Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_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 Amp Peak 1(1p34.2) 63 (16%) 334 0.027997 1 0.48064 1 0.00089229 0.637 0.64436 1 0.36254 1 0.61878 1 0.04845 1 0.24108 1 0.22181 1 0.65363 1 Amp Peak 2(1q21.2) 205 (52%) 192 0.041886 1 0.0061823 1 1.9829e-07 0.000163 0.0011299 0.798 0.16014 1 0.049238 1 0.00068518 0.495 0.00048787 0.357 0.1783 1 0.037678 1 Amp Peak 3(2p16.1) 216 (54%) 181 0.00030485 0.227 0.0016452 1 3.1822e-13 2.66e-10 5.8257e-05 0.045 0.95017 1 0.6427 1 0.00033312 0.247 0.0011329 0.799 0.79026 1 0.042984 1 Amp Peak 4(2q31.2) 132 (33%) 265 0.020695 1 0.00094798 0.675 6.5211e-06 0.00523 1.985e-07 0.000163 0.72406 1 0.88737 1 0.00080111 0.575 0.00093222 0.665 0.42612 1 0.3698 1 Amp Peak 5(3p11.1) 80 (20%) 317 0.074773 1 0.84409 1 0.74389 1 0.95744 1 0.21385 1 0.0012981 0.913 0.05549 1 0.44422 1 0.38239 1 0.7724 1 Amp Peak 6(3q26.33) 364 (92%) 33 0.00042663 0.314 1.7146e-05 0.0135 7.0488e-12 5.88e-09 6.6908e-07 0.000545 0.19288 1 0.077644 1 3.8139e-05 0.0297 0.00016431 0.125 0.23795 1 1.3728e-05 0.0109 Amp Peak 7(4q12) 93 (23%) 304 0.67906 1 0.75873 1 0.00035284 0.261 0.12421 1 0.3558 1 0.13102 1 0.55476 1 0.74982 1 0.16314 1 0.43871 1 Amp Peak 8(5p15.33) 314 (79%) 83 0.85286 1 0.86716 1 1.0671e-05 0.00852 0.012895 1 0.40531 1 0.50196 1 0.38708 1 0.32784 1 0.71029 1 0.17979 1 Amp Peak 9(5p12) 261 (66%) 136 0.91917 1 0.51401 1 7.5793e-10 6.29e-07 0.0087387 1 0.5626 1 1 1 0.063491 1 0.58557 1 0.039702 1 0.11559 1 Amp Peak 10(6p12.1) 130 (33%) 267 0.55703 1 0.38314 1 0.0018014 1 0.16779 1 0.96213 1 0.30014 1 0.17806 1 0.84067 1 0.93254 1 0.46405 1 Amp Peak 11(6q12) 117 (29%) 280 1 1 0.87303 1 0.0011385 0.802 0.045379 1 0.34826 1 0.40804 1 0.39467 1 0.23611 1 0.59468 1 0.21395 1 Amp Peak 12(7p11.2) 193 (49%) 204 0.18606 1 0.09391 1 0.00097005 0.687 0.0036616 1 0.68745 1 0.80108 1 0.075977 1 0.014833 1 0.46043 1 0.15736 1 Amp Peak 13(7q21.2) 209 (53%) 188 0.10132 1 0.24997 1 5.3382e-10 4.44e-07 1.2724e-05 0.0101 0.057338 1 0.3893 1 0.016544 1 0.022055 1 0.12223 1 0.089184 1 Amp Peak 14(8p11.23) 184 (46%) 213 0.0081177 1 0.16822 1 0.02545 1 0.035179 1 0.1916 1 0.098781 1 0.0063053 1 0.71976 1 0.13093 1 0.77125 1 Amp Peak 15(8q24.21) 280 (71%) 117 0.8715 1 0.64417 1 0.55402 1 0.96883 1 0.91657 1 0.70842 1 0.7345 1 0.42772 1 0.39241 1 0.93542 1 Amp Peak 16(9p24.1) 73 (18%) 324 0.37518 1 0.029533 1 0.00035369 0.261 0.17742 1 0.0016979 1 0.0050133 1 0.041333 1 0.0029351 1 0.46117 1 0.236 1 Amp Peak 17(9p13.3) 109 (27%) 