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 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 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 Amp Peak 1(1p22.3) 0 (0%) 705 1.2909e-13 6.27e-11 6.6693e-12 3e-09 6.6066e-18 3.63e-15 1.9538e-17 1.06e-14 0.00013949 0.0318 1.2827e-07 4.5e-05 9.2457e-16 4.88e-13 2.3992e-16 1.28e-13 1.3556e-13 6.57e-11 1.3621e-15 7.14e-13 Amp Peak 2(1q21.3) 0 (0%) 254 1.542e-07 5.37e-05 0.0018488 0.322 6.4517e-09 2.54e-06 1.6622e-06 0.000504 0.058626 1 0.0070266 1 0.00016729 0.0373 0.00020475 0.045 0.001015 0.184 0.0026165 0.434 Amp Peak 3(1q44) 0 (0%) 258 3.9045e-06 0.00113 0.26345 1 1.3715e-07 4.8e-05 9.2238e-06 0.0025 0.86382 1 0.32448 1 0.20618 1 0.38322 1 0.71104 1 0.027745 1 Amp Peak 4(3p26.1) 0 (0%) 725 0.012356 1 0.0080285 1 1.0082e-13 4.93e-11 2.9518e-06 0.000868 0.0057272 0.848 0.0086881 1 5.1084e-09 2.03e-06 6.5674e-07 0.000213 5.9715e-06 0.00168 1.179e-08 4.49e-06 Amp Peak 5(3q26.32) 0 (0%) 625 6.8833e-11 2.96e-08 7.835e-10 3.2e-07 8.7247e-36 5.38e-33 8.0052e-17 4.32e-14 7.1633e-07 0.000231 2.9244e-06 0.000863 4.3122e-22 2.52e-19 5.8797e-21 3.36e-18 1.6347e-15 8.53e-13 6.3915e-24 3.78e-21 Amp Peak 6(4q13.3) 0 (0%) 770 5.6271e-05 0.0137 0.00023006 0.0495 7.8651e-14 3.87e-11 3.9708e-07 0.000131 0.047129 1 0.52372 1 6.9972e-06 0.00195 2.3977e-05 0.00628 0.0013768 0.246 1.1087e-07 3.92e-05 Amp Peak 7(6p23) 0 (0%) 670 3.5923e-07 0.00012 1.9221e-07 6.59e-05 5.6524e-34 3.48e-31 2.4398e-17 1.33e-14 1.9752e-06 0.000593 8.4193e-05 0.0201 1.0106e-13 4.93e-11 3.5611e-11 1.56e-08 1.5184e-18 8.5e-16 2.5064e-15 1.29e-12 Amp Peak 8(6q21) 0 (0%) 743 8.1981e-14 4.03e-11 4.5353e-10 1.87e-07 1.6737e-39 1.04e-36 4.114e-13 1.95e-10 1.0432e-08 4e-06 4.6358e-07 0.000153 7.5918e-22 4.42e-19 2.7198e-18 1.51e-15 3.4224e-19 1.93e-16 4.3321e-23 2.55e-20 Amp Peak 9(8p11.23) 0 (0%) 567 1.6422e-06 0.000501 0.00561 0.836 1.4359e-24 8.5e-22 1.2172e-12 5.64e-10 0.039927 1 0.0047255 0.718 0.00022688 0.049 3.3369e-05 0.00851 0.0447 1 0.033209 1 Amp Peak 10(8p11.21) 0 (0%) 559 0.014371 1 0.042207 1 1.0092e-22 5.92e-20 4.028e-08 1.46e-05 0.79102 1 0.63322 1 0.00022439 0.0487 0.00010386 0.0242 0.036101 1 0.021461 1 Amp Peak 11(8q24.21) 