Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Amp Peak 1(1q31.1) 0 (0%) 452 0.58357 1 0.30814 1 1.3765e-05 0.0106 0.47561 1 0.36908 1 0.2894 1 0.89043 1 0.13428 1 0.44118 1 0.60971 1 0.022902 1 0.96168 1 Amp Peak 2(2q33.1) 0 (0%) 462 0.088273 1 0.00031948 0.227 0.00034022 0.241 0.0032192 1 0.22912 1 0.90087 1 0.0018628 1 0.017696 1 0.068432 1 0.024258 1 0.17032 1 0.12866 1 Amp Peak 3(5p12) 0 (0%) 480 0.097746 1 0.43491 1 2.4768e-06 0.00196 0.8507 1 0.001027 0.697 0.72076 1 0.00084403 0.579 0.00063463 0.444 0.91425 1 0.68284 1 5.417e-05 0.0406 0.12878 1 Amp Peak 4(5q22.3) 0 (0%) 529 0.56517 1 0.88657 1 0.0061905 1 0.24252 1 0.66238 1 0.81532 1 0.15029 1 0.020528 1 0.45906 1 0.31361 1 0.17072 1 0.90862 1 Amp Peak 5(6p21.1) 0 (0%) 440 0.022387 1 0.0018435 1 8.6206e-15 7.5e-12 0.12235 1 0.57504 1 0.36883 1 0.035144 1 0.074328 1 0.25164 1 0.21606 1 0.0058834 1 0.20638 1 Amp Peak 6(7p21.3) 0 (0%) 245 0.0022982 1 0.00093227 0.636 5.4779e-20 4.86e-17 3.3181e-06 0.00262 0.030472 1 0.026569 1 3.1793e-08 2.59e-05 2.2223e-07 0.000178 0.0065009 1 0.0021882 1 3.5836e-06 0.00282 0.3025 1 Amp Peak 7(8p11.23) 0 (0%) 387 0.39583 1 0.048564 1 8.555e-14 7.37e-11 0.37284 1 0.73206 1 0.49971 1 0.10946 1 0.14195 1 0.017399 1 0.13887 1 0.10307 1 0.20155 1 Amp Peak 8(8p11.21) 0 (0%) 345 0.17312 1 0.0085408 1 5.4133e-25 4.83e-22 0.27942 1 0.70031 1 0.39445 1 0.043475 1 0.15783 1 0.1032 1 0.14726 1 0.44582 1 0.39915 1 Amp Peak 9(8q12.1) 0 (0%) 274 0.14319 1 0.00074934 0.518 4.5316e-44 4.1e-41 0.024798 1 0.02185 1 0.054607 1 2.5512e-05 0.0194 0.0092917 1 0.16534 1 0.16528 1 0.0057232 1 0.030467 1 Amp Peak 10(8q24.21) 0 (0%) 237 0.23902 1 0.00022654 0.162 2.312e-45 2.09e-42 0.0028047 1 0.021434 1 0.28329 1 1.6341e-05 0.0125 0.00079163 0.545 0.17993 1 0.17314 1 0.0013404 0.894 0.11111 1 Amp Peak 11(10q22.3) 0 (0%) 553 1 1 0.18228 1 0.77863 1 0.61575 1 0.2974 1 0.8502 1 0.77929 1 0.20563 1 0.43539 1 0.56278 1 0.0060162 1 0.48166 1 Amp Peak 12(11p15.5) 0 (0%) 457 0.00020189 0.146 0.00068431 0.476 4.7955e-05 0.0361 0.001909 1 0.029355 1 0.23771 1 9.9591e-05 0.0735 5.0899e-05 0.0382 0.43731 1 0.97329 1 0.00019498 0.141 2.5663e-06 0.00203 Amp Peak 13(12p13.32) 0 (0%) 445 0.55635 1 0.78684 1 0.10439 1 0.049117 1 0.47758 1 0.81342 1 0.81699 1 0.88821 1 0.66753 1 0.51686 1 0.44258 1 0.31149 1 Amp