Clinical Features CN_CNMF METHLYATION_CNMF MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_CHIERARCHICAL nCNV (%) nWild-Type Chi-square test_P Chi-square 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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 5 (3%) 192 0.033097 1 8.8425e-07 0.000451 0.021736 1 0.19386 1 0.12964 1 0.2892 1 0.10632 1 0.026635 1 1q gain 14 (7%) 183 8.7071e-05 0.0415 2.5677e-10 1.39e-07 3.8806e-05 0.0187 0.0038611 1 0.41336 1 0.12478 1 0.61049 1 0.010526 1 2p gain 36 (18%) 161 9.398e-29 5.25e-26 9.4638e-05 0.0449 0.028346 1 0.048794 1 0.083843 1 0.65904 1 0.013459 1 0.566 1 2q gain 39 (20%) 158 1.1905e-28 6.64e-26 3.1254e-05 0.0152 0.048258 1 0.043012 1 0.10759 1 0.89609 1 0.024188 1 0.88199 1 3p gain 55 (28%) 142 9.2714e-18 5.15e-15 1.0585e-05 0.00523 9.0956e-07 0.000463 4.7753e-06 0.00239 0.079459 1 0.28356 1 0.091455 1 0.012962 1 3q gain 65 (33%) 132 1.456e-16 8.07e-14 7.1149e-06 0.00354 2.5634e-07 0.000133 0.0001514 0.0712 0.048944 1 0.093667 1 0.16174 1 0.0028505 1 4p gain 6 (3%) 191 0.33294 1 0.54191 1 0.39338 1 0.87706 1 1 1 0.37255 1 1 1 0.25062 1 4q gain 5 (3%) 192 0.68733 1 0.54191 1 0.62751 1 1 1 1 1 0.84983 1 0.74207 1 0.6753 1 5p gain 26 (13%) 171 1.3447e-06 0.000678 0.1014 1 0.038851 1 2.1209e-05 0.0104 0.11099 1 0.19056 1 0.037396 1 0.35493 1 5q gain 26 (13%) 171 1.7617e-05 0.00863 0.16927 1 0.072859 1 2.1209e-05 0.0104 0.11099 1 0.42899 1 0.11998 1 0.70711 1 6p gain 8 (4%) 189 0.21738 1 0.0055626 1 0.020981 1 0.22642 1 0.07533 1 0.37319 1 0.35634 1 0.046533 1 6q gain 6 (3%) 191 0.032635 1 0.00037038 0.171 0.13098 1 0.67292 1 0.12652 1 0.74502 1 0.24438 1 0.16573 1 7p gain 117 (59%) 80 2.2218e-16 1.23e-13 2.1026e-06 0.00106 3.6158e-14 1.99e-11 2.7608e-13 1.5e-10 0.1609 1 0.49181 1 0.099267 1 0.0012773 0.567 7q gain 118 (60%) 79 6.0492e-16 3.34e-13 5.1375e-06 0.00256 1.4523e-13 7.96e-11 6.288e-13 3.42e-10 0.22078 1 0.65254 1 0.14261 1 0.004702 1 8p gain 14 (7%) 183 0.40557 1 0.13903 1 0.024776 1 0.26648 1 0.22676 1 0.17163 1 0.61049 1 0.11169 1 8q gain 17 (9%) 180 0.17328 1 0.001422 0.626 0.0026622 1 0.1154 1 0.046402 1 0.081971 1 0.14435 1 0.037723 1 9p gain 3 (2%) 194 0.54257 1 NA NA 0.19427 1 0.28429 1 1 1 0.18729 1 0.50811 1 0.087353 1 10p gain 5 (3%) 192 0.10574 1 0.61924 1 0.51669 1 1 1 0.37403 1 0.45856 1 0.23063 1 0.42333 1 10q gain 5 (3%) 192 0.10574 1 0.61924 1 0.51669 1 1 1 0.37403 1 0.45856 1 0.23063 1 0.42333 1 11p gain 10 (5%) 187 0.026906 1 0.0038431 1 0.14439 1 0.032606 1 0.43489 1 0.82414 1 0.36067 1 0.52935 1 11q gain 8 (4%) 189 0.00043535 0.199 0.0012421 0.553 0.14572 1 0.031701 1 0.36295 1 1 1 0.28792 1 0.59324 1 12p gain 80 (41%) 117 0.00080523 0.364 0.15613 1 0.045194 1 0.0013956 0.618 0.19365 1 0.024929 1 0.10888 1 0.059959 1 12q gain 80 (41%) 117 0.00080523 0.364 0.15613 1 0.045194 