Clinical Features 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 1p gain 7 (4%) 155 0.11922 0.402 0.78488 0.953 NA NA NA NA 0.67342 0.877 0.82203 0.968 0.89471 1 0.52556 0.777 0.8348 0.971 0.65591 0.866 1q gain 19 (12%) 143 0.00085999 0.016 0.35395 0.671 0.91263 1 1 1 0.48955 0.763 0.59417 0.822 0.90746 1 0.66443 0.872 0.48704 0.763 0.84678 0.977 2p gain 6 (4%) 156 0.50717 0.774 0.0057299 0.0638 0.74753 0.927 1 1 0.24016 0.563 0.34704 0.666 0.13504 0.437 0.33504 0.662 0.1913 0.512 0.46204 0.744 4p gain 4 (2%) 158 0.67556 0.877 0.36653 0.681 NA NA NA NA 0.81925 0.968 0.55198 0.79 0.45102 0.743 0.78926 0.953 0.77027 0.944 1 1 4q gain 3 (2%) 159 0.062229 0.277 0.80263 0.961 NA NA NA NA 0.47168 0.75 0.73855 0.927 0.61466 0.835 0.83645 0.971 0.81365 0.965 0.46336 0.744 5p gain 11 (7%) 151 0.62007 0.836 0.43368 0.741 0.6021 0.827 1 1 0.91594 1 0.6598 0.869 0.85412 0.98 0.61435 0.835 0.82959 0.971 0.21445 0.546 5q gain 7 (4%) 155 0.89648 1 0.0052699 0.0606 NA NA NA NA 0.073069 0.298 0.29731 0.635 0.48409 0.763 0.37958 0.691 0.94142 1 0.28647 0.63 6p gain 15 (9%) 147 0.88666 1 0.25692 0.583 0.10044 0.361 0.2008 0.53 0.30768 0.638 0.37034 0.681 0.23843 0.563 0.30535 0.638 0.56117 0.791 0.5095 0.775 6q gain 8 (5%) 154 0.14777 0.449 0.00177 0.0269 NA NA NA NA 0.03672 0.198 0.11093 0.392 0.12889 0.421 0.18308 0.495 0.080949 0.317 0.2674 0.599 7p gain 27 (17%) 135 0.02124 0.146 0.073789 0.298 0.53303 0.78 0.14892 0.449 0.13943 0.443 0.38123 0.691 0.23926 0.563 0.072649 0.298 0.31555 0.64 0.088389 0.331 7q gain 22 (14%) 140 0.0074299 0.076 0.0062799 0.0688 0.44798 0.741 0.01867 0.136 0.17238 0.484 0.28385 0.628 0.14269 0.444 0.11399 0.398 0.52213 0.777 0.46027 0.744 8p gain 10 (6%) 152 0.01903 0.137 0.36897 0.681 0.81562 0.965 1 1 0.086879 0.331 0.090979 0.336 0.071039 0.298 0.15477 0.452 0.45396 0.744 0.10042 0.361 8q gain 13 (8%) 149 0.24098 0.563 0.75109 0.929 0.5976 0.825 1 1 0.082339 0.319 0.075029 0.3 0.11421 0.398 0.20122 0.53 0.8041 0.961 0.090749 0.336 9p gain 4 (2%) 158 0.2309 0.563 0.070439 0.298 NA NA NA NA 0.15203 0.449 0.22466 0.563 0.29008 0.631 0.25413 0.579 0.30259 0.638 0.51131 0.775 9q gain 3 (2%) 159 0.45989 0.744 0.13915 0.443 NA NA NA NA 0.23968 0.563 0.23939 0.563 0.46208 0.744 0.34625 0.666 0.29337 0.631 0.55711 0.79 10p gain 12 (7%) 150 0.51286 0.775 0.073299 0.298 0.71912 0.915 0.1177 0.402 0.51713 0.775 0.51661 0.775 1 1 0.84189 0.975 0.48881 0.763 0.17857 0.493 10q gain 10 (6%) 152 0.10313 0.369 0.69331 0.894 0.71828 0.915 0.12027 0.403 0.49158 0.763 0.59202 0.821 0.70547 0.906 0.50696 0.774 0.42556 0.736 0.15436 0.452 11p gain 5 (3%) 157 0.087509 0.331 0.51395 0.775 0.83089 0.971 1 1 