0 (0%) 329 1.1713e-16 6.3e-14 2.6199e-07 8.88e-05 2.6252e-43 1.65e-40 1.7018e-27 1.02e-24 4.583e-08 1.66e-05 9.359e-07 0.000297 3.4667e-21 1.99e-18 5.5437e-15 2.83e-12 1.3145e-21 7.6e-19 2.3712e-19 1.34e-16 Amp Peak 12(10p15.1) 0 (0%) 655 1.7203e-21 9.93e-19 1.0553e-18 5.92e-16 9.9502e-35 6.13e-32 1.9349e-26 1.16e-23 6.9975e-11 3e-08 2.332e-12 1.07e-09 2.0548e-28 1.24e-25 1.1655e-28 7.06e-26 6.2326e-28 3.76e-25 1.2008e-30 7.31e-28 Amp Peak 13(10q22.3) 0 (0%) 781 2.1956e-05 0.00582 0.068118 1 8.1809e-09 3.16e-06 0.00014898 0.0337 0.0025043 0.423 0.021128 1 1.8301e-07 6.31e-05 0.00068881 0.129 3.749e-05 0.00949 0.00067482 0.127 Amp Peak 14(11p13) 0 (0%) 721 0.3112 1 0.14832 1 1.8363e-10 7.73e-08 4.8373e-05 0.012 0.10499 1 0.22904 1 2.6058e-05 0.00675 0.020359 1 1.335e-06 0.000417 1.912e-08 7.15e-06 Amp Peak 15(11q13.3) 0 (0%) 564 0.0031946 0.511 0.033582 1 4.9077e-41 3.08e-38 4.0012e-10 1.66e-07 0.96626 1 0.146 1 0.045286 1 0.16774 1 0.00029163 0.0604 0.039571 1 Amp Peak 16(11q14.1) 0 (0%) 679 0.12011 1 0.10093 1 1.801e-19 1.02e-16 7.9266e-06 0.0022 0.14811 1 0.19923 1 8.5651e-05 0.0203 0.0014633 0.259 8.9761e-07 0.000285 1.3899e-05 0.00372 Amp Peak 17(12p13.33) 0 (0%) 675 1.9128e-12 8.84e-10 2.5309e-11 1.11e-08 1.6758e-28 1.01e-25 7.2884e-17 3.94e-14 2.6973e-08 9.98e-06 2.3692e-07 8.07e-05 1.6687e-17 9.11e-15 1.4479e-15 7.57e-13 9.1778e-22 5.32e-19 5.4996e-18 3.04e-15 Amp Peak 18(12q15) 0 (0%) 678 1.8053e-08 6.79e-06 0.00013106 0.0301 1.859e-25 1.11e-22 1.4919e-13 7.21e-11 0.18817 1 0.065182 1 6.0186e-06 0.00169 1.7075e-05 0.00456 9.1555e-08 3.25e-05 0.00064375 0.124 Amp Peak 19(13q12.3) 0 (0%) 785 0.070845 1 0.055699 1 2.2211e-05 0.00586 0.0089465 1 0.015517 1 0.14227 1 2.6307e-05 0.00679 0.0026917 0.441 0.00019615 0.0433 0.00042977 0.086 Amp Peak 20(13q34) 0 (0%) 754 9.1367e-10 3.72e-07 5.7789e-09 2.28e-06 1.5072e-17 8.24e-15 1.3297e-14 6.7e-12 8.2143e-06 0.00226 5.0995e-08 1.84e-05 8.4412e-14 4.14e-11 1.168e-14 5.9e-12 1.4101e-13 6.83e-11 5.5869e-20 3.17e-17 Amp Peak 21(14q21.1) 0 (0%) 732 0.00025922 0.0547 0.004778 0.721 1.9688e-09 7.89e-07 5.1636e-05 0.0127 0.082292 1 0.03852 1 3.9159e-05 0.00987 2.4488e-06 0.000725 1.9393e-06 0.000584 0.069259 