Clinical Features 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 12 (7%) 150 0.51325 1 0.94108 1 0.44997 1 0.52977 1 0.03208 1 0.01782 1 0.21962 1 0.77034 1 0.9406 1 0.45758 1 0.93122 1 0.71014 1 1q gain 32 (20%) 130 0.67037 1 0.61365 1 0.02199 1 0.38444 1 0.033 1 0.18198 1 0.31886 1 0.78409 1 0.57146 1 0.79574 1 0.14981 1 0.32504 1 2p gain 39 (24%) 123 0.50379 1 0.01985 1 0.055469 1 0.066369 1 0.66799 1 0.63949 1 0.04572 1 0.04144 1 0.18513 1 0.076669 1 0.9144 1 0.47063 1 2q gain 41 (25%) 121 0.092139 1 0.058169 1 0.01375 1 0.16266 1 0.72032 1 0.82673 1 0.081379 1 0.0092299 1 0.21586 1 0.30557 1 0.53507 1 0.23878 1 3p gain 27 (17%) 135 1 1 0.90448 1 0.18807 1 0.68296 1 0.086719 1 0.45577 1 0.42902 1 0.62671 1 0.37815 1 0.35712 1 0.63839 1 0.56052 1 3q gain 34 (21%) 128 0.60416 1 0.61227 1 0.064459 1 0.90838 1 0.25259 1 0.4203 1 0.41874 1 0.22578 1 0.22214 1 0.31859 1 0.93479 1 0.84008 1 4p gain 9 (6%) 153 1 1 0.79187 1 1 1 0.76323 1 0.088909 1 0.17102 1 0.35747 1 0.43695 1 0.22205 1 0.37343 1 0.60155 1 1 1 4q gain 5 (3%) 157 0.29446 1 0.64958 1 1 1 NA NA 0.21986 1 0.48694 1 0.55534 1 1 1 0.89084 1 1 1 NA NA NA NA 5p gain 34 (21%) 128 0.204 1 0.098719 1 0.02705 1 0.1253 1 0.21528 1 0.68828 1 0.0447 1 0.004 1 0.19174 1 0.92217 1 0.20045 1 0.62594 1 5q gain 22 (14%) 140 0.24406 1 0.088489 1 0.41445 1 0.02676 1 0.072419 1 0.91802 1 0.24018 1 0.060799 1 0.29664 1 0.61131 1 0.25275 1 0.21813 1 6p gain 40 (25%) 122 0.33558 1 0.56481 1 8.9999e-05 0.0812 0.00475 1 0.77238 1 0.25591 1 0.6166 1 0.59186 1 0.23869 1 0.30043 1 0.42343 1 0.62485 1 6q gain 35 (22%) 127 0.67144 1 0.2281 1 2e-05 0.0181 0.0107 1 0.84383 1 0.47151 1 0.66425 1 0.32897 1 0.33741 1 0.58102 1 0.78809 1 0.68203 1 7p gain 100 (62%) 62 0.00219 1 0.00266 1 9.9999e-06 0.00911 0.0087799 1 0.48581 1 0.37453 1 0.01972 1 0.00019 0.171 0.04088 1 0.096459 1 0.03632 1 0.384 1 7q gain 83 (51%) 79 0.04807 1 0.0075599 1 5e-05 0.0451 0.25949 1 0.61787 1 0.94862 1 0.04121 1 0.00266 1 0.49859 1 0.82932 1 0.37928 1 0.62097 1 8p gain 39 (24%) 123 0.58632 1 0.35839 1 0.01384 1 0.73422 1 0.30417 1 0.04253 1 0.21382 1 0.39139 1 0.77116 1 0.20346 1 0.195 1 0.94721 1 8q gain 88 (54%) 74 0.0077499 1 0.21263 1 9.9999e-06 0.00911 0.1928 1 0.54788 1 0.78513 1 0.5692 1 0.074779 1 0.24473 1 0.066009 1 0.89376 1 1 1 9p gain 42 (26%) 120 0.0182 1 0.20001 1 0.62635 1 0.20379 1 0.65361 1 0.229 1 0.02206 1 0.99411 1 0.27299 1 0.33059 1 0.13184 1 0.63158 1 9q gain 33 (20%) 129 0.01511 1 0.20999 1 0.32757 1 0.49687 1 0.56376 1 0.099939 1 0.24404 1 0.16192 1 0.78503 1 0.62206 1 0.29936 1 0.69428 1 10p gain 12 (7%) 150 1 1 0.91833 1 0.15503 1 0.2741 1 0.66815 1 0.74804 1 0.089459 1 0.04146 1 0.6512 1 0.91863 1 0.38596 1 0.0065399 