This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 79 arm-level results and 10 molecular subtypes across 563 patients, 60 significant findings detected with Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF'.
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1q gain cnv correlated to 'CN_CNMF'.
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2q gain cnv correlated to 'MIR_CNMF'.
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7p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
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7q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
-
18p gain cnv correlated to 'CN_CNMF'.
-
18q gain cnv correlated to 'CN_CNMF'.
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19p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
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19q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
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20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
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20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
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3q loss cnv correlated to 'CN_CNMF'.
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6p loss cnv correlated to 'CN_CNMF'.
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6q loss cnv correlated to 'CN_CNMF'.
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10p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
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10q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CNMF'.
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11p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
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11q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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13q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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14q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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15q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
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17p loss cnv correlated to 'CN_CNMF'.
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22q loss cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 60 significant findings detected.
Molecular subtypes |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
19p gain | 0 (0%) | 387 |
2.15e-14 (1.48e-11) |
3.12e-10 (2.12e-07) |
0.236 (1.00) |
0.000117 (0.0755) |
1.02e-23 (7.09e-21) |
0.000451 (0.286) |
0.0175 (1.00) |
3.09e-06 (0.00205) |
0.102 (1.00) |
0.00821 (1.00) |
19q gain | 0 (0%) | 412 |
7.22e-16 (4.99e-13) |
3.75e-12 (2.57e-09) |
0.0671 (1.00) |
2.31e-05 (0.015) |
1.64e-28 (1.14e-25) |
0.0112 (1.00) |
0.0528 (1.00) |
4.31e-06 (0.00285) |
0.025 (1.00) |
0.0124 (1.00) |
10q loss | 0 (0%) | 113 |
2.16e-06 (0.00144) |
4.5e-06 (0.00297) |
0.0242 (1.00) |
7.65e-06 (0.00501) |
3.09e-31 (2.15e-28) |
0.00202 (1.00) |
6.96e-05 (0.045) |
0.00164 (1.00) |
0.729 (1.00) |
0.0908 (1.00) |
15q loss | 0 (0%) | 501 |
5.43e-05 (0.0352) |
0.000315 (0.201) |
0.000622 (0.393) |
4.06e-06 (0.00269) |
6.26e-06 (0.00412) |
0.000258 (0.165) |
0.108 (1.00) |
0.0224 (1.00) |
0.0153 (1.00) |
0.452 (1.00) |
7p gain | 0 (0%) | 129 |
4.5e-08 (3.02e-05) |
7.2e-07 (0.000482) |
0.000718 (0.451) |
1.82e-09 (1.23e-06) |
2e-16 (1.38e-13) |
0.0011 (0.687) |
0.00162 (0.995) |
0.471 (1.00) |
0.0411 (1.00) |
0.00552 (1.00) |
7q gain | 0 (0%) | 124 |
3.49e-06 (0.00231) |
1.75e-05 (0.0114) |