288 0.16996 1 0.37287 1 0.043013 1 0.038723 1 0.070796 1 0.0089805 1 0.021999 1 0.18844 1 0.41054 1 0.97251 1 Amp Peak 18(11q13.3) 143 (36%) 254 0.06969 1 0.030551 1 0.0048628 1 0.00051779 0.377 0.19004 1 0.035798 1 0.012508 1 0.13883 1 0.14236 1 0.21367 1 Amp Peak 19(12p13.33) 198 (50%) 199 0.010156 1 0.057062 1 1.2263e-05 0.00977 0.00049216 0.359 0.31262 1 0.72944 1 0.00057533 0.418 0.0051835 1 0.58289 1 0.53899 1 Amp Peak 20(12q15) 144 (36%) 253 0.31238 1 0.5273 1 0.0053063 1 0.0013616 0.956 0.76381 1 0.52436 1 0.10546 1 0.049145 1 0.50901 1 0.9298 1 Amp Peak 21(13q34) 71 (18%) 326 0.96435 1 0.048907 1 0.038423 1 0.18194 1 0.87024 1 0.083384 1 0.80276 1 0.40688 1 0.066393 1 0.21594 1 Amp Peak 22(14q13.3) 121 (30%) 276 0.34486 1 0.24581 1 0.12677 1 0.096921 1 0.57003 1 0.0082634 1 0.61652 1 0.084716 1 0.027483 1 0.097221 1 Amp Peak 23(15q26.3) 139 (35%) 258 0.15118 1 0.02098 1 1.5595e-05 0.0123 9.3889e-06 0.0075 0.35379 1 0.01826 1 0.00062217 0.45 0.0042628 1 0.024131 1 0.00043706 0.321 Amp Peak 24(17q25.1) 191 (48%) 206 0.017661 1 0.060794 1 6.01e-07 0.00049 2.169e-05 0.017 0.26742 1 0.29175 1 0.027422 1 0.0080673 1 0.61101 1 0.89337 1 Amp Peak 25(18p11.32) 137 (35%) 260 0.095767 1 0.0098077 1 2.4815e-05 0.0195 0.00012602 0.096 0.23136 1 0.4508 1 0.40971 1 0.12147 1 0.65972 1 0.13509 1 Amp Peak 26(18q11.2) 126 (32%) 271 0.00045553 0.334 0.0022679 1 1.3658e-05 0.0108 0.00034191 0.253 0.27235 1 0.74038 1 0.0043758 1 0.00057779 0.419 0.31963 1 0.012015 1 Amp Peak 27(19q12) 167 (42%) 230 0.45483 1 0.24902 1 4.0708e-06 0.00328 0.1821 1 0.23063 1 0.028698 1 0.19265 1 0.081975 1 0.95091 1 0.60924 1 Amp Peak 28(19q13.2) 170 (43%) 227 0.71537 1 1 1 0.00019499 0.147 0.070833 1 0.35617 1 0.11719 1 0.62577 1 0.052994 1 0.87157 1 0.45393 1 Amp Peak 29(20p12.2) 211 (53%) 186 0.00098685 0.698 0.0042983 1 8.924e-08 7.34e-05 0.00016098 0.123 0.96651 1 0.22098 1 0.1497 1 0.013404 1 0.61101 1 0.27941 1 Amp Peak 30(20q11.21) 229 (58%) 168 0.99122 1 0.84394 1 0.00051999 0.379 0.013224 1 0.66891 1 0.5881 1 0.59324 1 0.54885 1 0.90444 1 0.51928 1 Amp Peak 31(22q11.21) 199 (50%) 198 0.11066 1 0.12309 1 0.00029562 0.22 0.00047739 0.349 0.88793 1 0.34914 1 0.067121 1 0.067683 1 0.72724 1 0.10342 1 Amp Peak 32(Xq28) 106 (27%) 291 0.63266 1 0.63565 1 0.038982 1 0.081483 1 0.070072 1 0.069028 1 0.13574 1 0.16498 1 0.50179 1 0.73437 1 Del Peak 1(1p36.22) 172 (43%) 225 1.4274e-06 0.00116 1.7833e-08 1.47e-05 1.6133e-28 1.36e-25 2.1042e-14 1.76e-11 0.41213 1 0.026199 1 1.0915e-09 9.05e-07 1.35e-08 1.12e-05 