This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 71 arm-level results and 12 molecular subtypes across 504 patients, 133 significant findings detected with Q value < 0.25.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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7q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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8p gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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8q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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12q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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20q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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1p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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1q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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2p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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2q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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3q loss cnv correlated to 'CN_CNMF'.
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4q loss cnv correlated to 'CN_CNMF'.
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6p loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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10p loss cnv correlated to 'CN_CNMF'.
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13q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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17p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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18p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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18q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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21q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 71 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 significant findings detected.
Molecular subtypes |
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
17p loss | 0 (0%) | 478 |
0.000117 (0.0786) |
0.000197 (0.131) |
6.44e-07 (0.000474) |
0.713 (1.00) |
2.92e-05 (0.0201) |
5.18e-06 (0.0037) |
1.9e-06 (0.00139) |
1.5e-08 (1.14e-05) |
2.83e-06 (0.00204) |
2.73e-11 (2.1e-08) |
0.225 (1.00) |
0.0348 (1.00) |
2p loss | 0 (0%) | 494 |
0.000249 (0.164) |
0.000389 (0.255) |
6.13e-07 (0.000451) |
0.484 (1.00) |
1.37e-05 (0.00961) |
0.000189 (0.126) |
4.72e-07 (0.000349) |
1.87e-08 (1.42e-05) |
0.000232 (0.154) |
1.38e-12 (1.07e-09) |
1 (1.00) |
0.204 (1.00) |
2q loss | 0 (0%) | 493 |
0.000249 (0.164) |
0.000389 (0.255) |
2.38e-06 (0.00172) |
1 (1.00) |
0.000129 (0.0866) |
4.42e-05 (0.0301) |
8.96e-08 (6.72e-05) |
7.91e-08 (5.95e-05) |
0.000101 (0.0681) |
1.44e-11 (1.11e-08) |
1 (1.00) |
0.204 (1.00) |
3p loss | 0 (0%) | 193 |
0.0106 (1.00) |
0.00929 (1.00) |
9.35e-35 (7.38e-32) |
4.94e-06 (0.00353) |
0.000105 (0.071) |
1.54e-05 (0.0108) |
2.09e-11 (1.61e-08) |
7.09e-10 (5.42e-07) |
1.97e-06 (0.00143) |
8.3e-12 (6.44e-09) |
0.00165 (1.00) |
0.000785 (0.502) |
9p loss | 0 (0%) | 415 |
0.378 (1.00) |
0.124 (1.00) |
6.57e-33 (5.17e-30) |
7.23e-12 (5.61e-09) |
0.00463 (1.00) |
0.00726 (1.00) |
1.39e-11 (1.07e-08) |
2.71e-12 (2.11e-09) |
2.42e-07 (0.00018) |
0.038 (1.00) |
4.42e-06 (0.00317) |
3.42e-05 (0.0234) |
14q loss | 0 (0%) | 342 |
0.00179 (1.00) |
0.00197 (1.00) |
7.35e-13 (5.76e-10) |
3.84e-05 (0.0262) |
6.61e-12 (5.13e-09) |
2.08e-07 (0.000155) |
6.97e-11 (5.35e-08) |
2.8e-07 (0.000208) |
7.43e-06 (0.00525) |
0.535 (1.00) |
0.0203 (1.00) |
0.622 (1.00) |
17q loss | 0 (0%) | 492 |
0.000668 (0.431) |
0.000893 (0.564) |
6.84e-06 (0.00485) |
0.484 (1.00) |
1.46e-05 (0.0102) |
1.02e-05 (0.00722) |
1.91e-06 (0.00139) |
7.91e-08 (5.95e-05) |
2.95e-05 (0.0203) |
8.59e-13 (6.71e-10) |
1 (1.00) |
0.204 (1.00) |
12p gain | 0 (0%) | 424 |
0.194 (1.00) |
0.201 (1.00) |
1.35e-08 (1.02e-05) |
0.00262 (1.00) |
5.67e-07 (0.000418) |
0.0139 (1.00) |
1.1e-05 (0.00775) |
1.89e-05 (0.0131) |
3.26e-06 (0.00235) |
0.237 (1.00) |
2.07e-06 (0.0015) |
0.0455 (1.00) |
12q gain | 0 (0%) | 423 |
0.194 (1.00) |
0.201 (1.00) |
6.42e-09 (4.89e-06) |
0.00262 (1.00) |
1.46e-07 (0.000109) |
0.0104 (1.00) |
6.06e-06 (0.00431) |
9.22e-06 (0.00651) |
1.72e-06 (0.00125) |
0.206 (1.00) |
8.85e-07 (0.000649) |
0.0299 (1.00) |
20q gain | 0 (0%) | 435 |
0.0753 (1.00) |
0.106 (1.00) |
1.37e-15 (1.08e-12) |
0.00326 (1.00) |
3.54e-05 (0.0242) |
0.000855 (0.544) |
3.3e-07 (0.000244) |
1.47e-06 (0.00107) |
1.54e-08 (1.17e-05) |
0.00296 (1.00) |
7.31e-08 (5.51e-05) |
0.0081 (1.00) |
9q loss | 0 (0%) | 410 |
0.378 (1.00) |
0.124 (1.00) |
2.79e-34 (2.2e-31) |
7.61e-13 (5.95e-10) |
0.000999 (0.628) |
0.0104 (1.00) |
1.31e-12 (1.03e-09) |
3.94e-14 (3.09e-11) |
9.59e-09 (7.28e-06) |
0.0159 (1.00) |
2.33e-05 (0.0161) |
0.00122 (0.757) |
8q gain | 0 (0%) | 468 |
0.0536 (1.00) |
0.0623 (1.00) |
5.94e-11 (4.57e-08) |
0.000901 (0.568) |
0.0102 (1.00) |
0.0449 (1.00) |
1.15e-07 (8.58e-05) |
4.88e-05 (0.0332) |
2.15e-06 (0.00156) |
0.00446 (1.00) |
1.11e-07 (8.29e-05) |
0.0242 (1.00) |
20p gain | 0 (0%) | 437 |
0.102 (1.00) |
0.149 (1.00) |
1.93e-14 (1.51e-11) |
0.00326 (1.00) |
0.000453 (0.295) |
0.000979 (0.616) |
3.59e-06 (0.00258) |
5.29e-06 (0.00377) |
3.18e-07 (0.000236) |
0.00242 (1.00) |
6.47e-07 (0.000475) |
0.0211 (1.00) |
1p loss | 0 (0%) | 472 |
0.000836 (0.532) |
5.38e-05 (0.0365) |
2.77e-05 (0.0191) |
0.483 (1.00) |
5.05e-08 (3.81e-05) |
0.000435 (0.284) |
0.0123 (1.00) |
4.64e-06 (0.00332) |
0.112 (1.00) |
9.78e-12 (7.57e-09) |
0.493 (1.00) |
0.0348 (1.00) |
6p loss | 0 (0%) | 445 |
0.0139 (1.00) |
0.00408 (1.00) |
7.13e-11 (5.47e-08) |
0.00369 (1.00) |
0.000122 (0.0815) |
7.03e-06 (0.00498) |
0.000722 (0.463) |
0.00105 (0.658) |
1.42e-07 (0.000106) |
0.000119 (0.0795) |
0.011 (1.00) |
0.0427 (1.00) |
1q loss | 0 (0%) | 484 |
0.0107 (1.00) |
0.0133 (1.00) |
6.85e-07 (0.000503) |
1 (1.00) |
0.000863 (0.548) |
0.00112 (0.695) |
1.9e-05 (0.0131) |
3.17e-06 (0.00229) |
0.128 (1.00) |
2.88e-10 (2.2e-07) |
0.488 (1.00) |
0.0896 (1.00) |
18p loss | 0 (0%) | 458 |
0.194 (1.00) |
0.486 (1.00) |
4.41e-05 (0.0301) |
0.0457 (1.00) |
0.0183 (1.00) |
0.00473 (1.00) |
6.06e-06 (0.00431) |
0.000196 (0.13) |
0.000231 (0.153) |
0.00146 (0.901) |
0.00259 (1.00) |
0.00109 (0.68) |
3q gain | 0 (0%) | 475 |
0.0249 (1.00) |
0.0289 (1.00) |
4.38e-07 (0.000324) |
0.0593 (1.00) |
