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 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 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 0.40106 1 1 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 0.000173 0.005342 1 0.0012254 0.555 0.00071538 0.333 3.3148e-06 0.00182 9.2345e-07 0.000518 2.9429e-09 1.8e-06 7.7964e-06 0.00421 2p gain 51 (10%) 441 0.23344 1 0.29788 1 5.4103e-11 3.42e-08 0.058815 1 0.17655 1 0.8017 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 3.06e-08 0.175 1 0.065268 1 0.5746 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 2.82e-16 0.12145 1 0.52525 1 0.65189 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 2.34e-19 2.4886e-05 0.0131 0.38821 1 0.30068 1 1.1907e-06 0.000666 5.1415e-05 0.0265 0.0012499 0.565 1.0011e-06 0.000561 4p gain 6 (1%) 486 NA NA NA NA 0.0038953 1 0.12499 1 NA NA 0.14038 1 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 1.84e-06 0.00013587 0.0678 0.031072 1 0.71241 1 3.9528e-06 0.00216 0.00041955 0.201 1.6955e-05 0.00904 1.0385e-05 0.00556 5q gain 9 (2%) 483 NA NA NA NA 0.002863 1 0.42348 1 NA NA 1 1 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 1.02e-13 0.034667 1 0.66066 1 1 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 1.04e-10 0.33135 1 0.40106 1 1 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 5.85e-16 0.011813 1 0.73304 1 0.21665 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 1.63e-16 0.024395 1 0.88873 1 0.055165 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 5.05e-15 0.91294 1 0.13349 1 1 1 0.47386 1 0.43448 1 0.47978 1 0.0001072 0.0541 8q gain 118 (24%) 374 0.0046103 1 0.042441 1 1.6503e-21 1.13e-18 0.36766 1 0.0049518 1 1 1 0.0059062 1 0.00029937 0.145 0.0029833 1 1.3738e-07 7.97e-05 9p gain 14 (3%) 478 NA NA NA NA 0.048355 1 0.078573 1 NA NA 1 1 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 0.326 0.20411 1 0.28359 1 0.13573 1 0.015488 1 0.25464 1 0.12699 1 0.01727 1 10q gain 79 (16%) 413 0.0015046 0.672 0.030274 1 9.3428e-05 0.0474 0.17582 1 0.38785 1 0.25211 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 0.10904 1 1 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 0.10904 1 0.29906 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 2.83e-05 0.0090941 1 0.9373 1 1 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 0.00021 0.12086 1 0.90119 1 1 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 5.58e-05 0.0055648 1 0.73455 1 0.36663 1 7.1356e-05 0.0365 0.00046225 0.22 0.0018201 0.797 0.00043361 0.207 14q gain 20 (4%) 472 1 1 1 1 2.159e-05 0.0114 0.22681 1 0.2387 1 0.29227 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 1 1 0.828 1 0.69879 1 1 1 0.90162 1 16p gain 12 (2%) 480 NA NA NA NA 0.00079405 0.365 0.031322 1 0.24267 1 1 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 1 1 NA NA NA NA 1 1 0.92013 1 17p gain 7 (1%) 485 NA NA NA NA 2.602e-05 0.0136 0.24392 1 NA NA 1 1 0.31635 1 0.31542 1 0.18625 1 0.043322 1 17q gain 13 (3%) 479 NA NA NA NA 0.00072729 0.337 0.0035743 1 0.053132 1 1 1 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 3.27e-11 6.6366e-05 0.034 0.092984 1 0.42867 1 3.3389e-05 0.0175 7.2822e-07 0.000411 1.4011e-10 8.79e-08 2.362e-09 1.45e-06 18q gain 20 (4%) 472 0.17647 1 0.054256 1 8.2613e-06 0.00444 0.0056176 1 NA NA 1 1 0.017254 1 0.0056462 1 1.6708e-05 0.00892 4.6256e-05 0.0239 19p gain 31 (6%) 461 0.059073 1 0.015111 1 2.4038e-13 1.58e-10 