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) 125 (26%) 347 0.55259 1 0.38427 1 5.4121e-07 0.000372 0.0081638 1 0.16949 1 0.24291 1 0.023728 1 0.05909 1 0.2415 1 0.70826 1 Amp Peak 2(1p22.3) 124 (26%) 348 0.87647 1 1 1 4.7979e-07 0.000332 0.0025252 1 0.18268 1 0.39935 1 0.052725 1 0.007032 1 0.43425 1 0.10754 1 Amp Peak 3(1q21.3) 336 (71%) 136 0.36172 1 0.46484 1 5.6363e-06 0.00356 8.3208e-07 0.000565 0.45774 1 0.35692 1 0.20291 1 0.86582 1 0.020179 1 0.00011638 0.0658 Amp Peak 4(3q26.2) 157 (33%) 315 0.00026431 0.142 0.0033217 1 5.0092e-10 3.89e-07 5.5192e-08 4.06e-05 0.00063119 0.329 0.0030724 1 1.1146e-08 8.4e-06 3.4696e-07 0.000243 8.6573e-08 6.31e-05 9.7968e-08 7.12e-05 Amp Peak 5(4q12) 88 (19%) 384 0.70327 1 0.20593 1 6.061e-09 4.6e-06 0.031374 1 0.022089 1 0.026495 1 0.072455 1 0.0072767 1 0.022848 1 0.0048931 1 Amp Peak 6(5p15.33) 304 (64%) 168 0.87754 1 0.90125 1 2.7489e-21 2.24e-18 0.039672 1 0.056507 1 0.00079802 0.405 1.2915e-07 9.29e-05 0.0032374 1 0.0035662 1 0.0021311 1 Amp Peak 7(5p13.1) 280 (59%) 192 0.26327 1 0.8973 1 5.6698e-18 4.58e-15 0.013505 1 0.44264 1 0.018662 1 6.7585e-07 0.000461 0.074023 1 0.0016004 0.773 0.0054963 1 Amp Peak 8(5q35.1) 110 (23%) 362 0.086231 1 0.45314 1 0.0039139 1 8.7965e-07 0.000595 0.090912 1 0.2003 1 0.0013973 0.683 0.00015343 0.0858 0.0010829 0.543 0.023312 1 Amp Peak 9(6p21.1) 173 (37%) 299 0.67463 1 0.20593 1 0.00016824 0.0934 1.0457e-07 7.55e-05 0.080965 1 0.60902 1 0.029843 1 0.94007 1 0.14982 1 0.024231 1 Amp Peak 10(7p21.1) 261 (55%) 211 0.74305 1 1 1 6.9487e-20 5.65e-17 4.9289e-06 0.00313 0.0018446 0.884 0.0010365 0.523 7.9789e-08 5.83e-05 2.31e-08 1.73e-05 0.00020964 0.115 0.00023808 0.129 Amp Peak 11(7p11.2) 252 (53%) 220 1 1 1 1 1.2656e-18 1.02e-15 1.9966e-05 0.0118 0.0011393 0.568 0.00026343 0.142 2.092e-11 1.64e-08 1.3572e-09 1.05e-06 1.7154e-06 0.00113 4.7527e-07 0.000329 Amp Peak 12(7q31.2) 200 (42%) 272 0.48233 1 0.4288 1 2.8556e-09 2.19e-06 5.4754e-05 0.0315 0.2063 1 0.052026 1 1.0272e-09 7.94e-07 1.0315e-07 7.46e-05 0.0065887 1 0.00076006 0.388 Amp Peak 13(8p11.23) 126 (27%) 346 0.29434 1 0.10708 1 2.1702e-16 1.75e-13 8.2511e-06 0.00512 0.08441 1 0.026704 1 0.00033358 0.178 1.9349e-05 0.0116 0.0064601 1 0.012037 1 Amp Peak 14(8p11.21) 162 (34%) 310 0.25289 1 0.12373 1 3.4203e-21 2.78e-18 0.00012766 0.0719 0.014879 1 0.0053405 1 4.592e-07 0.000319 2.536e-07 