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 Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q Chi-square test_P Chi-square test_Q Chi-square test_P Chi-square 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 Chi-square test_P Chi-square test_Q 1p gain 21 (4%) 471 0.68266 1 0.1836 1 0.035042 1 0.66105 1 0.053216 1 0.58903 1 0.18151 1 0.28962 1 0.032045 1 0.043001 1 1q gain 138 (28%) 354 0.11087 1 0.63732 1 3.0433e-07 0.000169 0.005342 1 0.0023621 0.99 0.00042747 0.197 3.3148e-06 0.00177 9.2345e-07 0.000505 2.9429e-09 1.76e-06 7.7964e-06 0.0041 2p gain 51 (10%) 441 0.23344 1 0.29788 1 5.4103e-11 3.34e-08 0.058815 1 0.30877 1 0.76195 1 0.23768 1 0.43383 1 0.021466 1 0.02922 1 2q gain 40 (8%) 452 0.51784 1 0.76949 1 4.8278e-11 2.99e-08 0.175 1 0.12729 1 0.40662 1 0.30009 1 0.62396 1 0.02411 1 0.0073024 1 3p gain 28 (6%) 464 NA NA NA NA 4.1488e-19 2.76e-16 0.12145 1 0.63226 1 0.26551 1 0.014933 1 0.042907 1 0.87926 1 0.1055 1 3q gain 50 (10%) 442 0.17647 1 0.054256 1 3.4119e-22 2.29e-19 2.4886e-05 0.0127 0.41161 1 0.2205 1 1.1907e-06 0.000649 5.1415e-05 0.0257 0.0012499 0.545 1.0011e-06 0.000547 4p gain 6 (1%) 486 NA NA NA NA 0.0038953 1 0.12499 1 NA NA NA NA 0.039552 1 0.15399 1 0.0091217 1 0.01315 1 5p gain 32 (7%) 460 0.86016 1 0.6235 1 3.0144e-09 1.8e-06 0.00013587 0.0656 0.028371 1 0.87879 1 3.9528e-06 0.0021 0.00041955 0.193 1.6955e-05 0.0088 1.0385e-05 0.00541 5q gain 9 (2%) 483 NA NA NA NA 0.002863 1 0.42348 1 NA NA NA NA 0.06786 1 0.28634 1 0.031436 1 0.046709 1 6p gain 38 (8%) 454 0.42965 1 0.2431 1 1.5228e-16 1e-13 0.034667 1 0.75229 1 0.76092 1 0.0066461 1 0.0074982 1 0.0069553 1 0.014363 1 6q gain 30 (6%) 462 0.42965 1 0.2431 1 1.5822e-13 1.02e-10 0.33135 1 0.48834 1 0.88323 1 0.0083914 1 0.0079272 1 0.12999 1 0.28213 1 7p gain 43 (9%) 449 1 1 0.86704 1 8.6204e-19 5.73e-16 0.011813 1 0.75143 1 0.45454 1 1 1 0.47476 1 0.42962 1 0.29736 1 7q gain 43 (9%) 449 0.94364 1 0.77558 1 2.3979e-19 1.6e-16 0.024395 1 0.77476 1 0.327 1 0.38457 1 0.033117 1 0.7338 1 0.18791 1 8p gain 86 (17%) 406 0.3955 1 1 1 7.4822e-18 4.95e-15 0.91294 1 0.26286 1 0.63163 1 0.47386 1 0.43448 1 0.47978 1 0.0001072 0.0524 8q gain 118 (24%) 374 0.0046103 1 0.042441 1 1.6503e-21 1.11e-18 0.36766 1 0.0015867 0.676 0.44891 1 0.0059062 1 0.00029937 0.14 0.0029833 1 1.3738e-07 7.78e-05 9p gain 14 (3%) 478 NA NA NA NA 0.048355 1 