Peak 14(13q12.13) 0 (0%) 208 1.9206e-07 0.000155 4.1221e-06 0.00324 5.1645e-41 4.66e-38 1.0525e-11 8.87e-09 0.022088 1 0.063964 1 1.9436e-07 0.000156 1.1338e-08 9.31e-06 0.00042962 0.302 0.43785 1 9.885e-10 8.21e-07 0.0013519 0.9 Amp Peak 15(13q12.2) 0 (0%) 213 4.6534e-06 0.00365 5.2465e-05 0.0393 6.9325e-43 6.26e-40 2.3075e-12 1.95e-09 0.024336 1 0.16887 1 2.7359e-07 0.000219 4.6587e-09 3.84e-06 0.0011363 0.767 0.49702 1 2.7355e-09 2.26e-06 0.012493 1 Amp Peak 16(13q22.1) 0 (0%) 208 9.7292e-06 0.00755 0.00019346 0.14 2.1376e-39 1.92e-36 3.9106e-10 3.28e-07 0.1146 1 0.17377 1 4.9141e-07 0.000392 2.1246e-08 1.74e-05 0.00094125 0.641 0.24805 1 1.207e-07 9.75e-05 0.041 1 Amp Peak 17(15q26.1) 0 (0%) 545 0.52717 1 0.062925 1 0.070886 1 0.76956 1 0.098526 1 0.2763 1 0.18766 1 0.68553 1 0.62759 1 1 1 0.77125 1 1 1 Amp Peak 18(16p11.2) 0 (0%) 427 0.017934 1 0.005738 1 1.6045e-20 1.43e-17 0.00054054 0.379 0.014124 1 0.015693 1 1.3704e-05 0.0106 2.5893e-05 0.0197 0.57563 1 0.83802 1 0.00040666 0.287 0.12208 1 Amp Peak 19(17q12) 0 (0%) 442 0.044286 1 0.027559 1 8.5548e-10 7.12e-07 0.0032886 1 0.13633 1 0.059168 1 0.0011027 0.745 2.9257e-05 0.0221 0.0063927 1 0.1825 1 0.26411 1 0.28818 1 Amp Peak 20(17q24.1) 0 (0%) 458 0.025694 1 0.0012574 0.84 1.8998e-10 1.6e-07 0.00034134 0.241 0.080541 1 0.005577 1 0.0031394 1 0.00018615 0.135 0.00014785 0.108 0.16307 1 0.41441 1 0.2481 1 Amp Peak 21(19p13.2) 0 (0%) 489 0.10769 1 0.43683 1 2.1011e-07 0.000169 0.01009 1 0.66275 1 0.39022 1 0.059207 1 0.1647 1 0.23247 1 0.21898 1 0.15471 1 0.1063 1 Amp Peak 22(19q12) 0 (0%) 465 0.028073 1 0.038973 1 7.1032e-08 5.77e-05 0.12919 1 0.080864 1 0.32613 1 0.051421 1 0.14486 1 0.35154 1 0.90261 1 0.29396 1 0.25662 1 Amp Peak 23(20p11.23) 0 (0%) 283 0.0034567 1 0.0026539 1 1.6929e-08 1.39e-05 0.019561 1 0.0058797 1 0.22648 1 0.00016393 0.119 0.00069475 0.482 0.31084 1 0.22626 1 0.00014225 0.104 0.16532 1 Amp Peak 24(20q11.21) 0 (0%) 140 1.1905e-13 1.02e-10 9.5932e-13 8.15e-10 4.4529e-36 3.99e-33 1.987e-18 1.75e-15 0.0068831 1 0.010343 1 4.4629e-17 3.92e-14 2.236e-20 1.99e-17 0.017296 1 0.16362 1 9.0934e-13 7.74e-10 0.00073349 0.508 Amp Peak 25(20q12) 0 (0%) 138 1.0598e-14 9.2e-12 4.1828e-14 3.62e-11 1.0827e-36 9.7e-34 4.8422e-17 4.25e-14 0.011155 1 0.005549 1 1.7642e-16 1.55e-13 2.0808e-19 1.84e-16 