 1 0.020216 1 0.00091327 0.578 0.0073931 1 0.23346 1 0.13015 1 1.1618e-05 0.00777 0.014993 1 0.058064 1 0.75324 1 18p gain 15 (4%) 398 0.11798 1 0.63749 1 0.0054775 1 0.013908 1 0.47625 1 0.61814 1 0.17065 1 0.058059 1 0.14412 1 0.3884 1 18q gain 9 (2%) 404 NA NA NA NA 0.023231 1 0.030293 1 0.1283 1 0.069729 1 0.14202 1 0.26749 1 0.27437 1 0.32669 1 19p gain 34 (8%) 379 0.14153 1 0.23992 1 0.0055403 1 0.051177 1 0.74701 1 0.16527 1 0.32105 1 0.48103 1 0.58806 1 0.57289 1 19q gain 41 (10%) 372 0.071786 1 0.10441 1 0.43743 1 0.066588 1 0.14615 1 0.049292 1 0.14546 1 0.29663 1 0.92434 1 0.94219 1 20p gain 188 (46%) 225 0.001417 0.883 1.4709e-06 0.00101 4.2881e-20 3.07e-17 0.012719 1 0.11383 1 0.016779 1 3.3451e-05 0.0222 0.00019663 0.128 0.17412 1 0.075786 1 20q gain 267 (65%) 146 1.2389e-11 8.67e-09 1.886e-13 1.34e-10 9.4158e-47 6.81e-44 1.0617e-09 7.37e-07 0.010519 1 2.2689e-06 0.00155 2.6055e-13 1.84e-10 3.5822e-11 2.5e-08 0.10269 1 0.42883 1 21q gain 11 (3%) 402 0.19372 1 0.19462 1 0.085831 1 0.33915 1 0.071712 1 0.52322 1 0.28201 1 0.73007 1 0.70412 1 0.68448 1 Xq gain 12 (3%) 401 0.48687 1 0.77692 1 0.033071 1 0.63094 1 0.11053 1 0.23172 1 0.44618 1 0.76497 1 0.35201 1 0.40967 1 1p loss 51 (12%) 362 0.0048918 1 0.0007651 0.487 7.0876e-08 4.9e-05 0.0032853 1 0.51777 1 0.61108 1 0.098391 1 0.28609 1 0.18025 1 0.27379 1 1q loss 18 (4%) 395 0.45164 1 0.13542 1 0.01032 1 0.26876 1 0.47187 1 0.68704 1 0.1506 1 0.19603 1 0.94083 1 0.44046 1 2p loss 4 (1%) 409 0.57247 1 0.1105 1 0.43319 1 NA NA NA NA NA NA NA NA NA NA 0.66171 1 0.13188 1 2q loss 6 (1%) 407 1 1 0.15638 1 0.60146 1 NA NA 0.096581 1 0.22364 1 NA NA NA NA 0.17503 1 0.0588 1 3p loss 27 (7%) 386 0.25348 1 0.10441 1 0.0025064 1 0.25233 1 0.55113 1 1 1 0.45836 1 0.55629 1 0.21162 1 0.14292 1 3q loss 12 (3%) 401 0.41487 1 0.56376 1 0.22379 1 1 1 0.17185 1 0.32301 1 0.2672 1 0.68335 1 0.42323 1 0.82207 1 4p loss 84 (20%) 329 0.0046945 1 0.052076 1 1.0515e-11 7.38e-09 0.0029908 1 0.24001 1 0.30901 1 0.00075446 0.481 0.00059947 0.384 0.08301 1 0.29045 1 4q loss 68 (16%) 345 0.007356 1 0.038081 1 2.2559e-10 1.57e-07 0.0022265 1 0.37204 1 0.33449 1 0.0034832 1 0.015793 1 0.0026607 1 0.035856 1 5p loss 25 (6%) 388 0.87467 1 0.17177 1 0.0017575 1 0.10207 1 0.64237 1 0.62482 1 0.12574 1 0.41591 1 0.84064 1 0.90748 1 5q loss 38 (9%) 375 0.12578 1 0.056322 1 1.1142e-05 0.00746 0.29312 1 0.53657 1 0.23424 1 0.0076323 1 0.10496 1 0.55089 1 0.47951 1 6p loss 12 (3%) 401 0.54027 1 0.25087 1 0.0028528 1 1 1 0.71917 1 1 1 0.66626 1 0.44955 1 0.64237 1 0.62386 1 6q loss 21 (5%) 392 0.94313 1 0.73195 1 0.074255 1 0.69654 1 0.23537 1 0.61741 1 1 1 0.84505 1 0.86383 1 1 1 8p loss 93 (23%) 320 0.0003169 0.205 0.0015632 0.972 7.7588e-17 5.55e-14 0.0010382 0.653 0.49858 1 0.013853 1 0.14082 1 0.066457 1 0.19995 1 0.35649 1 8q loss 8 (2%) 405 0.40267 1 0.77692 1 0.0096561 1 0.85153 1 0.21345 1 0.68625 1 1 1 1 1 0.19663 1 0.43569 1 9p loss 27 (7%) 386 0.87467 1 0.10976 1 4.3967e-05 0.0291 0.074568 1 0.42904 1 0.13443 1 0.042381 1 0.10496 1 0.5304 1 