0.00102 (0.637) |
1.56e-06 (0.00104) |
9.36e-15 (6.46e-12) |
0.00348 (1.00) |
0.0199 (1.00) |
0.361 (1.00) |
0.0916 (1.00) |
0.0115 (1.00) |
20p gain | 0 (0%) | 383 |
2.17e-13 (1.49e-10) |
3.72e-12 (2.55e-09) |
0.201 (1.00) |
6.21e-05 (0.0402) |
1.54e-09 (1.04e-06) |
0.0645 (1.00) |
0.0946 (1.00) |
0.00228 (1.00) |
0.914 (1.00) |
0.000713 (0.448) |
20q gain | 0 (0%) | 385 |
3.25e-13 (2.23e-10) |
4.38e-11 (2.98e-08) |
0.157 (1.00) |
6.8e-06 (0.00446) |
2.98e-09 (2.01e-06) |
0.011 (1.00) |
0.0595 (1.00) |
0.00116 (0.72) |
0.834 (1.00) |
0.000403 (0.257) |
10p loss | 0 (0%) | 126 |
1.2e-06 (0.000799) |
8.37e-06 (0.00548) |
0.0358 (1.00) |
1.58e-08 (1.07e-05) |
1.8e-28 (1.25e-25) |
0.00348 (1.00) |
0.000567 (0.358) |
0.000656 (0.413) |
0.531 (1.00) |
0.0603 (1.00) |
11p loss | 0 (0%) | 499 |
1.2e-07 (8.04e-05) |
6.61e-06 (0.00434) |
0.0946 (1.00) |
2.43e-06 (0.00162) |
7.77e-12 (5.31e-09) |
0.00107 (0.668) |
0.679 (1.00) |
0.0659 (1.00) |
0.0443 (1.00) |
0.426 (1.00) |
11q loss | 0 (0%) | 508 |
9.72e-05 (0.0627) |
0.00427 (1.00) |
0.512 (1.00) |
0.00501 (1.00) |
2.1e-10 (1.43e-07) |
0.254 (1.00) |
0.577 (1.00) |
0.0933 (1.00) |
0.648 (1.00) |
0.868 (1.00) |
13q loss | 0 (0%) | 425 |
0.000801 (0.502) |
4.42e-05 (0.0287) |
0.569 (1.00) |
0.647 (1.00) |
4.3e-13 (2.95e-10) |
0.00114 (0.712) |
0.601 (1.00) |
0.0182 (1.00) |
0.22 (1.00) |
0.309 (1.00) |
14q loss | 0 (0%) | 442 |
4.49e-07 (0.000301) |
0.025 (1.00) |
0.595 (1.00) |
0.714 (1.00) |
8.63e-34 (6.02e-31) |
0.0159 (1.00) |
0.753 (1.00) |
0.0604 (1.00) |
0.0359 (1.00) |
0.00494 (1.00) |
1p gain | 0 (0%) | 523 |
0.681 (1.00) |
0.0934 (1.00) |
0.934 (1.00) |
0.0651 (1.00) |
1.1e-05 (0.00719) |
0.388 (1.00) |
0.478 (1.00) |
0.925 (1.00) |
0.46 (1.00) |
0.0696 (1.00) |
1q gain | 0 (0%) | 518 |
0.621 (1.00) |
0.116 (1.00) |
0.44 (1.00) |
0.343 (1.00) |
2.64e-08 (1.78e-05) |
0.295 (1.00) |
0.713 (1.00) |
0.882 (1.00) |
1 (1.00) |
0.152 (1.00) |
2q gain | 0 (0%) | 545 |
0.173 (1.00) |
0.447 (1.00) |
3.9e-05 (0.0254) |
0.0743 (1.00) |
0.372 (1.00) |
0.46 (1.00) |
0.535 (1.00) |
0.52 (1.00) |
0.795 (1.00) |
0.366 (1.00) |
18p gain | 0 (0%) | 535 |
0.501 (1.00) |
0.188 (1.00) |
0.509 (1.00) |
0.364 (1.00) |
0.000326 (0.208) |
0.313 (1.00) |
0.408 (1.00) |
0.548 (1.00) |
0.0656 (1.00) |
0.259 (1.00) |
18q gain | 0 (0%) | 533 |
0.11 (1.00) |
0.186 (1.00) |
0.356 (1.00) |
0.597 (1.00) |
0.000159 (0.102) |
0.313 (1.00) |
0.722 (1.00) |
0.407 (1.00) |
0.0209 (1.00) |
0.103 (1.00) |
3q loss | 0 (0%) | 547 |
0.643 (1.00) |
0.473 (1.00) |
0.0271 (1.00) |
0.383 (1.00) |
0.000297 (0.19) |
0.807 (1.00) |
1 (1.00) |
0.454 (1.00) |
0.278 (1.00) |
|
6p loss | 0 (0%) | 516 |
0.98 (1.00) |
0.553 (1.00) |
0.375 (1.00) |
0.538 (1.00) |
2.84e-09 (1.92e-06) |
0.622 (1.00) |
0.914 (1.00) |
0.592 (1.00) |
0.896 (1.00) |
0.604 (1.00) |
6q loss | 0 (0%) | 483 |
0.672 (1.00) |
0.58 (1.00) |
0.462 (1.00) |
0.112 (1.00) |
1.87e-08 (1.26e-05) |
0.0853 (1.00) |
0.896 (1.00) |
0.678 (1.00) |
0.824 (1.00) |
0.383 (1.00) |
17p loss | 0 (0%) | 527 |
0.429 (1.00) |
0.62 (1.00) |
0.835 (1.00) |
0.633 (1.00) |
5.94e-06 (0.00391) |
0.18 (1.00) |
0.0555 (1.00) |
0.826 (1.00) |
0.503 (1.00) |
1 (1.00) |
22q loss | 0 (0%) | 423 |
0.809 (1.00) |
1 (1.00) |
0.511 (1.00) |
0.886 (1.00) |
0.000148 (0.0952) |
0.275 (1.00) |
0.731 (1.00) |
0.955 (1.00) |
0.156 (1.00) |
0.885 (1.00) |
2p gain | 0 (0%) | 543 |
0.11 (1.00) |
0.786 (1.00) |
0.002 (1.00) |
0.128 (1.00) |
0.252 (1.00) |
0.46 (1.00) |
0.685 (1.00) |
0.385 (1.00) |
0.577 (1.00) |
0.797 (1.00) |
3p gain | 0 (0%) | 533 |
0.0036 (1.00) |
0.0573 (1.00) |
0.551 (1.00) |
0.677 (1.00) |
0.0193 (1.00) |
0.15 (1.00) |