0.022659 1 0.0038708 1 Del Peak 2(1p13.2) 172 (43%) 225 0.00023715 0.178 0.0005497 0.4 1.2332e-15 1.03e-12 5.745e-09 4.75e-06 0.11875 1 0.071159 1 2.352e-05 0.0185 7.0749e-05 0.0545 0.16539 1 0.024633 1 Del Peak 3(2p25.3) 37 (9%) 360 0.046105 1 0.17884 1 0.077265 1 0.37008 1 0.10991 1 0.83838 1 0.31965 1 0.22609 1 0.096013 1 0.067636 1 Del Peak 4(2q22.1) 105 (26%) 292 0.25483 1 0.31825 1 0.00027109 0.203 0.019796 1 0.66724 1 0.077676 1 0.18815 1 0.23144 1 0.64846 1 0.55075 1 Del Peak 5(2q36.2) 132 (33%) 265 0.00023576 0.178 4.7565e-05 0.037 1.6951e-12 1.42e-09 2.1435e-06 0.00174 0.1769 1 0.1255 1 8.4879e-05 0.0653 6.1471e-06 0.00494 0.98626 1 0.58724 1 Del Peak 6(3p25.3) 313 (79%) 84 0.54042 1 0.17616 1 0.027817 1 0.0022082 1 0.63742 1 0.18016 1 0.32711 1 0.008757 1 0.7587 1 0.0074259 1 Del Peak 7(3p13) 340 (86%) 57 0.41881 1 0.54863 1 2.6689e-06 0.00216 0.0008576 0.613 0.88237 1 0.037948 1 0.36874 1 0.013408 1 0.92625 1 0.0046008 1 Del Peak 8(3p12.3) 332 (84%) 65 0.25764 1 0.34172 1 3.0279e-05 0.0236 0.0025909 1 1 1 0.091957 1 0.24013 1 0.016209 1 0.89392 1 0.0089897 1 Del Peak 9(3q11.1) 59 (15%) 338 0.75853 1 0.47773 1 0.11709 1 0.053816 1 0.76467 1 0.28212 1 0.92486 1 0.67444 1 0.73999 1 0.89098 1 Del Peak 10(4p15.2) 239 (60%) 158 0.00080707 0.579 0.001708 1 6.5154e-06 0.00523 0.0003406 0.252 0.66155 1 0.034313 1 0.088333 1 0.0514 1 0.32508 1 0.9208 1 Del Peak 11(4q22.1) 217 (55%) 180 0.0068481 1 0.057857 1 0.00010209 0.0782 0.008289 1 0.12263 1 0.38079 1 0.025247 1 0.0063574 1 0.21932 1 0.24156 1 Del Peak 12(4q32.3) 248 (62%) 149 0.0096682 1 0.025274 1 3.4983e-07 0.000286 0.0005961 0.432 0.10077 1 0.52301 1 0.005697 1 0.036026 1 0.34393 1 0.097415 1 Del Peak 13(4q35.2) 253 (64%) 144 0.10047 1 0.20573 1 2.8407e-06 0.0023 0.00012369 0.0944 0.45478 1 0.46976 1 0.0053154 1 0.10683 1 0.62975 1 0.30856 1 Del Peak 14(5q11.2) 290 (73%) 107 0.84151 1 0.30269 1 2.0341e-12 1.7e-09 0.00019205 0.145 0.95874 1 0.24402 1 0.24758 1 0.56007 1 0.95278 1 8.0587e-05 0.0621 Del Peak 15(5q31.1) 308 (78%) 89 0.33159 1 0.2283 1 5.7045e-09 4.72e-06 2.9999e-05 0.0235 0.27154 1 0.16591 1 0.2938 1 0.44504 1 0.70938 1 0.00046199 0.339 Del Peak 16(6p25.3) 100 (25%) 297 0.21975 1 0.10989 1 0.0087794 1 0.0014284 1 0.39303 1 0.013046 1 0.010038 1 0.020398 1 0.15878 1 0.18065 1 Del Peak 17(6q22.31) 95 (24%) 302 0.019183 1 0.0022397 1 0.0051316 1 0.00081841 0.586 0.62886 1 0.35397 1 0.021655 1 0.013314 1 0.19409 1 0.2426 1 Del Peak 18(6q26) 103 (26%) 294 0.065853 1 0.0029759 1 0.0023386 1 0.00072654 0.523 