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 15 (3%) 560 0.40379 1 0.11161 1 0.93194 1 0.49686 1 0.22398 1 0.021338 1 0.86431 1 0.82875 1 0.11131 1 0.91089 1 1q gain 80 (14%) 495 0.50855 1 0.9267 1 0.015823 1 0.92569 1 0.13658 1 0.47695 1 0.0034264 1 0.68127 1 0.072884 1 0.97845 1 2p gain 60 (10%) 515 0.014923 1 0.0023214 1 0.0081555 1 0.00025563 0.174 0.28728 1 0.41413 1 0.00063229 0.424 0.0055327 1 0.2161 1 0.020869 1 2q gain 59 (10%) 516 0.0039614 1 0.0026158 1 0.0010069 0.672 5.8199e-06 0.00409 0.55043 1 0.49702 1 0.002176 1 0.0023277 1 0.25079 1 0.050357 1 3p gain 36 (6%) 539 0.13149 1 0.48961 1 0.00018128 0.124 0.25722 1 0.082715 1 0.48833 1 0.51365 1 0.48369 1 0.20792 1 0.36632 1 3q gain 53 (9%) 522 0.23939 1 0.13772 1 2.4908e-06 0.00176 0.035341 1 0.027661 1 0.39769 1 0.69028 1 0.26875 1 0.11128 1 0.54357 1 4p gain 6 (1%) 569 NA NA NA NA 0.062196 1 0.22614 1 0.17038 1 0.080969 1 NA NA NA NA 0.13662 1 0.052496 1 4q gain 7 (1%) 568 0.70318 1 0.32105 1 0.24967 1 0.787 1 0.56819 1 0.73216 1 0.43522 1 0.7455 1 0.38271 1 0.80878 1 5p gain 60 (10%) 515 0.1166 1 0.68118 1 0.0015014 0.992 0.17846 1 0.17225 1 0.94858 1 0.061132 1 0.054405 1 0.7844 1 0.35435 1 5q gain 33 (6%) 542 0.45561 1 0.61736 1 0.0035603 1 0.35577 1 0.66143 1 0.63879 1 0.43179 1 0.46292 1 0.81846 1 0.48285 1 6p gain 77 (13%) 498 0.23811 1 0.0038625 1 1.5453e-06 0.00109 0.40135 1 0.36062 1 0.53227 1 0.03791 1 0.17817 1 0.84813 1 0.39161 1 6q gain 71 (12%) 504 0.3841 1 0.04477 1 7.4722e-07 0.000532 0.15877 1 0.27477 1 0.17031 1 0.06571 1 0.40924 1 0.74931 1 0.25108 1 7p gain 290 (50%) 285 0.00029113 0.197 0.0082373 1 1.8943e-21 1.42e-18 7.2886e-07 0.00052 0.030273 1 0.0041616 1 5.7235e-07 0.000409 5.1771e-07 0.000371 0.070344 1 0.030432 1 7q gain 255 (44%) 320 0.00040574 0.273 0.039255 1 6.9527e-16 5.16e-13 8.6118e-06 0.00603 0.31448 1 0.022715 1 7.4939e-07 0.000533 8.39e-06 0.00588 0.24522 1 0.15535 1 8p gain 108 (19%) 467 0.89962 1 0.65317 1 1.0033e-08 7.29e-06 0.43331 1 0.12137 1 0.078438 1 0.70795 1 0.69234 1 0.49022 1 0.89065 1 8q gain 235 (41%) 340 0.053147 1 0.58855 1 1.0571e-33 8e-31 0.0094198 1 0.044454 1 0.40774 1 0.01124 1 0.071859 1 0.45899 1 0.63306 1 9p gain 79 (14%) 496 0.49142 1 0.90688 1 0.17843 1 0.79019 1 0.40713 1 0.44565 1 0.043512 1 0.05195 1 0.78008 1 0.78126 1 9q gain 64 (11%) 511 0.47006 1 0.85659 1 0.214 1 0.43338 1 0.18653 1 0.22648 1 0.096484 1 0.067707 1 0.4082 1 0.73861 1 10p gain 28 (5%) 547 0.080429 1 1 1 0.009811 1 0.012541 1 0.88682 1 0.83514 1 0.44915 1 0.6739 1 0.6164 1 0.49637 1 10q gain 13 (2%) 562 0.68886 1 0.59527 1 0.19283 1 0.043666 