0.0073642 1 0.054319 1 2.7212e-13 2.33e-10 6.6018e-05 0.0493 Amp Peak 26(20q13.32) 0 (0%) 135 7.7972e-14 6.73e-11 2.0156e-12 1.71e-09 7.2996e-37 6.55e-34 4.576e-16 4e-13 0.014228 1 0.0044002 1 1.7642e-16 1.55e-13 2.0808e-19 1.84e-16 0.014983 1 0.11442 1 3.1874e-12 2.7e-09 6.6018e-05 0.0493 Amp Peak 27(Xq28) 0 (0%) 465 0.43576 1 0.88431 1 7.3779e-05 0.0547 0.08163 1 0.0017389 1 0.0093042 1 0.094984 1 0.025674 1 0.91286 1 0.97198 1 0.039739 1 0.59559 1 Del Peak 1(1p36.11) 0 (0%) 365 0.00011447 0.084 0.0037923 1 7.7771e-13 6.63e-10 4.5612e-06 0.00358 0.059604 1 0.14778 1 0.00017203 0.125 0.00013759 0.101 0.44952 1 0.87627 1 0.014193 1 0.024066 1 Del Peak 2(1p33) 0 (0%) 432 0.030575 1 0.091327 1 7.122e-12 6.01e-09 0.00035332 0.249 0.85894 1 0.57447 1 0.0064954 1 0.0034415 1 0.58454 1 0.15672 1 0.009549 1 0.0021933 1 Del Peak 3(1p13.2) 0 (0%) 430 0.28805 1 0.12889 1 7.0446e-09 5.79e-06 0.010933 1 0.56737 1 0.7023 1 0.0063242 1 0.0026436 1 0.65352 1 0.38234 1 0.038025 1 0.13099 1 Del Peak 4(2p12) 0 (0%) 569 1 1 0.81015 1 0.0016921 1 0.0077534 1 0.29643 1 1 1 0.74038 1 0.73176 1 0.010798 1 0.061487 1 1 1 0.7046 1 Del Peak 5(2q22.1) 0 (0%) 555 0.92642 1 0.31059 1 0.17166 1 0.89992 1 0.33923 1 0.90131 1 0.24803 1 0.59112 1 0.58016 1 0.1209 1 0.70961 1 0.91622 1 Del Peak 6(2q37.2) 0 (0%) 559 0.91149 1 0.86255 1 0.53915 1 0.88572 1 0.92351 1 0.16188 1 0.37226 1 0.11181 1 0.61301 1 0.36976 1 0.20761 1 0.39331 1 Del Peak 7(3p26.3) 0 (0%) 503 0.35771 1 0.75263 1 0.041381 1 0.35384 1 0.56183 1 0.82449 1 0.25926 1 0.76935 1 0.6925 1 0.13537 1 0.038208 1 0.10637 1 Del Peak 8(3p14.2) 0 (0%) 482 0.61954 1 0.9908 1 0.6145 1 0.62298 1 0.5008 1 0.67377 1 0.96337 1 0.795 1 0.26124 1 0.15295 1 0.094736 1 0.75399 1 Del Peak 9(3q26.31) 0 (0%) 530 0.54351 1 0.78763 1 0.063396 1 0.53224 1 0.33131 1 0.51007 1 0.59189 1 0.58311 1 0.22889 1 0.40211 1 0.3793 1 0.039601 1 Del Peak 10(4p16.1) 0 (0%) 402 0.065426 1 0.43666 1 7.6492e-14 6.61e-11 0.0014983 0.995 0.40166 1 0.92296 1 0.0047719 1 2.2989e-05 0.0175 0.43794 1 0.073038 1 0.00024997 0.178 0.18766 1 Del Peak 11(4q22.1) 0 (0%) 385 0.021594 1 0.030995 1 2.0608e-14 1.79e-11 1.7904e-05 0.0137 0.54076 1 0.77009 1 0.0012269 0.822 0.012407 1 0.033918 1 0.0068659 1 0.0026251 1 0.039236 1 Del Peak 12(4q35.1) 0 (0%) 374 0.021025 1 0.1701 1 2.2447e-14 