1 10q gain 6 (4%) 156 0.51593 1 0.082989 1 0.26847 1 0.7798 1 1 1 0.87269 1 0.40874 1 0.083579 1 0.77153 1 0.86447 1 NA NA NA NA 11p gain 30 (19%) 132 0.13391 1 0.38708 1 0.01806 1 0.39306 1 0.8432 1 0.39608 1 0.19085 1 0.02734 1 0.03105 1 0.28477 1 0.12871 1 0.16988 1 11q gain 25 (15%) 137 0.23919 1 0.42994 1 0.00124 1 0.03368 1 0.57391 1 0.30178 1 0.050489 1 0.00107 0.958 0.02556 1 0.5875 1 0.23253 1 1 1 12p gain 33 (20%) 129 0.69263 1 0.48243 1 0.00322 1 0.72479 1 0.18266 1 0.124 1 0.23133 1 0.32257 1 0.37428 1 0.5512 1 0.37937 1 0.68061 1 12q gain 23 (14%) 139 0.91166 1 0.51284 1 0.094569 1 0.30649 1 0.37336 1 0.25781 1 0.19054 1 0.94862 1 0.29904 1 0.33081 1 0.068799 1 0.28212 1 13q gain 110 (68%) 52 0.28208 1 0.38061 1 8.9999e-05 0.0812 0.084289 1 0.83703 1 0.32053 1 0.00436 1 0.02644 1 0.00278 1 0.065909 1 0.18982 1 0.58014 1 14q gain 8 (5%) 154 0.83372 1 0.91578 1 0.14584 1 0.17584 1 0.51895 1 0.54571 1 0.41291 1 0.39885 1 0.1283 1 0.86311 1 NA NA NA NA 15q gain 3 (2%) 159 NA NA NA NA 0.71809 1 0.48438 1 NA NA NA NA 0.35173 1 0.69675 1 NA NA NA NA NA NA NA NA 16p gain 39 (24%) 123 0.14778 1 0.85143 1 0.00133 1 0.51213 1 0.92258 1 1 1 0.25387 1 0.32232 1 0.15323 1 0.67561 1 0.058499 1 0.14334 1 16q gain 39 (24%) 123 0.04923 1 0.59529 1 2e-05 0.0181 0.48564 1 1 1 0.67048 1 0.02943 1 0.04306 1 0.02091 1 0.24327 1 0.02426 1 0.060629 1 17p gain 8 (5%) 154 0.11099 1 0.37848 1 0.02738 1 0.37585 1 1 1 0.87119 1 0.14529 1 0.55563 1 0.48776 1 0.44199 1 0.22852 1 0.79358 1 17q gain 30 (19%) 132 0.19881 1 0.9429 1 0.00032 0.287 0.38683 1 0.87791 1 0.94024 1 0.41953 1 0.37296 1 0.054199 1 0.46056 1 0.41494 1 1 1 18p gain 8 (5%) 154 0.51857 1 0.38922 1 0.0059299 1 0.73037 1 0.8066 1 0.73896 1 0.88656 1 0.92377 1 0.50129 1 0.56072 1 0.62108 1 0.45643 1 18q gain 6 (4%) 156 NA NA NA NA 0.079459 1 0.46056 1 0.49171 1 0.89215 1 0.45711 1 0.89148 1 0.65284 1 0.62909 1 0.62314 1 0.45832 1 19p gain 31 (19%) 131 0.066939 1 0.41828 1 0.01063 1 1 1 0.54882 1 0.4613 1 0.88105 1 0.63596 1 0.13528 1 0.95624 1 0.66711 1 1 1 19q gain 30 (19%) 132 0.081089 1 0.53097 1 0.01308 1 0.87944 1 0.95708 1 0.59213 1 0.25998 1 0.35321 1 0.35595 1 0.57947 1 0.25569 1 0.40848 1 20p gain 104 (64%) 58 0.096279 1 0.72535 1 0.38197 1 0.56192 1 0.056299 1 0.50059 1 0.48642 1 0.27951 1 0.42782 1 0.073819 1 0.57467 1 0.20772 1 20q gain 142 (88%) 20 0.0081899 1 0.16239 1 0.00041 0.367 0.34034 1 0.16162 1 0.33687 1 0.12283 1 0.02022 1 0.04372 1 0.36167 1 0.33727 1 0.3098 1 21q gain 10 (6%) 152 0.53754 1 0.65833 1 0.17134 1 1 1 0.62244 1 0.7942 1 0.88651 1 0.73925 1 0.29104 1 0.72372 1 0.69432 1 0.70647 1 22q gain 9 (6%) 153 0.72909 1 0.060849 1 0.2787 1 1 1 0.42499 1 0.23696 1 0.47623 1 0.081869 1 