1 0.72072 1 0.21014 1 1 1 0.79532 1 0.69363 1 0.90189 1 11p gain 39 (7%) 536 0.06836 1 0.66349 1 1.7136e-05 0.0119 0.00021429 0.146 0.81461 1 0.93018 1 0.0097121 1 0.059332 1 0.24559 1 0.88201 1 11q gain 39 (7%) 536 0.10493 1 0.045848 1 1.3278e-06 0.000941 0.00091055 0.608 0.50555 1 0.33191 1 0.00048721 0.328 0.0068436 1 0.55893 1 0.40622 1 12p gain 93 (16%) 482 0.3536 1 0.87209 1 0.25584 1 0.017053 1 0.55594 1 0.14248 1 0.053622 1 0.06651 1 0.21996 1 0.11247 1 12q gain 78 (14%) 497 0.233 1 0.80126 1 0.098608 1 0.0019341 1 0.89257 1 0.14534 1 0.14551 1 0.15691 1 0.22169 1 0.16642 1 13q gain 314 (55%) 261 1.3056e-07 9.44e-05 2.6706e-05 0.0186 1.6222e-37 1.23e-34 1.7064e-08 1.24e-05 0.011966 1 0.12547 1 5.4793e-08 3.97e-05 3.7457e-10 2.73e-07 0.010037 1 0.44955 1 14q gain 19 (3%) 556 0.49275 1 0.48023 1 0.030087 1 0.70858 1 0.35152 1 0.27726 1 0.16915 1 0.069902 1 1 1 0.37109 1 15q gain 7 (1%) 568 NA NA NA NA 0.51457 1 0.88163 1 0.024671 1 0.060576 1 NA NA NA NA 0.86981 1 0.37371 1 16p gain 96 (17%) 479 0.10937 1 0.09264 1 1.2625e-16 9.39e-14 0.010804 1 0.42568 1 0.02825 1 0.03518 1 0.0063358 1 0.57733 1 0.34666 1 16q gain 96 (17%) 479 0.049245 1 0.071183 1 3.0211e-18 2.25e-15 0.0039079 1 0.19047 1 0.015545 1 0.01025 1 0.0053383 1 0.46459 1 0.27723 1 17p gain 13 (2%) 562 0.77944 1 0.0078853 1 1 1 0.84961 1 0.37254 1 0.67272 1 0.30844 1 0.47995 1 0.69363 1 0.90189 1 17q gain 67 (12%) 508 0.050374 1 0.04235 1 0.00026856 0.182 0.0014284 0.946 0.2781 1 0.076049 1 0.0001175 0.0805 0.0021178 1 0.078543 1 0.35388 1 18p gain 21 (4%) 554 0.18989 1 0.013971 1 0.00061013 0.409 0.0095456 1 0.36482 1 0.71333 1 0.031133 1 0.0081684 1 0.56836 1 0.39747 1 18q gain 12 (2%) 563 NA NA NA NA 0.17246 1 0.0072864 1 0.26926 1 0.31397 1 NA NA NA NA 0.10546 1 0.13438 1 19p gain 52 (9%) 523 0.17831 1 0.2994 1 5.843e-05 0.0402 0.023588 1 0.065616 1 0.077059 1 0.021726 1 0.12222 1 0.71797 1 0.74542 1 19q gain 61 (11%) 514 0.013287 1 0.017832 1 0.012239 1 0.071518 1 0.0080504 1 0.036565 1 0.0034005 1 0.00026229 0.178 0.83213 1 0.49525 1 20p gain 288 (50%) 287 5.9034e-05 0.0406 5.8857e-08 4.26e-05 4.248e-22 3.2e-19 7.6737e-05 0.0526 0.030338 1 0.092448 1 1.222e-05 0.00853 4.0842e-10 2.97e-07 0.62537 1 0.47156 1 20q gain 403 (70%) 172 6.9517e-19 5.19e-16 2.9349e-16 2.18e-13 2.2246e-46 1.69e-43 9.0386e-13 6.64e-10 0.0010995 0.732 0.0011261 0.749 2.4236e-20 1.82e-17 5.5161e-24 4.16e-21 0.46311 1 0.10066 1 21q gain 19 (3%) 556 0.43486 1 0.40075 1 0.0026802 1 0.70858 1 0.21405 1 0.21885 1 0.26556 1 1 1 0.68566 1 0.14321 1 22q gain 7 (1%) 568 0.68886 1 0.0078853 1 0.23406 1 0.46578 1 