0.00718 (1.00) |
0.000107 (0.0722) |
0.000705 (0.453) |
0.00522 (1.00) |
1.06e-05 (0.00744) |
0.00177 (1.00) |
0.0268 (1.00) |
0.329 (1.00) |
8p gain | 0 (0%) | 488 |
1.74e-05 (0.0121) |
0.089 (1.00) |
0.0868 (1.00) |
0.146 (1.00) |
0.000978 (0.616) |
0.000683 (0.44) |
0.000136 (0.0909) |
0.0286 (1.00) |
0.000293 (0.193) |
0.26 (1.00) |
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21q loss | 0 (0%) | 470 |
0.0145 (1.00) |
0.0238 (1.00) |
0.000106 (0.0715) |
0.236 (1.00) |
0.00501 (1.00) |
0.0399 (1.00) |
0.00192 (1.00) |
1.72e-05 (0.012) |
0.195 (1.00) |
1.65e-05 (0.0115) |
0.749 (1.00) |
0.937 (1.00) |
7p gain | 0 (0%) | 376 |
0.877 (1.00) |
1 (1.00) |
1.75e-09 (1.33e-06) |
0.0604 (1.00) |
0.000268 (0.177) |
0.00565 (1.00) |
0.068 (1.00) |
0.0824 (1.00) |
0.0165 (1.00) |
0.667 (1.00) |
0.0334 (1.00) |
0.715 (1.00) |
7q gain | 0 (0%) | 374 |
0.877 (1.00) |
1 (1.00) |
1.84e-09 (1.4e-06) |
0.0441 (1.00) |
0.000118 (0.0791) |
0.000718 (0.461) |
0.0581 (1.00) |
0.131 (1.00) |
0.00739 (1.00) |
0.466 (1.00) |
0.0485 (1.00) |
0.253 (1.00) |
6q loss | 0 (0%) | 419 |
0.0393 (1.00) |
0.0205 (1.00) |
2.46e-09 (1.87e-06) |
0.147 (1.00) |
0.0014 (0.866) |
0.00103 (0.647) |
0.204 (1.00) |
0.478 (1.00) |
1.78e-05 (0.0124) |
0.000884 (0.561) |
0.0911 (1.00) |
0.18 (1.00) |
13q loss | 0 (0%) | 473 |
0.0253 (1.00) |
0.0381 (1.00) |
5.97e-06 (0.00425) |
0.148 (1.00) |
0.00137 (0.852) |
0.00139 (0.859) |
0.0025 (1.00) |
0.00046 (0.299) |
0.000157 (0.105) |
0.000796 (0.508) |
0.155 (1.00) |
0.00467 (1.00) |
18q loss | 0 (0%) | 456 |
0.259 (1.00) |
0.302 (1.00) |
6.3e-05 (0.0427) |
0.0627 (1.00) |
0.0551 (1.00) |
0.0128 (1.00) |
2.87e-05 (0.0197) |
0.000574 (0.371) |
0.000536 (0.348) |
0.000642 (0.414) |
0.00238 (1.00) |
0.00293 (1.00) |
1q gain | 0 (0%) | 472 |
0.611 (1.00) |
0.617 (1.00) |
2.09e-08 (1.57e-05) |
0.518 (1.00) |
0.434 (1.00) |
0.19 (1.00) |
0.00972 (1.00) |
0.15 (1.00) |
0.0387 (1.00) |
0.473 (1.00) |
0.288 (1.00) |
0.811 (1.00) |
2p gain | 0 (0%) | 455 |
0.561 (1.00) |
0.4 (1.00) |
1.96e-05 (0.0136) |
0.6 (1.00) |
0.0462 (1.00) |
0.783 (1.00) |
0.144 (1.00) |
0.0785 (1.00) |
0.303 (1.00) |
0.335 (1.00) |
0.388 (1.00) |
0.508 (1.00) |
5p gain | 0 (0%) | 361 |
0.593 (1.00) |
0.516 (1.00) |
0.000273 (0.18) |
0.228 (1.00) |
0.0817 (1.00) |
0.0546 (1.00) |
0.0458 (1.00) |
0.00844 (1.00) |
0.0185 (1.00) |
0.141 (1.00) |
0.0355 (1.00) |
0.561 (1.00) |
19p gain | 0 (0%) | 479 |
0.189 (1.00) |
0.207 (1.00) |
1.47e-05 (0.0103) |
0.326 (1.00) |
0.0448 (1.00) |
0.397 (1.00) |
0.0428 (1.00) |
0.0115 (1.00) |
0.0567 (1.00) |
0.0142 (1.00) |
0.124 (1.00) |
1 (1.00) |
19q gain | 0 (0%) | 476 |
0.0536 (1.00) |
0.0623 (1.00) |
1.53e-06 (0.00112) |
0.221 (1.00) |
0.056 (1.00) |
0.154 (1.00) |
0.0185 (1.00) |
0.00414 (1.00) |
0.0166 (1.00) |
0.00276 (1.00) |
0.0641 (1.00) |
0.913 (1.00) |
3q loss | 0 (0%) | 430 |
0.701 (1.00) |
0.7 (1.00) |
2.72e-06 (0.00197) |
0.132 (1.00) |
0.0955 (1.00) |
0.00661 (1.00) |
0.518 (1.00) |
0.804 (1.00) |
0.649 (1.00) |
0.0751 (1.00) |
0.074 (1.00) |
0.462 (1.00) |
4q loss | 0 (0%) | 476 |
1 (1.00) |
1 (1.00) |
2.66e-05 (0.0183) |
0.104 (1.00) |
0.251 (1.00) |
0.313 (1.00) |
0.0631 (1.00) |
0.0573 (1.00) |
0.969 (1.00) |
0.745 (1.00) |
0.453 (1.00) |
0.15 (1.00) |
10p loss | 0 (0%) | 472 |
0.026 (1.00) |
0.0306 (1.00) |
3.88e-06 (0.00279) |
0.151 (1.00) |
0.195 (1.00) |
0.037 (1.00) |
0.0123 (1.00) |
0.0197 (1.00) |
0.161 (1.00) |
0.000543 (0.352) |
0.354 (1.00) |
0.181 (1.00) |
1p gain | 0 (0%) | 499 |
0.105 (1.00) |
0.439 (1.00) |
0.0359 (1.00) |
0.846 (1.00) |
0.85 (1.00) |
0.62 (1.00) |
1 (1.00) |
|||||
2q gain | 0 (0%) | 454 |
0.561 (1.00) |
0.4 (1.00) |
0.000406 (0.266) |
0.579 (1.00) |
0.0528 (1.00) |
0.862 (1.00) |
0.0519 (1.00) |
0.0498 (1.00) |
0.135 (1.00) |
0.335 (1.00) |
0.699 (1.00) |
0.508 (1.00) |
3p gain | 0 (0%) | 497 |
0.204 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.00329 (1.00) |
0.294 (1.00) |
0.161 (1.00) |
0.00488 (1.00) |
0.0529 (1.00) |
0.606 (1.00) |
0.694 (1.00) |
||
4p gain | 0 (0%) | 496 |
0.121 (1.00) |
0.625 (1.00) |
0.428 (1.00) |
0.0803 (1.00) |
0.0257 (1.00) |
0.378 (1.00) |
0.00158 (0.974) |
0.147 (1.00) |
||||
4q gain | 0 (0%) | 496 |
0.486 (1.00) |
0.785 (1.00) |
0.878 (1.00) |
0.338 (1.00) |
0.0112 (1.00) |
0.509 (1.00) |
0.00158 (0.974) |
0.179 (1.00) |
||||
5q gain | 0 (0%) | 345 |
0.105 (1.00) |
0.0689 (1.00) |
0.00308 (1.00) |
0.197 (1.00) |
0.158 (1.00) |
0.175 (1.00) |
0.0381 (1.00) |
0.00512 (1.00) |
0.0596 (1.00) |
0.0184 (1.00) |
0.0563 (1.00) |
0.23 (1.00) |
6p gain | 0 (0%) | 498 |
0.876 (1.00) |
0.569 (1.00) |
0.819 (1.00) |
0.877 (1.00) |
0.215 (1.00) |
0.449 (1.00) |
0.33 (1.00) |
0.101 (1.00) |
||||
6q gain | 0 (0%) | 499 |
0.536 (1.00) |
0.625 (1.00) |
0.571 (1.00) |
0.626 (1.00) |
0.442 (1.00) |
0.571 (1.00) |
0.725 (1.00) |
0.055 (1.00) |
||||
9p gain | 0 (0%) | 496 |
0.385 (1.00) |
0.785 (1.00) |
0.17 (1.00) |
0.17 (1.00) |
0.103 (1.00) |
0.0571 (1.00) |
0.907 (1.00) |
0.0309 (1.00) |
0.356 (1.00) |
0.0195 (1.00) |
||
9q gain | 0 (0%) | 496 |
0.068 (1.00) |
0.534 (1.00) |
0.104 (1.00) |
0.338 (1.00) |
0.523 (1.00) |
0.636 (1.00) |
0.533 (1.00) |
0.179 (1.00) |
0.685 (1.00) |
1 (1.00) |
||
10p gain | 0 (0%) | 498 |
0.446 (1.00) |
1 (1.00) |
0.981 (1.00) |
1 (1.00) |
0.267 (1.00) |
0.311 (1.00) |
0.769 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.694 (1.00) |
||
10q gain | 0 (0%) | 500 |
0.164 (1.00) |
1 (1.00) |
0.716 (1.00) |
0.615 (1.00) |
0.688 (1.00) |
0.508 (1.00) |
0.822 (1.00) |
0.367 (1.00) |
||||
11p gain | 0 (0%) | 487 |
0.769 (1.00) |
0.783 (1.00) |
0.0169 (1.00) |
0.559 (1.00) |
0.437 (1.00) |
0.395 (1.00) |
0.491 (1.00) |
0.265 (1.00) |
0.701 (1.00) |
0.411 (1.00) |
0.188 (1.00) |
0.325 (1.00) |
11q gain | 0 (0%) | 489 |
0.769 (1.00) |
0.783 (1.00) |
0.0471 (1.00) |
0.578 (1.00) |
0.541 (1.00) |
0.48 (1.00) |
0.586 (1.00) |
0.505 (1.00) |
0.842 (1.00) |
0.356 (1.00) |
0.528 (1.00) |
0.787 (1.00) |
13q gain | 0 (0%) | 490 |
0.832 (1.00) |
0.0277 (1.00) |
0.467 (1.00) |
0.771 (1.00) |
0.0685 (1.00) |
0.636 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.867 (1.00) |
||
14q gain | 0 (0%) | 499 |
0.061 (1.00) |
0.625 (1.00) |
0.869 (1.00) |
0.0596 (1.00) |
0.00354 (1.00) |
0.0477 (1.00) |
0.0297 (1.00) |
0.0249 (1.00) |
||||
15q gain | 0 (0%) | 490 |
0.0652 (1.00) |
0.513 (1.00) |
0.644 (1.00) |
0.237 (1.00) |
0.116 (1.00) |
0.379 (1.00) |
0.885 (1.00) |
0.504 (1.00) |
0.33 (1.00) |
0.127 (1.00) |
||
16p gain | 0 (0%) | 436 |
0.1 (1.00) |
0.302 (1.00) |
0.105 (1.00) |
0.715 (1.00) |
0.0115 (1.00) |
0.0663 (1.00) |
0.635 (1.00) |
0.113 (1.00) |
0.175 (1.00) |
0.56 (1.00) |
0.34 (1.00) |
0.651 (1.00) |
16q gain | 0 (0%) | 443 |
