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 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 Fisher's exact test_P Fisher's exact test_Q Amp Peak 1(1p34.2) 0 (0%) 334 0.027997 1 0.48064 1 0.00089229 0.621 0.64436 1 0.36254 1 0.61878 1 0.024164 1 0.057238 1 0.087982 1 0.66932 1 Amp Peak 2(1q21.2) 0 (0%) 192 0.041886 1 0.0061823 1 1.9829e-07 0.000162 0.0011299 0.777 0.16014 1 0.049238 1 1.8709e-05 0.0146 4.1074e-05 0.0316 0.039291 1 0.0018052 1 Amp Peak 3(2p16.1) 0 (0%) 181 0.00030485 0.222 0.0016452 1 3.1822e-13 2.66e-10 5.8257e-05 0.0443 0.95017 1 0.6427 1 1.8804e-05 0.0146 7.5521e-05 0.0573 0.88705 1 0.017101 1 Amp Peak 4(2q31.2) 0 (0%) 265 0.020695 1 0.00094798 0.659 6.5211e-06 0.00517 1.985e-07 0.000162 0.72406 1 0.88737 1 0.00019414 0.144 0.00024752 0.182 0.3702 1 0.51141 1 Amp Peak 5(3p11.1) 0 (0%) 317 0.074773 1 0.84409 1 0.74389 1 0.95744 1 0.21385 1 0.0012981 0.887 0.23901 1 0.54119 1 0.8452 1 0.60157 1 Amp Peak 6(3q26.33) 0 (0%) 33 0.00042663 0.306 1.7146e-05 0.0134 7.0488e-12 5.86e-09 6.6908e-07 0.000541 0.19288 1 0.077644 1 1.255e-06 0.00101 5.0381e-05 0.0384 0.14828 1 3.0658e-06 0.00245 Amp Peak 7(4q12) 0 (0%) 304 0.67906 1 0.75873 1 0.00035284 0.255 0.12421 1 0.3558 1 0.13102 1 0.22096 1 0.10577 1 0.17772 1 0.39261 1 Amp Peak 8(5p15.33) 0 (0%) 83 0.85286 1 0.86716 1 1.0671e-05 0.00841 0.012895 1 0.40531 1 0.50196 1 0.26226 1 0.48743 1 0.45018 1 0.73544 1 Amp Peak 9(5p12) 0 (0%) 136 0.91917 1 0.51401 1 7.5793e-10 6.28e-07 0.0087387 1 0.5626 1 1 1 0.22451 1 0.20982 1 0.79153 1 0.23553 1 Amp Peak 10(6p12.1) 0 (0%) 267 0.55703 1 0.38314 1 0.0018014 1 0.16779 1 0.96213 1 0.30014 1 0.10601 1 0.52176 1 0.27034 1 0.26703 1 Amp Peak 11(6q12) 0 (0%) 280 1 1 0.87303 1 0.0011385 0.781 0.045379 1 0.34826 1 0.40804 1 0.19028 1 0.42016 1 0.19795 1 0.078417 1 Amp Peak 12(7p11.2) 0 (0%) 204 0.18606 1 0.09391 1 0.00097005 0.669 0.0036616 1 0.68745 1 0.80108 1 0.027313 1 0.0005424 0.386 0.63408 1 0.064445 1 Amp Peak 13(7q21.2) 0 (0%) 188 0.10132 1 0.24997 1 5.3382e-10 4.43e-07 1.2724e-05 0.00999 0.057338 1 0.3893 1 0.0006615 0.468 0.00018506 0.138 0.035824 1 0.052721 1 Amp Peak 14(8p11.23) 0 (0%) 213 0.0081177 1 0.16822 1 0.02545 1 0.035179 1 0.1916 1 0.098781 1 0.36341 1 0.5366 1 0.13548 1 0.37147 1 Amp Peak 15(8q24.21) 0 (0%) 117 0.8715 1 0.64417 1 0.55402 1 0.96883 1 0.91657 1 0.70842 1 0.99485 1 0.50901 1 0.86567 1 0.49675 1 Amp Peak 16(9p24.1) 0 (0%) 324 0.37518 1 0.029533 1 0.00035369 0.255 0.17742 1 0.0016979 1 0.0050133 1 0.006989 1 0.00076736 0.539 0.11675 1 