0.078573 1 NA NA NA NA 0.82159 1 0.07871 1 0.043203 1 0.11926 1 9q gain 4 (1%) 488 NA NA NA NA 0.35164 1 0.36274 1 NA NA NA NA 0.78103 1 0.36079 1 0.31228 1 0.17268 1 10p gain 87 (18%) 405 0.0035467 1 0.063958 1 0.00069957 0.313 0.20411 1 0.26564 1 0.54392 1 0.015488 1 0.25464 1 0.12699 1 0.01727 1 10q gain 79 (16%) 413 0.0015046 0.648 0.030274 1 9.3428e-05 0.0459 0.17582 1 0.29058 1 0.71619 1 0.026202 1 0.25647 1 0.019238 1 0.0085046 1 11p gain 8 (2%) 484 0.17647 1 0.054256 1 0.0099016 1 0.037261 1 0.10432 1 0.22164 1 0.15748 1 0.44673 1 0.90991 1 0.22728 1 11q gain 8 (2%) 484 NA NA NA NA 0.011078 1 0.46209 1 0.10432 1 0.02839 1 0.19408 1 0.39556 1 0.67031 1 0.39759 1 12p gain 37 (8%) 455 0.81541 1 0.82481 1 4.7807e-08 2.76e-05 0.0090941 1 0.99258 1 0.21908 1 0.04547 1 0.090624 1 0.026256 1 0.013493 1 12q gain 28 (6%) 464 0.81541 1 0.82481 1 3.6845e-07 0.000204 0.12086 1 0.86847 1 0.060223 1 0.081103 1 0.22715 1 0.19182 1 0.12342 1 13q gain 20 (4%) 472 NA NA NA NA 9.5474e-08 5.44e-05 0.0055648 1 0.7006 1 0.6848 1 7.1356e-05 0.0353 0.00046225 0.212 0.0018201 0.764 0.00043361 0.199 14q gain 20 (4%) 472 1 1 1 1 2.159e-05 0.0111 0.22681 1 0.36492 1 0.63645 1 0.40121 1 0.073693 1 0.045735 1 0.19871 1 15q gain 6 (1%) 486 NA NA NA NA 0.0041566 1 0.84602 1 NA NA NA NA 0.828 1 0.69879 1 1 1 0.90162 1 16p gain 12 (2%) 480 NA NA NA NA 0.00079405 0.352 0.031322 1 0.23219 1 0.91448 1 0.06786 1 0.07871 1 0.060853 1 0.23388 1 16q gain 4 (1%) 488 NA NA NA NA 0.046028 1 1 1 NA NA NA NA NA NA NA NA 1 1 0.92013 1 17p gain 7 (1%) 485 NA NA NA NA 2.602e-05 0.0133 0.24392 1 NA NA NA NA 0.31635 1 0.31542 1 0.18625 1 0.043322 1 17q gain 13 (3%) 479 NA NA NA NA 0.00072729 0.324 0.0035743 1 0.071012 1 6.6387e-05 0.0331 0.027619 1 0.28381 1 0.072583 1 0.024343 1 18p gain 37 (8%) 455 0.059073 1 0.1325 1 4.9415e-14 3.2e-11 6.6366e-05 0.0331 0.087733 1 0.051394 1 3.3389e-05 0.017 7.2822e-07 0.000401 1.4011e-10 8.59e-08 2.362e-09 1.42e-06 18q gain 20 (4%) 472 0.17647 1 0.054256 1 8.2613e-06 0.00432 0.0056176 1 NA NA NA NA 0.017254 1 0.0056462 1 1.6708e-05 0.00869 4.6256e-05 0.0232 19p gain 31 (6%) 461 0.059073 1 0.015111 1 2.4038e-13 1.54e-10 0.0042875 1 0.50613 1 0.43066 1 4.7344e-06 0.00251 1.8393e-05 0.00951 1.776e-05 0.0092 0.0013121 0.571 19q gain 28 (6%) 464 NA NA NA NA 4.2813e-13 2.74e-10 0.0014709 0.635 0.08343 1 0.084981 1 4.7344e-06 0.00251 