0.74427 1 9q loss 26 (6%) 387 0.34792 1 0.12399 1 2.5495e-06 0.00173 0.00061883 0.396 0.42904 1 0.13443 1 0.0008984 0.57 0.03599 1 0.11437 1 0.6754 1 10p loss 22 (5%) 391 0.66975 1 0.67198 1 0.00082829 0.526 0.28523 1 0.27906 1 0.975 1 0.51767 1 0.35247 1 0.23963 1 0.68136 1 10q loss 24 (6%) 389 0.60573 1 0.70978 1 0.00052594 0.338 0.15234 1 0.27906 1 1 1 0.29513 1 0.039998 1 0.69659 1 0.39298 1 11p loss 22 (5%) 391 0.47001 1 0.067421 1 8.336e-05 0.0548 0.00028101 0.182 0.80588 1 0.59969 1 0.048906 1 0.018363 1 0.040081 1 0.16178 1 11q loss 27 (7%) 386 0.37169 1 0.038707 1 7.9223e-06 0.00534 9.6071e-06 0.00645 0.91681 1 0.68704 1 0.2072 1 0.12893 1 0.35754 1 0.20161 1 12p loss 21 (5%) 392 0.090887 1 0.10976 1 7.1022e-05 0.0469 0.20684 1 0.67164 1 0.94732 1 0.080236 1 0.081727 1 0.71974 1 0.20758 1 12q loss 20 (5%) 393 0.16986 1 0.12399 1 0.00010141 0.0663 0.15257 1 0.68548 1 0.91336 1 0.016133 1 0.039998 1 0.41103 1 0.36188 1 13q loss 6 (1%) 407 NA NA NA NA 0.020925 1 0.23224 1 0.035882 1 0.016259 1 0.42521 1 0.46356 1 0.86925 1 0.7227 1 14q loss 94 (23%) 319 2.0915e-07 0.000144 1.1836e-06 0.000812 1.5793e-22 1.13e-19 1.1969e-06 0.00082 0.00071669 0.457 0.0010247 0.646 1.4971e-06 0.00102 8.7803e-05 0.0576 0.53245 1 0.19414 1 15q loss 99 (24%) 314 0.01932 1 0.012231 1 9.291e-22 6.66e-19 0.0045786 1 0.13449 1 0.3143 1 4.0684e-05 0.0269 7.3474e-05 0.0483 0.48797 1 0.043531 1 16p loss 9 (2%) 404 0.2512 1 0.55383 1 0.30453 1 0.029781 1 0.73379 1 1 1 1 1 1 1 0.71093 1 1 1 16q loss 7 (2%) 406 0.46416 1 1 1 0.22757 1 NA NA NA NA NA NA NA NA NA NA 0.17503 1 0.16959 1 17p loss 164 (40%) 249 1.7497e-05 0.0117 3.0491e-05 0.0203 4.4431e-23 3.19e-20 2.3112e-07 0.000159 0.13409 1 0.020681 1 2.6536e-06 0.0018 8.2008e-06 0.00552 0.14682 1 0.04636 1 17q loss 32 (8%) 381 0.11329 1 0.2246 1 0.0021573 1 0.21993 1 0.7314 1 0.36578 1 0.081268 1 0.10925 1 0.32156 1 0.29072 1 18p loss 209 (51%) 204 2.8122e-13 1.99e-10 2.9191e-10 2.03e-07 2.4423e-46 1.76e-43 5.149e-13 3.63e-10 0.0019121 1 3.1779e-05 0.0211 6.9843e-15 4.97e-12 5.8662e-09 4.07e-06 0.25052 1 0.49723 1 18q loss 225 (54%) 188 1.9205e-12 1.35e-09 3.831e-10 2.66e-07 8.8765e-46 6.4e-43 3.6165e-15 2.57e-12 0.023774 1 0.0001811 0.118 4.465e-14 3.17e-11 1.3634e-08 9.43e-06 0.061165 1 0.49873 1 19p loss 14 (3%) 399 1 1 0.31875 1 0.0027471 1 0.095687 1 0.19526 1 0.13399 1 0.0070759 1 0.078889 1 0.69276 1 0.087585 1 19q loss 13 (3%) 400 0.92159 1 0.38044 1 0.011541 1 0.095687 1 0.67899 1 0.18842 1 0.0070759 1 0.078889 1 0.56958 1 0.061113 1 20p loss 33 (8%) 380 0.013178 1 0.0071318 1 8.8788e-08 6.13e-05 0.051364 1 0.83945 1 0.63022 1 0.35278 1 0.30826 1 0.90557 1 0.52983 1 21q loss 71 (17%) 342 0.0026617 1 0.0048603 1 2.5982e-06 0.00176 0.25825 1 0.84825 1 0.64608 1 0.12188 1 0.34163 1 0.073098 1 0.60765 1 22q loss 81 (20%) 332 0.00091619 0.579 0.00045496 0.293 1.0613e-11 7.44e-09 0.089431 1 0.069953 1 0.020462 1 0.0097172 1 0.0011021 0.691 0.62418 1 0.12297 1 Xq loss 5 (1%) 408 NA NA NA NA 0.84236 1 1 1 0.072635 1 0.68228 1 NA NA NA NA 0.85062 1 0.14029 1