0.405 (1.00) |
0.137 (1.00) |
0.808 (1.00) |
0.779 (1.00) |
3q gain | 0 (0%) | 533 |
0.0036 (1.00) |
0.0573 (1.00) |
0.551 (1.00) |
0.907 (1.00) |
0.0473 (1.00) |
0.15 (1.00) |
0.405 (1.00) |
0.137 (1.00) |
0.748 (1.00) |
0.58 (1.00) |
4p gain | 0 (0%) | 548 |
0.747 (1.00) |
0.656 (1.00) |
0.382 (1.00) |
0.0456 (1.00) |
0.29 (1.00) |
0.444 (1.00) |
0.149 (1.00) |
|||
4q gain | 0 (0%) | 549 |
0.733 (1.00) |
0.633 (1.00) |
0.206 (1.00) |
0.0828 (1.00) |
0.193 (1.00) |
0.444 (1.00) |
0.149 (1.00) |
|||
5p gain | 0 (0%) | 533 |
0.112 (1.00) |
0.31 (1.00) |
0.241 (1.00) |
0.353 (1.00) |
0.0037 (1.00) |
0.169 (1.00) |
0.652 (1.00) |
0.201 (1.00) |
0.202 (1.00) |
|
5q gain | 0 (0%) | 540 |
0.0427 (1.00) |
0.183 (1.00) |
0.0508 (1.00) |
0.0905 (1.00) |
0.0152 (1.00) |
0.442 (1.00) |
0.365 (1.00) |
|||
6p gain | 0 (0%) | 556 |
0.79 (1.00) |
0.769 (1.00) |
0.657 (1.00) |
0.395 (1.00) |
0.161 (1.00) |
|||||
6q gain | 0 (0%) | 554 |
0.237 (1.00) |
0.601 (1.00) |
0.595 (1.00) |
0.746 (1.00) |
0.0295 (1.00) |
|||||
8p gain | 0 (0%) | 537 |
0.00124 (0.767) |
0.0814 (1.00) |
0.335 (1.00) |
0.00812 (1.00) |
0.0015 (0.924) |
0.15 (1.00) |
0.0641 (1.00) |
0.06 (1.00) |
0.808 (1.00) |
0.551 (1.00) |
8q gain | 0 (0%) | 532 |
0.000511 (0.324) |
0.0416 (1.00) |
0.286 (1.00) |
0.00535 (1.00) |
0.00362 (1.00) |
0.0434 (1.00) |
0.0641 (1.00) |
0.06 (1.00) |
0.338 (1.00) |
0.547 (1.00) |
9p gain | 0 (0%) | 546 |
0.234 (1.00) |
0.0394 (1.00) |
0.738 (1.00) |
0.56 (1.00) |
0.0422 (1.00) |
0.544 (1.00) |
0.215 (1.00) |
0.305 (1.00) |
0.319 (1.00) |
0.766 (1.00) |
9q gain | 0 (0%) | 529 |
0.431 (1.00) |
0.0317 (1.00) |
0.619 (1.00) |
0.739 (1.00) |
0.169 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.116 (1.00) |
0.588 (1.00) |
0.67 (1.00) |
10p gain | 0 (0%) | 551 |
0.00052 (0.329) |
0.00472 (1.00) |
0.0911 (1.00) |
0.00145 (0.893) |
0.00123 (0.762) |
0.307 (1.00) |
0.384 (1.00) |
|||
11p gain | 0 (0%) | 559 |
1 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.497 (1.00) |
0.259 (1.00) |
|||||
11q gain | 0 (0%) | 556 |
0.152 (1.00) |
0.209 (1.00) |
0.265 (1.00) |
0.0781 (1.00) |
0.161 (1.00) |
1 (1.00) |
0.421 (1.00) |
|||
12p gain | 0 (0%) | 520 |
0.413 (1.00) |
0.201 (1.00) |
1 (1.00) |
0.265 (1.00) |
0.00126 (0.78) |
0.446 (1.00) |
0.36 (1.00) |
0.8 (1.00) |
0.0427 (1.00) |
0.259 (1.00) |
12q gain | 0 (0%) | 530 |
0.32 (1.00) |
0.0664 (1.00) |
0.993 (1.00) |
0.209 (1.00) |
0.00567 (1.00) |
0.634 (1.00) |
0.55 (1.00) |
0.695 (1.00) |
0.109 (1.00) |
0.7 (1.00) |
13q gain | 0 (0%) | 560 |
0.777 (1.00) |
0.792 (1.00) |
0.156 (1.00) |
0.497 (1.00) |
0.289 (1.00) |
1 (1.00) |
0.527 (1.00) |
|||
14q gain | 0 (0%) | 556 |
0.706 (1.00) |
0.674 (1.00) |
0.0567 (1.00) |
0.564 (1.00) |
0.638 (1.00) |
|||||
15q gain | 0 (0%) | 557 |
0.379 (1.00) |
0.536 (1.00) |
0.512 (1.00) |
0.588 (1.00) |
0.0126 (1.00) |
|||||
16p gain | 0 (0%) | 545 |
0.0318 (1.00) |
0.297 (1.00) |
0.6 (1.00) |
0.263 (1.00) |
0.0155 (1.00) |
0.332 (1.00) |
0.442 (1.00) |
|||
16q gain | 0 (0%) | 545 |
0.048 (1.00) |
0.253 (1.00) |
0.439 (1.00) |
0.0325 (1.00) |
0.0155 (1.00) |
0.433 (1.00) |
0.442 (1.00) |
|||
17p gain | 0 (0%) | 552 |
0.0188 (1.00) |
0.389 (1.00) |
0.721 (1.00) |
0.349 (1.00) |
0.108 (1.00) |
1 (1.00) |
0.284 (1.00) |
|||
17q gain | 0 (0%) | 544 |
0.22 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.609 (1.00) |
0.0584 (1.00) |
0.786 (1.00) |
0.384 (1.00) |
0.208 (1.00) |
0.562 (1.00) |
|
21q gain | 0 (0%) | 527 |
0.00268 (1.00) |
0.0318 (1.00) |
0.00816 (1.00) |
0.00191 (1.00) |
0.0469 (1.00) |
0.411 (1.00) |
0.912 (1.00) |
0.0171 (1.00) |
0.0329 (1.00) |
|
22q gain | 0 (0%) | 552 |