1.5912e-06 0.000866 2.7243e-06 0.00146 0.0002309 0.109 20p gain 65 (13%) 427 0.17647 1 0.054256 1 2.2767e-18 1.51e-15 3.4709e-05 0.0176 0.27385 1 0.69333 1 9.0371e-05 0.0445 0.011949 1 4.1797e-08 2.42e-05 8.4322e-08 4.83e-05 20q gain 78 (16%) 414 0.059073 1 0.015111 1 3.6242e-24 2.44e-21 8.601e-08 4.92e-05 0.17078 1 0.45589 1 1.7451e-06 0.000946 0.00062065 0.28 2.0002e-11 1.25e-08 2.8103e-11 1.76e-08 21q gain 25 (5%) 467 NA NA NA NA 1.1349e-08 6.68e-06 0.079381 1 0.22156 1 0.67703 1 0.00020408 0.0965 0.0094958 1 0.00012253 0.0594 0.0071818 1 22q gain 9 (2%) 483 NA NA NA NA 0.0047256 1 0.00053691 0.244 NA NA NA NA 0.11476 1 0.36079 1 0.00098888 0.434 0.0051804 1 Xq gain 12 (2%) 480 NA NA NA NA 0.00025705 0.121 0.32236 1 NA NA NA NA 0.15748 1 0.44673 1 0.0065229 1 0.12795 1 1p loss 13 (3%) 479 NA NA NA NA 1.8216e-08 1.07e-05 0.00095455 0.421 NA NA NA NA 0.040252 1 0.088379 1 0.0097374 1 0.0083303 1 1q loss 4 (1%) 488 NA NA NA NA 0.03655 1 0.057423 1 NA NA NA NA 0.11476 1 0.36079 1 0.041673 1 0.2426 1 2p loss 6 (1%) 486 NA NA NA NA 0.019044 1 0.51798 1 NA NA NA NA 0.15748 1 0.087811 1 0.77465 1 0.024413 1 2q loss 8 (2%) 484 NA NA NA NA 0.0063665 1 0.19926 1 NA NA NA NA 0.15748 1 0.087811 1 0.45184 1 0.04581 1 3p loss 31 (6%) 461 NA NA NA NA 1.3351e-14 8.7e-12 0.00014128 0.0681 0.00036283 0.168 0.014083 1 1.7855e-07 1e-04 8.6312e-08 4.93e-05 5.4366e-05 0.0271 0.00011133 0.0543 3q loss 12 (2%) 480 NA NA NA NA 4.3108e-05 0.0217 0.05836 1 0.020119 1 0.33257 1 0.0047873 1 0.0027388 1 0.022642 1 0.29666 1 4p loss 66 (13%) 426 0.07289 1 0.013284 1 4.7865e-25 3.23e-22 7.079e-11 4.37e-08 0.029521 1 0.20974 1 2.45e-09 1.47e-06 1.2904e-07 7.33e-05 1.5324e-13 9.9e-11 4.2932e-09 2.55e-06 4q loss 64 (13%) 428 0.68266 1 0.37121 1 1.3603e-26 9.2e-24 2.656e-11 1.66e-08 0.12432 1 0.075139 1 2.643e-08 1.54e-05 2.4453e-08 1.43e-05 1.2284e-10 7.54e-08 1.9382e-08 1.13e-05 5p loss 27 (5%) 465 0.35228 1 0.1325 1 1.1633e-10 7.15e-08 0.00033435 0.156 0.16545 1 0.14444 1 0.0007823 0.347 0.00067185 0.302 0.0015379 0.658 0.010391 1 5q loss 45 (9%) 447 0.07289 1 0.013284 1 1.1786e-18 7.83e-16 7.2617e-09 4.29e-06 0.0048669 1 0.035896 1 6.2834e-08 3.61e-05 2.9609e-08 1.72e-05 2.5825e-07 0.000145 1.3766e-07 7.78e-05 6p loss 10 (2%) 482 0.68266 1 0.37121 1 0.00086192 0.381 0.096217 1 0.82832 1 0.38638 1 0.19389 1 0.24853 1 0.030919 1 0.046053 1 6q loss 12 (2%) 