0.41184 0.723 0.30497 0.638 0.53909 0.784 0.49402 0.763 0.34514 0.666 0.69 0.892 12p gain 11 (7%) 151 0.01097 0.101 0.0073699 0.076 0.49553 0.763 0.11931 0.402 0.33683 0.662 0.32383 0.653 0.01925 0.137 0.21563 0.547 0.13114 0.427 0.42903 0.736 12q gain 14 (9%) 148 0.068649 0.296 0.2254 0.563 0.85055 0.98 0.4905 0.763 0.60273 0.827 0.65325 0.865 0.061219 0.277 0.29098 0.631 0.22281 0.561 0.43607 0.741 13q gain 9 (6%) 153 0.01858 0.136 0.02141 0.146 0.24307 0.565 0.62283 0.836 0.0097399 0.0921 0.0093999 0.0914 0.02403 0.156 0.053549 0.257 0.0096399 0.0921 0.35964 0.678 14q gain 4 (2%) 158 0.061829 0.277 0.3685 0.681 NA NA NA NA 0.55094 0.79 0.55435 0.79 0.28683 0.63 0.78893 0.953 0.76939 0.944 0.87171 0.994 15q gain 14 (9%) 148 0.25033 0.576 0.03256 0.184 0.83713 0.971 0.35017 0.666 0.31439 0.64 0.77015 0.944 0.42716 0.736 0.79174 0.953 0.55682 0.79 0.92534 1 16p gain 6 (4%) 156 0.23904 0.563 0.55723 0.79 NA NA NA NA 0.74412 0.927 0.74021 0.927 0.38432 0.692 0.81518 0.965 0.29226 0.631 0.50151 0.771 16q gain 6 (4%) 156 0.01448 0.119 1 1 NA NA NA NA 0.26983 0.603 0.70055 0.902 1 1 0.76848 0.944 0.39665 0.707 0.42788 0.736 17q gain 5 (3%) 157 0.54462 0.786 0.31242 0.638 0.2196 0.555 0.33674 0.662 0.2998 0.636 0.30407 0.638 0.54075 0.784 0.77385 0.945 0.541 0.784 0.21194 0.544 18p gain 8 (5%) 154 0.14947 0.449 0.22992 0.563 1 1 0.1195 0.402 0.38256 0.691 0.65079 0.864 0.46544 0.745 0.56103 0.791 0.12862 0.421 0.85491 0.98 18q gain 10 (6%) 152 0.34658 0.666 0.58309 0.816 1 1 0.03863 0.206 0.36506 0.681 0.53359 0.78 0.84523 0.977 0.43902 0.741 0.19584 0.52 0.53216 0.78 19p gain 20 (12%) 142 0.01537 0.123 0.076889 0.304 0.40832 0.719 0.78113 0.952 0.74856 0.927 0.64401 0.859 0.27469 0.611 0.9257 1 0.20965 0.543 0.72704 0.922 19q gain 14 (9%) 148 0.15185 0.449 0.0084999 0.0838 0.44343 0.741 0.53884 0.784 0.37556 0.688 0.22846 0.563 0.45942 0.744 0.66684 0.873 0.52337 0.777 0.48946 0.763 20p gain 12 (7%) 150 0.64557 0.859 0.36688 0.681 0.62267 0.836 0.72898 0.922 0.18045 0.493 0.34306 0.666 0.16854 0.475 0.38275 0.691 0.59288 0.821 0.5904 0.821 20q gain 10 (6%) 152 0.54222 0.784 0.16652 0.475 0.48501 0.763 1 1 0.0302 0.18 0.061969 0.277 0.0391 0.206 0.077029 0.304 0.03908 0.206 0.51439 0.775 21q gain 3 (2%) 159 0.25112 0.576 0.13638 0.439 NA NA NA NA 0.23787 0.563 0.068189 0.296 0.184 0.495 0.40875 0.719 0.29103 0.631 0.80599 0.961 22q gain 3 (2%) 159 0.25234 0.577 0.081669 0.318 NA NA NA NA 0.23772 0.563 0.14981 0.449 0.18046 0.493 0.40752 0.719 0.056279 0.262 0.80678 0.961 xp gain 6 (4%) 156 0.15213 0.449 0.01804 0.135 NA NA NA NA 0.03503 0.195 0.01679 0.132 0.15725 0.454 0.069729 0.297 0.0202 0.141 0.29921 0.636 xq gain 