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 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 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 Amp Peak 1(1p34.3) 0 (0%) 347 0.55259 1 0.38427 1 5.4121e-07 0.000365 0.0081638 1 0.16949 1 0.24291 1 4.9631e-06 0.00311 0.14855 1 0.18394 1 0.14747 1 Amp Peak 2(1p22.3) 0 (0%) 348 0.87647 1 1 1 4.7979e-07 0.000324 0.0025252 1 0.18268 1 0.39935 1 0.0016833 0.788 0.0091011 1 0.13646 1 0.13148 1 Amp Peak 3(1q21.3) 0 (0%) 136 0.36172 1 0.46484 1 5.6363e-06 0.00351 8.3208e-07 0.000556 0.45774 1 0.35692 1 4.426e-06 0.00279 0.47278 1 0.00069543 0.35 0.00021065 0.112 Amp Peak 4(3q26.2) 0 (0%) 315 0.00026431 0.139 0.0033217 1 5.0092e-10 3.85e-07 5.5192e-08 3.98e-05 0.00063119 0.32 0.0030724 1 1.6207e-09 1.23e-06 5.6153e-09 4.22e-06 1.458e-06 0.000956 2.2068e-07 0.000153 Amp Peak 5(4q12) 0 (0%) 384 0.70327 1 0.20593 1 6.061e-09 4.55e-06 0.031374 1 0.022089 1 0.026495 1 0.15498 1 0.025809 1 0.0024111 1 0.0042896 1 Amp Peak 6(5p15.33) 0 (0%) 168 0.87754 1 0.90125 1 2.7489e-21 2.24e-18 0.039672 1 0.056507 1 0.00079802 0.396 1.769e-07 0.000124 0.0016566 0.777 0.00022482 0.119 0.00030354 0.159 Amp Peak 7(5p13.1) 0 (0%) 192 0.26327 1 0.8973 1 5.6698e-18 4.58e-15 0.013505 1 0.44264 1 0.018662 1 0.00011946 0.0661 0.0034201 1 0.00012221 0.0671 0.00027402 0.144 Amp Peak 8(5q35.1) 0 (0%) 362 0.086231 1 0.45314 1 0.0039139 1 8.7965e-07 0.000585 0.090912 1 0.2003 1 4.725e-05 0.0272 0.00015887 0.0858 0.013436 1 0.0029379 1 Amp Peak 9(6p21.1) 0 (0%) 299 0.67463 1 0.20593 1 0.00016824 0.0903 1.0457e-07 7.46e-05 0.080965 1 0.60902 1 0.0091755 1 0.72669 1 0.011992 1 0.016843 1 Amp Peak 10(7p21.1) 0 (0%) 211 0.74305 1 1 1 6.9487e-20 5.65e-17 4.9289e-06 0.00309 0.0018446 0.858 0.0010365 0.508 7.6563e-09 5.73e-06 7.9824e-08 5.73e-05 8.3848e-06 0.00515 0.0020343 0.938 Amp Peak 11(7p11.2) 0 (0%) 220 1 1 1 1 1.2656e-18 1.02e-15 1.9966e-05 0.0118 0.0011393 0.554 0.00026343 0.139 1.0644e-08 7.91e-06 1.4854e-10 1.16e-07 2.5923e-07 0.000179 6.854e-05 0.0388 Amp Peak 12(7q31.2) 0 (0%) 272 0.48233 1 0.4288 1 2.8556e-09 2.16e-06 5.4754e-05 0.0313 0.2063 1 0.052026 1 2.9669e-06 0.0019 1.3685e-08 1.01e-05 0.0063711 1 0.0097813 1 Amp Peak 13(8p11.23) 0 (0%) 346 0.29434 1 0.10708 1 2.1702e-16 1.75e-13 8.2511e-06 0.00507 0.08441 1 0.026704 1 0.0030875 1 7.1648e-06 0.00443 0.013132 1 0.00047866 0.247 Amp Peak 14(8p11.21) 