0.016656 1 Amp Peak 17(9p13.3) 0 (0%) 288 0.16996 1 0.37287 1 0.043013 1 0.038723 1 0.070796 1 0.0089805 1 0.011366 1 0.0014888 1 0.82279 1 0.55455 1 Amp Peak 18(11q13.3) 0 (0%) 254 0.06969 1 0.030551 1 0.0048628 1 0.00051779 0.37 0.19004 1 0.035798 1 0.012289 1 0.12379 1 0.045422 1 0.006693 1 Amp Peak 19(12p13.33) 0 (0%) 199 0.010156 1 0.057062 1 1.2263e-05 0.00965 0.00049216 0.352 0.31262 1 0.72944 1 0.00041818 0.301 0.01028 1 0.83672 1 0.21832 1 Amp Peak 20(12q15) 0 (0%) 253 0.31238 1 0.5273 1 0.0053063 1 0.0013616 0.927 0.76381 1 0.52436 1 0.058838 1 0.080687 1 1 1 0.43736 1 Amp Peak 21(13q34) 0 (0%) 326 0.96435 1 0.048907 1 0.038423 1 0.18194 1 0.87024 1 0.083384 1 0.57829 1 0.80869 1 0.15522 1 0.38131 1 Amp Peak 22(14q13.3) 0 (0%) 276 0.34486 1 0.24581 1 0.12677 1 0.096921 1 0.57003 1 0.0082634 1 0.067544 1 0.016404 1 0.0031957 1 0.53228 1 Amp Peak 23(15q26.3) 0 (0%) 258 0.15118 1 0.02098 1 1.5595e-05 0.0122 9.3889e-06 0.00741 0.35379 1 0.01826 1 0.00033367 0.242 0.0025266 1 0.015863 1 0.0012251 0.838 Amp Peak 24(17q25.1) 0 (0%) 206 0.017661 1 0.060794 1 6.01e-07 0.000487 2.169e-05 0.0168 0.26742 1 0.29175 1 0.0038965 1 0.00016477 0.123 0.79633 1 0.078334 1 Amp Peak 25(18p11.32) 0 (0%) 260 0.095767 1 0.0098077 1 2.4815e-05 0.0192 0.00012602 0.0949 0.23136 1 0.4508 1 0.13123 1 0.040221 1 0.89834 1 0.020937 1 Amp Peak 26(18q11.2) 0 (0%) 271 0.00045553 0.327 0.0022679 1 1.3658e-05 0.0107 0.00034191 0.248 0.27235 1 0.74038 1 0.00084074 0.587 5.0385e-06 0.00401 0.40198 1 0.0053858 1 Amp Peak 27(19q12) 0 (0%) 230 0.45483 1 0.24902 1 4.0708e-06 0.00324 0.1821 1 0.23063 1 0.028698 1 0.0082289 1 0.12997 1 0.91317 1 0.37004 1 Amp Peak 28(19q13.2) 0 (0%) 227 0.71537 1 1 1 0.00019499 0.144 0.070833 1 0.35617 1 0.11719 1 0.10567 1 0.084976 1 0.77013 1 0.24639 1 Amp Peak 29(20p12.2) 0 (0%) 186 0.00098685 0.68 0.0042983 1 8.924e-08 7.3e-05 0.00016098 0.121 0.96651 1 0.22098 1 0.040833 1 0.0027288 1 0.25882 1 0.094536 1 Amp Peak 30(20q11.21) 0 (0%) 168 0.99122 1 0.84394 1 0.00051999 0.371 0.013224 1 0.66891 1 0.5881 1 0.58481 1 0.75667 1 0.94128 1 0.37333 1 Amp Peak 31(22q11.21) 0 (0%) 198 0.11066 1 0.12309 1 0.00029562 0.216 0.00047739 0.342 0.88793 1 0.34914 1 0.012165 1 0.046272 1 0.75068 1 0.026984 1 Amp Peak 32(Xq28) 0 (0%) 291 0.63266 1 0.63565 1 0.038982 1 0.081483 1 0.070072 1 0.069028 1 0.10944 1 0.078102 1 0.51833 1 0.30324 1 Del Peak 1(1p36.22) 0 (0%) 225 1.4274e-06 0.00115 1.7833e-08 1.47e-05 1.6133e-28 1.36e-25 2.1042e-14 1.76e-11 0.41213 1 0.026199 1 8.6687e-14 7.25e-11 9.4466e-15 