1 Amp Peak 22(15q26.3) 0 (0%) 747 3.3123e-07 0.000111 0.0067928 0.978 1.8764e-15 9.76e-13 0.00032648 0.0669 0.00015335 0.0345 0.038405 1 2.0742e-08 7.72e-06 7.9771e-06 0.0022 5.9169e-08 2.11e-05 7.5562e-09 2.93e-06 Amp Peak 23(17q12) 0 (0%) 618 1.4882e-14 7.49e-12 0.0002998 0.0618 7.2942e-34 4.48e-31 5.7605e-09 2.28e-06 0.049046 1 0.0082103 1 0.00010117 0.0237 0.00045379 0.0903 0.014778 1 0.019607 1 Amp Peak 24(17q23.1) 0 (0%) 539 2.4249e-14 1.21e-11 0.0014925 0.263 6.1853e-38 3.84e-35 1.4475e-10 6.12e-08 0.19142 1 0.33414 1 0.0006437 0.124 0.0057452 0.848 3.1035e-07 0.000104 3.5668e-06 0.00103 Amp Peak 25(19q12) 0 (0%) 680 2.1218e-12 9.74e-10 9.106e-11 3.9e-08 1.2837e-21 7.43e-19 4.2012e-12 1.91e-09 6.1858e-07 0.000202 9.6773e-07 0.000306 1.1112e-15 5.84e-13 2.081e-15 1.08e-12 6.4861e-13 3.04e-10 2.8187e-18 1.57e-15 Amp Peak 26(19q13.42) 0 (0%) 678 0.00077451 0.143 0.021165 1 2.501e-14 1.25e-11 6.2303e-07 0.000202 0.0023269 0.4 0.054933 1 0.0026433 0.436 0.028964 1 4.2746e-06 0.00123 0.004411 0.675 Amp Peak 27(20q13.2) 0 (0%) 448 1.3488e-09 5.42e-07 0.00027817 0.0581 9.7821e-50 6.22e-47 5.1753e-25 3.07e-22 0.00060413 0.117 0.015396 1 6.6787e-09 2.62e-06 2.1367e-07 7.31e-05 7.4063e-10 3.03e-07 1.1633e-06 0.000364 Del Peak 1(1p36.13) 0 (0%) 533 3.2706e-05 0.00837 0.00065137 0.124 6.0173e-32 3.68e-29 2.8107e-09 1.12e-06 0.0072615 1 0.080488 1 1.1107e-05 0.00299 6.0197e-05 0.0146 2.3659e-07 8.07e-05 0.0005596 0.11 Del Peak 2(1p22.1) 0 (0%) 608 0.002341 0.4 8.3892e-05 0.0201 5.7684e-22 3.36e-19 0.0010349 0.186 0.023059 1 0.048955 1 0.00057402 0.113 3.0555e-06 0.000892 0.012512 1 0.032926 1 Del Peak 3(2q37.3) 0 (0%) 648 1.3934e-06 0.000432 3.7757e-08 1.38e-05 1.5745e-20 8.99e-18 2.6063e-10 1.09e-07 1.0318e-08 3.96e-06 1.1079e-07 3.92e-05 1.8138e-11 8.04e-09 2.0274e-08 7.56e-06 4.6621e-11 2.02e-08 2.6339e-07 8.9e-05 Del Peak 4(3p14.3) 0 (0%) 635 1.0584e-10 4.51e-08 3.1107e-08 1.14e-05 2.9303e-33 1.8e-30 5.7835e-13 2.72e-10 1.1804e-09 4.77e-07 5.2076e-06 0.00148 4.6082e-18 2.56e-15 4.4231e-13 2.09e-10 2.2945e-19 1.3e-16 2.5745e-14 1.28e-11 Del Peak 5(4p16.3) 0 (0%) 632 5.6305e-11 2.44e-08 6.3043e-12 2.84e-09 1.9767e-26 1.18e-23 8.4122e-13 3.94e-10 4.6e-07 