0 (0%) 310 0.25289 1 0.12373 1 3.4203e-21 2.78e-18 0.00012766 0.0697 0.014879 1 0.0053405 1 1.5923e-05 0.00949 4.9e-07 0.000331 4.1857e-05 0.0242 6.296e-06 0.0039 Amp Peak 15(8q11.1) 0 (0%) 258 0.0047198 1 0.013376 1 3.0403e-22 2.49e-19 1.1385e-07 8.08e-05 0.034394 1 0.0046706 1 5.3451e-06 0.00334 2.2621e-05 0.0133 1.942e-07 0.000136 8.8443e-07 0.000587 Amp Peak 16(8q24.21) 0 (0%) 174 0.034332 1 0.034084 1 8.4035e-20 6.82e-17 3.7208e-08 2.71e-05 0.15673 1 0.0016243 0.763 6.6465e-05 0.0378 3.27e-06 0.00209 8.4079e-07 0.00056 1.259e-05 0.00762 Amp Peak 17(10p15.1) 0 (0%) 348 0.023032 1 0.026244 1 4.1719e-06 0.00264 2.5854e-07 0.000179 0.0043432 1 0.034625 1 6.7817e-05 0.0385 2.0837e-08 1.54e-05 0.00023703 0.125 6.075e-05 0.0346 Amp Peak 18(11q13.3) 0 (0%) 315 0.0011838 0.573 0.00073647 0.368 5.9442e-14 4.76e-11 1.9354e-05 0.0115 0.012667 1 0.0068904 1 3.0732e-08 2.25e-05 9.4872e-07 0.000629 2.0794e-10 1.61e-07 2.032e-07 0.000141 Amp Peak 19(12p12.1) 0 (0%) 309 0.19753 1 0.032954 1 5.4536e-22 4.46e-19 4.137e-06 0.00262 0.034536 1 0.083445 1 1.4435e-05 0.00863 2.7391e-07 0.000188 6.0512e-06 0.00376 1.0145e-05 0.00621 Amp Peak 20(12q14.1) 0 (0%) 324 0.40563 1 0.30226 1 2.6454e-24 2.17e-21 1.4549e-07 0.000103 0.021505 1 0.0072217 1 2.9329e-07 0.000201 3.8782e-10 2.98e-07 6.2443e-09 4.68e-06 4.0876e-09 3.09e-06 Amp Peak 21(12q15) 0 (0%) 321 0.2214 1 0.10317 1 1.495e-21 1.22e-18 2.3526e-08 1.73e-05 0.014601 1 0.0047126 1 7.2425e-08 5.21e-05 4.3947e-09 3.31e-06 2.1686e-09 1.65e-06 1.1039e-07 7.86e-05 Amp Peak 22(13q33.3) 0 (0%) 400 0.17198 1 0.1048 1 0.43267 1 0.0028503 1 0.66321 1 0.29824 1 0.029299 1 0.22896 1 0.12856 1 0.082398 1 Amp Peak 23(14q13.3) 0 (0%) 261 0.56244 1 0.25359 1 2.034e-11 1.6e-08 4.728e-06 0.00297 0.0021261 0.972 0.012225 1 1.2809e-09 9.76e-07 3.8398e-05 0.0223 8.7005e-08 6.23e-05 2.6139e-09 1.98e-06 Amp Peak 24(17q12) 0 (0%) 264 0.17898 1 0.048967 1 6.0833e-14 4.87e-11 8.2659e-07 0.000553 0.063813 1 0.00015951 0.086 9.5604e-11 7.47e-08 2.0173e-06 0.0013 7.3338e-07 0.000491 1.0969e-06 0.000724 Amp Peak 25(17q23.1) 0 (0%) 242 0.081011 1 0.2078 1 2.2542e-14 1.81e-11 2.1073e-08 1.55e-05 0.001563 0.742 4.1217e-07 0.000279 2.7021e-13 2.15e-10 5.9854e-10 4.58e-07 1.5417e-06 0.00101 5.675e-06 0.00353 Amp Peak 26(18q11.2) 0 (0%) 378 0.195 1 0.015087 1 0.00091766 0.451 1.0692e-08 7.93e-06 0.043061 1 0.0008163 0.402 