0.0042875 1 0.52818 1 0.15057 1 4.7344e-06 0.00258 1.8393e-05 0.00977 1.776e-05 0.00945 0.0013121 0.592 19q gain 28 (6%) 464 NA NA NA NA 4.2813e-13 2.8e-10 0.0014709 0.659 0.084981 1 1 1 4.7344e-06 0.00258 1.5912e-06 0.000888 2.7243e-06 0.0015 0.0002309 0.113 20p gain 65 (13%) 427 0.17647 1 0.054256 1 2.2767e-18 1.54e-15 3.4709e-05 0.0181 0.29078 1 1 1 9.0371e-05 0.0459 0.011949 1 4.1797e-08 2.48e-05 8.4322e-08 4.95e-05 20q gain 78 (16%) 414 0.059073 1 0.015111 1 3.6242e-24 2.49e-21 8.601e-08 5.04e-05 0.19154 1 0.58017 1 1.7451e-06 0.00097 0.00062065 0.291 2.0002e-11 1.28e-08 2.8103e-11 1.8e-08 21q gain 25 (5%) 467 NA NA NA NA 1.1349e-08 6.84e-06 0.079381 1 0.2367 1 0.55767 1 0.00020408 0.0998 0.0094958 1 0.00012253 0.0614 0.0071818 1 22q gain 9 (2%) 483 NA NA NA NA 0.0047256 1 0.00053691 0.253 NA NA 0.37629 1 0.11476 1 0.36079 1 0.00098888 0.451 0.0051804 1 Xq gain 12 (2%) 480 NA NA NA NA 0.00025705 0.125 0.32236 1 NA NA 0.37629 1 0.15748 1 0.44673 1 0.0065229 1 0.12795 1 1p loss 13 (3%) 479 NA NA NA NA 1.8216e-08 1.09e-05 0.00095455 0.437 NA NA 1 1 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 0.14038 1 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 0.14038 1 0.15748 1 0.087811 1 0.45184 1 0.04581 1 3p loss 31 (6%) 461 NA NA NA NA 1.3351e-14 8.89e-12 0.00014128 0.0704 0.00052575 0.249 0.027968 1 1.7855e-07 0.000103 8.6312e-08 5.05e-05 5.4366e-05 0.0279 0.00011133 0.0561 3q loss 12 (2%) 480 NA NA NA NA 4.3108e-05 0.0223 0.05836 1 0.024047 1 0.55767 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 3.3e-22 7.079e-11 4.47e-08 0.033892 1 0.39315 1 2.45e-09 1.5e-06 1.2904e-07 7.51e-05 1.5324e-13 1.01e-10 4.2932e-09 2.61e-06 4q loss 64 (13%) 428 0.68266 1 0.37121 1 1.3603e-26 9.39e-24 2.656e-11 1.7e-08 0.13113 1 0.77642 1 2.643e-08 1.58e-05 2.4453e-08 1.46e-05 1.2284e-10 7.71e-08 1.9382e-08 1.16e-05 5p loss 27 (5%) 465 0.35228 1 0.1325 1 1.1633e-10 7.32e-08 0.00033435 0.161 0.16154 1 0.18109 1 0.0007823 0.361 0.00067185 0.314 0.0015379 0.684 0.010391 1 5q loss 45 (9%) 447 0.07289 1 0.013284 1 1.1786e-18 7.99e-16 7.2617e-09 4.39e-06 0.04811 1 0.15296 1 6.2834e-08 3.7e-05 2.9609e-08 1.76e-05 2.5825e-07 0.000148 1.3766e-07 7.97e-05 6p loss 10 (2%) 482 0.68266 1 0.37121 1 0.00086192 0.396 0.096217 1 0.85846 1 0.55767 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 0.115 0.035408 1 0.85846 1 0.55767 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 6.11e-07 0.006562 1 0.15846 1 0.20053 1 0.00016195 0.0803 2.2672e-05 0.0119 0.0080538 1 0.011117 1 7q loss 27 (5%) 465 NA NA NA NA 4.9115e-14 3.26e-11 0.00018012 0.0888 0.19732 1 0.012085 1 1.3201e-07 7.67e-05 1.5912e-06 0.000888 0.0015379 0.684 0.0001718 0.0849 8p loss 53 (11%) 439 0.019107 1 0.0040321 1 4.0085e-24 2.75e-21 1.0774e-11 6.95e-09 0.165 1 0.18109 1 4.8415e-12 3.13e-09 6.9006e-10 4.29e-07 2.8658e-14 1.91e-11 5.4483e-14 3.6e-11 8q loss 12 (2%) 480 NA NA NA NA 2.228e-05 0.0117 0.00095455 0.437 NA NA 1 1 0.039552 1 0.15399 1 0.0018038 0.792 0.021967 1 9p loss 76 (15%) 416 0.022668 1 0.0037915 1 2.631e-29 1.82e-26 2.341e-06 0.00129 0.011722 1 0.24436 1 2.1227e-12 1.38e-09 7.6036e-15 5.07e-12 5.7377e-09 3.48e-06 5.5232e-09 3.35e-06 9q loss 93 (19%) 399 0.0015041 0.672 0.0002482 0.121 1.5312e-37 1.07e-34 5.863e-07 0.000331 0.0060055 1 0.37819 1 2.5645e-13 1.68e-10 2.816e-16 1.89e-13 1.4294e-11 9.19e-09 1.3978e-07 8.08e-05 10p loss 23 (5%) 469 0.17647 1 0.054256 1 3.9966e-11 