5 (3%) 157 0.17743 0.493 0.04467 0.225 NA NA NA NA 0.052769 0.256 0.054469 0.258 0.1419 0.444 0.067859 0.296 0.0305 0.18 0.096629 0.353 1p loss 98 (60%) 64 9.9999e-06 0.00115 0.01524 0.123 0.0056199 0.0636 0.00012 0.0046 0.00291 0.0372 0.00183 0.0269 5.9999e-05 0.00244 0.01358 0.114 0.00056999 0.0119 0.13666 0.439 1q loss 27 (17%) 135 0.89509 1 0.30891 0.638 0.90817 1 0.1478 0.449 0.1237 0.412 0.51767 0.775 0.66288 0.871 0.26397 0.593 0.03127 0.183 0.23881 0.563 2p loss 10 (6%) 152 0.38218 0.691 0.075119 0.3 0.74728 0.927 0.42624 0.736 0.00464 0.0543 0.18037 0.493 0.19513 0.52 0.00074999 0.0144 0.14691 0.449 0.0074899 0.076 2q loss 13 (8%) 149 0.82195 0.968 0.4498 0.742 0.74839 0.927 0.42745 0.736 0.41656 0.728 0.14278 0.444 0.53031 0.78 0.097649 0.355 0.32762 0.657 0.34045 0.665 3p loss 62 (38%) 100 0.00060999 0.0124 0.095279 0.35 0.0034 0.0421 0.25832 0.584 0.00032 0.00843 9.9999e-06 0.00115 0.00088999 0.0162 0.00121 0.0199 0.00025 0.00747 0.00018 0.00654 3q loss 88 (54%) 74 5.9999e-05 0.00244 0.52087 0.777 0.056489 0.262 0.02609 0.164 0.04291 0.219 9.9999e-06 0.00115 0.00354 0.0429 0.03045 0.18 0.0119 0.108 0.01601 0.127 4p loss 11 (7%) 151 0.00342 0.0421 0.14561 0.449 0.46955 0.75 0.34995 0.666 0.0067999 0.0733 0.18442 0.495 0.29321 0.631 0.39084 0.699 0.057999 0.267 0.14559 0.449 4q loss 10 (6%) 152 0.072949 0.298 0.24106 0.563 0.47197 0.75 0.34966 0.666 0.01753 0.134 0.3381 0.663 0.41668 0.728 0.52463 0.777 0.32749 0.657 0.32273 0.653 5p loss 5 (3%) 157 0.064429 0.285 0.37597 0.688 NA NA NA NA 0.03634 0.197 0.03617 0.197 0.14139 0.444 0.1681 0.475 0.16811 0.475 0.054639 0.258 5q loss 7 (4%) 155 0.38578 0.693 0.78458 0.953 0.49442 0.763 1 1 0.64635 0.859 0.52447 0.777 0.89557 1 0.35839 0.677 0.22673 0.563 0.3038 0.638 6q loss 19 (12%) 143 0.00096999 0.0167 0.00049 0.0117 0.02018 0.141 0.11604 0.399 0.00049 0.0117 5e-05 0.00244 0.00033 0.00843 2e-05 0.00138 0.01237 0.111 0.00237 0.0321 7q loss 6 (4%) 156 0.03222 0.184 0.48027 0.762 NA NA NA NA 0.0404 0.211 0.17385 0.486 0.02978 0.18 0.02485 0.159 0.24707 0.572 0.12866 0.421 8p loss 20 (12%) 142 0.02163 0.146 0.39098 0.699 0.44524 0.741 0.815 0.965 0.12417 0.412 0.10778 0.383 0.71472 0.915 0.95232 1 0.2797 0.621 0.48782 0.763 8q loss 12 (7%) 150 0.04341 0.22 0.73938 0.927 0.15131 0.449 1 1 0.32999 0.66 0.61987 0.836 0.11142 0.392 0.4369 0.741 0.9275 1 0.42707 0.736 9p loss 11 (7%) 151 0.0492 0.244 0.71788 0.915 0.084499 0.324 0.01753 0.134 0.18212 0.495 0.18081 0.493 0.67241 0.877 0.068639 0.296 0.54806 0.789 0.31149 0.638 9q loss 11 (7%) 151 0.0078599 0.0786 0.61016 0.834 0.45628 0.744 0.34859 0.666 0.51124 0.775 0.62682 0.84 0.72466 0.921 0.40052 0.712 