0.0706 (1.00) |
0.174 (1.00) |
0.101 (1.00) |
0.945 (1.00) |
0.0443 (1.00) |
0.122 (1.00) |
0.696 (1.00) |
0.336 (1.00) |
0.229 (1.00) |
0.628 (1.00) |
0.2 (1.00) |
0.772 (1.00) |
17p gain | 0 (0%) | 488 |
0.00522 (1.00) |
0.00665 (1.00) |
0.00405 (1.00) |
0.537 (1.00) |
0.321 (1.00) |
0.0336 (1.00) |
0.191 (1.00) |
0.0327 (1.00) |
0.551 (1.00) |
0.0077 (1.00) |
0.25 (1.00) |
0.694 (1.00) |
17q gain | 0 (0%) | 482 |
0.00827 (1.00) |
0.0106 (1.00) |
0.00919 (1.00) |
0.169 (1.00) |
0.553 (1.00) |
0.0547 (1.00) |
0.253 (1.00) |
0.00949 (1.00) |
0.281 (1.00) |
0.0017 (1.00) |
0.0768 (1.00) |
0.282 (1.00) |
18p gain | 0 (0%) | 486 |
0.0764 (1.00) |
0.0436 (1.00) |
0.436 (1.00) |
0.144 (1.00) |
0.319 (1.00) |
0.143 (1.00) |
0.0977 (1.00) |
0.41 (1.00) |
0.827 (1.00) |
0.288 (1.00) |
0.421 (1.00) |
0.152 (1.00) |
18q gain | 0 (0%) | 486 |
0.0764 (1.00) |
0.0436 (1.00) |
0.436 (1.00) |
0.144 (1.00) |
0.319 (1.00) |
0.143 (1.00) |
0.0977 (1.00) |
0.41 (1.00) |
0.827 (1.00) |
0.288 (1.00) |
0.421 (1.00) |
0.152 (1.00) |
21q gain | 0 (0%) | 469 |
0.82 (1.00) |
0.818 (1.00) |
0.000757 (0.485) |
0.087 (1.00) |
0.0368 (1.00) |
0.836 (1.00) |
0.0709 (1.00) |
0.08 (1.00) |
0.377 (1.00) |
0.375 (1.00) |
0.05 (1.00) |
0.0476 (1.00) |
22q gain | 0 (0%) | 479 |
0.58 (1.00) |
0.0436 (1.00) |
0.00243 (1.00) |
0.0394 (1.00) |
0.452 (1.00) |
0.217 (1.00) |
0.826 (1.00) |
0.846 (1.00) |
1 (1.00) |
0.564 (1.00) |
0.528 (1.00) |
0.367 (1.00) |
Xq gain | 0 (0%) | 495 |
0.472 (1.00) |
0.742 (1.00) |
0.126 (1.00) |
0.338 (1.00) |
0.0651 (1.00) |
0.153 (1.00) |
0.465 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.787 (1.00) |
||
4p loss | 0 (0%) | 469 |
0.289 (1.00) |
0.298 (1.00) |
0.00354 (1.00) |
0.136 (1.00) |
0.816 (1.00) |
0.948 (1.00) |
0.0888 (1.00) |
0.366 (1.00) |
0.552 (1.00) |
0.96 (1.00) |
0.729 (1.00) |
0.289 (1.00) |
8p loss | 0 (0%) | 405 |
0.777 (1.00) |
0.784 (1.00) |
0.00339 (1.00) |
0.767 (1.00) |
0.738 (1.00) |
0.656 (1.00) |
0.141 (1.00) |
0.561 (1.00) |
0.422 (1.00) |
0.891 (1.00) |
0.785 (1.00) |
0.446 (1.00) |
8q loss | 0 (0%) | 464 |
0.49 (1.00) |
0.591 (1.00) |
0.934 (1.00) |
0.307 (1.00) |
0.476 (1.00) |
0.7 (1.00) |
0.188 (1.00) |
0.0552 (1.00) |
0.812 (1.00) |
0.587 (1.00) |
0.574 (1.00) |
0.754 (1.00) |
10q loss | 0 (0%) | 456 |
0.0972 (1.00) |
0.121 (1.00) |
0.00107 (0.67) |
0.0115 (1.00) |
0.22 (1.00) |
0.0125 (1.00) |
0.095 (1.00) |
0.126 (1.00) |
0.239 (1.00) |
0.0129 (1.00) |
0.68 (1.00) |
0.147 (1.00) |
11p loss | 0 (0%) | 499 |
0.0313 (1.00) |
0.625 (1.00) |
0.156 (1.00) |
0.0359 (1.00) |
0.359 (1.00) |
0.462 (1.00) |
0.452 (1.00) |
0.329 (1.00) |
||||
11q loss | 0 (0%) | 497 |
0.00534 (1.00) |
0.83 (1.00) |
0.0533 (1.00) |
0.215 (1.00) |
0.377 (1.00) |
0.311 (1.00) |
0.226 (1.00) |
0.214 (1.00) |
0.102 (1.00) |
0.204 (1.00) |
||
15q loss | 0 (0%) | 492 |
0.58 (1.00) |
0.586 (1.00) |
0.00461 (1.00) |
0.534 (1.00) |
0.451 (1.00) |
0.704 (1.00) |
0.0733 (1.00) |
0.136 (1.00) |
0.341 (1.00) |
0.309 (1.00) |
0.126 (1.00) |
0.787 (1.00) |
16q loss | 0 (0%) | 498 |
0.244 (1.00) |
0.363 (1.00) |
0.167 (1.00) |
0.456 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.452 (1.00) |
0.125 (1.00) |
0.449 (1.00) |
0.282 (1.00) |
||
19p loss | 0 (0%) | 500 |
0.126 (1.00) |
0.363 (1.00) |
0.279 (1.00) |
0.0359 (1.00) |
0.341 (1.00) |
0.379 (1.00) |
0.822 (1.00) |
0.723 (1.00) |
||||
20p loss | 0 (0%) | 498 |
0.209 (1.00) |
1 (1.00) |
0.0172 (1.00) |
0.877 (1.00) |
0.267 (1.00) |
0.747 (1.00) |
0.0489 (1.00) |
0.233 (1.00) |
||||
22q loss | 0 (0%) | 492 |
0.00143 (0.881) |
0.0167 (1.00) |
0.0462 (1.00) |
0.393 (1.00) |
0.000888 (0.562) |
0.0191 (1.00) |
0.191 (1.00) |
0.812 (1.00) |
1 (1.00) |
0.867 (1.00) |
||
Xq loss | 0 (0%) | 494 |
0.256 (1.00) |
0.272 (1.00) |
0.717 (1.00) |
0.631 (1.00) |
0.31 (1.00) |
0.287 (1.00) |
0.0676 (1.00) |
0.00763 (1.00) |
0.031 (1.00) |
0.000416 (0.272) |
0.795 (1.00) |
0.694 (1.00) |
P value = 2.09e-08 (Fisher's exact test), Q value = 1.6e-05
Table S1. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
1Q GAIN CNV | 26 | 5 | 1 |
1Q GAIN WILD-TYPE | 138 | 211 | 123 |
Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D2V3.png)
P value = 1.96e-05 (Fisher's exact test), Q value = 0.014
Table S2. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
2P GAIN CNV | 31 | 12 | 6 |
2P GAIN WILD-TYPE | 133 | 204 | 118 |
Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 4.38e-07 (Fisher's exact test), Q value = 0.00032
Table S3. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
3Q GAIN CNV | 23 | 3 | 3 |
3Q GAIN WILD-TYPE | 141 | 213 | 121 |
Figure S3. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D6V3.png)
P value = 0.000107 (Fisher's exact test), Q value = 0.072
Table S4. Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
3Q GAIN CNV | 3 | 8 | 15 |
3Q GAIN WILD-TYPE | 183 | 144 | 94 |
Figure S4. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D6V6.png)
P value = 1.06e-05 (Fisher's exact test), Q value = 0.0074
Table S5. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
3Q GAIN CNV | 5 | 3 | 21 |
3Q GAIN WILD-TYPE | 110 | 208 | 139 |
Figure S5. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D6V9.png)
P value = 0.000273 (Fisher's exact test), Q value = 0.18
Table S6. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
5P GAIN CNV | 64 | 57 | 22 |
5P GAIN WILD-TYPE | 100 | 159 | 102 |
Figure S6. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 1.75e-09 (Fisher's exact test), Q value = 1.3e-06
Table S7. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
7P GAIN CNV | 69 | 29 | 30 |
7P GAIN WILD-TYPE | 95 | 187 | 94 |
Figure S7. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 0.000268 (Chi-square test), Q value = 0.18
Table S8. Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
7P GAIN CNV | 18 | 11 | 26 | 31 | 11 | 19 |
7P GAIN WILD-TYPE | 82 | 77 | 58 | 44 | 32 | 38 |
Figure S8. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D13V5.png)
P value = 1.84e-09 (Fisher's exact test), Q value = 1.4e-06
Table S9. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
7Q GAIN CNV | 69 | 29 | 32 |
7Q GAIN WILD-TYPE | 95 | 187 | 92 |
Figure S9. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 0.000118 (Chi-square test), Q value = 0.079
Table S10. Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
7Q GAIN CNV | 17 | 12 | 27 | 31 | 10 | 21 |
7Q GAIN WILD-TYPE | 83 | 76 | 57 | 44 | 33 | 36 |
Figure S10. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D14V5.png)
P value = 1.74e-05 (Fisher's exact test), Q value = 0.012
Table S11. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
8P GAIN CNV | 13 | 0 | 3 |
8P GAIN WILD-TYPE | 151 | 216 | 121 |