0.0378 (1.00) |
0.143 (1.00) |
0.127 (1.00) |
0.48 (1.00) |
0.0767 (1.00) |
1 (1.00) |
0.284 (1.00) |
|||
Xq gain | 0 (0%) | 559 |
0.331 (1.00) |
0.468 (1.00) |
0.757 (1.00) |
0.259 (1.00) |
0.0702 (1.00) |
|||||
1p loss | 0 (0%) | 558 |
0.849 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.0996 (1.00) |
0.532 (1.00) |
|||||
1q loss | 0 (0%) | 559 |
0.218 (1.00) |
1 (1.00) |
0.682 (1.00) |
1 (1.00) |
1 (1.00) |
|||||
2p loss | 0 (0%) | 553 |
0.0274 (1.00) |
0.0705 (1.00) |
0.656 (1.00) |
0.112 (1.00) |
0.163 (1.00) |
0.135 (1.00) |
0.724 (1.00) |
1 (1.00) |
0.0393 (1.00) |
0.12 (1.00) |
2q loss | 0 (0%) | 554 |
0.035 (1.00) |
0.071 (1.00) |
0.236 (1.00) |
0.0562 (1.00) |
0.183 (1.00) |
0.135 (1.00) |
0.724 (1.00) |
1 (1.00) |
0.0393 (1.00) |
0.12 (1.00) |
3p loss | 0 (0%) | 541 |
0.854 (1.00) |
0.513 (1.00) |
0.582 (1.00) |
0.502 (1.00) |
0.00763 (1.00) |
0.15 (1.00) |
0.0835 (1.00) |
0.653 (1.00) |
0.37 (1.00) |
0.436 (1.00) |
4p loss | 0 (0%) | 537 |
0.0199 (1.00) |
0.669 (1.00) |
0.175 (1.00) |
0.0211 (1.00) |
0.876 (1.00) |
0.761 (1.00) |
0.0903 (1.00) |
0.43 (1.00) |
0.14 (1.00) |
0.436 (1.00) |
4q loss | 0 (0%) | 538 |
0.0426 (1.00) |
0.644 (1.00) |
0.162 (1.00) |
0.145 (1.00) |
0.101 (1.00) |
0.701 (1.00) |
0.0985 (1.00) |
0.551 (1.00) |
0.517 (1.00) |
0.562 (1.00) |
5p loss | 0 (0%) | 542 |
0.00423 (1.00) |
0.0947 (1.00) |
0.186 (1.00) |
0.0966 (1.00) |
0.11 (1.00) |
0.0858 (1.00) |
0.469 (1.00) |
1 (1.00) |
0.785 (1.00) |
0.495 (1.00) |
5q loss | 0 (0%) | 543 |
0.0743 (1.00) |
0.872 (1.00) |
0.304 (1.00) |
0.122 (1.00) |
0.0512 (1.00) |
0.0858 (1.00) |
0.873 (1.00) |
1 (1.00) |
0.465 (1.00) |
0.483 (1.00) |
7p loss | 0 (0%) | 558 |
0.542 (1.00) |
0.453 (1.00) |
0.81 (1.00) |
0.0341 (1.00) |
0.532 (1.00) |
|||||
7q loss | 0 (0%) | 559 |
0.849 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.0996 (1.00) |
0.833 (1.00) |
|||||
8p loss | 0 (0%) | 529 |
0.894 (1.00) |
0.593 (1.00) |
0.783 (1.00) |
0.239 (1.00) |
0.272 (1.00) |
0.134 (1.00) |
0.651 (1.00) |
0.912 (1.00) |
0.726 (1.00) |
0.7 (1.00) |
8q loss | 0 (0%) | 542 |
0.717 (1.00) |
0.144 (1.00) |
0.384 (1.00) |
0.185 (1.00) |
0.0154 (1.00) |
0.212 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.365 (1.00) |
|
9p loss | 0 (0%) | 399 |
0.0137 (1.00) |
0.00133 (0.822) |
0.832 (1.00) |
0.147 (1.00) |
0.227 (1.00) |
0.921 (1.00) |
0.282 (1.00) |
0.0585 (1.00) |
0.0348 (1.00) |
0.026 (1.00) |
9q loss | 0 (0%) | 500 |
0.0461 (1.00) |
0.0252 (1.00) |
0.564 (1.00) |
0.262 (1.00) |
0.0587 (1.00) |
0.552 (1.00) |
0.0367 (1.00) |
0.0528 (1.00) |
0.636 (1.00) |
0.184 (1.00) |
12p loss | 0 (0%) | 525 |
0.0116 (1.00) |
0.0172 (1.00) |
0.151 (1.00) |
0.0306 (1.00) |
0.756 (1.00) |
0.425 (1.00) |
0.1 (1.00) |
0.474 (1.00) |
1 (1.00) |
1 (1.00) |
12q loss | 0 (0%) | 528 |
0.00882 (1.00) |
0.0185 (1.00) |
0.61 (1.00) |
0.0536 (1.00) |
0.127 (1.00) |
0.14 (1.00) |
0.102 (1.00) |
0.695 (1.00) |
0.839 (1.00) |
0.547 (1.00) |
16p loss | 0 (0%) | 540 |
0.2 (1.00) |
0.684 (1.00) |
0.46 (1.00) |
0.793 (1.00) |
0.127 (1.00) |
0.397 (1.00) |
0.644 (1.00) |
0.89 (1.00) |
0.501 (1.00) |
0.185 (1.00) |
16q loss | 0 (0%) | 522 |
0.112 (1.00) |
0.0209 (1.00) |
0.122 (1.00) |
0.52 (1.00) |
0.287 (1.00) |
0.228 (1.00) |
0.0754 (1.00) |
0.945 (1.00) |
0.706 (1.00) |
0.569 (1.00) |
17q loss | 0 (0%) | 544 |
0.39 (1.00) |
0.136 (1.00) |
0.402 (1.00) |
0.347 (1.00) |
0.0017 (1.00) |
0.214 (1.00) |
0.277 (1.00) |
0.168 (1.00) |
0.0933 (1.00) |
|
18p loss | 0 (0%) | 519 |
0.0244 (1.00) |
0.0871 (1.00) |
0.504 (1.00) |
0.712 (1.00) |
0.00156 (0.96) |
0.0747 (1.00) |
0.246 (1.00) |
0.0387 (1.00) |
0.0596 (1.00) |
0.521 (1.00) |