0.00018 3.7377e-05 0.0218 0.00048699 0.258 Amp Peak 15(8q11.1) 214 (45%) 258 0.0047198 1 0.013376 1 3.0403e-22 2.49e-19 1.1385e-07 8.2e-05 0.034394 1 0.0046706 1 4.2118e-06 0.0027 2.9343e-05 0.0173 3.2585e-07 0.000228 4.9055e-06 0.00312 Amp Peak 16(8q24.21) 298 (63%) 174 0.034332 1 0.034084 1 8.4035e-20 6.82e-17 3.7208e-08 2.76e-05 0.15673 1 0.0016243 0.781 3.0624e-07 0.000215 1.3668e-05 0.00824 1.154e-05 0.00703 1.733e-05 0.0104 Amp Peak 17(10p15.1) 124 (26%) 348 0.023032 1 0.026244 1 4.1719e-06 0.00267 2.5854e-07 0.000183 0.0043432 1 0.034625 1 0.0002203 0.12 2.2556e-06 0.00148 0.00072403 0.372 0.00017533 0.097 Amp Peak 18(11q13.3) 157 (33%) 315 0.0011838 0.588 0.00073647 0.377 5.9442e-14 4.76e-11 1.9354e-05 0.0116 0.012667 1 0.0068904 1 3.1767e-05 0.0186 3.55e-07 0.000248 4.7723e-08 3.52e-05 8.564e-08 6.25e-05 Amp Peak 19(12p12.1) 163 (35%) 309 0.19753 1 0.032954 1 5.4536e-22 4.46e-19 4.137e-06 0.00266 0.034536 1 0.083445 1 9.6903e-07 0.000652 3.9606e-06 0.00255 1.0367e-05 0.00637 7.4593e-06 0.00465 Amp Peak 20(12q14.1) 148 (31%) 324 0.40563 1 0.30226 1 2.6454e-24 2.17e-21 1.4549e-07 0.000104 0.021505 1 0.0072217 1 2.6805e-07 0.000189 2.2578e-09 1.73e-06 2.6316e-08 1.96e-05 9.7928e-09 7.41e-06 Amp Peak 21(12q15) 151 (32%) 321 0.2214 1 0.10317 1 1.495e-21 1.22e-18 2.3526e-08 1.76e-05 0.014601 1 0.0047126 1 4.8578e-07 0.000336 2.1824e-07 0.000155 1.9228e-07 0.000137 3.9781e-09 3.04e-06 Amp Peak 22(13q33.3) 72 (15%) 400 0.17198 1 0.1048 1 0.43267 1 0.0028503 1 0.66321 1 0.29824 1 0.91695 1 0.2675 1 0.26954 1 0.098199 1 Amp Peak 23(14q13.3) 211 (45%) 261 0.56244 1 0.25359 1 2.034e-11 1.6e-08 4.728e-06 0.00302 0.0021261 1 0.012225 1 2.5468e-10 1.98e-07 5.2475e-05 0.0303 2.373e-06 0.00155 3.6048e-09 2.76e-06 Amp Peak 24(17q12) 208 (44%) 264 0.17898 1 0.048967 1 6.0833e-14 4.86e-11 8.2659e-07 0.000562 0.063813 1 0.00015951 0.0888 1.0515e-06 0.000706 6.7054e-08 4.93e-05 3.1893e-06 0.00207 1.0062e-07 7.3e-05 Amp Peak 25(17q23.1) 230 (49%) 242 0.081011 1 0.2078 1 2.2542e-14 1.81e-11 2.1073e-08 1.58e-05 0.001563 0.758 4.1217e-07 0.000287 1.842e-07 0.000132 2.9005e-10 2.26e-07 1.7066e-05 0.0102 5.3939e-06 0.00341 Amp Peak 26(18q11.2) 94 (20%) 378 0.195 1 0.015087 1 0.00091766 0.464 1.0692e-08 8.08e-06 0.043061 1 0.0008163 0.414 0.012129 1 0.0031493 1 0.002652 1 1.445e-06 0.000961 Amp Peak 27(19q12) 126 (27%) 346 0.05139 1 0.021931 1 1.2875e-08 