0.90794 1 0.49331 1 0.13995 1 0.47995 1 0.45861 1 0.59561 1 Xq gain 17 (3%) 558 0.14489 1 0.64382 1 0.016685 1 0.33848 1 0.1409 1 0.34423 1 0.75925 1 0.86915 1 0.48172 1 0.70461 1 1p loss 68 (12%) 507 0.057568 1 0.0028037 1 7.5476e-06 0.0053 3.8428e-05 0.0265 0.78421 1 0.68655 1 0.064324 1 0.051439 1 0.19261 1 0.62049 1 1q loss 25 (4%) 550 0.40436 1 0.011513 1 0.082264 1 0.031495 1 0.64964 1 0.82476 1 0.14783 1 0.33215 1 0.42483 1 0.72532 1 2p loss 10 (2%) 565 1 1 0.48497 1 0.073513 1 NA NA 0.003485 1 0.77992 1 0.23187 1 0.018607 1 0.015125 1 0.013286 1 2q loss 8 (1%) 567 0.74121 1 0.45558 1 0.54823 1 NA NA 0.079184 1 0.37432 1 0.19756 1 0.012658 1 0.058427 1 0.045527 1 3p loss 35 (6%) 540 0.93797 1 0.45115 1 0.83112 1 0.83463 1 0.92667 1 0.9171 1 0.37574 1 0.89025 1 0.10485 1 0.72944 1 3q loss 17 (3%) 558 0.61793 1 0.73598 1 0.75688 1 0.015667 1 0.1344 1 0.44011 1 0.77345 1 0.63231 1 0.73957 1 0.7721 1 4p loss 122 (21%) 453 0.059837 1 0.11702 1 5.4975e-11 4.02e-08 0.0035973 1 0.35044 1 0.75914 1 0.12284 1 0.068242 1 0.045027 1 0.76936 1 4q loss 113 (20%) 462 0.075165 1 0.13597 1 3.1754e-12 2.33e-09 0.0016838 1 0.39156 1 0.54777 1 0.23847 1 0.045606 1 0.012191 1 0.56362 1 5p loss 34 (6%) 541 0.26054 1 0.29696 1 0.00054432 0.366 0.034068 1 0.30584 1 0.50549 1 0.78678 1 0.88042 1 0.96862 1 0.82879 1 5q loss 60 (10%) 515 0.014457 1 0.027363 1 5.5316e-07 0.000396 0.081603 1 0.43095 1 0.87835 1 0.063737 1 0.19653 1 0.96346 1 0.57856 1 6p loss 18 (3%) 557 0.11 1 0.096247 1 0.026043 1 0.2767 1 0.476 1 0.85529 1 0.072336 1 0.149 1 0.60161 1 0.92285 1 6q loss 33 (6%) 542 0.45201 1 0.43263 1 0.09827 1 1 1 0.092797 1 0.66783 1 0.24713 1 0.4567 1 0.26225 1 0.29769 1 7q loss 3 (1%) 572 NA NA NA NA 0.21176 1 NA NA 0.81833 1 1 1 NA NA NA NA 0.76387 1 1 1 8p loss 145 (25%) 430 0.014973 1 0.0063117 1 1.1426e-18 8.52e-16 0.00037323 0.252 0.074422 1 0.18411 1 4.2326e-05 0.0292 0.0028634 1 0.51503 1 0.73021 1 8q loss 12 (2%) 563 0.60231 1 0.74106 1 0.082808 1 0.58001 1 0.020699 1 0.59992 1 0.22102 1 0.22645 1 0.15853 1 0.27077 1 9p loss 39 (7%) 536 0.57149 1 0.18219 1 2.8967e-05 0.0201 0.0015809 1 0.18837 1 0.20084 1 0.31696 1 0.37747 1 0.12745 1 1 1 9q loss 37 (6%) 538 0.051767 1 0.016107 1 1.9547e-06 0.00138 3.4176e-05 0.0236 0.3571 1 0.29431 1 0.031424 1 0.0062802 1 0.049149 1 0.81952 1 10p loss 40 (7%) 535 0.88427 1 0.52136 1 0.00086224 0.577 0.41929 1 0.082083 1 0.62077 1 0.95393 1 0.26231 1 0.13213 1 0.59051 1 10q loss 46 (8%) 529 0.76192 1 0.31077 1 1.4367e-06 0.00102 0.15314 1 0.023912 1 0.99055 1 0.9684 1 0.28567 1 0.71404 1 0.81051 1 11p loss 40 (7%) 535 0.74503 