18q loss | 0 (0%) | 524 |
0.28 (1.00) |
0.381 (1.00) |
0.337 (1.00) |
0.923 (1.00) |
0.0795 (1.00) |
0.0599 (1.00) |
0.154 (1.00) |
0.00651 (1.00) |
0.567 (1.00) |
0.687 (1.00) |
19p loss | 0 (0%) | 550 |
0.00284 (1.00) |
0.024 (1.00) |
0.000418 (0.266) |
0.00738 (1.00) |
0.158 (1.00) |
0.592 (1.00) |
0.371 (1.00) |
0.574 (1.00) |
0.577 (1.00) |
0.157 (1.00) |
19q loss | 0 (0%) | 545 |
0.00902 (1.00) |
0.047 (1.00) |
0.00964 (1.00) |
0.00144 (0.888) |
0.0738 (1.00) |
0.592 (1.00) |
0.371 (1.00) |
0.574 (1.00) |
0.858 (1.00) |
0.365 (1.00) |
20p loss | 0 (0%) | 552 |
0.054 (1.00) |
0.129 (1.00) |
0.116 (1.00) |
0.0621 (1.00) |
0.00377 (1.00) |
0.414 (1.00) |
0.384 (1.00) |
|||
20q loss | 0 (0%) | 553 |
0.0789 (1.00) |
0.171 (1.00) |
0.656 (1.00) |
0.399 (1.00) |
0.019 (1.00) |
0.414 (1.00) |
0.384 (1.00) |
|||
21q loss | 0 (0%) | 538 |
0.0133 (1.00) |
0.0152 (1.00) |
0.0903 (1.00) |
0.0121 (1.00) |
0.0284 (1.00) |
0.219 (1.00) |
0.0279 (1.00) |
0.326 (1.00) |
0.602 (1.00) |
0.848 (1.00) |
Xq loss | 0 (0%) | 552 |
0.443 (1.00) |
0.468 (1.00) |
0.116 (1.00) |
0.37 (1.00) |
0.153 (1.00) |
0.636 (1.00) |
0.316 (1.00) |
0.517 (1.00) |
0.454 (1.00) |
P value = 1.1e-05 (Fisher's exact test), Q value = 0.0072
Table S1. Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
1P GAIN CNV | 25 | 6 | 9 |
1P GAIN WILD-TYPE | 136 | 208 | 179 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D1V5.png)
P value = 2.64e-08 (Fisher's exact test), Q value = 1.8e-05
Table S2. Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
1Q GAIN CNV | 30 | 4 | 11 |
1Q GAIN WILD-TYPE | 131 | 210 | 177 |
Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D2V5.png)
P value = 3.9e-05 (Fisher's exact test), Q value = 0.025
Table S3. Gene #4: '2q gain' versus Molecular Subtype #3: 'MIR_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 139 | 157 | 72 | 104 |
2Q GAIN CNV | 6 | 0 | 0 | 10 |
2Q GAIN WILD-TYPE | 133 | 157 | 72 | 94 |
Figure S3. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'MIR_CNMF'
![](D4V3.png)
P value = 4.5e-08 (Fisher's exact test), Q value = 3e-05
Table S4. Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
7P GAIN CNV | 141 | 104 | 145 |
7P GAIN WILD-TYPE | 31 | 66 | 22 |
Figure S4. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D13V1.png)
P value = 7.2e-07 (Fisher's exact test), Q value = 0.00048
Table S5. Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
7P GAIN CNV | 179 | 108 | 103 |
7P GAIN WILD-TYPE | 38 | 18 | 63 |
Figure S5. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D13V2.png)
P value = 1.82e-09 (Fisher's exact test), Q value = 1.2e-06
Table S6. Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
7P GAIN CNV | 135 | 157 | 75 |
7P GAIN WILD-TYPE | 28 | 22 | 55 |
Figure S6. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D13V4.png)
P value = 2e-16 (Fisher's exact test), Q value = 1.4e-13
Table S7. Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
7P GAIN CNV | 140 | 190 | 104 |
7P GAIN WILD-TYPE | 21 | 24 | 84 |
Figure S7. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D13V5.png)
P value = 3.49e-06 (Fisher's exact test), Q value = 0.0023
Table S8. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
7Q GAIN CNV | 140 | 109 | 144 |
7Q GAIN WILD-TYPE | 32 | 61 | 23 |
Figure S8. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D14V1.png)
P value = 1.75e-05 (Fisher's exact test), Q value = 0.011
Table S9. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
7Q GAIN CNV | 179 | 107 | 107 |
7Q GAIN WILD-TYPE | 38 | 19 | 59 |
Figure S9. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D14V2.png)