0.00079949 0.396 9.6053e-05 0.0538 1.0551e-05 0.00643 6.7326e-07 0.000452 Amp Peak 27(19q12) 0 (0%) 346 0.05139 1 0.021931 1 1.2875e-08 9.54e-06 0.00030411 0.159 0.068451 1 0.079108 1 0.00043758 0.226 4.2165e-08 3.06e-05 1.2652e-06 0.000834 1.4571e-06 0.000956 Amp Peak 28(20p11.21) 0 (0%) 293 0.061134 1 0.095316 1 1.1008e-05 0.00669 0.0070836 1 0.33779 1 0.037876 1 0.00022071 0.117 0.0015876 0.749 0.00014475 0.0785 7.5125e-05 0.0424 Amp Peak 29(20q13.33) 0 (0%) 247 0.005592 1 0.030109 1 1.0299e-07 7.35e-05 0.0029575 1 0.0042556 1 0.0033453 1 1.3661e-05 0.00821 0.018408 1 2.5339e-06 0.00163 4.2355e-07 0.000287 Amp Peak 30(22q11.22) 0 (0%) 391 0.26763 1 0.16206 1 0.0014007 0.671 0.60075 1 0.023163 1 0.11945 1 0.44027 1 0.053175 1 0.040192 1 0.1251 1 Amp Peak 31(Xq28) 0 (0%) 321 0.30129 1 0.12324 1 3.0132e-10 2.33e-07 5.9382e-05 0.0338 0.024391 1 0.030781 1 0.0014563 0.696 9.713e-05 0.0543 0.0058966 1 0.033047 1 Del Peak 1(1p36.13) 0 (0%) 364 0.79481 1 0.44137 1 1.5935e-06 0.00104 2.1754e-05 0.0129 0.43706 1 0.3635 1 8.0632e-06 0.00497 8.9874e-06 0.00551 0.025333 1 0.0048561 1 Del Peak 2(1p13.3) 0 (0%) 333 0.84359 1 0.89631 1 9.9668e-07 0.000659 9.8087e-05 0.0547 0.62591 1 0.7171 1 0.0070527 1 0.05738 1 0.069257 1 0.0063777 1 Del Peak 3(1p13.1) 0 (0%) 335 0.70327 1 0.70728 1 1.9336e-06 0.00125 2.1957e-05 0.013 0.12392 1 0.5348 1 0.0022115 1 0.034857 1 0.07021 1 0.013103 1 Del Peak 4(2q22.1) 0 (0%) 425 0.86935 1 0.77984 1 0.0023837 1 0.037851 1 0.030649 1 0.47148 1 0.15061 1 0.021298 1 0.073903 1 0.0079982 1 Del Peak 5(2q37.3) 0 (0%) 409 0.70327 1 0.20593 1 0.00033016 0.171 0.0016045 0.756 0.22002 1 0.15128 1 0.17776 1 0.0090463 1 0.0069076 1 0.00015287 0.0827 Del Peak 6(3p21.31) 0 (0%) 245 0.13236 1 0.47785 1 7.5324e-06 0.00465 3.2149e-06 0.00206 0.041069 1 0.0073749 1 3.353e-05 0.0195 6.2253e-09 4.67e-06 1.1778e-05 0.00715 0.00074304 0.371 Del Peak 7(3q11.1) 0 (0%) 339 0.60921 1 0.60234 1 0.04139 1 0.02737 1 0.36648 1 0.29817 1 0.047248 1 0.016203 1 0.18281 1 0.93624 1 Del Peak 8(3q29) 0 (0%) 343 0.71049 1 0.60234 1 0.14505 1 8.1101e-05 0.0457 0.0051543 1 0.016843 1 3.2717e-08 2.39e-05 0.017096 1 0.66647 1 0.68392 1 Del Peak 9(4p16.3) 0 (0%) 356 0.59513 1 0.45337 1 1.5601e-05 0.00931 2.3123e-05 0.0136 0.023211 1 0.049931 1 8.397e-07 0.00056 6.3637e-11 4.98e-08 2.8228e-07 0.000194 1.1051e-07 7.86e-05 Del Peak 10(4q22.1) 0 (0%) 330 0.00021406 