1 0.0013956 0.618 0.19365 1 0.024929 1 0.10888 1 0.059959 1 13q gain 22 (11%) 175 0.21943 1 0.52615 1 0.24193 1 0.83191 1 0.74501 1 1 1 0.72221 1 0.7531 1 14q gain 3 (2%) 194 0.72169 1 0.066597 1 0.19427 1 0.28429 1 1 1 0.18729 1 1 1 0.087353 1 15q gain 5 (3%) 192 0.033097 1 0.17444 1 0.20211 1 0.16454 1 0.53598 1 0.57167 1 0.44297 1 0.6753 1 16p gain 105 (53%) 92 3.446e-08 1.82e-05 7.3383e-09 3.91e-06 1.2759e-06 0.000646 3.398e-10 1.83e-07 0.012248 1 0.01848 1 0.00067678 0.307 0.00096364 0.431 16q gain 101 (51%) 96 2.1293e-09 1.14e-06 1.1317e-08 6.01e-06 8.3159e-08 4.36e-05 1.2595e-09 6.75e-07 0.0016004 0.699 0.01323 1 9.5806e-05 0.0453 0.00022545 0.105 17p gain 118 (60%) 79 6.5056e-16 3.58e-13 2.0447e-07 0.000106 2.5471e-13 1.39e-10 9.3436e-12 5.06e-09 0.09366 1 0.17792 1 0.025426 1 0.0032744 1 17q gain 133 (68%) 64 5.3958e-12 2.93e-09 0.0014724 0.646 6.3129e-08 3.32e-05 5.7918e-08 3.05e-05 0.44817 1 0.31574 1 0.3636 1 0.072173 1 18p gain 9 (5%) 188 0.41238 1 0.22554 1 0.66052 1 0.6927 1 0.25015 1 0.0045802 1 0.19541 1 0.067503 1 18q gain 5 (3%) 192 0.23161 1 0.45156 1 0.58901 1 0.22974 1 1 1 0.063309 1 0.62891 1 0.6753 1 19p gain 3 (2%) 194 0.16204 1 0.5613 1 0.19427 1 0.50296 1 0.32327 1 0.53569 1 0.28867 1 0.49115 1 19q gain 3 (2%) 194 0.16204 1 0.5613 1 0.19427 1 0.50296 1 0.32327 1 0.53569 1 0.28867 1 0.49115 1 20p gain 66 (34%) 131 0.00055427 0.252 0.010467 1 0.025515 1 0.06273 1 0.045285 1 0.69049 1 0.16054 1 0.34428 1 20q gain 68 (35%) 129 0.0019702 0.857 0.0071662 1 0.062365 1 0.084809 1 0.031312 1 0.82324 1 0.18325 1 0.52008 1 21q gain 12 (6%) 185 0.24789 1 0.52999 1 0.035317 1 0.23137 1 0.93068 1 0.43771 1 0.53099 1 0.76213 1 22q gain 3 (2%) 194 0.36534 1 0.79051 1 0.51233 1 0.77821 1 0.069616 1 0.27984 1 0.19837 1 0.23007 1 xq gain 63 (32%) 134 7.7736e-18 4.33e-15 2.444e-07 0.000127 1.5024e-07 7.84e-05 6.0793e-10 3.26e-07 0.0076507 1 0.064856 1 0.00042692 0.196 0.0024899 1 1p loss 21 (11%) 176 1.2994e-06 0.000656 0.011388 1 0.0074583 1 0.41192 1 1 1 0.34257 1 1 1 0.87914 1 1q loss 13 (7%) 184 0.00044077 0.201 0.23577 1 0.32807 1 0.51013 1 0.67781 1 0.14186 1 0.72019 1 0.29764 1 3p loss 14 (7%) 183 8.7071e-05 0.0415 1.2035e-06 0.00061 3.8806e-05 0.0187 0.00044625 0.203 0.26737 1 0.0053014 1 0.040367 1 5.064e-06 0.00253 3q loss 4 (2%) 193 0.073884 1 0.0054513 1 0.065225 1 0.10128 1 0.12814 1 0.50298 1 0.20656 1 0.082398 1 4p loss 18 (9%) 179 2.9292e-05 0.0143 1.6144e-13 8.83e-11 9.9507e-07 0.000505 0.0038267 1 0.3319 1 0.17262 1 0.70625 1 0.0058636 1 4q loss 19 (10%) 178 2.2526e-07 0.000117 8.736e-11 4.73e-08 3.4059e-07 0.000175 0.0061968 1 0.40876 1 0.37357 1 0.84182 1 0.052739 1 5p loss 7 (4%) 190 0.33307 1 8.2977e-07 0.000425 0.030873 1 0.0035776 1 0.0063375 1 0.058443 1 0.011091 1 0.045203 1 5q loss 7 (4%) 190 0.43888 1 8.2977e-07 