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 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 Amp Peak 1(1q31.1) 134 (23%) 441 0.4442 1 0.81342 1 0.00020463 0.122 0.72236 1 0.4195 1 0.87385 1 0.089288 1 0.3201 1 0.76478 1 0.94434 1 Amp Peak 2(2q33.1) 123 (21%) 452 0.04804 1 0.060868 1 1.5207e-06 0.000978 0.0050196 1 0.31104 1 0.35953 1 0.00017266 0.103 0.0001656 0.0992 0.18061 1 0.0012944 0.725 Amp Peak 3(5p12) 107 (19%) 468 0.097844 1 0.97392 1 6.5452e-06 0.00414 0.7939 1 0.47066 1 0.39976 1 0.10221 1 0.018933 1 0.88927 1 0.34721 1 Amp Peak 4(5q22.3) 59 (10%) 516 0.89444 1 1 1 0.0037006 1 0.3195 1 0.68971 1 0.76879 1 0.24841 1 0.020002 1 0.46039 1 0.89428 1 Amp Peak 5(6p21.1) 146 (25%) 429 0.026325 1 0.0030838 1 3.9711e-14 2.78e-11 0.16938 1 0.18907 1 0.57828 1 0.00093145 0.529 0.015078 1 0.53094 1 0.0067783 1 Amp Peak 6(7p21.3) 337 (59%) 238 0.00063586 0.368 0.0068793 1 7.9137e-22 5.77e-19 7.1064e-06 0.00448 0.41594 1 0.0075144 1 6.8733e-10 4.69e-07 3.1463e-06 0.002 0.022382 1 0.0025921 1 Amp Peak 7(8p11.23) 196 (34%) 379 0.57345 1 0.40042 1 2.8317e-23 2.07e-20 0.30365 1 0.88421 1 0.65326 1 0.2349 1 0.78078 1 0.015361 1 0.077226 1 Amp Peak 8(8p11.21) 238 (41%) 337 0.30634 1 0.25613 1 3.3334e-31 2.45e-28 0.23711 1 0.49049 1 0.61284 1 0.41011 1 0.735 1 0.081506 1 0.20055 1 Amp Peak 9(8q12.1) 309 (54%) 266 0.079837 1 0.11835 1 1.9068e-36 1.41e-33 0.015312 1 0.10139 1 0.40856 1 0.00051184 0.298 0.0072851 1 0.10208 1 0.1461 1 Amp Peak 10(8q24.21) 345 (60%) 230 0.24015 1 0.19563 1 3.1776e-35 2.35e-32 0.0042881 1 0.34453 1 0.43979 1 0.00029443 0.174 0.010935 1 0.25116 1 0.17643 1 Amp Peak 11(10q22.3) 35 (6%) 540 0.90315 1 0.14493 1 0.65461 1 0.56037 1 0.37964 1 0.3414 1 0.57912 1 0.1871 1 0.58747 1 0.28086 1 Amp Peak 12(11p15.5) 129 (22%) 446 4.3117e-05 0.0263 0.0011533 0.649 1.8397e-06 0.00118 0.0034433 1 0.010806 1 0.10027 1 4.7475e-05 0.029 7.6788e-06 0.00482 0.35173 1 0.0090568 1 Amp Peak 13(12p13.32) 144 (25%) 431 0.18079 1 0.78626 1 0.25212 1 0.13658 1 1 1 0.87363 1 0.20541 1 0.3483 1 0.67615 1 0.88617 1 Amp Peak 14(13q12.13) 371 (65%) 204 3.2507e-08 2.16e-05 1.565e-06 0.001 6.4175e-44 4.79e-41 8.9135e-11 6.11e-08 0.077968 1 0.060103 1 8.0009e-11 5.5e-08 4.9743e-07 0.000324 0.013611 1 0.23666 1 Amp Peak 15(13q12.2) 366 (64%) 209 9.9561e-07 0.000646 1.9696e-05 0.0122 2.2045e-45 1.65e-42 2.3112e-11 1.59e-08 0.20878 1 0.13462 1 2.1277e-10 