1 0.94823 1 0.0097676 1 0.70583 1 0.17945 1 0.27693 1 0.080784 1 0.38999 1 0.11333 1 0.35936 1 11q loss 51 (9%) 524 0.97536 1 0.95223 1 0.0016581 1 0.23178 1 0.84064 1 0.2502 1 0.25268 1 0.17791 1 0.12883 1 0.83548 1 12p loss 33 (6%) 542 0.11645 1 0.18844 1 5.424e-07 0.000388 0.25849 1 0.70692 1 0.66426 1 0.56781 1 0.077255 1 0.54148 1 0.22186 1 12q loss 28 (5%) 547 0.1355 1 0.047551 1 1.1071e-06 0.000786 0.52201 1 0.91844 1 0.86567 1 0.20779 1 0.041592 1 0.6164 1 0.6809 1 13q loss 12 (2%) 563 0.29429 1 0.11456 1 0.049459 1 0.22645 1 0.42534 1 0.093235 1 0.28039 1 0.23184 1 0.7263 1 0.40273 1 14q loss 143 (25%) 432 3.4103e-06 0.0024 2.029e-07 0.000146 1.1184e-31 8.46e-29 1.9699e-07 0.000142 2.8208e-05 0.0196 0.0061784 1 1.0866e-05 0.0076 3.0922e-07 0.000222 0.11445 1 0.70906 1 15q loss 156 (27%) 419 0.0072292 1 0.0047672 1 2.0874e-24 1.58e-21 0.015774 1 0.021763 1 0.98712 1 0.35727 1 0.0013665 0.906 0.3675 1 0.24605 1 16p loss 15 (3%) 560 0.2543 1 0.34884 1 0.09948 1 0.22645 1 0.56989 1 0.64645 1 0.44085 1 0.65232 1 1 1 0.91089 1 16q loss 17 (3%) 558 0.013213 1 0.19425 1 0.0022089 1 0.49228 1 0.52636 1 0.75763 1 0.73887 1 0.83118 1 0.13425 1 0.25684 1 17p loss 252 (44%) 323 0.00015906 0.109 0.0012407 0.824 5.4882e-22 4.13e-19 2.4395e-07 0.000176 0.18403 1 0.53849 1 0.0034427 1 0.00018787 0.128 0.027 1 0.49718 1 17q loss 45 (8%) 530 0.77587 1 0.44092 1 0.0023038 1 0.85708 1 0.9226 1 0.96968 1 0.25327 1 0.12058 1 0.11572 1 0.63456 1 18p loss 324 (56%) 251 2.4529e-15 1.82e-12 2.18e-12 1.6e-09 4.2634e-47 3.24e-44 4.3282e-19 3.24e-16 0.013937 1 0.0074165 1 6.9762e-14 5.16e-11 7.3041e-14 5.39e-11 0.065035 1 0.7872 1 18q loss 352 (61%) 223 4.0764e-13 3e-10 5.3218e-12 3.9e-09 6.8004e-51 5.18e-48 8.0336e-21 6.03e-18 0.028641 1 0.079562 1 9.1925e-11 6.71e-08 5.5051e-14 4.07e-11 0.0093757 1 0.37782 1 19p loss 20 (3%) 555 0.4888 1 0.60371 1 1.4622e-05 0.0102 0.024428 1 0.75557 1 0.72431 1 0.68974 1 0.52508 1 0.23499 1 0.37109 1 19q loss 18 (3%) 557 0.4888 1 0.60371 1 0.00023546 0.16 0.096499 1 0.56989 1 0.64645 1 0.68974 1 0.52508 1 0.42424 1 0.097617 1 20p loss 47 (8%) 528 0.18145 1 0.22804 1 4.5625e-07 0.000328 0.039019 1 0.20554 1 0.5838 1 0.035329 1 0.17745 1 0.55412 1 0.48621 1 21q loss 114 (20%) 461 0.047073 1 0.22252 1 3.6397e-05 0.0252 0.055504 1 0.33189 1 0.5314 1 0.61435 1 0.28666 1 0.11838 1 0.3424 1 22q loss 122 (21%) 453 0.056679 1 0.0048373 1 7.7977e-14 5.75e-11 0.35208 1 0.19378 1 0.46368 1 0.33507 1 0.019564 1 0.066218 1 0.10019 1 Xq loss 11 (2%) 564 0.76407 1 0.84019 1 0.33904 1 0.44599 1 0.014792 1 0.40186 1 0.40978 1 1 1 0.51495 1 0.65187 1