Figure S11. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 0.000136 (Fisher's exact test), Q value = 0.091
Table S12. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
8P GAIN CNV | 2 | 1 | 13 |
8P GAIN WILD-TYPE | 113 | 210 | 147 |
Figure S12. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D15V9.png)
P value = 0.000293 (Fisher's exact test), Q value = 0.19
Table S13. Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
8P GAIN CNV | 0 | 0 | 8 |
8P GAIN WILD-TYPE | 52 | 97 | 67 |
Figure S13. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D15V11.png)
P value = 5.94e-11 (Fisher's exact test), Q value = 4.6e-08
Table S14. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
8Q GAIN CNV | 27 | 0 | 9 |
8Q GAIN WILD-TYPE | 137 | 216 | 115 |
Figure S14. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 1.15e-07 (Fisher's exact test), Q value = 8.6e-05
Table S15. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
8Q GAIN CNV | 1 | 25 | 5 |
8Q GAIN WILD-TYPE | 196 | 154 | 92 |
Figure S15. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D16V7.png)
P value = 4.88e-05 (Fisher's exact test), Q value = 0.033
Table S16. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
8Q GAIN CNV | 3 | 4 | 24 |
8Q GAIN WILD-TYPE | 66 | 210 | 166 |
Figure S16. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D16V8.png)
P value = 2.15e-06 (Fisher's exact test), Q value = 0.0016
Table S17. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
8Q GAIN CNV | 6 | 4 | 25 |
8Q GAIN WILD-TYPE | 109 | 207 | 135 |
Figure S17. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D16V9.png)
P value = 1.11e-07 (Fisher's exact test), Q value = 8.3e-05
Table S18. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
8Q GAIN CNV | 0 | 0 | 14 |
8Q GAIN WILD-TYPE | 52 | 97 | 61 |
Figure S18. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D16V11.png)
P value = 1.35e-08 (Fisher's exact test), Q value = 1e-05
Table S19. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
12P GAIN CNV | 48 | 14 | 18 |
12P GAIN WILD-TYPE | 116 | 202 | 106 |
Figure S19. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D23V3.png)
P value = 5.67e-07 (Chi-square test), Q value = 0.00042
Table S20. Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
12P GAIN CNV | 4 | 9 | 20 | 9 | 6 | 21 |
12P GAIN WILD-TYPE | 96 | 79 | 64 | 66 | 37 | 36 |
Figure S20. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D23V5.png)
P value = 1.1e-05 (Fisher's exact test), Q value = 0.0077
Table S21. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
12P GAIN CNV | 15 | 45 | 12 |
12P GAIN WILD-TYPE | 182 | 134 | 85 |
Figure S21. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D23V7.png)
P value = 1.89e-05 (Fisher's exact test), Q value = 0.013
Table S22. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
12P GAIN CNV | 7 | 18 | 47 |
12P GAIN WILD-TYPE | 62 | 196 | 143 |
Figure S22. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D23V8.png)
P value = 3.26e-06 (Fisher's exact test), Q value = 0.0023
Table S23. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
12P GAIN CNV | 14 | 20 | 46 |
12P GAIN WILD-TYPE | 101 | 191 | 114 |
Figure S23. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D23V9.png)
P value = 2.07e-06 (Fisher's exact test), Q value = 0.0015
Table S24. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
12P GAIN CNV | 7 | 4 | 24 |
12P GAIN WILD-TYPE | 45 | 93 | 51 |
Figure S24. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D23V11.png)
P value = 6.42e-09 (Fisher's exact test), Q value = 4.9e-06
Table S25. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
12Q GAIN CNV | 49 | 14 | 18 |
12Q GAIN WILD-TYPE | 115 | 202 | 106 |
Figure S25. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D24V3.png)
P value = 1.46e-07 (Chi-square test), Q value = 0.00011
Table S26. Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
12Q GAIN CNV | 4 | 9 | 20 | 9 | 6 | 22 |
12Q GAIN WILD-TYPE | 96 | 79 | 64 | 66 | 37 | 35 |
Figure S26. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D24V5.png)
P value = 6.06e-06 (Fisher's exact test), Q value = 0.0043
Table S27. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
12Q GAIN CNV | 15 | 46 | 12 |
12Q GAIN WILD-TYPE | 182 | 133 | 85 |
Figure S27. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D24V7.png)
P value = 9.22e-06 (Fisher's exact test), Q value = 0.0065
Table S28. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
12Q GAIN CNV | 7 | 18 | 48 |
12Q GAIN WILD-TYPE | 62 | 196 | 142 |
Figure S28. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D24V8.png)
P value = 1.72e-06 (Fisher's exact test), Q value = 0.0013
Table S29. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
12Q GAIN CNV | 14 | 20 | 47 |
12Q GAIN WILD-TYPE | 101 | 191 | 113 |
Figure S29. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D24V9.png)
P value = 8.85e-07 (Fisher's exact test), Q value = 0.00065
Table S30. Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
12Q GAIN CNV | 7 | 4 | 25 |
12Q GAIN WILD-TYPE | 45 | 93 | 50 |
Figure S30. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D24V11.png)
P value = 1.47e-05 (Fisher's exact test), Q value = 0.01
Table S31. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
19P GAIN CNV | 16 | 1 | 8 |
19P GAIN WILD-TYPE | 148 | 215 | 116 |
Figure S31. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D34V3.png)
P value = 1.53e-06 (Fisher's exact test), Q value = 0.0011
Table S32. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
19Q GAIN CNV | 19 | 1 | 8 |
19Q GAIN WILD-TYPE | 145 | 215 | 116 |
Figure S32. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D35V3.png)
P value = 1.93e-14 (Fisher's exact test), Q value = 1.5e-11
Table S33. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
20P GAIN CNV | 44 | 3 | 20 |
20P GAIN WILD-TYPE | 120 | 213 | 104 |
Figure S33. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 3.59e-06 (Fisher's exact test), Q value = 0.0026
Table S34. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
20P GAIN CNV | 12 | 42 | 10 |
20P GAIN WILD-TYPE | 185 | 137 | 87 |
Figure S34. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D36V7.png)
P value = 5.29e-06 (Fisher's exact test), Q value = 0.0038
Table S35. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
20P GAIN CNV | 8 | 13 | 43 |
20P GAIN WILD-TYPE | 61 | 201 | 147 |
Figure S35. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D36V8.png)
P value = 3.18e-07 (Fisher's exact test), Q value = 0.00024
Table S36. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
20P GAIN CNV | 11 | 14 | 42 |
20P GAIN WILD-TYPE | 104 | 197 | 118 |
Figure S36. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D36V9.png)