1.46e-07 1.0832e-06 0.000701 0.026046 1 0.28461 1 Amp Peak 16(13q22.1) 371 (65%) 204 7.5802e-06 0.00477 7.2369e-05 0.0439 7.6851e-42 5.7e-39 2.9909e-09 2.02e-06 0.16925 1 0.081763 1 9.8228e-10 6.68e-07 5.3606e-07 0.000349 0.03008 1 0.04712 1 Amp Peak 17(15q26.1) 43 (7%) 532 0.52584 1 0.39376 1 0.24946 1 0.84162 1 0.63974 1 0.59102 1 0.19087 1 0.2414 1 0.92601 1 1 1 Amp Peak 18(16p11.2) 161 (28%) 414 0.013406 1 0.0069521 1 1.3311e-20 9.68e-18 0.0015397 0.859 0.036894 1 0.0317 1 2.1703e-05 0.0134 0.0036874 1 0.81077 1 0.11023 1 Amp Peak 19(17q12) 144 (25%) 431 0.015027 1 0.1003 1 3.4581e-09 2.33e-06 0.0072631 1 0.50619 1 0.044214 1 0.00042372 0.248 0.0021241 1 0.038998 1 0.23162 1 Amp Peak 20(17q24.1) 128 (22%) 447 0.0096287 1 0.0080793 1 1.5413e-08 1.03e-05 0.00034993 0.206 0.088685 1 0.012439 1 0.0002006 0.12 0.0030881 1 0.0012716 0.715 0.041926 1 Amp Peak 21(19p13.2) 97 (17%) 478 0.043869 1 0.37731 1 8.872e-08 5.83e-05 0.031724 1 0.62231 1 0.74495 1 0.32934 1 0.41774 1 0.27415 1 0.13138 1 Amp Peak 22(19q12) 122 (21%) 453 0.030799 1 0.010651 1 6.2256e-08 4.12e-05 0.25113 1 0.29029 1 0.46249 1 0.074742 1 0.078878 1 0.70958 1 0.49006 1 Amp Peak 23(20p11.23) 301 (52%) 274 0.011702 1 0.00040084 0.235 5.5572e-17 3.98e-14 0.014078 1 0.068775 1 0.37584 1 1.065e-05 0.00663 2.2906e-05 0.0141 0.35274 1 0.42547 1 Amp Peak 24(20p11.21) 339 (59%) 236 0.00023856 0.141 1.5383e-06 0.000988 8.5661e-23 6.25e-20 6.9846e-06 0.00441 0.13479 1 0.26756 1 4.8331e-09 3.24e-06 3.8008e-09 2.55e-06 0.10712 1 0.18811 1 Amp Peak 25(20q11.21) 439 (76%) 136 4.1451e-15 2.93e-12 7.4821e-14 5.22e-11 1.5402e-42 1.14e-39 2.1295e-16 1.52e-13 0.12124 1 0.00091279 0.519 1.5937e-19 1.16e-16 5.246e-18 3.78e-15 0.12378 1 0.018878 1 Amp Peak 26(20q12) 441 (77%) 134 3.226e-16 2.31e-13 3.2727e-15 2.32e-12 5.8367e-43 4.34e-40 3.5601e-15 2.52e-12 0.054733 1 0.00089654 0.511 5.4214e-19 3.92e-16 1.8134e-17 1.3e-14 0.065014 1 0.0077889 1 Amp Peak 27(20q13.32) 444 (77%) 131 2.88e-15 2.04e-12 1.2514e-13 8.71e-11 5.6648e-43 4.22e-40 3.2142e-14 2.25e-11 0.076835 1 0.00045984 0.269 5.4214e-19 3.92e-16 1.8134e-17 1.3e-14 0.11691 1 0.032951 1 Amp Peak 28(Xq28) 121 (21%) 454 0.34508 1 0.58069 1 1.7197e-06 0.0011 0.10043 1 0.00068292 0.392 0.13281 1 0.17084 1 0.024028 1 0.98952 1 0.78345 1 Del Peak 1(1p36.11) 222 (39%) 353 7.4515e-05 0.0452 0.0021128 1 2.207e-13 1.53e-10 2.1039e-05 0.013 0.033102 1 0.058686 1 