P value = 1.56e-06 (Fisher's exact test), Q value = 0.001
Table S10. Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
7Q GAIN CNV | 135 | 153 | 80 |
7Q GAIN WILD-TYPE | 28 | 26 | 50 |
Figure S10. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D14V4.png)
P value = 9.36e-15 (Fisher's exact test), Q value = 6.5e-12
Table S11. Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
7Q GAIN CNV | 137 | 193 | 109 |
7Q GAIN WILD-TYPE | 24 | 21 | 79 |
Figure S11. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D14V5.png)
P value = 0.000326 (Fisher's exact test), Q value = 0.21
Table S12. Gene #31: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
18P GAIN CNV | 17 | 3 | 8 |
18P GAIN WILD-TYPE | 144 | 211 | 180 |
Figure S12. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D31V5.png)
P value = 0.000159 (Fisher's exact test), Q value = 0.1
Table S13. Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
18Q GAIN CNV | 18 | 3 | 9 |
18Q GAIN WILD-TYPE | 143 | 211 | 179 |
Figure S13. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D32V5.png)
P value = 2.15e-14 (Fisher's exact test), Q value = 1.5e-11
Table S14. Gene #33: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
19P GAIN CNV | 46 | 23 | 88 |
19P GAIN WILD-TYPE | 126 | 147 | 79 |
Figure S14. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D33V1.png)
P value = 3.12e-10 (Fisher's exact test), Q value = 2.1e-07
Table S15. Gene #33: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
19P GAIN CNV | 64 | 66 | 27 |
19P GAIN WILD-TYPE | 153 | 60 | 139 |
Figure S15. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D33V2.png)
P value = 0.000117 (Fisher's exact test), Q value = 0.075
Table S16. Gene #33: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
19P GAIN CNV | 52 | 75 | 25 |
19P GAIN WILD-TYPE | 111 | 104 | 105 |
Figure S16. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D33V4.png)
P value = 1.02e-23 (Fisher's exact test), Q value = 7.1e-21
Table S17. Gene #33: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
19P GAIN CNV | 24 | 122 | 30 |
19P GAIN WILD-TYPE | 137 | 92 | 158 |
Figure S17. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D33V5.png)
P value = 3.09e-06 (Fisher's exact test), Q value = 0.002
Table S18. Gene #33: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 64 | 33 | 104 |
19P GAIN CNV | 35 | 6 | 20 |
19P GAIN WILD-TYPE | 29 | 27 | 84 |
Figure S18. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
![](D33V8.png)
P value = 7.22e-16 (Fisher's exact test), Q value = 5e-13
Table S19. Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
19Q GAIN CNV | 41 | 14 | 79 |
19Q GAIN WILD-TYPE | 131 | 156 | 88 |
Figure S19. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D34V1.png)
P value = 3.75e-12 (Fisher's exact test), Q value = 2.6e-09
Table S20. Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
19Q GAIN CNV | 57 | 60 | 17 |
19Q GAIN WILD-TYPE | 160 | 66 | 149 |
Figure S20. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D34V2.png)
P value = 2.31e-05 (Fisher's exact test), Q value = 0.015
Table S21. Gene #34: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
19Q GAIN CNV | 48 | 66 | 18 |
19Q GAIN WILD-TYPE | 115 | 113 | 112 |
Figure S21. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D34V4.png)
P value = 1.64e-28 (Fisher's exact test), Q value = 1.1e-25
Table S22. Gene #34: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
19Q GAIN CNV | 14 | 115 | 22 |
19Q GAIN WILD-TYPE | 147 | 99 | 166 |
Figure S22. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D34V5.png)
P value = 4.31e-06 (Fisher's exact test), Q value = 0.0029