480 0.68266 1 0.37121 1 0.00023581 0.111 0.035408 1 0.82832 1 0.38638 1 0.015969 1 0.03837 1 0.047625 1 0.23949 1 7p loss 29 (6%) 463 0.17647 1 0.054256 1 9.8778e-10 5.98e-07 0.006562 1 0.18147 1 0.71391 1 0.00016195 0.0777 2.2672e-05 0.0116 0.0080538 1 0.011117 1 7q loss 27 (5%) 465 NA NA NA NA 4.9115e-14 3.19e-11 0.00018012 0.0859 0.18014 1 0.38489 1 1.3201e-07 7.48e-05 1.5912e-06 0.000866 0.0015379 0.658 0.0001718 0.0822 8p loss 53 (11%) 439 0.019107 1 0.0040321 1 4.0085e-24 2.7e-21 1.0774e-11 6.8e-09 0.018756 1 0.48121 1 4.8415e-12 3.06e-09 6.9006e-10 4.2e-07 2.8658e-14 1.87e-11 5.4483e-14 3.53e-11 8q loss 12 (2%) 480 NA NA NA NA 2.228e-05 0.0114 0.00095455 0.421 NA NA NA NA 0.039552 1 0.15399 1 0.0018038 0.759 0.021967 1 9p loss 76 (15%) 416 0.022668 1 0.0037915 1 2.631e-29 1.78e-26 2.341e-06 0.00126 0.00055245 0.25 0.44742 1 2.1227e-12 1.35e-09 7.6036e-15 4.97e-12 5.7377e-09 3.4e-06 5.5232e-09 3.28e-06 9q loss 93 (19%) 399 0.0015041 0.648 0.0002482 0.117 1.5312e-37 1.04e-34 5.863e-07 0.000323 0.00033368 0.156 0.84614 1 2.5645e-13 1.64e-10 2.816e-16 1.85e-13 1.4294e-11 8.99e-09 1.3978e-07 7.88e-05 10p loss 23 (5%) 469 0.17647 1 0.054256 1 3.9966e-11 2.49e-08 0.00033435 0.156 0.45106 1 0.46628 1 0.0004688 0.214 0.0015999 0.68 2.6057e-06 0.0014 0.0067191 1 10q loss 24 (5%) 468 NA NA NA NA 2.9446e-10 1.8e-07 0.0001924 0.0914 0.42387 1 0.71033 1 0.0004688 0.214 0.0056992 1 7.0242e-05 0.0348 0.0094157 1 11p loss 53 (11%) 439 NA NA NA NA 1.4445e-21 9.69e-19 7.4418e-07 0.000409 0.27517 1 0.45929 1 4.4598e-08 2.58e-05 2.5957e-07 0.000145 5.5758e-10 3.4e-07 2.1416e-06 0.00116 11q loss 45 (9%) 447 NA NA NA NA 1.1505e-15 7.54e-13 7.5322e-05 0.0372 0.71251 1 0.36952 1 0.00039705 0.183 8.0744e-06 0.00423 1.7438e-07 9.82e-05 7.756e-06 0.00409 12p loss 25 (5%) 467 NA NA NA NA 3.8618e-11 2.41e-08 0.0001924 0.0914 0.0060418 1 0.32785 1 3.6189e-05 0.0183 0.0056992 1 1.6267e-08 9.57e-06 8.916e-06 0.00465 12q loss 18 (4%) 474 NA NA NA NA 1.23e-09 7.43e-07 0.00010017 0.0491 0.043548 1 0.31162 1 0.0010551 0.461 0.006701 1 5.0797e-07 0.000281 0.00018142 0.0864 13q loss 60 (12%) 432 0.68266 1 0.37121 1 2.4269e-18 1.61e-15 0.00011254 0.0548 0.08043 1 0.21144 1 0.00039515 0.183 3.8892e-06 0.00207 8.5294e-05 0.0421 0.00492 1 14q loss 42 (9%) 450 0.019107 1 0.0040321 1 8.9369e-17 5.89e-14 1.4782e-09 8.9e-07 0.068262 1 0.011705 1 3.3753e-08 