P value = 6.47e-07 (Fisher's exact test), Q value = 0.00048
Table S37. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
20P GAIN CNV | 4 | 2 | 21 |
20P GAIN WILD-TYPE | 48 | 95 | 54 |
Figure S37. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D36V11.png)
P value = 1.37e-15 (Fisher's exact test), Q value = 1.1e-12
Table S38. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
20Q GAIN CNV | 47 | 3 | 19 |
20Q GAIN WILD-TYPE | 117 | 213 | 105 |
Figure S38. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 3.54e-05 (Chi-square test), Q value = 0.024
Table S39. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
20Q GAIN CNV | 4 | 8 | 14 | 15 | 4 | 18 |
20Q GAIN WILD-TYPE | 96 | 80 | 70 | 60 | 39 | 39 |
Figure S39. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D37V5.png)
P value = 3.3e-07 (Fisher's exact test), Q value = 0.00024
Table S40. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
20Q GAIN CNV | 12 | 45 | 9 |
20Q GAIN WILD-TYPE | 185 | 134 | 88 |
Figure S40. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 1.47e-06 (Fisher's exact test), Q value = 0.0011
Table S41. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
20Q GAIN CNV | 8 | 13 | 45 |
20Q GAIN WILD-TYPE | 61 | 201 | 145 |
Figure S41. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 1.54e-08 (Fisher's exact test), Q value = 1.2e-05
Table S42. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
20Q GAIN CNV | 10 | 14 | 45 |
20Q GAIN WILD-TYPE | 105 | 197 | 115 |
Figure S42. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D37V9.png)
P value = 7.31e-08 (Fisher's exact test), Q value = 5.5e-05
Table S43. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
20Q GAIN CNV | 4 | 2 | 23 |
20Q GAIN WILD-TYPE | 48 | 95 | 52 |
Figure S43. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D37V11.png)
P value = 5.38e-05 (Fisher's exact test), Q value = 0.037
Table S44. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 32 | 24 |
1P LOSS CNV | 8 | 2 | 1 |
1P LOSS WILD-TYPE | 6 | 30 | 23 |
Figure S44. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D41V2.png)
P value = 2.77e-05 (Fisher's exact test), Q value = 0.019
Table S45. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
1P LOSS CNV | 10 | 4 | 18 |
1P LOSS WILD-TYPE | 154 | 212 | 106 |
Figure S45. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D41V3.png)
P value = 5.05e-08 (Chi-square test), Q value = 3.8e-05
Table S46. Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
1P LOSS CNV | 3 | 1 | 3 | 16 | 3 | 0 |
1P LOSS WILD-TYPE | 97 | 87 | 81 | 59 | 40 | 57 |
Figure S46. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D41V5.png)
P value = 4.64e-06 (Fisher's exact test), Q value = 0.0033
Table S47. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
1P LOSS CNV | 15 | 9 | 6 |
1P LOSS WILD-TYPE | 54 | 205 | 184 |
Figure S47. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D41V8.png)
P value = 9.78e-12 (Fisher's exact test), Q value = 7.6e-09
Table S48. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
1P LOSS CNV | 4 | 16 | 12 |
1P LOSS WILD-TYPE | 159 | 20 | 275 |
Figure S48. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D41V10.png)
P value = 6.85e-07 (Fisher's exact test), Q value = 5e-04
Table S49. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
1Q LOSS CNV | 4 | 1 | 15 |
1Q LOSS WILD-TYPE | 160 | 215 | 109 |
Figure S49. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D42V3.png)
P value = 1.9e-05 (Fisher's exact test), Q value = 0.013
Table S50. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
1Q LOSS CNV | 5 | 2 | 13 |
1Q LOSS WILD-TYPE | 192 | 177 | 84 |
Figure S50. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D42V7.png)
P value = 3.17e-06 (Fisher's exact test), Q value = 0.0023
Table S51. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
1Q LOSS CNV | 12 | 5 | 3 |
1Q LOSS WILD-TYPE | 57 | 209 | 187 |
Figure S51. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D42V8.png)
P value = 2.88e-10 (Fisher's exact test), Q value = 2.2e-07
Table S52. Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
1Q LOSS CNV | 2 | 12 | 6 |
1Q LOSS WILD-TYPE | 161 | 24 | 281 |
Figure S52. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D42V10.png)
P value = 0.000249 (Fisher's exact test), Q value = 0.16
Table S53. Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 24 | 13 |
2P LOSS CNV | 0 | 1 | 5 |
2P LOSS WILD-TYPE | 33 | 23 | 8 |
Figure S53. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D43V1.png)
P value = 6.13e-07 (Fisher's exact test), Q value = 0.00045
Table S54. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
2P LOSS CNV | 0 | 0 | 10 |
2P LOSS WILD-TYPE | 164 | 216 | 114 |
Figure S54. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D43V3.png)
P value = 1.37e-05 (Chi-square test), Q value = 0.0096
Table S55. Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
2P LOSS CNV | 0 | 0 | 0 | 6 | 0 | 0 |
2P LOSS WILD-TYPE | 100 | 88 | 84 | 69 | 43 | 57 |
Figure S55. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D43V5.png)
P value = 0.000189 (Fisher's exact test), Q value = 0.13
Table S56. Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
2P LOSS CNV | 0 | 0 | 6 |
2P LOSS WILD-TYPE | 186 | 152 | 103 |
Figure S56. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D43V6.png)
P value = 4.72e-07 (Fisher's exact test), Q value = 0.00035
Table S57. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
2P LOSS CNV | 0 | 0 | 9 |
2P LOSS WILD-TYPE | 197 | 179 | 88 |
Figure S57. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D43V7.png)
P value = 1.87e-08 (Fisher's exact test), Q value = 1.4e-05
Table S58. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
2P LOSS CNV | 9 | 0 | 0 |
2P LOSS WILD-TYPE | 60 | 214 | 190 |
Figure S58. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D43V8.png)
P value = 0.000232 (Fisher's exact test), Q value = 0.15
Table S59. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
2P LOSS CNV | 1 | 0 | 9 |
2P LOSS WILD-TYPE | 114 | 211 | 151 |
Figure S59. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D43V9.png)
P value = 1.38e-12 (Fisher's exact test), Q value = 1.1e-09
Table S60. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
2P LOSS CNV | 0 | 10 | 0 |
2P LOSS WILD-TYPE | 163 | 26 | 287 |
Figure S60. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D43V10.png)
P value = 0.000249 (Fisher's exact test), Q value = 0.16
Table S61. Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 24 | 13 |
2Q LOSS CNV | 0 | 1 | 5 |
2Q LOSS WILD-TYPE | 33 | 23 | 8 |
Figure S61. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D44V1.png)