Table S23. Gene #34: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 64 | 33 | 104 |
19Q GAIN CNV | 30 | 4 | 15 |
19Q GAIN WILD-TYPE | 34 | 29 | 89 |
Figure S23. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'
![](D34V8.png)
P value = 2.17e-13 (Fisher's exact test), Q value = 1.5e-10
Table S24. Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
20P GAIN CNV | 41 | 27 | 88 |
20P GAIN WILD-TYPE | 131 | 143 | 79 |
Figure S24. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D35V1.png)
P value = 3.72e-12 (Fisher's exact test), Q value = 2.5e-09
Table S25. Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
20P GAIN CNV | 59 | 70 | 27 |
20P GAIN WILD-TYPE | 158 | 56 | 139 |
Figure S25. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D35V2.png)
P value = 6.21e-05 (Fisher's exact test), Q value = 0.04
Table S26. Gene #35: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
20P GAIN CNV | 58 | 69 | 22 |
20P GAIN WILD-TYPE | 105 | 110 | 108 |
Figure S26. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D35V4.png)
P value = 1.54e-09 (Fisher's exact test), Q value = 1e-06
Table S27. Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
20P GAIN CNV | 42 | 102 | 36 |
20P GAIN WILD-TYPE | 119 | 112 | 152 |
Figure S27. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D35V5.png)
P value = 3.25e-13 (Fisher's exact test), Q value = 2.2e-10
Table S28. Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
20Q GAIN CNV | 42 | 26 | 87 |
20Q GAIN WILD-TYPE | 130 | 144 | 80 |
Figure S28. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D36V1.png)
P value = 4.38e-11 (Fisher's exact test), Q value = 3e-08
Table S29. Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
20Q GAIN CNV | 62 | 67 | 26 |
20Q GAIN WILD-TYPE | 155 | 59 | 140 |
Figure S29. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D36V2.png)
P value = 6.8e-06 (Fisher's exact test), Q value = 0.0045
Table S30. Gene #36: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
20Q GAIN CNV | 57 | 71 | 20 |
20Q GAIN WILD-TYPE | 106 | 108 | 110 |
Figure S30. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D36V4.png)
P value = 2.98e-09 (Fisher's exact test), Q value = 2e-06
Table S31. Gene #36: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
20Q GAIN CNV | 40 | 101 | 37 |
20Q GAIN WILD-TYPE | 121 | 113 | 151 |
Figure S31. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'
![](D36V5.png)
P value = 0.000297 (Fisher's exact test), Q value = 0.19
Table S32. Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
3Q LOSS CNV | 10 | 0 | 6 |
3Q LOSS WILD-TYPE | 151 | 214 | 182 |
Figure S32. Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D45V5.png)
P value = 2.84e-09 (Fisher's exact test), Q value = 1.9e-06
Table S33. Gene #50: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
6P LOSS CNV | 33 | 6 | 8 |
6P LOSS WILD-TYPE | 128 | 208 | 180 |
Figure S33. Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D50V5.png)
P value = 1.87e-08 (Fisher's exact test), Q value = 1.3e-05
Table S34. Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
6Q LOSS CNV | 46 | 21 | 13 |
6Q LOSS WILD-TYPE | 115 | 193 | 175 |
Figure S34. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D51V5.png)
P value = 1.2e-06 (Fisher's exact test), Q value = 8e-04
Table S35. Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
10P LOSS CNV | 131 | 112 | 149 |
10P LOSS WILD-TYPE | 41 | 58 | 18 |
Figure S35. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D58V1.png)
P value = 8.37e-06 (Fisher's exact test), Q value = 0.0055
Table S36. Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
10P LOSS CNV | 169 | 113 | 110 |
10P LOSS WILD-TYPE | 48 | 13 | 56 |
