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 1p gain 0 (0%) 416 NA NA NA NA 0.28763 1 0.69775 1 0.17792 1 0.38396 1 0.76751 1 0.2439 1 0.59751 1 0.73342 1 1 1 1 1 1q gain 0 (0%) 378 0.040536 1 0.53602 1 0.068244 1 0.19906 1 0.28159 1 0.048087 1 0.2243 1 0.29141 1 0.69748 1 0.71034 1 0.14959 1 0.44377 1 2p gain 0 (0%) 386 0.124 1 0.074608 1 0.017312 1 0.0092079 1 0.027828 1 0.39257 1 0.0022673 1 0.080023 1 0.23447 1 0.48791 1 0.10736 1 0.0079929 1 2q gain 0 (0%) 388 0.073705 1 0.050976 1 0.0065166 1 0.0016508 1 0.046379 1 0.45047 1 0.0291 1 0.14102 1 0.27504 1 0.40969 1 0.11295 1 0.12104 1 3p gain 0 (0%) 407 0.29804 1 0.42991 1 0.15845 1 0.38775 1 0.36361 1 0.72105 1 0.84424 1 1 1 0.86007 1 0.71392 1 0.75554 1 0.6213 1 3q gain 0 (0%) 397 0.37494 1 0.16405 1 0.0047223 1 0.23384 1 0.53594 1 0.75209 1 0.1315 1 0.62922 1 0.43585 1 0.74622 1 0.90669 1 0.26524 1 4p gain 0 (0%) 424 NA NA NA NA 0.24353 1 0.18519 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4q gain 0 (0%) 422 NA NA NA NA 0.25126 1 0.78972 1 NA NA NA NA NA NA NA NA 0.52699 1 0.54257 1 NA NA NA NA 5p gain 0 (0%) 387 0.21767 1 0.098835 1 0.0020345 1 0.11981 1 0.66219 1 0.97123 1 0.42788 1 0.75957 1 0.57529 1 0.63666 1 0.074765 1 0.88243 1 5q gain 0 (0%) 405 0.54511 1 0.63094 1 0.055489 1 0.18979 1 0.53291 1 0.29256 1 0.68626 1 0.25016 1 1 1 0.73751 1 0.26109 1 0.73285 1 6p gain 0 (0%) 374 0.58873 1 0.013558 1 0.00061307 0.467 0.37295 1 0.56827 1 0.44268 1 0.24983 1 0.1063 1 0.41432 1 0.5155 1 0.45432 1 0.89697 1 6q gain 0 (0%) 380 0.34847 1 0.027446 1 0.0043711 1 0.22816 1 0.48409 1 0.43338 1 0.46619 1 0.74348 1 0.35909 1 0.58999 1 0.11529 1 0.54927 1 7p gain 0 (0%) 221 0.00304 1 0.0022344 1 1.0053e-14 8.48e-12 6.7399e-05 0.0534 0.0059037 1 0.039715 1 1.2495e-06 0.00102 7.3702e-06 0.00596 0.65392 1 0.15045 1 5.9525e-05 0.0473 0.39411 1 7q gain 0 (0%) 247 0.014468 1 0.012963 1 2.4973e-09 2.07e-06 0.0047286 1 0.10508 1 0.071977 1 0.0001282 0.101 8.9079e-05 0.0704 0.83256 1 0.24161 1 0.00056332 0.433 0.81078 1 8p gain 0 (0%) 342 0.69139 1 0.35662 1 8.0329e-13 6.72e-10 0.051921 1 0.066874 1 0.16116 1 0.44604 1 0.060011 1 0.63034 1 0.19257 1 0.43573 1 0.85063 1 8q gain 0 (0%) 260 0.72973 1 0.69124 1 1.3151e-19 1.13e-16 0.00024258 0.19 0.55377 1 0.039861 1 0.035339 1 0.033076 1 0.15116 1 0.63075 1 0.012924 