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 24 (43%) 32 0.20051 0.744 0.75367 0.979 0.73685 0.979 0.69258 0.979 0.82005 1 0.90233 1 0.52728 0.944 0.28356 0.781 0.60563 0.952 0.56671 0.952 1q gain 31 (55%) 25 0.4375 0.907 0.76733 0.984 0.93541 1 0.59385 0.952 0.76167 0.979 0.61839 0.959 0.70672 0.979 0.45634 0.921 0.88321 1 0.81486 1 2p gain 23 (41%) 33 0.88659 1 0.0078199 0.375 0.10937 0.705 0.03477 0.584 0.01928 0.479 0.056099 0.616 0.49538 0.938 0.072209 0.663 0.10102 0.705 0.13517 0.716 2q gain 21 (38%) 35 0.37327 0.858 0.01848 0.479 0.13501 0.716 0.3133 0.798 0.01203 0.432 0.11184 0.705 0.6224 0.959 0.0488 0.595 0.19502 0.744 0.11201 0.705 3p gain 12 (21%) 44 0.21204 0.744 0.259 0.781 0.10422 0.705 0.2103 0.744 0.43141 0.901 0.19961 0.744 0.86073 1 0.26476 0.781 0.4508 0.919 0.55395 0.952 3q gain 23 (41%) 33 0.10059 0.705 0.04861 0.595 0.33697 0.824 0.56555 0.952 0.1958 0.744 0.12034 0.705 0.49712 0.938 0.19017 0.744 0.073849 0.663 0.22101 0.747 4p gain 9 (16%) 47 0.72953 0.979 0.70118 0.979 0.03209 0.552 0.02631 0.524 0.82271 1 0.86672 1 0.77485 0.984 0.3253 0.809 0.26066 0.781 0.36819 0.853 4q gain 3 (5%) 53 1 1 0.2556 0.781 NA NA NA NA 0.51389 0.944 0.79251 0.995 0.67455 0.979 0.56476 0.952 0.59808 0.952 0.69534 0.979 5p gain 23 (41%) 33 0.04465 0.595 0.37532 0.858 0.0060499 0.355 0.19883 0.744 0.45117 0.919 0.24292 0.768 0.74335 0.979 0.0288 0.542 0.59625 0.952 0.15161 0.734 5q gain 8 (14%) 48 0.51116 0.944 0.56456 0.952 0.02243 0.479 0.20921 0.744 0.31117 0.797 0.2473 0.769 0.080509 0.664 0.15447 0.734 0.1298 0.716 0.19234 0.744 6p gain 30 (54%) 26 0.19494 0.744 0.52304 0.944 0.5524 0.952 0.52135 0.944 0.60115 0.952 0.41506 0.896 1 1 0.47421 0.926 0.73709 0.979 0.32122 0.809 6q gain 27 (48%) 29 0.20823 0.744 0.20578 0.744 0.60764 0.952 0.62009 0.959 0.22416 0.747 0.16652 0.744 1 1 0.19011 0.744 0.64958 0.976 0.1397 0.716 7p gain 21 (38%) 35 0.20066 0.744 0.55654 0.952 0.9078 1 0.28994 0.781 0.1514 0.734 0.28193 0.781 0.59251 0.952 0.13169 0.716 0.32888 0.811 0.12101 0.705 7q gain 17 (30%) 39 0.58491 0.952 0.84205 1 0.69181 0.979 0.86984 1 0.33911 0.824 0.8098 0.997 0.74217 0.979 0.16719 0.744 1 1 0.1537 0.734 8p gain 19 (34%) 37 0.18763 0.744 0.74222 0.979 0.50252 0.942 0.27791 0.781 0.44483 0.919 0.87112 1 0.97003 1 0.55818 0.952 0.66451 0.979 0.59596 0.952 8q gain 30 (54%) 26 0.01441 0.474 0.19729 0.744 0.55176 0.952 