0.000152 1.6249e-06 0.000497 9.7486e-24 5.75e-21 2.1408e-18 1.19e-15 9.9689e-15 5.05e-12 4.699e-18 2.6e-15 Del Peak 6(4q35.2) 0 (0%) 630 3.1689e-06 0.000922 9.8064e-07 0.000309 2.706e-37 1.68e-34 1.6588e-13 8e-11 1.5119e-08 5.71e-06 1.7796e-06 0.000537 2.222e-21 1.28e-18 3.7865e-14 1.87e-11 2.8367e-13 1.36e-10 6.7335e-18 3.7e-15 Del Peak 7(5q11.2) 0 (0%) 679 1.1732e-27 7.04e-25 6.1137e-25 3.63e-22 5.9137e-60 3.78e-57 1.4321e-39 8.94e-37 3.3271e-16 1.77e-13 7.4321e-19 4.18e-16 1.3315e-40 8.35e-38 1.6995e-43 1.07e-40 8.3636e-40 5.24e-37 5.4087e-49 3.43e-46 Del Peak 8(5q21.3) 0 (0%) 688 1.3639e-29 8.28e-27 1.0003e-26 5.98e-24 6.1266e-70 3.92e-67 3.2548e-51 2.07e-48 2.5973e-15 1.34e-12 8.9738e-16 4.75e-13 5.8796e-48 3.73e-45 1.0637e-47 6.73e-45 1.2827e-39 8.02e-37 1.6726e-54 1.07e-51 Del Peak 9(6p25.3) 0 (0%) 743 0.3175 1 0.52211 1 8.5052e-07 0.000271 4.7147e-05 0.0117 0.43913 1 0.59688 1 0.0029248 0.477 0.0078573 1 0.29914 1 0.041663 1 Del Peak 10(6q15) 0 (0%) 612 1.5475e-06 0.000478 0.0013728 0.246 6.8301e-28 4.11e-25 3.7835e-08 1.38e-05 0.45649 1 0.087503 1 2.6907e-05 0.00692 0.00026186 0.055 0.013556 1 5.0416e-05 0.0124 Del Peak 11(6q27) 0 (0%) 599 0.018324 1 0.6098 1 2.8674e-14 1.42e-11 0.0037538 0.589 0.11289 1 0.7957 1 0.34137 1 0.56078 1 0.39265 1 0.11542 1 Del Peak 12(7p22.3) 0 (0%) 795 0.0029773 0.482 0.00036571 0.0742 2.0563e-15 1.07e-12 5.8917e-07 0.000193 0.021413 1 0.0055267 0.829 8.0737e-09 3.12e-06 5.3885e-08 1.93e-05 3.9557e-11 1.72e-08 1.3813e-10 5.86e-08 Del Peak 13(7q36.1) 0 (0%) 739 0.012946 1 0.042957 1 5.252e-10 2.16e-07 0.089713 1 0.55078 1 0.056216 1 0.00041367 0.0831 0.00049646 0.0983 5.264e-08 1.89e-05 1.6004e-06 0.000491 Del Peak 14(8p23.2) 0 (0%) 432 1.0843e-09 4.4e-07 2.5341e-05 0.00661 7.6285e-31 4.65e-28 1.1904e-13 5.8e-11 0.0095473 1 0.034055 1 2.0483e-11 9.03e-09 3.7053e-08 1.36e-05 5.6847e-06 0.00161 4.7884e-12 2.17e-09 Del Peak 15(8p11.21) 0 (0%) 740 0.00012588 0.0292 0.014068 1 6.186e-11 2.67e-08 0.047398 1 0.046466 1 0.019137 1 0.00059302 0.115 0.00091398 0.167 0.0040051 0.625 6.262e-06 0.00175 Del Peak 16(9p21.3) 0 (0%) 606 2.4284e-06 0.000721 0.00076043 0.141 1.1111e-29 6.76e-27 2.2104e-15 1.14e-12 0.0034135 0.543 