1 0.45183 1 9p gain 0 (0%) 379 0.0064524 1 0.19232 1 0.15206 1 0.29066 1 0.067883 1 0.17919 1 0.52042 1 0.83468 1 0.73066 1 0.43563 1 0.8879 1 0.6139 1 9q gain 0 (0%) 387 0.011043 1 0.07296 1 0.26963 1 0.093569 1 0.019498 1 0.033971 1 0.29385 1 0.58893 1 0.040153 1 0.036918 1 0.7566 1 0.038002 1 10p gain 0 (0%) 408 0.69067 1 0.51996 1 0.15194 1 0.023004 1 0.18433 1 0.7266 1 0.69468 1 0.43262 1 0.4482 1 0.51533 1 0.0028962 1 0.74938 1 10q gain 0 (0%) 416 NA NA NA NA 0.28763 1 0.013855 1 0.37729 1 0.4977 1 0.83178 1 0.36224 1 0.16677 1 0.21673 1 0.097272 1 0.76431 1 11p gain 0 (0%) 407 0.13759 1 0.0013887 1 6.9297e-05 0.0549 0.00017117 0.135 0.54774 1 0.80443 1 0.6818 1 0.36745 1 0.94704 1 0.76733 1 0.31718 1 0.24629 1 11q gain 0 (0%) 403 0.021447 1 0.0027657 1 4.5012e-06 0.00365 0.00029607 0.231 0.33374 1 0.80795 1 0.16638 1 0.034677 1 0.65879 1 0.18047 1 0.033554 1 0.2468 1 12p gain 0 (0%) 361 0.26725 1 0.38249 1 0.00054363 0.418 0.0050527 1 0.85042 1 0.8128 1 0.66521 1 0.65947 1 0.049946 1 0.1353 1 0.033203 1 0.24758 1 12q gain 0 (0%) 366 0.34121 1 0.54177 1 0.0004513 0.348 0.00076658 0.583 0.77922 1 0.66875 1 0.67847 1 0.81614 1 0.0060567 1 0.11505 1 0.035953 1 0.24293 1 13q gain 0 (0%) 210 1.0588e-05 0.00854 1.6648e-05 0.0134 2.2007e-29 1.89e-26 6.3672e-05 0.0506 0.0088414 1 0.0051019 1 1.4917e-05 0.012 2.2443e-07 0.000184 0.1947 1 0.21198 1 1.4804e-07 0.000122 0.81307 1 14q gain 0 (0%) 411 0.482 1 0.44276 1 0.13974 1 0.20339 1 0.28461 1 0.30896 1 0.064561 1 0.0097796 1 1 1 0.65875 1 1 1 0.65004 1 15q gain 0 (0%) 422 NA NA NA NA 0.10909 1 0.68497 1 0.058038 1 0.033319 1 0.65987 1 0.69436 1 0.48486 1 0.44038 1 0.3941 1 0.30231 1 16p gain 0 (0%) 360 0.0074852 1 0.00080364 0.611 9.2454e-15 7.81e-12 0.11786 1 0.72438 1 0.032865 1 0.038299 1 0.030102 1 0.080523 1 0.018276 1 0.085023 1 0.95593 1 16q gain 0 (0%) 361 0.0060209 1 0.0011609 0.873 1.4109e-15 1.2e-12 0.12979 1 0.84714 1 0.019909 1 0.038299 1 0.030102 1 0.16394 1 0.014938 1 0.0087357 1 0.67595 1 17p gain 0 (0%) 417 NA NA NA NA 1 1 0.81248 1 0.60292 1 0.18188 1 0.071771 1 0.13113 1 0.56793 1 0.59512 1 0.62887 1 1 1 17q gain 0 (0%) 381 0.029211 1 0.049528 1 0.0027024 1 0.0051126 1 0.90953 1 0.22627 1 0.0031678 1 0.0096072 1 0.037882 1 0.85425 1 0.12442 1 0.2208 1 18p gain 0 (0%) 412 0.1437 1 0.63479 1 0.0014538 1 