P value = 2.38e-06 (Fisher's exact test), Q value = 0.0017
Table S62. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
2Q LOSS CNV | 1 | 0 | 10 |
2Q LOSS WILD-TYPE | 163 | 216 | 114 |
Figure S62. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D44V3.png)
P value = 0.000129 (Chi-square test), Q value = 0.087
Table S63. Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
2Q LOSS CNV | 0 | 0 | 0 | 6 | 0 | 1 |
2Q LOSS WILD-TYPE | 100 | 88 | 84 | 69 | 43 | 56 |
Figure S63. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D44V5.png)
P value = 4.42e-05 (Fisher's exact test), Q value = 0.03
Table S64. Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
2Q LOSS CNV | 0 | 0 | 7 |
2Q LOSS WILD-TYPE | 186 | 152 | 102 |
Figure S64. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D44V6.png)
P value = 8.96e-08 (Fisher's exact test), Q value = 6.7e-05
Table S65. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
2Q LOSS CNV | 0 | 0 | 10 |
2Q LOSS WILD-TYPE | 197 | 179 | 87 |
Figure S65. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D44V7.png)
P value = 7.91e-08 (Fisher's exact test), Q value = 6e-05
Table S66. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
2Q LOSS CNV | 9 | 0 | 1 |
2Q LOSS WILD-TYPE | 60 | 214 | 189 |
Figure S66. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D44V8.png)
P value = 0.000101 (Fisher's exact test), Q value = 0.068
Table S67. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
2Q LOSS CNV | 1 | 0 | 10 |
2Q LOSS WILD-TYPE | 114 | 211 | 150 |
Figure S67. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D44V9.png)
P value = 1.44e-11 (Fisher's exact test), Q value = 1.1e-08
Table S68. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
2Q LOSS CNV | 0 | 10 | 1 |
2Q LOSS WILD-TYPE | 163 | 26 | 286 |
Figure S68. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D44V10.png)
P value = 9.35e-35 (Fisher's exact test), Q value = 7.4e-32
Table S69. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
3P LOSS CNV | 118 | 174 | 19 |
3P LOSS WILD-TYPE | 46 | 42 | 105 |
Figure S69. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D45V3.png)
P value = 4.94e-06 (Fisher's exact test), Q value = 0.0035
Table S70. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 114 | 76 |
3P LOSS CNV | 66 | 88 | 32 |
3P LOSS WILD-TYPE | 34 | 26 | 44 |
Figure S70. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D45V4.png)
P value = 0.000105 (Chi-square test), Q value = 0.071
Table S71. Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
3P LOSS CNV | 77 | 47 | 55 | 40 | 33 | 26 |
3P LOSS WILD-TYPE | 23 | 41 | 29 | 35 | 10 | 31 |
Figure S71. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D45V5.png)
P value = 1.54e-05 (Fisher's exact test), Q value = 0.011
Table S72. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
3P LOSS CNV | 130 | 101 | 47 |
3P LOSS WILD-TYPE | 56 | 51 | 62 |
Figure S72. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D45V6.png)
P value = 2.09e-11 (Fisher's exact test), Q value = 1.6e-08
Table S73. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
3P LOSS CNV | 154 | 96 | 38 |
3P LOSS WILD-TYPE | 43 | 83 | 59 |
Figure S73. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D45V7.png)
P value = 7.09e-10 (Fisher's exact test), Q value = 5.4e-07
Table S74. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
3P LOSS CNV | 23 | 160 | 105 |
3P LOSS WILD-TYPE | 46 | 54 | 85 |
Figure S74. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D45V8.png)
P value = 1.97e-06 (Fisher's exact test), Q value = 0.0014
Table S75. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
3P LOSS CNV | 63 | 156 | 79 |
3P LOSS WILD-TYPE | 52 | 55 | 81 |
Figure S75. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D45V9.png)
P value = 8.3e-12 (Fisher's exact test), Q value = 6.4e-09
Table S76. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
3P LOSS CNV | 80 | 8 | 210 |
3P LOSS WILD-TYPE | 83 | 28 | 77 |
Figure S76. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D45V10.png)
P value = 2.72e-06 (Fisher's exact test), Q value = 0.002
Table S77. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
3Q LOSS CNV | 33 | 38 | 3 |
3Q LOSS WILD-TYPE | 131 | 178 | 121 |
Figure S77. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D46V3.png)
P value = 2.66e-05 (Fisher's exact test), Q value = 0.018
Table S78. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
4Q LOSS CNV | 20 | 3 | 5 |
4Q LOSS WILD-TYPE | 144 | 213 | 119 |
Figure S78. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 7.13e-11 (Fisher's exact test), Q value = 5.5e-08
Table S79. Gene #49: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
6P LOSS CNV | 40 | 5 | 14 |
6P LOSS WILD-TYPE | 124 | 211 | 110 |
Figure S79. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D49V3.png)
P value = 0.000122 (Chi-square test), Q value = 0.082
Table S80. Gene #49: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
6P LOSS CNV | 10 | 3 | 9 | 14 | 1 | 15 |
6P LOSS WILD-TYPE | 90 | 85 | 75 | 61 | 42 | 42 |
Figure S80. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D49V5.png)
P value = 7.03e-06 (Fisher's exact test), Q value = 0.005
Table S81. Gene #49: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
6P LOSS CNV | 8 | 19 | 25 |
6P LOSS WILD-TYPE | 178 | 133 | 84 |
Figure S81. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D49V6.png)
P value = 1.42e-07 (Fisher's exact test), Q value = 0.00011
Table S82. Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
6P LOSS CNV | 5 | 14 | 38 |
6P LOSS WILD-TYPE | 110 | 197 | 122 |
Figure S82. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D49V9.png)
P value = 0.000119 (Fisher's exact test), Q value = 0.08
Table S83. Gene #49: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
6P LOSS CNV | 19 | 13 | 25 |
6P LOSS WILD-TYPE | 144 | 23 | 262 |
Figure S83. Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D49V10.png)
P value = 2.46e-09 (Fisher's exact test), Q value = 1.9e-06
Table S84. Gene #50: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
6Q LOSS CNV | 53 | 18 | 14 |
6Q LOSS WILD-TYPE | 111 | 198 | 110 |
Figure S84. Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D50V3.png)
P value = 1.78e-05 (Fisher's exact test), Q value = 0.012
Table S85. Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
6Q LOSS CNV | 9 | 29 | 45 |
6Q LOSS WILD-TYPE | 106 | 182 | 115 |
Figure S85. Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D50V9.png)
P value = 6.57e-33 (Fisher's exact test), Q value = 5.2e-30
Table S86. Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
9P LOSS CNV | 77 | 3 | 9 |
9P LOSS WILD-TYPE | 87 | 213 | 115 |
Figure S86. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D53V3.png)