0.114 9.8935e-05 0.0551 3.6672e-07 0.00025 9.8921e-08 7.07e-05 0.15053 1 0.028597 1 3.8108e-06 0.00242 9.9669e-14 7.96e-11 1.6594e-08 1.22e-05 1.5448e-06 0.00101 Del Peak 11(4q35.1) 0 (0%) 300 0.0020383 0.938 0.0011805 0.573 7.479e-10 5.71e-07 1.3625e-11 1.07e-08 0.038078 1 0.00019589 0.105 2.4668e-09 1.87e-06 7.3643e-18 5.94e-15 1.5731e-10 1.22e-07 1.0041e-10 7.83e-08 Del Peak 12(5q11.2) 0 (0%) 306 0.25999 1 0.25359 1 1.9005e-12 1.5e-09 2.0243e-07 0.000141 0.0042592 1 0.011309 1 1.3516e-06 0.000888 2.5683e-09 1.95e-06 4.5276e-08 3.28e-05 2.1069e-06 0.00136 Del Peak 13(5q22.1) 0 (0%) 283 0.044656 1 0.05154 1 1.0824e-12 8.57e-10 2.5624e-08 1.88e-05 0.0017014 0.795 0.0037686 1 1.5477e-08 1.14e-05 3.5591e-10 2.74e-07 5.9732e-10 4.58e-07 8.433e-09 6.29e-06 Del Peak 14(6q12) 0 (0%) 314 0.5324 1 1 1 0.059835 1 0.024441 1 0.24274 1 0.15879 1 0.57487 1 0.89101 1 0.053584 1 0.47634 1 Del Peak 15(6q22.31) 0 (0%) 238 0.54019 1 0.18678 1 0.022002 1 1.2902e-06 0.000849 0.30802 1 0.054436 1 0.018414 1 0.70899 1 0.9002 1 0.57065 1 Del Peak 16(6q26) 0 (0%) 234 0.36839 1 0.27624 1 0.011891 1 8.6432e-05 0.0486 0.16788 1 0.0094429 1 0.14055 1 0.80681 1 0.8101 1 0.40998 1 Del Peak 17(8p23.2) 0 (0%) 243 0.0052612 1 0.0038227 1 7.67e-17 6.18e-14 9.1653e-05 0.0514 0.017998 1 0.00035354 0.183 8.2151e-09 6.14e-06 2.2875e-07 0.000159 3.5805e-06 0.00228 0.0031177 1 Del Peak 18(8p12) 0 (0%) 267 0.10598 1 0.12046 1 1.826e-15 1.47e-12 1.9517e-05 0.0116 0.042395 1 0.022233 1 4.6121e-05 0.0267 5.3667e-06 0.00335 5.2594e-05 0.0301 0.0043223 1 Del Peak 19(8p11.21) 0 (0%) 365 0.79481 1 0.50418 1 2.7927e-11 2.2e-08 0.017983 1 0.72109 1 0.31842 1 0.00062651 0.318 0.18512 1 0.037601 1 0.51192 1 Del Peak 20(8q11.21) 0 (0%) 413 1 1 1 1 0.79583 1 0.062832 1 0.53688 1 0.67602 1 0.00083104 0.409 0.6036 1 0.15149 1 0.46448 1 Del Peak 21(9p23) 0 (0%) 214 0.52069 1 0.90125 1 3.2175e-07 0.000219 0.58236 1 0.61967 1 0.59796 1 0.015368 1 0.011883 1 0.63933 1 0.28646 1 Del Peak 22(9p21.3) 0 (0%) 208 0.52069 1 0.90125 1 1.7863e-06 0.00116 0.52113 1 0.328 1 0.28761 1 0.021992 1 0.0028449 1 0.93368 1 0.46383 1 Del Peak 23(9q21.11) 0 (0%) 241 0.033497 1 0.5971 1 1.491e-07 0.000105 5.0827e-05 0.0292 0.072606 1 0.011237 1 0.00011628 0.0644 1.6715e-07 0.000117 0.0033295 1 0.00012568 0.0689 Del Peak 24(10p15.3) 0 (0%) 359 1 1 1 1 0.00073507 0.368 0.00061385 0.313 0.5041 1 0.56009 1 