1 1 1 1 0.68816 1 0.088349 1 xq gain 32 (20%) 130 0.10584 1 0.33475 1 0.050089 1 0.43735 1 0.78031 1 0.44189 1 0.15803 1 0.43613 1 0.96487 1 0.95795 1 0.71998 1 0.70345 1 1p loss 44 (27%) 118 0.6918 1 0.02728 1 0.00026 0.234 0.27145 1 0.93468 1 0.20771 1 0.80432 1 0.070559 1 0.44026 1 0.60944 1 0.92035 1 0.19244 1 1q loss 25 (15%) 137 0.91128 1 0.057559 1 0.02188 1 0.04418 1 0.72618 1 0.38293 1 0.71763 1 0.60294 1 0.51708 1 0.23839 1 0.80493 1 0.10908 1 2p loss 11 (7%) 151 0.63732 1 0.75168 1 0.01106 1 0.48164 1 0.90766 1 0.53991 1 0.1235 1 0.24196 1 0.43478 1 0.60403 1 1 1 1 1 2q loss 6 (4%) 156 1 1 0.57037 1 0.15184 1 NA NA 0.10238 1 0.30407 1 0.19793 1 0.22485 1 0.20291 1 0.46746 1 NA NA NA NA 3p loss 15 (9%) 147 1 1 0.365 1 0.12369 1 0.84191 1 0.25625 1 0.8972 1 0.15871 1 0.53667 1 0.45401 1 0.13488 1 0.11449 1 1 1 3q loss 10 (6%) 152 0.51669 1 0.79154 1 0.062589 1 0.40674 1 0.32766 1 0.65919 1 0.03762 1 0.28662 1 0.49588 1 0.0096199 1 0.29205 1 1 1 4p loss 58 (36%) 104 0.66572 1 0.37191 1 9.9999e-06 0.00911 0.036 1 0.96995 1 0.51241 1 0.52387 1 0.64339 1 0.97431 1 0.098669 1 0.54327 1 0.62263 1 4q loss 65 (40%) 97 0.78119 1 0.27011 1 4e-05 0.0362 0.0408 1 0.81645 1 0.51507 1 0.7022 1 0.2682 1 0.81224 1 0.21749 1 0.92977 1 0.60273 1 5p loss 26 (16%) 136 0.23921 1 0.81716 1 0.23185 1 0.19593 1 0.52654 1 0.066299 1 0.69599 1 0.22643 1 0.72443 1 0.57805 1 0.31555 1 0.25519 1 5q loss 40 (25%) 122 0.090759 1 0.01128 1 0.0060999 1 0.3475 1 1 1 0.66943 1 0.96879 1 0.20517 1 0.94413 1 0.20726 1 0.64529 1 0.80145 1 6p loss 13 (8%) 149 0.54375 1 0.9282 1 0.85194 1 0.14241 1 0.30682 1 0.35916 1 0.72487 1 0.24184 1 0.56553 1 0.25633 1 0.38423 1 0.14678 1 6q loss 22 (14%) 140 0.16903 1 0.6425 1 0.13431 1 0.50175 1 0.45064 1 0.6054 1 0.1344 1 0.03838 1 0.26132 1 0.4101 1 0.16979 1 0.34516 1 7q loss 3 (2%) 159 NA NA NA NA 0.20364 1 NA NA 0.78566 1 0.7723 1 0.59915 1 1 1 0.85865 1 1 1 NA NA NA NA 8p loss 75 (46%) 87 0.18369 1 0.36791 1 0.01703 1 0.66896 1 0.70448 1 0.23786 1 0.28245 1 0.32815 1 0.84752 1 0.97352 1 0.01893 1 0.43198 1 8q loss 11 (7%) 151 0.17919 1 0.7395 1 0.16106 1 0.37739 1 0.79646 1 0.27733 1 0.18574 1 0.19236 1 0.86542 1 0.30307 1 0.74079 1 0.80569 1 9p loss 22 (14%) 140 0.6317 1 0.61712 1 0.2432 1 0.22582 1 0.74731 1 0.56688 1 0.82244 1 0.95549 1 0.30955 1 0.04723 1 0.15322 1 0.12228 1 9q loss 22 (14%) 140 0.20827 1 0.44682 1 0.36729 1 0.23887 1 0.94212 1 0.90206 1 0.98782 1 0.38023 1 0.069759 1 0.00181 1 0.16166 1 0.056389 1 10p loss 32 (20%) 130 0.14228 1 0.1728 1 0.60405 1 0.096549 1 0.14559 1 0.23977 1 0.87489 1 0.50226 1 0.83775 1 0.11508 1 0.8929 1 0.2213 1 10q loss 37 (23%) 125 0.17639 1 0.1554 1 0.097359 1 0.14339 1 0.12977 1 0.0331 1 0.49437 