1.94e-11 6.214e-05 0.0465 0.29543 1 0.88791 1 0.0017439 1 0.0066935 1 0.32526 1 0.036817 1 7.6802e-05 0.0569 0.011156 1 Del Peak 13(5q11.2) 0 (0%) 446 0.00059982 0.42 0.0046582 1 3.448e-11 2.9e-08 0.0012069 0.81 0.020526 1 0.54742 1 0.031231 1 0.020302 1 0.83906 1 0.028221 1 6.6786e-06 0.00521 0.0036436 1 Del Peak 14(5q22.2) 0 (0%) 414 0.0010635 0.72 0.031384 1 6.387e-10 5.35e-07 0.072018 1 0.16969 1 0.92197 1 0.11019 1 0.15324 1 0.51998 1 0.021369 1 0.00091366 0.624 0.051791 1 Del Peak 15(6p25.3) 0 (0%) 511 0.90663 1 0.55332 1 0.39963 1 0.31844 1 0.047218 1 0.94018 1 0.50002 1 0.52778 1 0.64145 1 0.8684 1 0.39669 1 0.42467 1 Del Peak 16(6q26) 0 (0%) 499 0.77681 1 0.33063 1 0.37272 1 0.86349 1 0.047137 1 0.45135 1 0.68691 1 0.86578 1 0.42323 1 0.61161 1 0.42403 1 0.31621 1 Del Peak 17(7q31.1) 0 (0%) 574 0.29223 1 0.93264 1 1 1 1 1 0.87262 1 0.27267 1 0.71229 1 1 1 0.15818 1 0.48775 1 0.25691 1 0.76114 1 Del Peak 18(8p23.3) 0 (0%) 312 0.0016832 1 0.00051819 0.364 3.054e-47 2.77e-44 4.1865e-07 0.000335 0.079165 1 0.0053293 1 7.4959e-06 0.00584 2.3372e-06 0.00185 0.1754 1 0.18365 1 1.6157e-05 0.0124 0.0085601 1 Del Peak 19(8p23.2) 0 (0%) 312 0.00025797 0.183 0.00014587 0.107 3.4426e-51 3.13e-48 1.0121e-07 8.2e-05 0.14986 1 0.0031593 1 2.604e-06 0.00206 8.3184e-07 0.000661 0.21868 1 0.090121 1 7.6715e-06 0.00597 0.0056626 1 Del Peak 20(8p22) 0 (0%) 299 0.0011796 0.794 0.00085665 0.587 5.7901e-54 5.27e-51 7.972e-08 6.47e-05 0.10894 1 0.0022544 1 1.1514e-05 0.00891 1.4905e-06 0.00118 0.27304 1 0.036939 1 2.2403e-05 0.0171 0.0011852 0.796 Del Peak 21(8q11.1) 0 (0%) 544 0.5801 1 0.55725 1 0.00021165 0.152 0.56542 1 0.34395 1 0.56794 1 0.15478 1 0.13705 1 0.12848 1 0.11029 1 0.51905 1 0.45348 1 Del Peak 22(9p24.2) 0 (0%) 510 0.45163 1 0.29858 1 0.0068027 1 0.048085 1 0.56407 1 0.59166 1 0.23264 1 0.34065 1 0.2702 1 0.085082 1 0.043362 1 0.26014 1 Del Peak 23(10p15.3) 0 (0%) 486 0.23157 1 0.16851 1 7.7747e-06 0.00604 0.028294 1 0.020505 1 0.15821 1 0.024051 1 0.0006612 0.462 0.70398 1 0.28912 1 0.062071 1 0.014342 1 Del Peak 24(10q21.1) 0 (0%) 469 0.17122 1 0.11962 1 8.5249e-10 7.1e-07 0.099339 1 0.072821 1 0.13262 1 0.016429 1 0.020272 1 0.75423 1 0.30144 1 0.023311 1 0.25191 1 Del Peak 25(10q23.31) 0 (0%) 441 0.13642 1 0.5197 1 4.434e-07 0.000354 0.15713 1 0.061014 1 0.24197 