0.000425 0.030873 1 0.0035776 1 0.0063375 1 0.058443 1 0.011091 1 0.045203 1 6p loss 13 (7%) 184 0.092613 1 0.019365 1 0.099742 1 0.33336 1 0.445 1 0.28261 1 0.46942 1 0.56314 1 6q loss 16 (8%) 181 0.015202 1 0.024727 1 0.023144 1 0.32741 1 1 1 0.56686 1 0.69224 1 0.10902 1 8p loss 7 (4%) 190 0.51603 1 0.99153 1 0.27794 1 0.50147 1 0.31226 1 0.10839 1 0.39564 1 0.066982 1 8q loss 4 (2%) 193 0.42596 1 0.66293 1 0.32788 1 0.68218 1 0.84651 1 0.65183 1 1 1 0.58554 1 9p loss 22 (11%) 175 3.4867e-06 0.00175 3.3915e-07 0.000175 1.0469e-07 5.48e-05 8.6146e-05 0.0412 0.15129 1 0.051439 1 0.16875 1 0.0016669 0.727 9q loss 24 (12%) 173 9.8368e-05 0.0464 2.1979e-09 1.17e-06 1.0945e-08 5.82e-06 3.489e-05 0.0169 0.10045 1 0.00086814 0.39 0.06345 1 8.3675e-06 0.00414 10p loss 12 (6%) 185 1.6125e-05 0.00792 8.8526e-05 0.0421 0.00034183 0.159 0.050925 1 0.56555 1 0.0044422 1 0.23471 1 0.0032788 1 10q loss 12 (6%) 185 0.00037858 0.175 7.1202e-06 0.00354 0.00034183 0.159 0.01865 1 0.18732 1 0.0015135 0.663 0.051443 1 0.00021737 0.102 11p loss 10 (5%) 187 0.023117 1 0.0020185 0.876 0.028978 1 0.33061 1 0.77665 1 0.18214 1 0.30314 1 0.070796 1 11q loss 14 (7%) 183 0.00037316 0.172 0.0012358 0.551 0.0034766 1 0.23411 1 0.55098 1 0.37754 1 0.24168 1 0.16492 1 13q loss 18 (9%) 179 0.01126 1 1.3134e-13 7.21e-11 1.5204e-05 0.00748 0.016292 1 0.026436 1 0.0087243 1 0.065927 1 0.00085149 0.383 14q loss 35 (18%) 162 8.0645e-17 4.48e-14 7.8228e-05 0.0375 0.00050621 0.23 0.0021046 0.911 0.38211 1 0.48915 1 0.25543 1 0.21588 1 15q loss 19 (10%) 178 3.7364e-05 0.0181 4.0742e-05 0.0196 0.0039954 1 0.0079162 1 0.18663 1 0.21431 1 0.12383 1 0.15976 1 16p loss 4 (2%) 193 0.064877 1 0.0054513 1 0.065225 1 0.10128 1 0.84651 1 0.3742 1 1 1 0.082398 1 16q loss 5 (3%) 192 0.01167 1 0.00034614 0.161 0.021736 1 0.19386 1 0.53598 1 0.37372 1 0.62891 1 0.019288 1 17p loss 8 (4%) 189 0.13958 1 7.9994e-05 0.0383 0.00092518 0.414 0.027173 1 0.17927 1 0.10896 1 0.22578 1 0.046533 1 18p loss 30 (15%) 167 0.0034948 1 7.625e-08 4e-05 4.0437e-07 0.000208 0.0030829 1 0.043226 1 0.46479 1 0.05149 1 0.044625 1 18q loss 32 (16%) 165 0.00038482 0.177 6.0029e-10 3.23e-07 4.5068e-08 2.38e-05 0.0014031 0.619 0.051874 1 0.32706 1 0.077794 1 0.016643 1 19p loss 12 (6%) 185 0.0040721 1 0.056199 1 0.046441 1 0.08555 1 0.29467 1 0.18483 1 0.073934 1 0.31027 1 19q loss 11 (6%) 186 0.012585 1 0.014569 1 0.070806 1 0.57518 1 0.46838 1 0.27992 1 0.13526 1 0.10631 1 21q loss 32 (16%) 165 0.00015121 0.0712 0.15333 1 0.54593 1 1 1 0.57715 1 0.70429 1 0.32086 1 0.84756 1 22q loss 44 (22%) 153 1.5176e-05 0.00748 1.2614e-08 6.69e-06 1.5019e-07 7.84e-05 0.0057168 1 0.5147 1 0.039425 1 0.10628 1 0.010659 1 xq loss 20 (10%) 177 2.4518e-06 0.00123 4.6419e-07 0.000238 0.00019531 0.0916 0.10519 1 0.097423 1 0.10241 1 0.16683 1 0.034818 1