9.68e-06 0.00030411 0.163 0.068451 1 0.079108 1 0.001046 0.526 4.5676e-05 0.0265 1.3577e-06 0.000904 5.1809e-07 0.000357 Amp Peak 28(20p11.21) 179 (38%) 293 0.061134 1 0.095316 1 1.1008e-05 0.00673 0.0070836 1 0.33779 1 0.037876 1 0.0029444 1 0.0047502 1 0.00023383 0.127 3.4447e-05 0.0201 Amp Peak 29(20q13.33) 225 (48%) 247 0.005592 1 0.030109 1 1.0299e-07 7.46e-05 0.0029575 1 0.0042556 1 0.0033453 1 1.149e-05 0.00701 0.0046718 1 1.0198e-05 0.00627 1.3381e-05 0.00808 Amp Peak 30(22q11.22) 81 (17%) 391 0.26763 1 0.16206 1 0.0014007 0.684 0.60075 1 0.023163 1 0.11945 1 0.4743 1 0.22163 1 0.060539 1 0.098212 1 Amp Peak 31(Xq28) 151 (32%) 321 0.30129 1 0.12324 1 3.0132e-10 2.34e-07 5.9382e-05 0.0341 0.024391 1 0.030781 1 0.00027201 0.146 0.0028744 1 0.026424 1 0.03379 1 Del Peak 1(1p36.13) 108 (23%) 364 0.79481 1 0.44137 1 1.5935e-06 0.00105 2.1754e-05 0.0129 0.43706 1 0.3635 1 5.3298e-05 0.0308 0.0001795 0.0991 0.00021545 0.118 0.0072377 1 Del Peak 2(1p13.3) 139 (29%) 333 0.84359 1 0.89631 1 9.9668e-07 0.00067 9.8087e-05 0.0557 0.62591 1 0.7171 1 0.00058094 0.305 0.0055676 1 0.035253 1 0.030442 1 Del Peak 3(1p13.1) 137 (29%) 335 0.70327 1 0.70728 1 1.9336e-06 0.00127 2.1957e-05 0.013 0.12392 1 0.5348 1 0.0012149 0.601 0.0066046 1 0.018689 1 0.028819 1 Del Peak 4(2q22.1) 47 (10%) 425 0.86935 1 0.77984 1 0.0023837 1 0.037851 1 0.030649 1 0.47148 1 0.05421 1 0.0024194 1 0.047638 1 0.12079 1 Del Peak 5(2q37.3) 63 (13%) 409 0.70327 1 0.20593 1 0.00033016 0.177 0.0016045 0.773 0.22002 1 0.15128 1 0.012546 1 0.0026718 1 0.0044777 1 0.0012957 0.639 Del Peak 6(3p21.31) 227 (48%) 245 0.13236 1 0.47785 1 7.5324e-06 0.00469 3.2149e-06 0.00208 0.041069 1 0.0073749 1 0.018864 1 3.352e-09 2.57e-06 8.432e-06 0.00522 3.0019e-06 0.00195 Del Peak 7(3q11.1) 133 (28%) 339 0.60921 1 0.60234 1 0.04139 1 0.02737 1 0.36648 1 0.29817 1 0.16817 1 0.027682 1 0.85621 1 0.72792 1 Del Peak 8(3q29) 129 (27%) 343 0.71049 1 0.60234 1 0.14505 1 8.1101e-05 0.0465 0.0051543 1 0.016843 1 8.8297e-05 0.0503 0.073158 1 0.63672 1 0.024893 1 Del Peak 9(4p16.3) 116 (25%) 356 0.59513 1 0.45337 1 1.5601e-05 0.00939 2.3123e-05 0.0136 0.023211 1 0.049931 1 9.4505e-07 0.000637 3.3381e-07 0.000234 6.1457e-07 0.000421 4.725e-08 3.49e-05 Del Peak 10(4q22.1) 142 (30%) 330 0.00021406 0.117 9.8935e-05 0.0561 3.6672e-07 0.000256 9.8921e-08 7.18e-05 0.15053 1 0.028597 1 5.4135e-07 