0.92144 1 0.68997 1 0.068692 1 0.14099 1 0.14935 1 0.088905 1 Del Peak 19(7q11.22) 37 (9%) 360 0.90823 1 0.40489 1 4.3951e-05 0.0342 0.82862 1 0.95833 1 0.74972 1 0.046282 1 0.064437 1 0.8366 1 0.52389 1 Del Peak 20(7q36.3) 81 (20%) 316 0.18723 1 0.11156 1 0.00094976 0.675 0.27435 1 1 1 0.31493 1 0.092794 1 0.069784 1 0.13787 1 0.16313 1 Del Peak 21(8p23.2) 267 (67%) 130 0.86415 1 0.45866 1 0.00096128 0.682 0.17289 1 0.34475 1 0.1409 1 0.15724 1 0.071999 1 0.34475 1 0.28515 1 Del Peak 22(9p23) 258 (65%) 139 0.005614 1 0.0029131 1 1.9708e-10 1.64e-07 0.10353 1 0.14638 1 0.20769 1 0.026141 1 0.087611 1 0.98626 1 0.065199 1 Del Peak 23(9p21.3) 302 (76%) 95 0.37246 1 0.17169 1 4.9922e-07 0.000408 0.40906 1 0.69525 1 0.38805 1 0.16414 1 0.84599 1 0.85165 1 0.29571 1 Del Peak 24(9q21.11) 191 (48%) 206 0.00017721 0.134 4.9247e-05 0.0382 5.9694e-11 4.97e-08 1.1436e-06 0.000931 0.65275 1 0.23857 1 4.4373e-06 0.00357 2.3951e-07 0.000196 0.064287 1 0.000283 0.211 Del Peak 25(10p15.3) 178 (45%) 219 0.37287 1 0.44184 1 4.8041e-05 0.0373 9.6005e-05 0.0736 0.3293 1 0.44338 1 0.0038329 1 0.016525 1 0.12237 1 0.0027272 1 Del Peak 26(10p15.1) 168 (42%) 229 0.072155 1 0.48421 1 0.00016166 0.123 4.0282e-06 0.00325 0.46906 1 0.35291 1 0.00025878 0.194 0.013136 1 0.044243 1 0.0051579 1 Del Peak 27(10q23.31) 203 (51%) 194 0.039232 1 0.0038632 1 2.1656e-05 0.017 2.0796e-06 0.00169 0.36004 1 0.38997 1 0.0001037 0.0793 2.6262e-05 0.0206 0.54122 1 0.017286 1 Del Peak 28(11p15.5) 183 (46%) 214 0.00068877 0.497 0.052775 1 1.284e-06 0.00104 0.035158 1 0.00076369 0.549 2.0219e-05 0.0159 0.019994 1 0.036223 1 0.043562 1 0.075408 1 Del Peak 29(11q22.1) 118 (30%) 279 0.49319 1 0.28778 1 0.005299 1 0.031392 1 0.10316 1 0.99545 1 0.25936 1 0.42647 1 0.21887 1 0.058387 1 Del Peak 30(11q25) 143 (36%) 254 0.7979 1 0.42926 1 0.074578 1 0.33284 1 0.1133 1 0.90777 1 0.44743 1 0.40585 1 0.14034 1 0.18885 1 Del Peak 31(12q24.31) 63 (16%) 334 0.96498 1 0.33211 1 0.42567 1 0.43534 1 0.32272 1 0.20712 1 0.90035 1 0.68912 1 0.28183 1 0.32164 1 Del Peak 32(13q12.11) 260 (65%) 137 0.054743 1 0.61102 1 0.034361 1 0.16435 1 0.90658 1 0.26832 1 0.69982 1 0.21445 1 0.97265 1 1 1 Del Peak 33(13q14.2) 271 (68%) 126 0.051249 1 0.096235 1 0.00096039 0.682 0.05298 1 0.70704 1 0.68237 1 0.028092 1 0.14722 1 0.90457 1 0.56076 1 Del Peak 34(14q11.2) 140 (35%) 257 0.054625 1 0.29339 1 0.16302 1 0.43658 1 0.20597 1 0.15948 1 0.0026496 1 0.0021291 1 0.25249 1 0.2737 1 Del Peak 35(15q12) 131 (33%) 266 0.72495 1 0.22782 1 0.4498 1 0.34728 1 