1 0.0021429 1 0.0041743 1 0.72306 1 0.013346 1 0.00096502 0.656 0.0080636 1 Del Peak 26(10q25.2) 0 (0%) 447 0.318 1 0.16237 1 6.6166e-09 5.45e-06 0.039876 1 0.0043082 1 0.24513 1 0.0016283 1 0.00024089 0.172 0.9908 1 0.003052 1 0.0015454 1 0.035956 1 Del Peak 27(11q22.3) 0 (0%) 484 0.47835 1 0.065843 1 0.074301 1 0.074974 1 0.25989 1 0.14737 1 1 1 0.96293 1 0.81832 1 0.74162 1 0.2681 1 0.54467 1 Del Peak 28(12p13.1) 0 (0%) 510 0.0059934 1 0.014154 1 7.0094e-10 5.85e-07 0.38857 1 0.89237 1 0.73193 1 0.42275 1 0.4872 1 0.69485 1 0.37638 1 0.019165 1 0.16768 1 Del Peak 29(12q21.31) 0 (0%) 510 0.062856 1 0.067723 1 2.7237e-08 2.22e-05 0.14422 1 0.57439 1 0.59067 1 0.02766 1 0.0026103 1 0.71842 1 0.97943 1 0.079297 1 0.029118 1 Del Peak 30(14q11.2) 0 (0%) 396 3.66e-05 0.0276 5.7118e-06 0.00447 1.8145e-40 1.63e-37 4.995e-05 0.0376 0.003661 1 0.18552 1 3.9978e-06 0.00315 9.4323e-05 0.0697 0.060881 1 0.59971 1 7.6344e-07 0.000608 0.075959 1 Del Peak 31(14q31.1) 0 (0%) 391 0.00077289 0.533 0.00025687 0.183 4.8226e-38 4.34e-35 0.00010537 0.0774 0.00069369 0.482 0.035715 1 1.5645e-05 0.012 0.00024402 0.174 0.26613 1 0.57224 1 3.1553e-07 0.000252 0.077841 1 Del Peak 32(14q31.1) 0 (0%) 387 0.0012318 0.824 0.00065312 0.457 1.617e-37 1.45e-34 4.5694e-05 0.0345 0.0010575 0.717 0.047194 1 1.1185e-05 0.00867 7.3458e-05 0.0546 0.40213 1 0.68244 1 1.1456e-07 9.27e-05 0.10694 1 Del Peak 33(15q11.2) 0 (0%) 353 0.0008209 0.565 0.0048717 1 3.1622e-21 2.82e-18 0.0049805 1 0.21321 1 0.35894 1 0.00014756 0.108 2.4594e-05 0.0187 0.39168 1 0.14878 1 4.9052e-06 0.00384 0.64793 1 Del Peak 34(15q21.1) 0 (0%) 360 0.0008361 0.574 0.02392 1 4.9646e-19 4.39e-16 0.010703 1 0.10571 1 0.13029 1 0.00025044 0.178 0.00067293 0.469 0.65513 1 0.2673 1 0.00010439 0.0768 0.59933 1 Del Peak 35(15q22.33) 0 (0%) 369 0.00019922 0.144 0.0011582 0.781 5.8046e-21 5.17e-18 0.001871 1 0.58637 1 0.46255 1 3.2923e-05 0.0249 6.5728e-06 0.00513 0.79182 1 0.46644 1 2.5781e-05 0.0196 0.20183 1 Del Peak 36(16p13.3) 0 (0%) 530 0.13856 1 0.11894 1 0.80791 1 0.6174 1 0.48982 1 0.78854 1 0.44437 1 0.11683 1 0.63787 1 0.23291 1 0.73403 1 0.54399 1 Del Peak 37(16q23.1) 0 (0%) 515 0.04389 1 0.0072891 1 0.31079 1 0.25236 1 0.2211 1 0.92463 1 0.40798 1 0.56664 1 0.72648 1 0.49481 1 0.55643 1 0.3615 1 Del Peak 38(17p12) 0 (0%) 240 8.379e-08 