0.000372 3.5238e-12 2.78e-09 5.1761e-07 0.000357 1.1411e-08 8.59e-06 Del Peak 11(4q35.1) 172 (36%) 300 0.0020383 0.964 0.0011805 0.588 7.479e-10 5.8e-07 1.3625e-11 1.07e-08 0.038078 1 0.00019589 0.108 2.0744e-11 1.63e-08 7.7097e-17 6.21e-14 1.0694e-08 8.08e-06 1.6695e-14 1.34e-11 Del Peak 12(5q11.2) 166 (35%) 306 0.25999 1 0.25359 1 1.9005e-12 1.51e-09 2.0243e-07 0.000144 0.0042592 1 0.011309 1 1.0073e-05 0.0062 7.7742e-08 5.69e-05 4.5433e-07 0.000316 7.4405e-08 5.46e-05 Del Peak 13(5q22.1) 189 (40%) 283 0.044656 1 0.05154 1 1.0824e-12 8.59e-10 2.5624e-08 1.91e-05 0.0017014 0.817 0.0037686 1 6.1821e-07 0.000423 2.4893e-08 1.86e-05 1.197e-09 9.24e-07 1.4533e-09 1.12e-06 Del Peak 14(6q12) 158 (33%) 314 0.5324 1 1 1 0.059835 1 0.024441 1 0.24274 1 0.15879 1 0.88178 1 0.92845 1 0.17176 1 0.0050001 1 Del Peak 15(6q22.31) 234 (50%) 238 0.54019 1 0.18678 1 0.022002 1 1.2902e-06 0.000861 0.30802 1 0.054436 1 0.054969 1 0.98092 1 0.37353 1 0.52676 1 Del Peak 16(6q26) 238 (50%) 234 0.36839 1 0.27624 1 0.011891 1 8.6432e-05 0.0494 0.16788 1 0.0094429 1 0.22644 1 0.63505 1 0.17973 1 0.10647 1 Del Peak 17(8p23.2) 229 (49%) 243 0.0052612 1 0.0038227 1 7.67e-17 6.19e-14 9.1653e-05 0.0522 0.017998 1 0.00035354 0.188 1.0516e-05 0.00644 1.829e-07 0.000131 0.0042512 1 1.6683e-06 0.0011 Del Peak 18(8p12) 205 (43%) 267 0.10598 1 0.12046 1 1.826e-15 1.47e-12 1.9517e-05 0.0116 0.042395 1 0.022233 1 0.00026165 0.141 7.8563e-06 0.00488 0.004237 1 7.8027e-06 0.00485 Del Peak 19(8p11.21) 107 (23%) 365 0.79481 1 0.50418 1 2.7927e-11 2.19e-08 0.017983 1 0.72109 1 0.31842 1 0.23409 1 0.1012 1 0.34046 1 0.041259 1 Del Peak 20(8q11.21) 59 (12%) 413 1 1 1 1 0.79583 1 0.062832 1 0.53688 1 0.67602 1 0.86067 1 0.48826 1 0.25953 1 0.18323 1 Del Peak 21(9p23) 258 (55%) 214 0.52069 1 0.90125 1 3.2175e-07 0.000226 0.58236 1 0.61967 1 0.59796 1 0.057228 1 0.022177 1 0.469 1 0.15328 1 Del Peak 22(9p21.3) 264 (56%) 208 0.52069 1 0.90125 1 1.7863e-06 0.00118 0.52113 1 0.328 1 0.28761 1 0.0045675 1 0.012981 1 0.8263 1 0.20431 1 Del Peak 23(9q21.11) 231 (49%) 241 0.033497 1 0.5971 1 1.491e-07 0.000107 5.0827e-05 0.0294 0.072606 1 0.011237 1 0.0056694 1 9.4131e-06 0.00581 0.0049495 1 1.2013e-05 0.00728 Del Peak 24(10p15.3) 113 (24%) 359 1 1 1 1 0.00073507 0.377 0.00061385 0.321 0.5041 1 0.56009 1 0.0043767 1 0.47558 1 0.0020016 0.949 0.022738 1 Del Peak 25(10q26.3) 130 (28%) 342 