0.00054591 0.28 0.36572 1 0.026642 1 0.010269 1 Del Peak 25(10q26.3) 0 (0%) 342 0.7482 1 0.28297 1 4.781e-06 0.003 0.00025572 0.135 0.002678 1 0.023698 1 5.6495e-05 0.0323 0.0020462 0.938 0.05324 1 0.0078915 1 Del Peak 26(11p15.5) 0 (0%) 346 0.26763 1 0.057583 1 4.0351e-06 0.00256 0.012035 1 0.0076669 1 0.0020423 0.938 0.0011065 0.54 4.3624e-06 0.00275 0.0045269 1 0.00010769 0.0598 Del Peak 27(11q23.2) 0 (0%) 363 0.43314 1 0.45337 1 0.00012159 0.0669 0.018434 1 0.0090008 1 0.0026588 1 0.0015619 0.742 0.0017231 0.803 0.0029556 1 0.0054454 1 Del Peak 28(11q25) 0 (0%) 367 0.1081 1 0.07995 1 0.0014903 0.711 0.045403 1 0.0012028 0.581 0.0064444 1 0.026387 1 0.0051693 1 0.14084 1 0.085396 1 Del Peak 29(12p13.2) 0 (0%) 346 0.25541 1 0.71867 1 0.00017186 0.0921 7.2125e-07 0.000484 0.077418 1 0.020954 1 0.0080213 1 0.1112 1 0.82418 1 1 1 Del Peak 30(12q12) 0 (0%) 382 0.59734 1 0.64431 1 1.1922e-05 0.00722 0.020959 1 0.1068 1 0.015755 1 0.0041488 1 0.047369 1 0.20392 1 0.052019 1 Del Peak 31(12q24.33) 0 (0%) 357 0.06298 1 0.039644 1 6.5364e-06 0.00405 0.0019493 0.901 0.022299 1 0.0032834 1 0.0006144 0.313 0.0003057 0.159 0.053816 1 0.015133 1 Del Peak 32(13q12.11) 0 (0%) 207 0.0011346 0.553 0.013376 1 1.378e-19 1.12e-16 0.00060839 0.311 0.0018816 0.873 1.4854e-06 0.000971 2.7306e-07 0.000188 4.0695e-08 2.95e-05 0.0024834 1 8.5063e-05 0.0479 Del Peak 33(13q12.13) 0 (0%) 206 0.0086219 1 0.021834 1 1.0462e-19 8.48e-17 0.00010727 0.0596 0.00052444 0.27 6.6845e-07 0.00045 1.2029e-07 8.53e-05 8.1745e-08 5.86e-05 0.0038594 1 0.00013791 0.0749 Del Peak 34(13q14.2) 0 (0%) 216 0.0086219 1 0.021834 1 7.6139e-22 6.22e-19 0.00078257 0.39 0.0006466 0.327 1.0418e-05 0.00636 4.1467e-09 3.13e-06 1.5408e-07 0.000109 0.00020565 0.11 4.6856e-05 0.027 Del Peak 35(13q34) 0 (0%) 255 0.03556 1 0.044535 1 2.2047e-15 1.77e-12 0.050765 1 0.0035915 1 0.0007897 0.392 3.7064e-06 0.00236 3.094e-05 0.018 0.021489 1 0.0046232 1 Del Peak 36(14q32.33) 0 (0%) 332 0.70327 1 0.30226 1 0.00013486 0.0734 0.52145 1 0.16025 1 0.062692 1 0.13133 1 0.045057 1 0.090929 1 0.011739 1 Del Peak 37(15q11.2) 0 (0%) 233 0.1678 1 0.15747 1 1.8115e-10 1.41e-07 0.00019302 0.103 0.09283 1 0.00016097 0.0866 1.9138e-13 1.53e-10 1.4023e-05 0.00841 2.8215e-05 0.0165 0.0008025 0.396 Del Peak 38(16q23.1) 0 (0%) 312 0.058714 1 0.31155 1 2.5866e-07 0.000179 0.00045989 0.237 0.00069818 0.35 0.017432 1 