7.92e-12 0.00083797 0.586 1.834e-05 0.0143 Del Peak 2(1p13.2) 0 (0%) 225 0.00023715 0.175 0.0005497 0.391 1.2332e-15 1.03e-12 5.745e-09 4.73e-06 0.11875 1 0.071159 1 5.5563e-07 0.000451 1.9622e-07 0.00016 0.1274 1 0.00078822 0.553 Del Peak 3(2p25.3) 0 (0%) 360 0.046105 1 0.17884 1 0.077265 1 0.37008 1 0.10991 1 0.83838 1 0.3191 1 0.12836 1 0.053345 1 0.024688 1 Del Peak 4(2q22.1) 0 (0%) 292 0.25483 1 0.31825 1 0.00027109 0.198 0.019796 1 0.66724 1 0.077676 1 0.021861 1 0.016461 1 0.51176 1 0.2262 1 Del Peak 5(2q36.2) 0 (0%) 265 0.00023576 0.174 4.7565e-05 0.0364 1.6951e-12 1.41e-09 2.1435e-06 0.00172 0.1769 1 0.1255 1 6.61e-07 0.000535 2.9848e-08 2.45e-05 0.88486 1 0.16258 1 Del Peak 6(3p25.3) 0 (0%) 84 0.54042 1 0.17616 1 0.027817 1 0.0022082 1 0.63742 1 0.18016 1 0.078017 1 0.043262 1 0.60195 1 0.059733 1 Del Peak 7(3p13) 0 (0%) 57 0.41881 1 0.54863 1 2.6689e-06 0.00214 0.0008576 0.598 0.88237 1 0.037948 1 0.075627 1 0.017081 1 0.432 1 0.0013423 0.915 Del Peak 8(3p12.3) 0 (0%) 65 0.25764 1 0.34172 1 3.0279e-05 0.0233 0.0025909 1 1 1 0.091957 1 0.1197 1 0.023469 1 0.70112 1 0.005772 1 Del Peak 9(3q11.1) 0 (0%) 338 0.75853 1 0.47773 1 0.11709 1 0.053816 1 0.76467 1 0.28212 1 0.88529 1 0.80254 1 0.28903 1 0.88743 1 Del Peak 10(4p15.2) 0 (0%) 158 0.00080707 0.566 0.001708 1 6.5154e-06 0.00517 0.0003406 0.247 0.66155 1 0.034313 1 0.013814 1 0.0068919 1 0.30222 1 0.86424 1 Del Peak 11(4q22.1) 0 (0%) 180 0.0068481 1 0.057857 1 0.00010209 0.0771 0.008289 1 0.12263 1 0.38079 1 0.0047314 1 0.007224 1 0.3498 1 0.16768 1 Del Peak 12(4q32.3) 0 (0%) 149 0.0096682 1 0.025274 1 3.4983e-07 0.000285 0.0005961 0.422 0.10077 1 0.52301 1 0.0011954 0.819 0.0045534 1 0.66272 1 0.24153 1 Del Peak 13(4q35.2) 0 (0%) 144 0.10047 1 0.20573 1 2.8407e-06 0.00227 0.00012369 0.0933 0.45478 1 0.46976 1 0.00014338 0.108 0.010451 1 0.43991 1 0.095738 1 Del Peak 14(5q11.2) 0 (0%) 107 0.84151 1 0.30269 1 2.0341e-12 1.69e-09 0.00019205 0.143 0.95874 1 0.24402 1 0.010429 1 0.085756 1 0.98713 1 0.0011302 0.777 Del Peak 15(5q31.1) 0 (0%) 89 0.33159 1 0.2283 1 5.7045e-09 4.71e-06 2.9999e-05 0.0232 0.27154 1 0.16591 1 0.058186 1 0.063853 1 0.68421 1 0.0071276 1 Del Peak 16(6p25.3) 0 (0%) 297 0.21975 1 0.10989 1 0.0087794 1 0.0014284 0.971 0.39303 1 0.013046 1 0.0021907 1 0.00030485 0.222 0.17904 1 0.079683 1 Del Peak 17(6q22.31) 0 (0%) 302 0.019183 1 0.0022397 1 0.0051316 1 0.00081841 0.573 0.62886 1 0.35397 1 0.00024921 0.183 0.00058659 0.416 0.3736 1 0.21756 1 Del Peak 18(6q26) 0 (0%) 294 0.065853 1 0.0029759 1 