0.44419 1 7.3085e-07 0.000235 2.6358e-07 8.9e-05 4.0189e-06 0.00116 4.1474e-12 1.89e-09 Del Peak 17(9q21.11) 0 (0%) 667 0.0025493 0.426 0.00028988 0.0603 3.4148e-16 1.81e-13 1.1898e-10 5.06e-08 1.0414e-05 0.00281 0.0065344 0.954 2.4102e-06 0.000718 8.3002e-06 0.00227 1.4099e-08 5.34e-06 9.3349e-13 4.36e-10 Del Peak 18(10q23.31) 0 (0%) 652 4.0908e-05 0.0103 9.5653e-05 0.0225 3.8281e-20 2.18e-17 4.7504e-12 2.16e-09 1.8996e-07 6.53e-05 7.3748e-05 0.0178 1.0624e-11 4.75e-09 6.9092e-09 2.69e-06 5.4734e-09 2.17e-06 3.9676e-09 1.58e-06 Del Peak 19(10q26.3) 0 (0%) 649 2.8798e-08 1.06e-05 1.4887e-07 5.2e-05 2.232e-22 1.31e-19 2.0718e-12 9.53e-10 3.0624e-08 1.13e-05 8.2479e-07 0.000264 1.7705e-15 9.22e-13 1.171e-12 5.44e-10 7.8055e-12 3.5e-09 3.4847e-15 1.79e-12 Del Peak 20(11p15.5) 0 (0%) 651 1.3439e-06 0.000418 1.6232e-07 5.62e-05 5.0122e-36 3.1e-33 1.9555e-12 9.01e-10 1.2732e-09 5.13e-07 1.6524e-06 0.000502 8.065e-18 4.42e-15 5.0697e-13 2.39e-10 3.8713e-15 1.98e-12 1.4174e-16 7.61e-14 Del Peak 21(11q13.1) 0 (0%) 719 0.0018482 0.322 0.058395 1 3.5102e-17 1.91e-14 4.3872e-06 0.00125 0.33089 1 0.39322 1 0.0082347 1 0.016887 1 0.59562 1 0.029681 1 Del Peak 22(11q23.2) 0 (0%) 464 2.0784e-08 7.72e-06 0.029644 1 3.218e-42 2.02e-39 7.6821e-12 3.45e-09 0.97534 1 0.47519 1 0.0030477 0.491 0.0025375 0.426 0.019604 1 0.00013729 0.0314 Del Peak 23(11q25) 0 (0%) 492 0.00024306 0.052 0.9595 1 6.1522e-38 3.83e-35 9.8899e-09 3.81e-06 0.12647 1 0.70695 1 0.35468 1 0.35086 1 0.092968 1 0.03309 1 Del Peak 24(12p13.1) 0 (0%) 756 0.043897 1 0.13961 1 0.00097911 0.178 0.014949 1 0.2216 1 0.042019 1 0.00020971 0.0458 0.013741 1 8.0331e-05 0.0194 8.677e-06 0.00237 Del Peak 25(12q24.21) 0 (0%) 739 9.5969e-11 4.1e-08 2.4963e-10 1.04e-07 2.3346e-15 1.2e-12 2.6833e-14 1.33e-11 0.00020918 0.0458 1.051e-06 0.00033 6.5499e-16 3.47e-13 3.4653e-13 1.65e-10 1.1669e-08 4.46e-06 3.2709e-13 1.56e-10 Del Peak 26(13q14.2) 0 (0%) 500 2.1522e-05 0.00572 4.2296e-05 0.0106 7.0739e-28 4.25e-25 1.8096e-08 6.79e-06 0.53804 1 0.11079 1 1.5495e-07 5.38e-05 6.3919e-06 0.00178 3.8647e-10 1.6e-07 1.1153e-07 3.93e-05 Del Peak 27(14q24.3) 0 (0%) 619 3.9962e-13 1.9e-10 1.5614e-08 5.89e-06 8.5986e-37 5.32e-34 