6.8e-05 2.2016e-05 0.0168 9.9638e-35 8.91e-32 5.8116e-09 4.79e-06 0.0085813 1 0.024703 1 1.5e-07 0.000121 1.8878e-09 1.56e-06 0.015745 1 0.054349 1 2.4753e-08 2.02e-05 0.15554 1 Del Peak 39(17q24.3) 0 (0%) 503 1 1 0.22422 1 0.01976 1 0.54816 1 0.94672 1 0.52344 1 0.37058 1 0.71345 1 0.82958 1 0.52392 1 0.033092 1 0.67106 1 Del Peak 40(18p11.31) 0 (0%) 239 5.7977e-12 4.9e-09 6.2426e-10 5.23e-07 1.0292e-44 9.31e-42 4.8979e-18 4.32e-15 0.041691 1 0.03053 1 2.2461e-16 1.97e-13 2.4185e-15 2.11e-12 0.0045851 1 0.65136 1 1.0009e-14 8.7e-12 0.00023653 0.169 Del Peak 41(18q12.2) 0 (0%) 194 1.0102e-09 8.38e-07 4.5892e-09 3.79e-06 1.1362e-52 1.03e-49 1.5853e-20 1.41e-17 0.034229 1 0.028019 1 1.7679e-15 1.54e-12 4.7635e-13 4.07e-10 0.00088348 0.604 0.089126 1 6.2499e-15 5.44e-12 0.00022042 0.158 Del Peak 42(18q21.2) 0 (0%) 177 3.7165e-10 3.12e-07 1.643e-08 1.35e-05 5.3209e-54 4.85e-51 1.1413e-17 1e-14 0.014853 1 0.024656 1 1.6806e-13 1.44e-10 3.4604e-13 2.96e-10 7.0759e-05 0.0526 0.17754 1 7.9929e-13 6.81e-10 0.00069667 0.483 Del Peak 43(18q22.1) 0 (0%) 182 2.012e-09 1.67e-06 1.232e-07 9.94e-05 4.4666e-56 4.07e-53 3.8013e-18 3.35e-15 0.031305 1 0.019973 1 3.8375e-13 3.28e-10 1.0686e-12 9.07e-10 6.6628e-05 0.0496 0.37731 1 2.1254e-13 1.82e-10 0.026958 1 Del Peak 44(19p13.3) 0 (0%) 496 0.11712 1 0.15089 1 2.611e-05 0.0198 0.6569 1 0.88007 1 0.66556 1 0.37058 1 0.31715 1 0.51735 1 9.9887e-05 0.0736 0.020615 1 0.014823 1 Del Peak 45(19q13.43) 0 (0%) 521 0.72014 1 0.21925 1 9.2409e-05 0.0684 0.29757 1 0.16503 1 0.93678 1 0.47672 1 0.14265 1 0.22484 1 0.13044 1 0.12146 1 0.5773 1 Del Peak 46(20p12.1) 0 (0%) 408 0.019713 1 0.020259 1 6.5632e-10 5.49e-07 1.2733e-05 0.00984 0.74141 1 0.0071167 1 0.025055 1 0.0048906 1 0.087334 1 0.10327 1 0.096386 1 0.0827 1 Del Peak 47(20p12.1) 0 (0%) 408 0.019713 1 0.020259 1 6.5632e-10 5.49e-07 1.2733e-05 0.00984 0.74141 1 0.0071167 1 0.025055 1 0.0048906 1 0.087334 1 0.10327 1 0.096386 1 0.0827 1 Del Peak 48(21q11.2) 0 (0%) 389 0.022381 1 0.021634 1 5.7434e-08 4.68e-05 0.0077924 1 0.57391 1 0.21291 1 0.0014835 0.986 0.0040076 1 0.041256 1 0.33574 1 0.00021983 0.158 0.083215 1 Del Peak 49(22q13.32) 0 (0%) 378 0.0047599 1 0.005782 1 1.1527e-13 9.93e-11 0.016506 1 0.46894 1 0.61741 1 0.046036 1 0.02901 1 0.93563 1 0.63834 1 0.0001765 0.128 0.502 1