0.7482 1 0.28297 1 4.781e-06 0.00305 0.00025572 0.138 0.002678 1 0.023698 1 0.00065289 0.338 0.017081 1 0.019629 1 0.0060133 1 Del Peak 26(11p15.5) 126 (27%) 346 0.26763 1 0.057583 1 4.0351e-06 0.00259 0.012035 1 0.0076669 1 0.0020423 0.964 0.0046339 1 5.2987e-06 0.00335 0.0077271 1 0.0021509 1 Del Peak 27(11q23.2) 109 (23%) 363 0.43314 1 0.45337 1 0.00012159 0.0686 0.018434 1 0.0090008 1 0.0026588 1 0.00051771 0.273 0.0019755 0.938 0.016493 1 0.12979 1 Del Peak 28(11q25) 105 (22%) 367 0.1081 1 0.07995 1 0.0014903 0.724 0.045403 1 0.0012028 0.597 0.0064444 1 0.00046366 0.246 0.0059601 1 0.11371 1 0.4325 1 Del Peak 29(12p13.2) 126 (27%) 346 0.25541 1 0.71867 1 0.00017186 0.0952 7.2125e-07 0.000491 0.077418 1 0.020954 1 0.024097 1 0.092832 1 0.98742 1 0.96805 1 Del Peak 30(12q12) 90 (19%) 382 0.59734 1 0.64431 1 1.1922e-05 0.00724 0.020959 1 0.1068 1 0.015755 1 0.039886 1 0.18367 1 0.1993 1 0.022216 1 Del Peak 31(12q24.33) 115 (24%) 357 0.06298 1 0.039644 1 6.5364e-06 0.00409 0.0019493 0.928 0.022299 1 0.0032834 1 0.0099537 1 0.0010362 0.523 0.0040486 1 5.8387e-06 0.00367 Del Peak 32(13q12.11) 265 (56%) 207 0.0011346 0.567 0.013376 1 1.378e-19 1.12e-16 0.00060839 0.319 0.0018816 0.898 1.4854e-06 0.000985 2.3601e-06 0.00154 3.9936e-09 3.05e-06 7.3532e-06 0.0046 8.6581e-07 0.000586 Del Peak 33(13q12.13) 266 (56%) 206 0.0086219 1 0.021834 1 1.0462e-19 8.48e-17 0.00010727 0.0607 0.00052444 0.276 6.6845e-07 0.000457 4.8006e-06 0.00306 8.61e-09 6.53e-06 3.207e-05 0.0188 3.5199e-06 0.00227 Del Peak 34(13q14.2) 256 (54%) 216 0.0086219 1 0.021834 1 7.6139e-22 6.22e-19 0.00078257 0.399 0.0006466 0.336 1.0418e-05 0.00639 8.8148e-07 0.000595 4.0669e-08 3.01e-05 3.2438e-05 0.0189 1.2615e-06 0.000844 Del Peak 35(13q34) 217 (46%) 255 0.03556 1 0.044535 1 2.2047e-15 1.77e-12 0.050765 1 0.0035915 1 0.0007897 0.402 3.8832e-05 0.0226 5.097e-06 0.00323 0.0014484 0.705 0.00024772 0.134 Del Peak 36(14q32.33) 140 (30%) 332 0.70327 1 0.30226 1 0.00013486 0.0757 0.52145 1 0.16025 1 0.062692 1 0.38885 1 0.075059 1 0.019721 1 0.18572 1 Del Peak 37(15q11.2) 239 (51%) 233 0.1678 1 0.15747 1 1.8115e-10 1.41e-07 0.00019302 0.106 0.09283 1 0.00016097 0.0895 1.8331e-09 1.41e-06 1.0545e-07 7.6e-05 0.0018751 0.896 0.00015628 0.0872 Del Peak 38(16q23.1) 160 (34%) 312 0.058714 1 0.31155 1 2.5866e-07 0.000183 0.00045989 0.244 0.00069818 0.36 0.017432 1 2.7384e-07 0.000193 