1 0.16283 1 0.68168 1 0.087249 1 0.85202 1 0.28957 1 11p loss 24 (15%) 138 0.24361 1 0.37256 1 0.00314 1 0.1388 1 0.20278 1 0.18138 1 0.30594 1 0.085699 1 0.99445 1 0.71218 1 0.48877 1 0.054199 1 11q loss 30 (19%) 132 0.056379 1 0.20451 1 0.00026 0.234 0.0303 1 0.60456 1 0.38485 1 0.11116 1 0.0073199 1 0.20598 1 0.37642 1 0.31282 1 0.085749 1 12p loss 22 (14%) 140 0.42497 1 0.28255 1 0.15533 1 0.43027 1 0.69502 1 0.079209 1 0.92034 1 0.21525 1 0.45046 1 0.77461 1 0.23608 1 0.79735 1 12q loss 20 (12%) 142 0.28143 1 0.4068 1 0.059519 1 0.93089 1 0.64278 1 0.32807 1 0.9372 1 0.072019 1 0.45833 1 0.20573 1 0.26705 1 0.61084 1 13q loss 8 (5%) 154 0.51742 1 1 1 0.24745 1 0.10651 1 0.055809 1 0.43304 1 1 1 0.89058 1 0.1755 1 1 1 0.74437 1 0.5665 1 14q loss 65 (40%) 97 0.49707 1 0.24829 1 0.0116 1 0.64606 1 0.80276 1 0.4912 1 0.1081 1 0.16387 1 0.33685 1 0.19905 1 0.79188 1 0.48081 1 15q loss 72 (44%) 90 0.45192 1 0.11041 1 0.00146 1 1 1 0.088769 1 0.25172 1 0.86616 1 0.50145 1 0.81657 1 0.63292 1 0.97583 1 0.8325 1 16p loss 9 (6%) 153 0.37921 1 0.75668 1 0.19612 1 0.062119 1 0.65262 1 0.63286 1 0.96309 1 0.96342 1 0.56373 1 1 1 0.67774 1 0.57035 1 16q loss 14 (9%) 148 0.27967 1 0.67662 1 0.00202 1 0.14794 1 0.64279 1 0.71253 1 0.75399 1 0.73009 1 0.56651 1 0.85765 1 0.79238 1 0.55177 1 17p loss 104 (64%) 58 0.20336 1 0.37455 1 0.04375 1 0.1693 1 0.97126 1 0.31999 1 0.79968 1 0.96159 1 0.98073 1 0.39546 1 0.52636 1 0.51558 1 17q loss 25 (15%) 137 0.90254 1 0.7371 1 0.00354 1 0.077449 1 0.74864 1 0.97446 1 0.31571 1 0.62624 1 0.86914 1 0.94544 1 0.39269 1 1 1 18p loss 125 (77%) 37 0.059349 1 0.70813 1 9.9999e-06 0.00911 0.0294 1 0.59882 1 0.15324 1 0.65886 1 0.23185 1 0.1698 1 0.16224 1 0.17686 1 1 1 18q loss 135 (83%) 27 0.02099 1 0.17333 1 3e-05 0.0271 0.01646 1 0.79708 1 0.48395 1 0.89021 1 0.68013 1 0.42361 1 0.02709 1 0.02291 1 0.63586 1 19p loss 22 (14%) 140 0.72758 1 0.83519 1 0.050559 1 0.04605 1 0.70043 1 0.83306 1 0.22174 1 0.21249 1 0.27347 1 0.02126 1 0.67563 1 1 1 19q loss 21 (13%) 141 0.83285 1 0.501 1 0.39051 1 0.13723 1 0.88226 1 0.77647 1 0.33223 1 0.26521 1 0.04535 1 0.0096199 1 0.75853 1 0.9299 1 20p loss 25 (15%) 137 1 1 0.95285 1 0.074439 1 0.41227 1 0.20647 1 0.68688 1 0.67472 1 0.68249 1 0.11125 1 0.061159 1 0.02968 1 0.16614 1 21q loss 66 (41%) 96 0.28587 1 0.24664 1 0.02666 1 0.96526 1 0.97208 1 0.53038 1 0.57847 1 0.83312 1 0.01519 1 0.18365 1 0.42688 1 0.47087 1 22q loss 57 (35%) 105 0.85278 1 0.31065 1 0.064899 1 0.73781 1 0.74803 1 0.29923 1 0.066429 1 0.094599 1 0.0060299 1 0.17926 1 0.36922 1 0.41056 1 xq loss 25 (15%) 137 1 1 0.71355 1 0.11545 1 0.46861 1 0.56705 1 0.97181 1 0.74387 1 0.90261 1 0.93461 1 0.6813 1 0.97204 1 0.51638 1