1.96e-05 1.9461e-07 0.000109 4.3208e-07 0.000239 9.9414e-09 5.87e-06 15q loss 81 (16%) 411 0.0067724 1 0.0010266 0.45 4.6791e-35 3.18e-32 1.6072e-13 1.03e-10 0.0015087 0.648 0.0091403 1 7.9229e-10 4.8e-07 1.0686e-10 6.58e-08 2.159e-15 1.41e-12 2.7286e-12 1.74e-09 16p loss 69 (14%) 423 0.019107 1 0.0040321 1 2.8194e-31 1.91e-28 2.7681e-09 1.66e-06 0.29321 1 0.84381 1 7.5166e-10 4.56e-07 1.4726e-09 8.88e-07 4.3008e-09 2.55e-06 4.7729e-11 2.96e-08 16q loss 110 (22%) 382 0.0068587 1 0.0017313 0.734 5.935e-40 4.05e-37 2.8603e-11 1.78e-08 0.40044 1 0.76552 1 1.006e-11 6.36e-09 2.3407e-10 1.43e-07 8.4138e-13 5.37e-10 1.532e-13 9.9e-11 17p loss 105 (21%) 387 0.0068587 1 0.0017313 0.734 8.6624e-53 5.93e-50 8.1447e-13 5.2e-10 4.5061e-05 0.0227 0.11928 1 1.6027e-20 1.07e-17 2.1472e-21 1.44e-18 2.0101e-16 1.32e-13 1.4152e-11 8.92e-09 17q loss 68 (14%) 424 0.019107 1 0.0040321 1 1.4783e-29 1e-26 3.4055e-05 0.0173 0.024551 1 0.19677 1 4.279e-09 2.55e-06 1.9474e-11 1.22e-08 2.8675e-07 0.00016 4.2665e-05 0.0215 18p loss 36 (7%) 456 NA NA NA NA 3.1519e-12 2e-09 2.091e-05 0.0108 0.12861 1 0.64888 1 0.00065956 0.297 0.00017153 0.0822 0.0034966 1 0.00013092 0.0634 18q loss 49 (10%) 443 NA NA NA NA 9.7475e-18 6.43e-15 1.978e-06 0.00107 0.41411 1 0.46384 1 3.8676e-06 0.00207 5.6503e-07 0.000312 8.8216e-07 0.000483 3.0061e-06 0.00161 19p loss 34 (7%) 458 NA NA NA NA 4.6331e-12 2.94e-09 1.066e-07 6.07e-05 0.31793 1 0.61809 1 1.8398e-05 0.00951 7.8364e-06 0.00411 5.7241e-06 0.00302 4.3371e-06 0.0023 19q loss 28 (6%) 464 NA NA NA NA 1.787e-08 1.05e-05 4.6494e-05 0.0233 0.71251 1 0.95813 1 0.00071886 0.321 0.002828 1 0.0014234 0.616 0.00049889 0.227 20p loss 15 (3%) 477 NA NA NA NA 0.00012225 0.0594 0.10685 1 0.23219 1 0.51636 1 0.03678 1 0.046533 1 0.0026484 1 0.040187 1 20q loss 7 (1%) 485 NA NA NA NA 0.010576 1 0.054039 1 NA NA NA NA 0.39137 1 0.47424 1 0.094326 1 0.039563 1 21q loss 32 (7%) 460 0.059073 1 0.015111 1 6.4739e-08 3.72e-05 0.0025241 1 0.011504 1 0.63835 1 0.00014817 0.0713 0.0013625 0.591 0.0017744 0.749 0.0035712 1 22q loss 87 (18%) 405 0.019107 1 0.0040321 1 1.4075e-36 9.58e-34 4.2349e-08 2.45e-05 0.017277 1 0.77242 1 4.876e-11 3.02e-08 3.2854e-14 2.14e-11 3.2041e-10 1.95e-07 5.6126e-08 3.23e-05 Xq loss 18 (4%) 474 NA NA NA NA 2.9675e-07 0.000165 0.00056938 0.257 0.87203 1 0.79099 1 0.015969 1 0.006701 1 0.0007641 0.34 0.011299 1