2.54e-08 0.00033435 0.161 0.47447 1 0.63255 1 0.0004688 0.223 0.0015999 0.709 2.6057e-06 0.00144 0.0067191 1 10q loss 24 (5%) 468 NA NA NA NA 2.9446e-10 1.84e-07 0.0001924 0.0945 0.45123 1 1 1 0.0004688 0.223 0.0056992 1 7.0242e-05 0.036 0.0094157 1 11p loss 53 (11%) 439 NA NA NA NA 1.4445e-21 9.89e-19 7.4418e-07 0.000419 0.18182 1 0.75005 1 4.4598e-08 2.64e-05 2.5957e-07 0.000149 5.5758e-10 3.47e-07 2.1416e-06 0.00119 11q loss 45 (9%) 447 NA NA NA NA 1.1505e-15 7.7e-13 7.5322e-05 0.0384 0.92479 1 0.71272 1 0.00039705 0.191 8.0744e-06 0.00434 1.7438e-07 0.000101 7.756e-06 0.0042 12p loss 25 (5%) 467 NA NA NA NA 3.8618e-11 2.46e-08 0.0001924 0.0945 0.057656 1 1 1 3.6189e-05 0.0188 0.0056992 1 1.6267e-08 9.79e-06 8.916e-06 0.00478 12q loss 18 (4%) 474 NA NA NA NA 1.23e-09 7.6e-07 0.00010017 0.0507 0.30993 1 0.42867 1 0.0010551 0.479 0.006701 1 5.0797e-07 0.000288 0.00018142 0.0893 13q loss 60 (12%) 432 0.68266 1 0.37121 1 2.4269e-18 1.64e-15 0.00011254 0.0566 0.16118 1 0.39315 1 0.00039515 0.19 3.8892e-06 0.00213 8.5294e-05 0.0434 0.00492 1 14q loss 42 (9%) 450 0.019107 1 0.0040321 1 8.9369e-17 6.01e-14 1.4782e-09 9.11e-07 0.084745 1 0.0051992 1 3.3753e-08 2.01e-05 1.9461e-07 0.000112 4.3208e-07 0.000245 9.9414e-09 6e-06 15q loss 81 (16%) 411 0.0067724 1 0.0010266 0.467 4.6791e-35 3.25e-32 1.6072e-13 1.06e-10 0.00259 1 0.26661 1 7.9229e-10 4.91e-07 1.0686e-10 6.73e-08 2.159e-15 1.44e-12 2.7286e-12 1.77e-09 16p loss 69 (14%) 423 0.019107 1 0.0040321 1 2.8194e-31 1.95e-28 2.7681e-09 1.7e-06 0.19252 1 0.79627 1 7.5166e-10 4.67e-07 1.4726e-09 9.09e-07 4.3008e-09 2.61e-06 4.7729e-11 3.03e-08 16q loss 110 (22%) 382 0.0068587 1 0.0017313 0.765 5.935e-40 4.14e-37 2.8603e-11 1.82e-08 0.23685 1 1 1 1.006e-11 6.5e-09 2.3407e-10 1.47e-07 8.4138e-13 5.49e-10 1.532e-13 1.01e-10 17p loss 105 (21%) 387 0.0068587 1 0.0017313 0.765 8.6624e-53 6.05e-50 8.1447e-13 5.32e-10 0.00057115 0.268 0.66522 1 1.6027e-20 1.09e-17 2.1472e-21 1.47e-18 2.0101e-16 1.35e-13 1.4152e-11 9.11e-09 17q loss 68 (14%) 424 0.019107 1 0.0040321 1 1.4783e-29 1.02e-26 3.4055e-05 0.0178 0.092362 1 0.61178 1 4.279e-09 2.61e-06 1.9474e-11 1.25e-08 2.8675e-07 0.000164 4.2665e-05 0.0221 18p loss 36 (7%) 456 NA NA NA NA 3.1519e-12 2.05e-09 2.091e-05 0.0111 0.32575 1 0.74551 1 0.00065956 0.309 0.00017153 0.0849 0.0034966 1 0.00013092 0.0655 18q loss 49 (10%) 443 NA NA NA NA 9.7475e-18 6.57e-15 1.978e-06 0.0011 0.72497 1 1 1 3.8676e-06 0.00212 5.6503e-07 0.00032 8.8216e-07 0.000496 3.0061e-06 0.00165 19p loss 34 (7%) 458 NA NA NA NA 4.6331e-12 3e-09 1.066e-07 6.21e-05 0.33053 1 1 1 1.8398e-05 0.00977 7.8364e-06 0.00422 5.7241e-06 0.0031 4.3371e-06 0.00236 19q loss 28 (6%) 464 NA NA NA NA 1.787e-08 1.07e-05 4.6494e-05 0.024 0.73417 1 0.71272 1 0.00071886 0.334 0.002828 1 0.0014234 0.639 0.00049889 0.236 20p loss 15 (3%) 477 NA NA NA NA 0.00012225 0.0614 0.10685 1 0.24267 1 0.63255 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 0.52818 1 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 3.81e-05 0.0025241 1 0.09504 1 0.75005 1 0.00014817 0.0736 0.0013625 0.613 0.0017744 0.781 0.0035712 1 22q loss 87 (18%) 405 0.019107 1 0.0040321 1 1.4075e-36 9.78e-34 4.2349e-08 2.51e-05 0.072103 1 1 1 4.876e-11 3.09e-08 3.2854e-14 2.18e-11 3.2041e-10 2e-07 5.6126e-08 3.31e-05 Xq loss 18 (4%) 474 NA NA NA NA 2.9675e-07 0.000169 0.00056938 0.268 0.61718 1 0.63255 1 0.015969 1 0.006701 1 0.0007641 0.353 0.011299 1