0.011894 1 0.72142 1 0.96788 1 0.21637 1 0.26204 1 0.1298 1 0.15475 1 0.80511 1 0.65975 1 18q gain 0 (0%) 418 NA NA NA NA 0.011733 1 0.019047 1 0.50152 1 0.15769 1 0.070847 1 0.14738 1 0.28456 1 0.15764 1 0.44951 1 0.62727 1 19p gain 0 (0%) 391 0.056278 1 0.20791 1 0.020928 1 0.03541 1 0.17716 1 0.078152 1 0.21315 1 0.39553 1 0.69933 1 0.75829 1 0.25699 1 0.13177 1 19q gain 0 (0%) 383 0.047596 1 0.053692 1 0.17649 1 0.10248 1 0.055465 1 0.012945 1 0.11441 1 0.23391 1 0.90359 1 0.75057 1 0.66406 1 0.35602 1 20p gain 0 (0%) 233 0.0017044 1 8.7011e-07 0.000712 6.8921e-17 5.89e-14 0.0028737 1 0.011195 1 0.037085 1 6.2459e-07 0.000512 2.2929e-08 1.89e-05 0.2097 1 0.0024497 1 7.965e-05 0.063 0.88064 1 20q gain 0 (0%) 153 1.1373e-12 9.5e-10 4.9702e-15 4.21e-12 1.2233e-44 1.05e-41 2.0071e-11 1.67e-08 3.0946e-05 0.0248 1.5779e-06 0.00128 2.5825e-14 2.17e-11 1.3891e-16 1.19e-13 0.47779 1 0.00035297 0.273 1.566e-12 1.31e-09 0.057047 1 21q gain 0 (0%) 414 0.16982 1 0.19519 1 0.43364 1 0.20339 1 0.30604 1 0.27487 1 0.58731 1 0.90875 1 0.84807 1 0.7936 1 1 1 0.85338 1 Xq gain 0 (0%) 415 0.065925 1 0.77725 1 0.0039366 1 0.20339 1 0.1315 1 0.42563 1 0.63693 1 1 1 0.56793 1 0.3418 1 0.18268 1 0.85338 1 1p loss 0 (0%) 376 0.0028289 1 0.00097194 0.735 3.5534e-05 0.0284 0.004922 1 0.45789 1 0.69838 1 0.15194 1 0.33325 1 0.49777 1 0.074717 1 0.26919 1 0.019884 1 1q loss 0 (0%) 409 0.35571 1 0.13462 1 0.13457 1 0.29495 1 0.37327 1 0.79115 1 0.14775 1 0.40316 1 0.88952 1 0.80232 1 0.43422 1 0.32743 1 2p loss 0 (0%) 422 0.89774 1 0.31456 1 0.065022 1 NA NA NA NA NA NA NA NA NA NA 0.39139 1 0.28782 1 NA NA NA NA 2q loss 0 (0%) 421 1 1 0.15598 1 0.31581 1 NA NA 0.20425 1 0.24525 1 NA NA NA NA 0.18083 1 0.21627 1 NA NA NA NA 3p loss 0 (0%) 397 0.413 1 0.18694 1 0.00047887 0.369 0.33047 1 0.31159 1 1 1 0.26035 1 0.15034 1 0.4134 1 0.64907 1 0.12265 1 0.40185 1 3q loss 0 (0%) 413 0.74475 1 0.63094 1 0.27787 1 1 1 0.016306 1 0.18667 1 0.15229 1 0.63518 1 0.85882 1 1 1 0.51308 1 0.17527 1 4p loss 0 (0%) 339 0.0027141 1 0.019893 1 1.2546e-13 1.05e-10 0.0025488 1 0.31695 1 0.70846 1 0.00030615 0.238 0.00059045 0.452 0.13003 1 0.38193 1 0.014501 1 0.080021 1 4q loss 0 (0%) 354 0.0036142 1 0.010724 1 3.5642e-11 2.96e-08 0.001402 1 0.1178 1 0.42703 1 0.00039233 0.303 0.0029328 1 0.0053306 1 0.029675 1 