0.59371 0.952 0.050539 0.595 0.50576 0.942 0.21485 0.744 0.3244 0.809 0.067459 0.65 0.12244 0.705 9p gain 6 (11%) 50 0.35145 0.839 0.70271 0.979 0.75845 0.979 0.12397 0.705 0.93553 1 0.66497 0.979 0.83187 1 0.80442 0.997 0.86132 1 1 1 10p gain 21 (38%) 35 0.32676 0.809 0.02031 0.479 0.17339 0.744 0.29951 0.781 0.03998 0.595 0.11992 0.705 0.32623 0.809 0.10639 0.705 0.67758 0.979 0.19894 0.744 10q gain 17 (30%) 39 0.87448 1 0.33718 0.824 0.23886 0.764 0.46496 0.926 0.55131 0.952 0.04807 0.595 0.22237 0.747 0.18242 0.744 0.38015 0.858 0.073409 0.663 11p gain 5 (9%) 51 0.71989 0.979 0.44663 0.919 0.20939 0.744 0.92526 1 0.26381 0.781 0.85098 1 0.49305 0.938 0.11862 0.705 0.51902 0.944 0.093339 0.696 11q gain 7 (12%) 49 0.68212 0.979 0.38757 0.862 0.0192 0.479 0.71647 0.979 0.22716 0.751 0.38175 0.859 0.75536 0.979 0.03631 0.59 0.57801 0.952 0.03106 0.552 12p gain 22 (39%) 34 0.2622 0.781 0.00431 0.355 0.31437 0.799 0.59428 0.952 0.37462 0.858 0.04268 0.595 0.80971 0.997 0.97716 1 0.52917 0.944 0.62913 0.961 12q gain 11 (20%) 45 0.53713 0.947 0.53246 0.945 0.65169 0.977 0.85455 1 0.80508 0.997 0.52474 0.944 1 1 0.29822 0.781 0.91032 1 0.27038 0.781 13q gain 15 (27%) 41 0.64841 0.976 0.070319 0.663 0.26579 0.781 0.54436 0.949 0.0215 0.479 0.02432 0.506 0.2223 0.747 0.04599 0.595 0.01013 0.405 0.14186 0.718 14q gain 7 (12%) 49 0.60705 0.952 0.57697 0.952 0.11324 0.705 0.04936 0.595 0.25477 0.781 0.26114 0.781 0.20594 0.744 0.73537 0.979 0.22574 0.749 0.4716 0.926 15q gain 4 (7%) 52 0.18927 0.744 0.25321 0.781 0.75913 0.979 0.57674 0.952 0.57632 0.952 0.3247 0.809 0.75584 0.979 0.34752 0.832 0.42452 0.899 0.35483 0.842 16p gain 10 (18%) 46 0.10974 0.705 0.28071 0.781 0.17972 0.744 0.82988 1 0.19696 0.744 0.27676 0.781 1 1 0.48102 0.933 0.90376 1 0.40698 0.887 16q gain 6 (11%) 50 0.17226 0.744 0.84908 1 0.74612 0.979 0.92561 1 0.54567 0.949 0.9684 1 0.77079 0.984 0.92622 1 0.475 0.926 0.86688 1 17p gain 9 (16%) 47 0.38953 0.864 0.89627 1 0.95285 1 0.82702 1 0.56907 0.952 0.5629 0.952 0.28389 0.781 0.060689 0.632 0.1286 0.716 0.1727 0.744 17q gain 18 (32%) 38 0.42141 0.896 0.27164 0.781 0.63343 0.963 0.80018 0.997 0.70182 0.979 0.51366 0.944 0.39259 0.869 0.30581 0.79 0.75949 0.979 0.4324 0.901 18p gain 18 (32%) 38 0.67597 0.979 0.04909 0.595 0.68893 0.979 0.78703 0.993 0.094349 0.697 0.3448 0.832 0.14558 0.728 0.19881 0.744 0.40775 0.887 0.431 0.901 