1.0504e-05 0.00655 6.5371e-05 0.0397 0.15838 1 0.018302 1 Del Peak 2(1p33) 156 (27%) 419 0.010261 1 0.071826 1 8.9471e-13 6.2e-10 0.00037065 0.218 0.21767 1 0.095474 1 0.0015984 0.89 0.0020772 1 0.53241 1 0.015895 1 Del Peak 3(1p13.2) 157 (27%) 418 0.18918 1 0.092345 1 3.379e-09 2.28e-06 0.015335 1 0.90798 1 0.069001 1 0.013159 1 0.00062049 0.36 0.75564 1 0.3515 1 Del Peak 4(2p12) 20 (3%) 555 1 1 0.43462 1 0.0019382 1 0.011104 1 0.47992 1 0.80739 1 0.173 1 0.73813 1 0.016497 1 0.021531 1 Del Peak 5(2q22.1) 33 (6%) 542 0.92685 1 0.85059 1 0.14635 1 0.83265 1 0.36323 1 0.61845 1 0.97396 1 0.79732 1 0.31564 1 0.27226 1 Del Peak 6(2q37.2) 30 (5%) 545 0.92384 1 0.69056 1 0.28501 1 0.83265 1 0.20452 1 0.44389 1 0.56014 1 0.09482 1 0.24408 1 0.36359 1 Del Peak 7(3p26.3) 84 (15%) 491 0.10463 1 0.81892 1 0.16257 1 0.35748 1 0.98369 1 0.34579 1 0.28049 1 0.0366 1 0.27674 1 0.72808 1 Del Peak 8(3p14.2) 104 (18%) 471 0.47522 1 0.89997 1 0.93155 1 0.59731 1 0.92799 1 0.784 1 0.55342 1 0.66263 1 0.059527 1 0.91843 1 Del Peak 9(3q26.31) 56 (10%) 519 0.29676 1 0.55419 1 0.4484 1 0.37333 1 0.13392 1 0.67614 1 0.30763 1 0.05159 1 0.093407 1 0.12285 1 Del Peak 10(4p16.1) 182 (32%) 393 0.052415 1 0.42363 1 1.6474e-12 1.14e-09 0.0020286 1 0.88241 1 0.4007 1 1.322e-06 0.000853 0.00014327 0.086 0.62193 1 0.11684 1 Del Peak 11(4q22.1) 198 (34%) 377 0.019286 1 0.05072 1 1.2505e-14 8.77e-12 7.6585e-05 0.0463 0.9259 1 0.36478 1 7.0961e-06 0.00448 0.00018004 0.107 0.14791 1 0.4088 1 Del Peak 12(4q35.1) 211 (37%) 364 0.016065 1 0.18529 1 1.2462e-13 8.69e-11 0.00064166 0.371 0.85993 1 0.66867 1 5.0681e-05 0.0309 3.7357e-05 0.0229 0.52329 1 0.74296 1 Del Peak 13(5q11.2) 140 (24%) 435 0.0019081 1 0.48007 1 2.1328e-12 1.47e-09 0.0028212 1 0.79264 1 0.1416 1 0.0003174 0.187 0.0020471 1 1 1 0.75785 1 Del Peak 14(5q22.2) 172 (30%) 403 0.0014099 0.788 0.058116 1 2.2261e-09 1.51e-06 0.11369 1 0.88423 1 0.71216 1 0.0016795 0.934 0.1687 1 0.77075 1 0.85443 1 Del Peak 15(6p25.3) 78 (14%) 497 0.83957 1 0.59942 1 0.08489 1 0.26246 1 1 1 0.31536 1 0.96051 1 0.38499 1 0.60986 1 0.95718 1 Del Peak 16(6q26) 90 (16%) 485 0.88608 1 0.69786 1 0.04006 1 0.76234 1 0.23479 1 0.58184 1 0.9192 1 0.94771 1 0.22283 1 0.50721 1 Del Peak 17(7q31.1) 15 (3%) 560 0.10252 1 1 1 1 1 1 1 0.43394 1 0.51037 1 0.66022 1 0.71365 1 0.23486 1 0.49815 1 Del Peak 18(8p23.2) 272 (47%) 303 0.00058553 0.34 0.032242 1 2.1272e-34 