P value = 7.23e-12 (Fisher's exact test), Q value = 5.6e-09
Table S87. Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 114 | 76 |
9P LOSS CNV | 39 | 3 | 11 |
9P LOSS WILD-TYPE | 61 | 111 | 65 |
Figure S87. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D53V4.png)
P value = 1.39e-11 (Fisher's exact test), Q value = 1.1e-08
Table S88. Gene #53: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
9P LOSS CNV | 14 | 60 | 9 |
9P LOSS WILD-TYPE | 183 | 119 | 88 |
Figure S88. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D53V7.png)
P value = 2.71e-12 (Fisher's exact test), Q value = 2.1e-09
Table S89. Gene #53: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
9P LOSS CNV | 5 | 15 | 63 |
9P LOSS WILD-TYPE | 64 | 199 | 127 |
Figure S89. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D53V8.png)
P value = 2.42e-07 (Fisher's exact test), Q value = 0.00018
Table S90. Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
9P LOSS CNV | 15 | 21 | 51 |
9P LOSS WILD-TYPE | 100 | 190 | 109 |
Figure S90. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D53V9.png)
P value = 4.42e-06 (Fisher's exact test), Q value = 0.0032
Table S91. Gene #53: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
9P LOSS CNV | 11 | 5 | 25 |
9P LOSS WILD-TYPE | 41 | 92 | 50 |
Figure S91. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D53V11.png)
P value = 3.42e-05 (Fisher's exact test), Q value = 0.023
Table S92. Gene #53: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 109 | 19 | 96 |
9P LOSS CNV | 11 | 0 | 30 |
9P LOSS WILD-TYPE | 98 | 19 | 66 |
Figure S92. Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D53V12.png)
P value = 2.79e-34 (Fisher's exact test), Q value = 2.2e-31
Table S93. Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
9Q LOSS CNV | 81 | 4 | 9 |
9Q LOSS WILD-TYPE | 83 | 212 | 115 |
Figure S93. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D54V3.png)
P value = 7.61e-13 (Fisher's exact test), Q value = 6e-10
Table S94. Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 114 | 76 |
9Q LOSS CNV | 41 | 3 | 11 |
9Q LOSS WILD-TYPE | 59 | 111 | 65 |
Figure S94. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D54V4.png)
P value = 1.31e-12 (Fisher's exact test), Q value = 1e-09
Table S95. Gene #54: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
9Q LOSS CNV | 15 | 64 | 9 |
9Q LOSS WILD-TYPE | 182 | 115 | 88 |
Figure S95. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D54V7.png)
P value = 3.94e-14 (Fisher's exact test), Q value = 3.1e-11
Table S96. Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
9Q LOSS CNV | 5 | 15 | 68 |
9Q LOSS WILD-TYPE | 64 | 199 | 122 |
Figure S96. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D54V8.png)
P value = 9.59e-09 (Fisher's exact test), Q value = 7.3e-06
Table S97. Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
9Q LOSS CNV | 15 | 21 | 55 |
9Q LOSS WILD-TYPE | 100 | 190 | 105 |
Figure S97. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D54V9.png)
P value = 2.33e-05 (Fisher's exact test), Q value = 0.016
Table S98. Gene #54: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 52 | 97 | 75 |
9Q LOSS CNV | 12 | 7 | 26 |
9Q LOSS WILD-TYPE | 40 | 90 | 49 |
Figure S98. Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D54V11.png)
P value = 3.88e-06 (Fisher's exact test), Q value = 0.0028
Table S99. Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
10P LOSS CNV | 14 | 2 | 16 |
10P LOSS WILD-TYPE | 150 | 214 | 108 |
Figure S99. Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 5.97e-06 (Fisher's exact test), Q value = 0.0043
Table S100. Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
13Q LOSS CNV | 20 | 2 | 9 |
13Q LOSS WILD-TYPE | 144 | 214 | 115 |
Figure S100. Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D59V3.png)
P value = 0.000157 (Fisher's exact test), Q value = 0.1
Table S101. Gene #59: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
13Q LOSS CNV | 7 | 4 | 20 |
13Q LOSS WILD-TYPE | 108 | 207 | 140 |
Figure S101. Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D59V9.png)
P value = 7.35e-13 (Fisher's exact test), Q value = 5.8e-10
Table S102. Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
14Q LOSS CNV | 90 | 46 | 26 |
14Q LOSS WILD-TYPE | 74 | 170 | 98 |
Figure S102. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D60V3.png)
P value = 3.84e-05 (Fisher's exact test), Q value = 0.026
Table S103. Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 114 | 76 |
14Q LOSS CNV | 44 | 19 | 27 |
14Q LOSS WILD-TYPE | 56 | 95 | 49 |
Figure S103. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D60V4.png)
P value = 6.61e-12 (Chi-square test), Q value = 5.1e-09
Table S104. Gene #60: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
14Q LOSS CNV | 20 | 18 | 54 | 18 | 11 | 28 |
14Q LOSS WILD-TYPE | 80 | 70 | 30 | 57 | 32 | 29 |
Figure S104. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D60V5.png)
P value = 2.08e-07 (Fisher's exact test), Q value = 0.00015
Table S105. Gene #60: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
14Q LOSS CNV | 37 | 73 | 39 |
14Q LOSS WILD-TYPE | 149 | 79 | 70 |
Figure S105. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D60V6.png)
P value = 6.97e-11 (Fisher's exact test), Q value = 5.4e-08
Table S106. Gene #60: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
14Q LOSS CNV | 54 | 88 | 11 |
14Q LOSS WILD-TYPE | 143 | 91 | 86 |
Figure S106. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D60V7.png)
P value = 2.8e-07 (Fisher's exact test), Q value = 0.00021
Table S107. Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
14Q LOSS CNV | 8 | 60 | 85 |
14Q LOSS WILD-TYPE | 61 | 154 | 105 |
Figure S107. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D60V8.png)
P value = 7.43e-06 (Fisher's exact test), Q value = 0.0053
Table S108. Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
14Q LOSS CNV | 24 | 59 | 75 |
14Q LOSS WILD-TYPE | 91 | 152 | 85 |
Figure S108. Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D60V9.png)
P value = 0.000117 (Fisher's exact test), Q value = 0.079
Table S109. Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 24 | 13 |
17P LOSS CNV | 0 | 3 | 6 |
17P LOSS WILD-TYPE | 33 | 21 | 7 |
Figure S109. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D63V1.png)
P value = 0.000197 (Fisher's exact test), Q value = 0.13
Table S110. Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 32 | 24 |
17P LOSS CNV | 6 | 0 | 3 |
17P LOSS WILD-TYPE | 8 | 32 | 21 |
Figure S110. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D63V2.png)
P value = 6.44e-07 (Fisher's exact test), Q value = 0.00047
Table S111. Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