0.038807 1 0.079153 1 5p loss 0 (0%) 403 0.40597 1 0.11759 1 0.0011168 0.841 0.082729 1 0.48671 1 0.74469 1 0.062284 1 0.037791 1 0.832 1 0.91573 1 0.15621 1 0.40185 1 5q loss 0 (0%) 388 0.05989 1 0.0075721 1 1.7879e-05 0.0144 0.20132 1 0.0077932 1 0.24187 1 0.0016257 1 0.010294 1 0.65865 1 0.53658 1 0.02868 1 0.47482 1 6p loss 0 (0%) 415 0.45647 1 0.24739 1 0.068393 1 1 1 0.40295 1 0.94247 1 0.64186 1 0.16721 1 0.65206 1 0.26219 1 1 1 0.30231 1 6q loss 0 (0%) 406 0.91546 1 0.78906 1 0.15735 1 0.83716 1 0.52784 1 0.87128 1 0.94394 1 0.39437 1 0.61438 1 0.60215 1 0.69432 1 0.78723 1 8p loss 0 (0%) 330 0.00033214 0.257 0.0005809 0.446 2.3198e-16 1.98e-13 0.0003133 0.243 0.061709 1 0.075269 1 0.020324 1 0.00088561 0.671 0.18953 1 0.031871 1 0.0001134 0.0894 0.27516 1 8q loss 0 (0%) 417 0.27385 1 0.38628 1 0.012081 1 0.57739 1 0.074997 1 0.33065 1 1 1 1 1 0.063367 1 0.37061 1 1 1 0.68912 1 9p loss 0 (0%) 400 0.80979 1 0.12326 1 0.00025415 0.198 0.057788 1 0.16348 1 0.33017 1 0.053544 1 0.045125 1 0.33979 1 0.90188 1 0.10504 1 0.045415 1 9q loss 0 (0%) 401 0.30814 1 0.13882 1 3.5789e-05 0.0286 0.00059347 0.453 0.23511 1 0.33017 1 0.0036083 1 0.0077546 1 0.093483 1 0.27876 1 0.0066926 1 0.07878 1 10p loss 0 (0%) 402 0.69986 1 0.67266 1 0.031432 1 0.81332 1 0.22615 1 0.96162 1 0.46061 1 0.11684 1 0.27065 1 0.32857 1 0.72184 1 1 1 10q loss 0 (0%) 401 0.59691 1 0.71065 1 0.0047593 1 0.66084 1 0.14312 1 1 1 0.23999 1 0.01944 1 0.67461 1 0.92069 1 0.39187 1 0.56432 1 11p loss 0 (0%) 405 0.44508 1 0.067986 1 0.0002537 0.198 0.00022575 0.177 0.4167 1 0.31686 1 0.0044125 1 0.0048641 1 0.046304 1 0.27424 1 0.0040894 1 0.036943 1 11q loss 0 (0%) 399 0.28782 1 0.038614 1 9.0064e-05 0.0711 1.3369e-06 0.00109 0.57969 1 0.59998 1 0.17629 1 0.037791 1 0.084203 1 0.5338 1 0.22064 1 0.56432 1 12p loss 0 (0%) 406 0.079183 1 0.12326 1 1.7279e-05 0.0139 0.22261 1 0.41852 1 0.92193 1 0.1296 1 0.0097672 1 0.42988 1 0.22843 1 0.28805 1 0.2054 1 12q loss 0 (0%) 407 0.2078 1 0.13882 1 5.7852e-06 0.00468 0.093821 1 0.82947 1 0.87951 1 0.01489 1 0.061692 1 0.35956 1 0.14457 1 0.075174 1 0.2054 1 13q loss 0 (0%) 420 NA NA NA NA 0.31178 1 0.26512 1 0.014449 1 0.093067 1 0.21142 1 0.62389 1 0.55388 1 0.3087 1 0.3941 1 0.046415 1 14q loss 0 (0%) 331 3.1842e-08 2.62e-05 2.1385e-06 0.00174 1.433e-20 1.23e-17 