0.0023386 1 0.00072654 0.512 0.92144 1 0.68997 1 0.0020357 1 0.0022341 1 0.18393 1 0.085039 1 Del Peak 19(7q11.22) 0 (0%) 360 0.90823 1 0.40489 1 4.3951e-05 0.0338 0.82862 1 0.95833 1 0.74972 1 0.046461 1 0.049252 1 0.61021 1 0.35776 1 Del Peak 20(7q36.3) 0 (0%) 316 0.18723 1 0.11156 1 0.00094976 0.659 0.27435 1 1 1 0.31493 1 0.0025355 1 0.0054011 1 0.028012 1 0.16607 1 Del Peak 21(8p23.2) 0 (0%) 130 0.86415 1 0.45866 1 0.00096128 0.665 0.17289 1 0.34475 1 0.1409 1 0.49392 1 0.042143 1 0.68008 1 0.070472 1 Del Peak 22(9p23) 0 (0%) 139 0.005614 1 0.0029131 1 1.9708e-10 1.64e-07 0.10353 1 0.14638 1 0.20769 1 0.0028103 1 0.074621 1 0.099105 1 0.032817 1 Del Peak 23(9p21.3) 0 (0%) 95 0.37246 1 0.17169 1 4.9922e-07 0.000406 0.40906 1 0.69525 1 0.38805 1 0.053538 1 0.47212 1 0.35138 1 0.42073 1 Del Peak 24(9q21.11) 0 (0%) 206 0.00017721 0.132 4.9247e-05 0.0376 5.9694e-11 4.96e-08 1.1436e-06 0.000923 0.65275 1 0.23857 1 4.4013e-09 3.64e-06 1.6275e-09 1.35e-06 0.00095785 0.664 0.00018395 0.137 Del Peak 25(10p15.3) 0 (0%) 219 0.37287 1 0.44184 1 4.8041e-05 0.0368 9.6005e-05 0.0727 0.3293 1 0.44338 1 0.0015552 1 0.00055382 0.393 0.054898 1 4.4536e-05 0.0342 Del Peak 26(10p15.1) 0 (0%) 229 0.072155 1 0.48421 1 0.00016166 0.121 4.0282e-06 0.00321 0.46906 1 0.35291 1 0.00016074 0.121 0.0014346 0.974 0.010667 1 9.0944e-06 0.00719 Del Peak 27(10q23.31) 0 (0%) 194 0.039232 1 0.0038632 1 2.1656e-05 0.0168 2.0796e-06 0.00167 0.36004 1 0.38997 1 8.5437e-06 0.00677 7.2301e-07 0.000584 0.2191 1 0.064403 1 Del Peak 28(11p15.5) 0 (0%) 214 0.00068877 0.486 0.052775 1 1.284e-06 0.00103 0.035158 1 0.00076369 0.538 2.0219e-05 0.0157 0.0029325 1 0.031004 1 0.0019272 1 0.045872 1 Del Peak 29(11q22.1) 0 (0%) 279 0.49319 1 0.28778 1 0.005299 1 0.031392 1 0.10316 1 0.99545 1 0.12974 1 0.263 1 0.38229 1 0.84867 1 Del Peak 30(11q25) 0 (0%) 254 0.7979 1 0.42926 1 0.074578 1 0.33284 1 0.1133 1 0.90777 1 0.13449 1 0.10375 1 0.49004 1 1 1 Del Peak 31(12q24.31) 0 (0%) 334 0.96498 1 0.33211 1 0.42567 1 0.43534 1 0.32272 1 0.20712 1 0.84936 1 0.80796 1 0.076635 1 0.36232 1 Del Peak 32(13q12.11) 0 (0%) 137 0.054743 1 0.61102 1 0.034361 1 0.16435 1 0.90658 1 0.26832 1 0.72995 1 0.28633 1 0.81209 1 0.68069 1 Del Peak 33(13q14.2) 0 (0%) 126 0.051249 1 0.096235 1 0.00096039 0.665 0.05298 1 0.70704 1 0.68237 1 0.10773 1 0.12054 1 0.89278 1 0.6716 1 Del Peak 34(14q11.2) 0 (0%) 257 0.054625 1 0.29339 1 0.16302 1 0.43658 1 0.20597 1 0.15948 1 0.00038568 0.278 9.7963e-05 0.0741 0.18304 1 0.49259 1 Del Peak 35(15q12) 0 (0%) 266 0.72495 