17P LOSS CNV | 15 | 0 | 11 |
17P LOSS WILD-TYPE | 149 | 216 | 113 |
Figure S111. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D63V3.png)
P value = 2.92e-05 (Chi-square test), Q value = 0.02
Table S112. Gene #63: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
17P LOSS CNV | 1 | 1 | 2 | 10 | 0 | 7 |
17P LOSS WILD-TYPE | 99 | 87 | 82 | 65 | 43 | 50 |
Figure S112. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D63V5.png)
P value = 5.18e-06 (Fisher's exact test), Q value = 0.0037
Table S113. Gene #63: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
17P LOSS CNV | 2 | 4 | 15 |
17P LOSS WILD-TYPE | 184 | 148 | 94 |
Figure S113. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D63V6.png)
P value = 1.9e-06 (Fisher's exact test), Q value = 0.0014
Table S114. Gene #63: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
17P LOSS CNV | 0 | 12 | 11 |
17P LOSS WILD-TYPE | 197 | 167 | 86 |
Figure S114. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D63V7.png)
P value = 1.5e-08 (Fisher's exact test), Q value = 1.1e-05
Table S115. Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
17P LOSS CNV | 12 | 0 | 11 |
17P LOSS WILD-TYPE | 57 | 214 | 179 |
Figure S115. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D63V8.png)
P value = 2.83e-06 (Fisher's exact test), Q value = 0.002
Table S116. Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
17P LOSS CNV | 4 | 2 | 20 |
17P LOSS WILD-TYPE | 111 | 209 | 140 |
Figure S116. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D63V9.png)
P value = 2.73e-11 (Fisher's exact test), Q value = 2.1e-08
Table S117. Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
17P LOSS CNV | 7 | 14 | 5 |
17P LOSS WILD-TYPE | 156 | 22 | 282 |
Figure S117. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D63V10.png)
P value = 6.84e-06 (Fisher's exact test), Q value = 0.0049
Table S118. Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
17Q LOSS CNV | 2 | 0 | 10 |
17Q LOSS WILD-TYPE | 162 | 216 | 114 |
Figure S118. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D64V3.png)
P value = 1.46e-05 (Chi-square test), Q value = 0.01
Table S119. Gene #64: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 100 | 88 | 84 | 75 | 43 | 57 |
17Q LOSS CNV | 0 | 0 | 0 | 7 | 0 | 1 |
17Q LOSS WILD-TYPE | 100 | 88 | 84 | 68 | 43 | 56 |
Figure S119. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D64V5.png)
P value = 1.02e-05 (Fisher's exact test), Q value = 0.0072
Table S120. Gene #64: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 152 | 109 |
17Q LOSS CNV | 0 | 0 | 8 |
17Q LOSS WILD-TYPE | 186 | 152 | 101 |
Figure S120. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D64V6.png)
P value = 1.91e-06 (Fisher's exact test), Q value = 0.0014
Table S121. Gene #64: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
17Q LOSS CNV | 0 | 1 | 9 |
17Q LOSS WILD-TYPE | 197 | 178 | 88 |
Figure S121. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D64V7.png)
P value = 7.91e-08 (Fisher's exact test), Q value = 6e-05
Table S122. Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
17Q LOSS CNV | 9 | 0 | 1 |
17Q LOSS WILD-TYPE | 60 | 214 | 189 |
Figure S122. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D64V8.png)
P value = 2.95e-05 (Fisher's exact test), Q value = 0.02
Table S123. Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
17Q LOSS CNV | 1 | 0 | 11 |
17Q LOSS WILD-TYPE | 114 | 211 | 149 |
Figure S123. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D64V9.png)
P value = 8.59e-13 (Fisher's exact test), Q value = 6.7e-10
Table S124. Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
17Q LOSS CNV | 0 | 11 | 1 |
17Q LOSS WILD-TYPE | 163 | 25 | 286 |
Figure S124. Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D64V10.png)
P value = 4.41e-05 (Fisher's exact test), Q value = 0.03
Table S125. Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
18P LOSS CNV | 28 | 8 | 10 |
18P LOSS WILD-TYPE | 136 | 208 | 114 |
Figure S125. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D65V3.png)
P value = 6.06e-06 (Fisher's exact test), Q value = 0.0043
Table S126. Gene #65: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
18P LOSS CNV | 8 | 32 | 4 |
18P LOSS WILD-TYPE | 189 | 147 | 93 |
Figure S126. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D65V7.png)
P value = 0.000196 (Fisher's exact test), Q value = 0.13
Table S127. Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
18P LOSS CNV | 7 | 8 | 29 |
18P LOSS WILD-TYPE | 62 | 206 | 161 |
Figure S127. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D65V8.png)
P value = 0.000231 (Fisher's exact test), Q value = 0.15
Table S128. Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 211 | 160 |
18P LOSS CNV | 10 | 9 | 27 |
18P LOSS WILD-TYPE | 105 | 202 | 133 |
Figure S128. Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D65V9.png)
P value = 6.3e-05 (Fisher's exact test), Q value = 0.043
Table S129. Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
18Q LOSS CNV | 29 | 9 | 10 |
18Q LOSS WILD-TYPE | 135 | 207 | 114 |
Figure S129. Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D66V3.png)
P value = 2.87e-05 (Fisher's exact test), Q value = 0.02
Table S130. Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 197 | 179 | 97 |
18Q LOSS CNV | 9 | 32 | 5 |
18Q LOSS WILD-TYPE | 188 | 147 | 92 |
Figure S130. Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D66V7.png)
P value = 0.000106 (Fisher's exact test), Q value = 0.072
Table S131. Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 216 | 124 |
21Q LOSS CNV | 11 | 5 | 18 |
21Q LOSS WILD-TYPE | 153 | 211 | 106 |
Figure S131. Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 1.72e-05 (Fisher's exact test), Q value = 0.012
Table S132. Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 69 | 214 | 190 |
21Q LOSS CNV | 14 | 6 | 9 |
21Q LOSS WILD-TYPE | 55 | 208 | 181 |
Figure S132. Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D69V8.png)
P value = 1.65e-05 (Fisher's exact test), Q value = 0.012
Table S133. Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 36 | 287 |
21Q LOSS CNV | 9 | 11 | 14 |
21Q LOSS WILD-TYPE | 154 | 25 | 273 |
Figure S133. Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D69V10.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt
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Number of patients = 504
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Number of significantly arm-level cnvs = 71
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Number of molecular subtypes = 12
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Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.