0.82822 0.971 0.4408 0.741 11p loss 54 (33%) 108 9.9999e-06 0.00115 0.00055999 0.0119 0.00115 0.0194 0.14038 0.444 0.00025 0.00747 9.9999e-06 0.00115 3e-05 0.00172 2e-05 0.00138 5e-05 0.00244 0.00247 0.0328 11q loss 40 (25%) 122 2e-05 0.00138 0.069269 0.297 0.02308 0.152 0.11562 0.399 0.00026 0.00747 0.00072999 0.0144 0.00019 0.00655 0.00031 0.00843 2e-04 0.00657 0.0262 0.164 13q loss 8 (5%) 154 0.03607 0.197 0.44697 0.741 0.01254 0.111 0.67113 0.877 0.31183 0.638 0.11613 0.399 0.5279 0.778 0.22638 0.563 0.54893 0.789 0.46333 0.744 14q loss 20 (12%) 142 0.23676 0.563 0.053189 0.257 0.16765 0.475 0.20416 0.536 0.31006 0.638 0.79273 0.953 0.15541 0.452 0.00198 0.0285 0.02897 0.177 0.00157 0.0246 15q loss 3 (2%) 159 0.3476 0.666 0.33264 0.661 NA NA NA NA 1 1 0.86566 0.99 0.61651 0.836 0.83623 0.971 0.90017 1 1 1 16p loss 9 (6%) 153 0.33468 0.662 0.04265 0.219 0.67731 0.877 0.44524 0.741 0.55389 0.79 0.36103 0.679 0.2493 0.575 0.40254 0.714 0.67753 0.877 0.77143 0.944 16q loss 5 (3%) 157 0.73942 0.927 0.44504 0.741 0.74622 0.927 0.78567 0.953 0.4458 0.741 0.0276 0.17 0.21018 0.543 0.58977 0.821 0.090549 0.336 0.82886 0.971 17p loss 61 (38%) 101 0.00050999 0.0117 0.00236 0.0321 0.49237 0.763 0.15858 0.456 0.071409 0.298 0.03344 0.188 0.02289 0.152 0.02224 0.149 0.21442 0.546 0.01387 0.115 17q loss 19 (12%) 143 5.9999e-05 0.00244 0.90278 1 0.15643 0.454 0.03235 0.184 0.29684 0.635 0.2305 0.563 0.37012 0.681 0.087939 0.331 0.88174 1 0.2615 0.59 18p loss 16 (10%) 146 0.50306 0.771 0.74378 0.927 0.4353 0.741 0.20805 0.542 0.85512 0.98 0.75788 0.935 0.89286 1 0.31222 0.638 0.60683 0.831 0.45487 0.744 18q loss 6 (4%) 156 0.28776 0.63 0.87383 0.995 0.83292 0.971 0.055009 0.258 0.58444 0.816 0.65629 0.866 0.57284 0.805 0.58257 0.816 0.43202 0.74 0.86679 0.99 19q loss 6 (4%) 156 0.24155 0.563 1 1 NA NA NA NA 0.94203 1 0.94336 1 0.33205 0.661 0.62256 0.836 0.92675 1 0.93189 1 20q loss 3 (2%) 159 1 1 1 1 NA NA NA NA 1 1 0.64308 0.859 0.79028 0.953 1 1 0.72961 0.922 0.80605 0.961 21q loss 36 (22%) 126 0.20644 0.54 0.050569 0.249 0.31027 0.638 0.45466 0.744 0.04136 0.215 0.93862 1 0.56149 0.791 0.60308 0.827 0.9079 1 0.71668 0.915 22q loss 58 (36%) 104 9.9999e-06 0.00115 0.01272 0.111 0.36504 0.681 0.084239 0.324 0.03222 0.184 0.00207 0.0291 0.0476 0.238 0.051539 0.252 0.02686 0.167 0.0244 0.157 xp loss 48 (30%) 114 2e-05 0.00138 0.00181 0.0269 0.058369 0.267 0.44112 0.741 0.01294 0.112 0.00095999 0.0167 0.00254 0.0331 0.01779 0.135 0.2401 0.563 0.01816 0.135 xq loss 49 (30%) 113 3e-05 0.00172 0.0014 0.0225 0.072429 0.298 0.61173 0.834 0.0073499 0.076 0.00054999 0.0119 0.00375 0.0446 0.01038 0.0968 0.21187 0.544 0.01328 0.113