0.071706 1 0.007983 1 0.13225 1 0.35649 1 0.072334 1 0.63616 1 Del Peak 36(15q21.1) 124 (31%) 273 0.64316 1 0.24163 1 0.29796 1 0.9693 1 0.13822 1 0.0076257 1 0.15583 1 0.35383 1 0.22845 1 0.31835 1 Del Peak 37(16p13.3) 148 (37%) 249 0.23929 1 0.24492 1 0.0052502 1 0.19657 1 0.14901 1 0.60559 1 0.53052 1 0.24668 1 0.61821 1 0.067668 1 Del Peak 38(16q23.1) 166 (42%) 231 0.94193 1 0.65907 1 0.08633 1 0.27078 1 0.35392 1 0.7607 1 0.20485 1 0.026365 1 0.53514 1 0.3373 1 Del Peak 39(17p11.2) 202 (51%) 195 0.19384 1 0.4015 1 0.0018499 1 0.16122 1 0.15048 1 0.018225 1 0.36815 1 0.86032 1 0.066574 1 0.031312 1 Del Peak 40(17q11.2) 96 (24%) 301 1.2614e-05 0.01 6.4433e-05 0.0497 3.0448e-08 2.51e-05 0.01773 1 0.49523 1 0.37803 1 0.00012202 0.0932 7.1613e-06 0.00574 0.42567 1 0.068256 1 Del Peak 41(17q25.3) 76 (19%) 321 0.0051505 1 0.042126 1 0.00040515 0.299 0.044583 1 0.62249 1 0.99436 1 0.12966 1 0.0021039 1 0.94595 1 0.11064 1 Del Peak 42(18q23) 179 (45%) 218 0.50803 1 0.78802 1 0.50245 1 0.89829 1 0.8006 1 0.39738 1 0.2296 1 0.11539 1 0.7725 1 0.50154 1 Del Peak 43(19p13.3) 173 (44%) 224 0.33425 1 0.023076 1 1.3758e-05 0.0109 0.1453 1 0.058795 1 0.25112 1 0.16017 1 0.012363 1 0.022888 1 0.069159 1 Del Peak 44(19q13.33) 106 (27%) 291 0.61681 1 0.06944 1 0.00016682 0.126 0.00018682 0.141 0.24377 1 0.71878 1 0.43647 1 0.2122 1 0.43783 1 0.12558 1 Del Peak 45(21q21.1) 189 (48%) 208 0.48146 1 0.13538 1 0.011714 1 0.02929 1 0.58502 1 0.88981 1 0.99588 1 0.8148 1 0.056199 1 0.068671 1 Del Peak 46(21q22.3) 224 (56%) 173 0.95746 1 0.1932 1 2.1292e-08 1.75e-05 0.0020622 1 0.39563 1 0.099114 1 0.5636 1 0.30219 1 0.0039492 1 0.34734 1 Del Peak 47(22q11.21) 68 (17%) 329 0.09039 1 0.0093024 1 0.067222 1 0.084138 1 0.1449 1 0.12939 1 0.59809 1 0.7479 1 0.17152 1 0.12563 1 Del Peak 48(22q13.32) 95 (24%) 302 0.00028103 0.21 8.6845e-05 0.0667 0.017238 1 0.35054 1 0.5426 1 0.075877 1 0.057468 1 0.16188 1 0.096088 1 0.016171 1 Del Peak 49(Xp22.2) 126 (32%) 271 0.59895 1 0.3507 1 0.00024911 0.187 0.010114 1 0.2774 1 0.78348 1 0.13988 1 0.12171 1 0.12182 1 0.24377 1 Del Peak 50(Xp21.1) 127 (32%) 270 0.35378 1 0.14801 1 5.3937e-05 0.0417 0.00024021 0.18 0.34428 1 0.6807 1 0.077879 1 0.0071601 1 0.32136 1 0.097394 1 Del Peak 51(Xp11.3) 125 (31%) 272 0.06204 1 0.17505 1 9.1854e-06 0.00735 4.0939e-05 0.0319 0.09227 1 0.12432 1 0.014157 1 0.017529 1 0.063544 1 0.19271 1 Del Peak 52(Xq22.3) 95 (24%) 302 0.0085301 1 0.10522 1 1.906e-05 0.015 0.00024914 0.187 0.66297 1 0.9198 1 0.051315 1 0.48519 1 0.53495 1 0.94201 1