3.4991e-14 1.73e-11 5.2946e-07 0.000174 5.5315e-06 0.00157 3.86e-15 1.98e-12 3.0431e-13 1.45e-10 5.4362e-18 3.01e-15 1.5189e-16 8.14e-14 Del Peak 28(15q13.1) 0 (0%) 598 3.4589e-07 0.000116 7.5675e-08 2.69e-05 6.7418e-31 4.12e-28 1.1986e-11 5.33e-09 0.00019256 0.0427 2.3206e-05 0.0061 6.0702e-15 3.09e-12 2.3219e-14 1.16e-11 6.3188e-19 3.56e-16 1.9625e-18 1.1e-15 Del Peak 29(16q24.3) 0 (0%) 326 1.6023e-16 8.57e-14 2.5109e-14 1.25e-11 1.6596e-14 8.33e-12 4.4729e-13 2.11e-10 1.1446e-09 4.64e-07 3.4541e-11 1.51e-08 2.8205e-16 1.5e-13 4.6216e-21 2.65e-18 9.2218e-15 4.68e-12 8.4866e-22 4.93e-19 Del Peak 30(17p12) 0 (0%) 367 2.14e-10 8.99e-08 0.16599 1 9.3314e-23 5.49e-20 7.404e-07 0.000238 8.0661e-05 0.0194 0.0077463 1 0.00058603 0.114 0.12057 1 0.0002551 0.0541 0.0001269 0.0293 Del Peak 31(17q21.31) 0 (0%) 598 1.0676e-14 5.4e-12 3.9073e-07 0.00013 5.421e-22 3.17e-19 1.1931e-11 5.32e-09 1.8581e-11 8.21e-09 3.1238e-11 1.37e-08 2.8586e-21 1.64e-18 8.315e-17 4.48e-14 1.1423e-12 5.32e-10 1.7604e-11 7.82e-09 Del Peak 32(18q23) 0 (0%) 620 0.00034744 0.0709 0.14873 1 1.3244e-15 6.95e-13 1.2001e-08 4.56e-06 0.0041271 0.64 0.58095 1 2.5421e-05 0.00661 0.0037051 0.585 0.00037498 0.0757 0.0001428 0.0324 Del Peak 33(19p13.3) 0 (0%) 608 5.9856e-11 2.59e-08 4.5737e-08 1.66e-05 1.2523e-44 7.91e-42 6.5313e-18 3.6e-15 3.0314e-06 0.000888 3.3891e-05 0.00861 1.1922e-12 5.53e-10 5.3985e-10 2.22e-07 9.6735e-16 5.1e-13 6.5412e-17 3.55e-14 Del Peak 34(19q13.32) 0 (0%) 730 1.5707e-06 0.000484 8.8007e-05 0.0208 4.4821e-20 2.55e-17 1.5222e-10 6.42e-08 0.00078305 0.144 4.9541e-05 0.0122 5.2784e-09 2.1e-06 6.7532e-09 2.64e-06 3.6046e-10 1.5e-07 5.7758e-12 2.61e-09 Del Peak 35(20p13) 0 (0%) 779 8.8144e-06 0.0024 0.0001582 0.0354 2.5928e-13 1.24e-10 7.1509e-09 2.78e-06 0.0015362 0.269 0.011875 1 2.4409e-10 1.02e-07 7.0566e-10 2.89e-07 2.6926e-12 1.23e-09 1.9074e-13 9.17e-11 Del Peak 36(21q11.2) 0 (0%) 731 0.00025239 0.0538 0.034183 1 4.3098e-11 1.87e-08 2.0147e-06 0.000602 0.22548 1 0.50164 1 0.058127 1 0.19667 1 0.014182 1 0.019373 1 Del Peak 37(22q13.32) 0 (0%) 503 0.16446 1 0.043759 1 0.062967 1 0.00067355 0.127 0.12127 1 0.0218 1 0.0066117 0.959 0.0024667 0.419 0.0043777 0.674 0.49157 1