18q gain 14 (25%) 42 0.68528 0.979 0.080859 0.664 0.59653 0.952 0.59024 0.952 0.15399 0.734 0.23996 0.764 0.20406 0.744 0.084769 0.676 0.1388 0.716 0.16915 0.744 19p gain 24 (43%) 32 0.11512 0.705 0.17741 0.744 0.33886 0.824 0.72414 0.979 0.27016 0.781 0.36431 0.846 0.53484 0.945 0.22938 0.751 0.41999 0.896 0.51019 0.944 19q gain 28 (50%) 28 0.12452 0.705 0.075569 0.664 0.73339 0.979 0.8737 1 0.37907 0.858 0.39897 0.878 0.92952 1 0.89797 1 0.88566 1 0.93759 1 20p gain 37 (66%) 19 0.28727 0.781 0.50352 0.942 0.10922 0.705 0.59536 0.952 0.92338 1 0.75864 0.979 0.87464 1 0.69603 0.979 0.22326 0.747 0.47214 0.926 20q gain 44 (79%) 12 0.051899 0.595 0.91888 1 0.21361 0.744 0.95179 1 0.96867 1 0.99646 1 0.58901 0.952 0.57622 0.952 0.21401 0.744 0.67967 0.979 21q gain 18 (32%) 38 0.073219 0.663 0.37681 0.858 0.48931 0.938 0.78578 0.993 0.9013 1 0.89202 1 0.91456 1 0.57152 0.952 1 1 0.94851 1 22q gain 8 (14%) 48 0.71129 0.979 0.96122 1 0.4536 0.919 0.3023 0.786 0.80477 0.997 0.92533 1 0.88575 1 0.94398 1 1 1 1 1 xp gain 18 (32%) 38 0.93799 1 0.01008 0.405 0.40376 0.886 0.48322 0.933 0.01945 0.479 0.24596 0.769 0.79979 0.997 0.56107 0.952 0.20319 0.744 0.43318 0.901 xq gain 15 (27%) 41 0.69603 0.979 0.36371 0.846 0.72298 0.979 0.76146 0.979 0.76206 0.979 0.71409 0.979 0.87005 1 0.29272 0.781 1 1 0.088949 0.689 1p loss 9 (16%) 47 0.59618 0.952 0.60369 0.952 0.48606 0.934 0.62603 0.959 0.92187 1 0.11798 0.705 0.11056 0.705 0.02997 0.551 0.054669 0.608 0.04924 0.595 1q loss 9 (16%) 47 0.48322 0.933 0.51844 0.944 0.73566 0.979 0.29772 0.781 0.51337 0.944 0.077839 0.664 0.42182 0.896 0.15617 0.734 0.21217 0.744 0.14553 0.728 3p loss 20 (36%) 36 0.01025 0.405 0.41971 0.896 0.40674 0.887 0.71487 0.979 0.0488 0.595 0.22997 0.751 0.37612 0.858 0.92751 1 0.4188 0.896 0.43044 0.901 3q loss 14 (25%) 42 0.13861 0.716 0.45836 0.921 0.83577 1 0.79563 0.996 0.1377 0.716 0.6023 0.952 0.52737 0.944 0.87907 1 0.3827 0.859 1 1 4p loss 31 (55%) 25 0.065889 0.65 0.062779 0.636 0.1684 0.744 0.082319 0.664 0.25718 0.781 0.20248 0.744 0.03742 0.59 0.71272 0.979 0.14775 0.73 0.44647 0.919 4q loss 33 (59%) 23 0.1883 0.744 0.01843 0.479 0.29178 0.781 0.090239 0.689 0.00495 0.355 0.03882 0.59 9.9999e-05 0.079 0.24637 0.769 0.02075 0.479 0.13537 0.716 5p loss 9 (16%) 47 0.90199 1 0.47587 0.926 0.01593 0.479 0.062369 0.636 0.88421 1 0.13498 0.716 1 1 0.29938 0.781 1 1 0.41669 0.896 