1.7313e-06 0.00112 3.2112e-07 0.000219 0.013008 1 0.055891 1 Del Peak 39(16q24.3) 0 (0%) 294 0.16033 1 0.63133 1 1.6596e-06 0.00108 0.0028187 1 0.018589 1 0.079995 1 2.903e-05 0.0169 4.8778e-05 0.028 0.02155 1 0.034487 1 Del Peak 40(17p13.3) 0 (0%) 220 0.38561 1 0.6094 1 2.7784e-13 2.21e-10 7.5644e-08 5.44e-05 0.033388 1 0.0015801 0.747 5.6037e-08 4.04e-05 9.7865e-07 0.000648 0.010242 1 0.0060283 1 Del Peak 41(18q21.32) 0 (0%) 239 0.11499 1 0.22677 1 8.5809e-10 6.55e-07 0.050772 1 0.001327 0.638 0.0022974 1 9.0795e-09 6.76e-06 0.00011996 0.0662 0.0092521 1 0.10487 1 Del Peak 42(18q23) 0 (0%) 244 0.029007 1 0.096811 1 9.3067e-13 7.39e-10 0.020478 1 0.0039452 1 0.0013536 0.65 1.0408e-08 7.74e-06 1.2826e-05 0.00773 0.003884 1 0.079792 1 Del Peak 43(19p13.3) 0 (0%) 220 0.57194 1 0.66451 1 2.5955e-12 2.05e-09 2.3524e-07 0.000163 0.56376 1 0.30589 1 3.4289e-10 2.64e-07 3.1444e-07 0.000215 3.6499e-06 0.00232 1.6314e-07 0.000115 Del Peak 44(19p13.2) 0 (0%) 226 0.69366 1 1 1 1.2528e-11 9.88e-09 2.2226e-08 1.63e-05 0.37799 1 0.18657 1 3.3382e-10 2.58e-07 4.0099e-07 0.000272 2.4594e-06 0.00158 2.8685e-07 0.000197 Del Peak 45(19p12) 0 (0%) 273 0.51884 1 0.65766 1 9.722e-13 7.71e-10 1.7072e-05 0.0102 0.60272 1 0.26611 1 0.0015256 0.726 0.0001202 0.0662 2.7949e-05 0.0164 1.2668e-05 0.00765 Del Peak 46(19q13.33) 0 (0%) 298 0.27231 1 0.38339 1 2.0218e-07 0.000141 0.0029212 1 0.08193 1 0.20781 1 0.018353 1 0.001943 0.9 2.5156e-05 0.0147 1.4098e-05 0.00844 Del Peak 47(20p13) 0 (0%) 351 0.10512 1 0.26812 1 2.3992e-06 0.00155 0.0006553 0.33 0.0055231 1 0.0010629 0.52 0.00012668 0.0693 0.011696 1 0.74194 1 0.7718 1 Del Peak 48(21q11.2) 0 (0%) 315 0.060411 1 0.050147 1 3.1031e-11 2.44e-08 0.00013079 0.0713 0.0062417 1 0.0046886 1 3.5874e-08 2.61e-05 3.7791e-07 0.000257 2.2467e-05 0.0132 3.5511e-08 2.59e-05 Del Peak 49(21q21.3) 0 (0%) 319 0.028769 1 0.032954 1 9.4524e-11 7.39e-08 1.2844e-05 0.00773 0.00052511 0.27 0.00065044 0.328 3.2407e-10 2.51e-07 5.5087e-10 4.23e-07 1.0353e-05 0.00633 1.2802e-07 9.06e-05 Del Peak 50(22q13.32) 0 (0%) 248 0.069155 1 0.087079 1 6.175e-13 4.91e-10 4.5678e-08 3.3e-05 0.0086263 1 0.017135 1 1.5054e-10 1.17e-07 6.2863e-11 4.93e-08 1.6607e-07 0.000117 2.7183e-08 1.99e-05 Del Peak 51(Xp22.2) 0 (0%) 335 0.69055 1 0.89631 1 1.9902e-07 0.000139 0.0013094 0.631 0.08854 1 0.028366 1 0.014054 1 0.00032178 0.167 0.49942 1 0.24355 1