1 0.22782 1 0.4498 1 0.34728 1 0.071706 1 0.007983 1 0.21486 1 0.14887 1 0.02395 1 0.18897 1 Del Peak 36(15q21.1) 0 (0%) 273 0.64316 1 0.24163 1 0.29796 1 0.9693 1 0.13822 1 0.0076257 1 0.29852 1 0.10409 1 0.026451 1 0.19897 1 Del Peak 37(16p13.3) 0 (0%) 249 0.23929 1 0.24492 1 0.0052502 1 0.19657 1 0.14901 1 0.60559 1 0.37062 1 0.26762 1 0.42741 1 0.40069 1 Del Peak 38(16q23.1) 0 (0%) 231 0.94193 1 0.65907 1 0.08633 1 0.27078 1 0.35392 1 0.7607 1 0.19812 1 0.20294 1 0.9315 1 0.55971 1 Del Peak 39(17p11.2) 0 (0%) 195 0.19384 1 0.4015 1 0.0018499 1 0.16122 1 0.15048 1 0.018225 1 0.044608 1 0.079787 1 0.18295 1 0.16485 1 Del Peak 40(17q11.2) 0 (0%) 301 1.2614e-05 0.00991 6.4433e-05 0.049 3.0448e-08 2.5e-05 0.01773 1 0.49523 1 0.37803 1 1.48e-06 0.00119 4.8283e-08 3.95e-05 0.14296 1 0.037298 1 Del Peak 41(17q25.3) 0 (0%) 321 0.0051505 1 0.042126 1 0.00040515 0.292 0.044583 1 0.62249 1 0.99436 1 0.14552 1 0.0018676 1 0.52929 1 0.2228 1 Del Peak 42(18q23) 0 (0%) 218 0.50803 1 0.78802 1 0.50245 1 0.89829 1 0.8006 1 0.39738 1 0.52364 1 0.022807 1 0.94214 1 0.44444 1 Del Peak 43(19p13.3) 0 (0%) 224 0.33425 1 0.023076 1 1.3758e-05 0.0108 0.1453 1 0.058795 1 0.25112 1 0.28379 1 0.02829 1 0.00022396 0.166 0.0029663 1 Del Peak 44(19q13.33) 0 (0%) 291 0.61681 1 0.06944 1 0.00016682 0.125 0.00018682 0.139 0.24377 1 0.71878 1 0.081938 1 0.039847 1 0.034123 1 0.33407 1 Del Peak 45(21q21.1) 0 (0%) 208 0.48146 1 0.13538 1 0.011714 1 0.02929 1 0.58502 1 0.88981 1 0.37264 1 0.53307 1 0.03785 1 0.027501 1 Del Peak 46(21q22.3) 0 (0%) 173 0.95746 1 0.1932 1 2.1292e-08 1.75e-05 0.0020622 1 0.39563 1 0.099114 1 0.1301 1 0.013114 1 0.058911 1 0.16125 1 Del Peak 47(22q11.21) 0 (0%) 329 0.09039 1 0.0093024 1 0.067222 1 0.084138 1 0.1449 1 0.12939 1 0.64508 1 0.32916 1 0.058283 1 0.097367 1 Del Peak 48(22q13.32) 0 (0%) 302 0.00028103 0.205 8.6845e-05 0.0658 0.017238 1 0.35054 1 0.5426 1 0.075877 1 0.11863 1 0.1003 1 0.018478 1 0.014418 1 Del Peak 49(Xp22.2) 0 (0%) 271 0.59895 1 0.3507 1 0.00024911 0.183 0.010114 1 0.2774 1 0.78348 1 0.2358 1 0.10271 1 0.17882 1 0.23508 1 Del Peak 50(Xp21.1) 0 (0%) 270 0.35378 1 0.14801 1 5.3937e-05 0.0411 0.00024021 0.177 0.34428 1 0.6807 1 0.1365 1 0.0070572 1 0.53774 1 0.16268 1 Del Peak 51(Xp11.3) 0 (0%) 272 0.06204 1 0.17505 1 9.1854e-06 0.00726 4.0939e-05 0.0315 0.09227 1 0.12432 1 0.063143 1 0.0039054 1 0.13065 1 0.13826 1 Del Peak 52(Xq22.3) 0 (0%) 302 0.0085301 1 0.10522 1 1.906e-05 0.0148 0.00024914 0.183 0.66297 1 0.9198 1 0.0422 1 0.43778 1 0.27631 1 0.79692 1