1.57e-31 1.9574e-06 0.00125 0.30663 1 0.014477 1 1.5158e-05 0.0094 0.00056078 0.326 0.80158 1 0.39873 1 Del Peak 19(8p22) 285 (50%) 290 0.0010879 0.617 0.033402 1 1.581e-37 1.17e-34 1.3157e-06 0.00085 0.27708 1 0.0011064 0.626 1.0532e-06 0.000682 0.00022349 0.133 0.76329 1 0.64202 1 Del Peak 20(8p11.21) 124 (22%) 451 0.011149 1 0.12636 1 4.8516e-07 0.000317 0.34128 1 0.3515 1 0.15854 1 0.062079 1 0.049746 1 0.1625 1 0.40038 1 Del Peak 21(8q11.1) 44 (8%) 531 0.27183 1 0.68653 1 0.0026632 1 0.66125 1 0.75678 1 0.096474 1 0.31533 1 0.32022 1 0.081906 1 0.019346 1 Del Peak 22(9p24.2) 78 (14%) 497 0.2561 1 0.14982 1 0.0017841 0.988 0.050595 1 0.29746 1 0.54105 1 0.029546 1 0.0024061 1 0.29637 1 0.2426 1 Del Peak 23(10p15.3) 102 (18%) 473 0.24648 1 0.41669 1 1.3776e-07 9.02e-05 0.028831 1 0.39481 1 0.038444 1 0.012185 1 0.057586 1 0.71014 1 0.30188 1 Del Peak 24(10q21.1) 118 (21%) 457 0.2001 1 0.1105 1 3.1348e-11 2.16e-08 0.14957 1 0.47561 1 0.0097587 1 0.072765 1 0.043804 1 0.69109 1 0.57652 1 Del Peak 25(10q23.31) 145 (25%) 430 0.13535 1 0.49569 1 9.0881e-08 5.96e-05 0.15474 1 0.35683 1 0.0035237 1 0.0026248 1 0.068467 1 0.76199 1 0.36526 1 Del Peak 26(10q25.2) 140 (24%) 435 0.31218 1 0.11639 1 3.0619e-12 2.11e-09 0.10548 1 0.80755 1 0.18913 1 0.0002385 0.141 0.00032441 0.191 0.97166 1 0.77949 1 Del Peak 27(11q22.3) 104 (18%) 471 0.58489 1 0.53036 1 0.03853 1 0.12502 1 0.45358 1 0.18433 1 0.03654 1 0.52358 1 0.65677 1 0.36295 1 Del Peak 28(12p13.1) 77 (13%) 498 0.0069737 1 0.017316 1 3.8948e-08 2.58e-05 0.42864 1 0.64276 1 0.66392 1 0.057107 1 0.42333 1 0.44647 1 0.91879 1 Del Peak 29(12q21.2) 80 (14%) 495 0.172 1 0.029424 1 5.5178e-07 0.000359 0.34774 1 0.9473 1 0.36008 1 0.035123 1 0.2942 1 0.52063 1 0.97871 1 Del Peak 30(14q22.1) 185 (32%) 390 0.00011737 0.0707 0.00012002 0.0721 1.9531e-28 1.43e-25 8.1404e-06 0.0051 0.00010769 0.065 0.036584 1 4.0917e-08 2.71e-05 3.0832e-05 0.0189 0.12679 1 0.43856 1 Del Peak 31(15q11.2) 233 (41%) 342 0.0006869 0.394 0.01779 1 1.2039e-23 8.82e-21 0.0057215 1 0.94729 1 0.11558 1 1.4108e-06 0.000909 1.375e-05 0.00854 0.47751 1 0.11089 1 Del Peak 32(15q21.1) 227 (39%) 348 0.0024331 1 0.076694 1 2.4292e-21 1.77e-18 0.0035788 1 0.72041 1 0.12209 1 2.2022e-07 0.000144 2.2976e-05 0.0141 0.74178 1 0.45864 1 Del Peak 33(15q22.33) 217 (38%) 358 0.00064515 0.372 0.0074628 1 4.4907e-23 3.28e-20 0.00084041 0.48 0.83873 1 0.18036 1 