5q loss 18 (32%) 38 0.77036 0.984 0.30805 0.793 0.10502 0.705 0.078009 0.664 0.26538 0.781 0.2321 0.755 0.35986 0.842 0.94658 1 0.35536 0.842 0.94812 1 6p loss 5 (9%) 51 0.42564 0.899 0.95574 1 0.46308 0.926 0.75099 0.979 0.75666 0.979 0.95545 1 0.54359 0.949 0.9102 1 1 1 1 1 6q loss 7 (12%) 49 0.064099 0.641 0.69926 0.979 0.38686 0.862 0.16469 0.744 0.63963 0.97 0.90095 1 0.70616 0.979 0.61787 0.959 0.67156 0.979 0.61552 0.959 7p loss 13 (23%) 43 1 1 0.66468 0.979 0.54517 0.949 0.28475 0.781 0.73716 0.979 0.49767 0.938 0.31186 0.797 0.45365 0.919 0.77359 0.984 0.59919 0.952 7q loss 13 (23%) 43 0.11937 0.705 0.85387 1 0.32515 0.809 0.49656 0.938 0.92019 1 0.8211 1 0.7174 0.979 0.22148 0.747 1 1 0.52875 0.944 8p loss 23 (41%) 33 0.28926 0.781 0.98202 1 0.53929 0.949 0.27359 0.781 0.82967 1 0.74506 0.979 0.68674 0.979 0.51244 0.944 0.60451 0.952 0.57684 0.952 8q loss 9 (16%) 47 1 1 0.75546 0.979 0.81131 0.997 0.68863 0.979 0.29801 0.781 0.71264 0.979 0.94834 1 0.75758 0.979 0.26048 0.781 0.66885 0.979 9p loss 34 (61%) 22 0.29768 0.781 0.0079099 0.375 0.051889 0.595 0.00047 0.186 0.67296 0.979 0.13472 0.716 0.86444 1 0.28763 0.781 1 1 0.060779 0.632 9q loss 39 (70%) 17 0.18953 0.744 0.00161 0.318 0.14053 0.716 0.02183 0.479 0.49632 0.938 0.0387 0.59 0.66372 0.979 0.11853 0.705 1 1 0.16176 0.744 10p loss 23 (41%) 33 0.62563 0.959 0.01331 0.457 0.66602 0.979 0.72128 0.979 0.02883 0.542 0.18679 0.744 0.2462 0.769 0.78992 0.994 0.88028 1 0.8958 1 10q loss 21 (38%) 35 0.8859 1 0.29772 0.781 0.27458 0.781 0.78295 0.991 0.17633 0.744 0.17025 0.744 0.12416 0.705 0.47146 0.926 0.39808 0.878 0.73766 0.979 11p loss 26 (46%) 30 1 1 0.00374 0.355 0.87997 1 0.85771 1 0.37774 0.858 0.51733 0.944 0.26892 0.781 0.57974 0.952 0.50543 0.942 0.36009 0.842 11q loss 24 (43%) 32 0.62574 0.959 0.0080699 0.375 0.71788 0.979 0.80627 0.997 0.80458 0.997 0.89157 1 0.29367 0.781 0.58966 0.952 0.21998 0.747 0.18304 0.744 12p loss 13 (23%) 43 0.30471 0.789 0.27556 0.781 0.52836 0.944 0.7403 0.979 0.57999 0.952 0.73445 0.979 0.54677 0.949 0.57826 0.952 1 1 0.21729 0.747 12q loss 14 (25%) 42 0.42732 0.9 0.88013 1 0.87346 1 0.12501 0.705 0.81986 1 0.91456 1 0.96527 1 0.90728 1 0.91996 1 0.60445 0.952 13q loss 26 (46%) 30 0.41662 0.896 0.00113 0.298 0.84727 1 0.14772 0.73 0.058559 0.627 0.02651 0.524 0.35722 0.842 0.11921 0.705 0.03865 0.59 0.1966 0.744 14q loss 27 (48%) 29 