4.0132e-06 0.00326 0.0010597 0.799 0.026613 1 1.9449e-05 0.0156 3.6265e-05 0.0289 0.26756 1 0.0059612 1 0.00059324 0.453 0.047757 1 15q loss 0 (0%) 326 0.010775 1 0.0027528 1 5.434e-18 4.65e-15 0.0045301 1 0.046704 1 0.3927 1 0.0017166 1 2.145e-05 0.0172 0.27925 1 0.0097363 1 0.0040981 1 0.46332 1 16p loss 0 (0%) 417 0.27385 1 0.5545 1 0.9004 1 0.015896 1 0.92726 1 0.90449 1 0.84957 1 0.53069 1 1 1 0.72691 1 1 1 0.49858 1 16q loss 0 (0%) 419 0.51949 1 1 1 0.5853 1 0.18519 1 0.25405 1 0.49319 1 NA NA NA NA 0.18083 1 0.21627 1 NA NA NA NA 17p loss 0 (0%) 255 3.7718e-05 0.03 5.3729e-06 0.00435 8.6959e-22 7.47e-19 4.7778e-08 3.93e-05 0.062301 1 0.055165 1 1.5886e-07 0.00013 2.1082e-08 1.74e-05 0.36709 1 0.15154 1 5.0755e-09 4.2e-06 0.014093 1 17q loss 0 (0%) 390 0.091774 1 0.22668 1 0.00017446 0.137 0.078988 1 0.53068 1 0.42811 1 0.0024728 1 0.024547 1 0.78271 1 0.45623 1 0.022897 1 0.07878 1 18p loss 0 (0%) 208 3.9306e-13 3.29e-10 3.8289e-10 3.17e-07 2.2233e-47 1.92e-44 8.4584e-15 7.16e-12 0.00027462 0.214 0.00038057 0.294 4.4688e-15 3.79e-12 1.3841e-14 1.17e-11 0.64821 1 0.023319 1 3.9209e-14 3.3e-11 0.00089228 0.675 18q loss 0 (0%) 193 3.4196e-13 2.87e-10 8.7941e-11 7.3e-08 1.1017e-44 9.5e-42 6.41e-16 5.46e-13 0.0036804 1 0.0013775 1 7.1581e-15 6.06e-12 9.0846e-16 7.73e-13 0.31599 1 0.028328 1 2.5017e-12 2.08e-09 0.045481 1 19p loss 0 (0%) 411 1 1 0.3199 1 0.03103 1 0.028939 1 0.55089 1 0.18296 1 0.00082222 0.624 0.02439 1 0.47065 1 0.59793 1 0.35793 1 0.036943 1 19q loss 0 (0%) 414 0.92438 1 0.3813 1 0.13263 1 0.13096 1 0.86446 1 0.36307 1 0.0099902 1 0.03406 1 0.48992 1 0.60047 1 0.13466 1 0.063764 1 20p loss 0 (0%) 390 0.050821 1 0.054425 1 0.0012996 0.975 0.083762 1 0.75768 1 0.32744 1 0.47182 1 0.047619 1 0.78923 1 0.56802 1 0.32219 1 0.23636 1 20q loss 0 (0%) 424 NA NA NA NA 0.16426 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21q loss 0 (0%) 351 0.014096 1 0.0022745 1 1.4356e-06 0.00117 0.59127 1 0.39327 1 0.57198 1 0.030115 1 0.071898 1 0.056569 1 0.40265 1 0.21734 1 0.13654 1 22q loss 0 (0%) 340 0.00032035 0.249 0.0005809 0.446 7.0639e-13 5.91e-10 0.034264 1 0.20645 1 0.13829 1 0.00098291 0.742 0.0012372 0.929 0.28878 1 0.11301 1 0.011056 1 0.26711 1 Xq loss 0 (0%) 422 NA NA NA NA 0.81994 1 1 1 0.15882 1 0.82096 1 NA NA NA NA 0.71597 1 0.52526 1 0.64095 1 1 1