5.8136e-09 3.89e-06 5.4971e-06 0.00349 0.86536 1 0.1165 1 Del Peak 34(16p13.3) 58 (10%) 517 0.14152 1 0.38223 1 0.21481 1 0.67595 1 0.81089 1 0.78404 1 0.92693 1 0.17584 1 0.63651 1 0.59521 1 Del Peak 35(16q23.1) 72 (13%) 503 0.064553 1 0.0011468 0.648 0.17918 1 0.32666 1 0.86696 1 0.26129 1 0.27086 1 0.22958 1 0.80518 1 0.63247 1 Del Peak 36(17p12) 343 (60%) 232 6.9273e-08 4.57e-05 2.789e-05 0.0171 2.0063e-34 1.48e-31 6.04e-09 4.03e-06 0.41222 1 0.0048567 1 1.5954e-08 1.06e-05 3.3152e-06 0.00211 0.051965 1 0.67329 1 Del Peak 37(17q24.3) 84 (15%) 491 0.90508 1 0.87587 1 0.029627 1 0.52806 1 0.49804 1 0.25779 1 0.18383 1 0.078066 1 0.91947 1 0.42487 1 Del Peak 38(18p11.31) 341 (59%) 234 5.5331e-13 3.84e-10 2.3459e-09 1.59e-06 1.1905e-41 8.82e-39 2.3143e-15 1.65e-12 0.62657 1 0.0017883 0.989 1.4029e-20 1.02e-17 5.0845e-15 3.58e-12 0.018344 1 0.38647 1 Del Peak 39(18q12.2) 386 (67%) 189 9.6445e-10 6.57e-07 7.3142e-08 4.82e-05 1.2945e-49 9.68e-47 8.059e-18 5.8e-15 0.26821 1 0.0041222 1 2.8352e-19 2.05e-16 1.22e-10 8.36e-08 0.0057877 1 0.059024 1 Del Peak 40(18q21.2) 403 (70%) 172 3.9826e-10 2.72e-07 8.2446e-08 5.42e-05 1.2388e-50 9.28e-48 3.4304e-15 2.43e-12 0.089592 1 0.0011476 0.648 2.8314e-15 2.02e-12 1.4217e-09 9.65e-07 0.00065728 0.378 0.12629 1 Del Peak 41(18q22.1) 398 (69%) 177 2.428e-09 1.64e-06 2.0701e-06 0.00132 9.5463e-53 7.16e-50 1.3687e-15 9.77e-13 0.14897 1 0.0029053 1 2.8314e-15 2.02e-12 5.8399e-09 3.9e-06 0.0012813 0.719 0.17094 1 Del Peak 42(19p13.3) 92 (16%) 483 0.088724 1 0.68379 1 1.3518e-05 0.00841 0.82504 1 0.49303 1 0.45578 1 0.032861 1 0.0086858 1 0.57921 1 0.91111 1 Del Peak 43(19q13.43) 68 (12%) 507 0.95095 1 0.69771 1 0.0001104 0.0666 0.59989 1 1 1 0.32273 1 0.0093455 1 0.0091629 1 0.25511 1 0.50243 1 Del Peak 44(20p12.1) 179 (31%) 396 0.023368 1 0.023571 1 6.5033e-15 4.58e-12 1.0094e-05 0.00632 0.25333 1 0.0033053 1 0.023187 1 0.015089 1 0.22326 1 0.97624 1 Del Peak 45(20p12.1) 179 (31%) 396 0.023368 1 0.023571 1 6.5033e-15 4.58e-12 1.0094e-05 0.00632 0.25333 1 0.0033053 1 0.023187 1 0.015089 1 0.22326 1 0.97624 1 Del Peak 46(21q11.2) 195 (34%) 380 0.0017735 0.984 0.12577 1 4.0688e-09 2.73e-06 0.010909 1 0.50126 1 0.049319 1 0.00064744 0.373 0.0052738 1 0.23351 1 0.049362 1 Del Peak 47(22q13.32) 204 (35%) 371 0.022573 1 0.0046102 1 9.8306e-15 6.9e-12 0.029932 1 0.11758 1 0.53247 1 0.00082402 0.471 0.034892 1 0.69579 1 0.011544 1