3.6572e-08 2.72e-05 0.0064378 1 0.0039631 1 Del Peak 39(16q24.3) 178 (38%) 294 0.16033 1 0.63133 1 1.6596e-06 0.0011 0.0028187 1 0.018589 1 0.079995 1 2.1246e-06 0.00139 3.2339e-06 0.00209 0.018422 1 0.0050916 1 Del Peak 40(17p13.3) 252 (53%) 220 0.38561 1 0.6094 1 2.7784e-13 2.22e-10 7.5644e-08 5.54e-05 0.033388 1 0.0015801 0.765 6.8306e-05 0.0392 6.3834e-06 0.004 0.0054147 1 0.0035187 1 Del Peak 41(18q21.32) 233 (49%) 239 0.11499 1 0.22677 1 8.5809e-10 6.64e-07 0.050772 1 0.001327 0.652 0.0022974 1 0.0045521 1 0.010898 1 0.040914 1 0.021725 1 Del Peak 42(18q23) 228 (48%) 244 0.029007 1 0.096811 1 9.3067e-13 7.41e-10 0.020478 1 0.0039452 1 0.0013536 0.663 0.00037994 0.202 0.00062836 0.328 0.013313 1 0.0027374 1 Del Peak 43(19p13.3) 252 (53%) 220 0.57194 1 0.66451 1 2.5955e-12 2.05e-09 2.3524e-07 0.000167 0.56376 1 0.30589 1 2.1504e-06 0.00141 1.9036e-08 1.43e-05 2.4011e-06 0.00156 9.3618e-06 0.00579 Del Peak 44(19p13.2) 246 (52%) 226 0.69366 1 1 1 1.2528e-11 9.88e-09 2.2226e-08 1.66e-05 0.37799 1 0.18657 1 1.0646e-06 0.000713 1.2784e-06 0.000854 1.4718e-06 0.000977 4.9886e-07 0.000344 Del Peak 45(19p12) 199 (42%) 273 0.51884 1 0.65766 1 9.722e-13 7.73e-10 1.7072e-05 0.0102 0.60272 1 0.26611 1 8.2377e-05 0.0471 5.8837e-06 0.00369 2.3419e-05 0.0138 0.00020036 0.11 Del Peak 46(19q13.33) 174 (37%) 298 0.27231 1 0.38339 1 2.0218e-07 0.000144 0.0029212 1 0.08193 1 0.20781 1 0.078211 1 0.0094452 1 0.00013692 0.0767 1.1716e-05 0.00712 Del Peak 47(20p13) 121 (26%) 351 0.10512 1 0.26812 1 2.3992e-06 0.00156 0.0006553 0.339 0.0055231 1 0.0010629 0.534 0.014565 1 0.013482 1 0.72164 1 0.6889 1 Del Peak 48(21q11.2) 157 (33%) 315 0.060411 1 0.050147 1 3.1031e-11 2.43e-08 0.00013079 0.0735 0.0062417 1 0.0046886 1 8.8345e-08 6.43e-05 4.6166e-09 3.52e-06 1.9833e-05 0.0118 5.827e-06 0.00367 Del Peak 49(21q21.3) 153 (32%) 319 0.028769 1 0.032954 1 9.4524e-11 7.39e-08 1.2844e-05 0.00777 0.00052511 0.276 0.00065044 0.338 1.1882e-10 9.28e-08 2.081e-12 1.65e-09 2.9756e-05 0.0175 8.3751e-07 0.000568 Del Peak 50(22q13.32) 224 (47%) 248 0.069155 1 0.087079 1 6.175e-13 4.92e-10 4.5678e-08 3.38e-05 0.0086263 1 0.017135 1 5.0837e-09 3.86e-06 4.8806e-09 3.71e-06 1.6651e-05 0.01 3.7647e-08 2.79e-05 Del Peak 51(Xp22.2) 137 (29%) 335 0.69055 1 0.89631 1 1.9902e-07 0.000142 0.0013094 0.644 0.08854 1 0.028366 1 0.00066756 0.344 0.0012383 0.612 0.54377 1 0.51373 1