0.94342 1 0.093329 0.696 0.52722 0.944 0.118 0.705 0.12115 0.705 0.12303 0.705 0.61635 0.959 0.89834 1 0.93938 1 0.93826 1 15q loss 32 (57%) 24 0.0062999 0.355 0.71273 0.979 0.77196 0.984 0.051989 0.595 0.93046 1 0.98116 1 0.93128 1 0.97775 1 1 1 0.89495 1 16p loss 32 (57%) 24 0.2416 0.767 0.4925 0.938 0.97676 1 0.089019 0.689 0.34601 0.832 0.10161 0.705 0.81064 0.997 0.91331 1 0.47004 0.926 0.89538 1 16q loss 37 (66%) 19 0.77682 0.985 0.79404 0.996 0.7389 0.979 0.12952 0.716 0.4497 0.919 0.090719 0.689 0.68319 0.979 0.92405 1 0.13996 0.716 0.85854 1 17p loss 34 (61%) 22 0.54617 0.949 0.2824 0.781 0.04389 0.595 0.27406 0.781 0.98059 1 0.75858 0.979 0.8059 0.997 0.89053 1 0.23508 0.76 0.88963 1 17q loss 17 (30%) 39 0.16383 0.744 0.35801 0.842 0.52725 0.944 0.63275 0.963 0.71579 0.979 0.38526 0.862 0.96697 1 0.21418 0.744 0.93165 1 0.27712 0.781 18p loss 18 (32%) 38 0.03215 0.552 0.01677 0.479 0.40964 0.889 0.28479 0.781 0.053849 0.608 0.089249 0.689 0.067379 0.65 0.079369 0.664 0.058709 0.627 0.04629 0.595 18q loss 20 (36%) 36 0.11688 0.705 0.072569 0.663 0.31657 0.802 0.29475 0.781 0.1841 0.744 0.11898 0.705 0.01174 0.432 0.0057699 0.355 0.0061499 0.355 0.00224 0.339 19p loss 15 (27%) 41 0.5606 0.952 0.46023 0.923 0.16275 0.744 0.47247 0.926 0.20299 0.744 0.35756 0.842 0.3463 0.832 0.71754 0.979 0.21086 0.744 0.70244 0.979 19q loss 13 (23%) 43 0.73456 0.979 0.15252 0.734 0.19539 0.744 0.81764 1 0.94417 1 0.61941 0.959 0.22935 0.751 0.87364 1 0.2372 0.762 1 1 20p loss 7 (12%) 49 0.53467 0.945 0.20765 0.744 0.00285 0.339 0.003 0.339 0.081559 0.664 0.075759 0.664 0.61729 0.959 0.69209 0.979 0.5781 0.952 0.6928 0.979 20q loss 4 (7%) 52 0.37174 0.858 0.60291 0.952 0.080429 0.664 0.1923 0.744 0.11815 0.705 0.47303 0.926 1 1 0.88539 1 0.66876 0.979 0.78875 0.994 21q loss 17 (30%) 39 0.6674 0.979 0.17896 0.744 0.73355 0.979 0.32959 0.811 0.63381 0.963 0.7443 0.979 0.68083 0.979 0.97167 1 0.93139 1 0.94292 1 22q loss 33 (59%) 23 0.17575 0.744 0.96941 1 0.25318 0.781 0.02095 0.479 0.96207 1 0.90197 1 0.70622 0.979 0.29054 0.781 0.4662 0.926 0.75929 0.979 xp loss 15 (27%) 41 0.64798 0.976 0.83891 1 0.2642 0.781 0.34454 0.832 0.92678 1 0.92792 1 0.44793 0.919 0.64959 0.976 0.50439 0.942 0.76098 0.979 xq loss 18 (32%) 38 0.76962 0.984 0.15539 0.734 0.48454 0.934 0.2192 0.747 0.23574 0.76 0.62608 0.959 0.4568 0.921 0.64816 0.976 0.53221 0.945 0.70815 0.979