Figure S36. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D58V2.png)
P value = 1.58e-08 (Fisher's exact test), Q value = 1.1e-05
Table S37. Gene #58: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
10P LOSS CNV | 136 | 156 | 77 |
10P LOSS WILD-TYPE | 27 | 23 | 53 |
Figure S37. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D58V4.png)
P value = 1.8e-28 (Fisher's exact test), Q value = 1.2e-25
Table S38. Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
10P LOSS CNV | 137 | 205 | 95 |
10P LOSS WILD-TYPE | 24 | 9 | 93 |
Figure S38. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D58V5.png)
P value = 2.16e-06 (Fisher's exact test), Q value = 0.0014
Table S39. Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
10Q LOSS CNV | 133 | 120 | 153 |
10Q LOSS WILD-TYPE | 39 | 50 | 14 |
Figure S39. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D59V1.png)
P value = 4.5e-06 (Fisher's exact test), Q value = 0.003
Table S40. Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
10Q LOSS CNV | 172 | 117 | 117 |
10Q LOSS WILD-TYPE | 45 | 9 | 49 |
Figure S40. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D59V2.png)
P value = 7.65e-06 (Fisher's exact test), Q value = 0.005
Table S41. Gene #59: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
10Q LOSS CNV | 137 | 159 | 87 |
10Q LOSS WILD-TYPE | 26 | 20 | 43 |
Figure S41. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D59V4.png)
P value = 3.09e-31 (Fisher's exact test), Q value = 2.2e-28
Table S42. Gene #59: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
10Q LOSS CNV | 140 | 210 | 100 |
10Q LOSS WILD-TYPE | 21 | 4 | 88 |
Figure S42. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D59V5.png)
P value = 6.96e-05 (Fisher's exact test), Q value = 0.045
Table S43. Gene #59: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 54 | 58 | 44 | 45 |
10Q LOSS CNV | 42 | 40 | 44 | 39 |
10Q LOSS WILD-TYPE | 12 | 18 | 0 | 6 |
Figure S43. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'
![](D59V7.png)
P value = 1.2e-07 (Fisher's exact test), Q value = 8e-05
Table S44. Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
11P LOSS CNV | 18 | 38 | 5 |
11P LOSS WILD-TYPE | 154 | 132 | 162 |
Figure S44. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D60V1.png)
P value = 6.61e-06 (Fisher's exact test), Q value = 0.0043
Table S45. Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
11P LOSS CNV | 22 | 4 | 35 |
11P LOSS WILD-TYPE | 195 | 122 | 131 |
Figure S45. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D60V2.png)
P value = 2.43e-06 (Fisher's exact test), Q value = 0.0016
Table S46. Gene #60: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
11P LOSS CNV | 18 | 9 | 32 |
11P LOSS WILD-TYPE | 145 | 170 | 98 |
Figure S46. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D60V4.png)
P value = 7.77e-12 (Fisher's exact test), Q value = 5.3e-09
Table S47. Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
11P LOSS CNV | 38 | 3 | 23 |
11P LOSS WILD-TYPE | 123 | 211 | 165 |
Figure S47. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D60V5.png)
P value = 9.72e-05 (Fisher's exact test), Q value = 0.063
Table S48. Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
11Q LOSS CNV | 18 | 30 | 6 |
11Q LOSS WILD-TYPE | 154 | 140 | 161 |
Figure S48. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D61V1.png)
P value = 2.1e-10 (Fisher's exact test), Q value = 1.4e-07
Table S49. Gene #61: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
11Q LOSS CNV | 36 | 4 | 15 |
11Q LOSS WILD-TYPE | 125 | 210 | 173 |
Figure S49. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D61V5.png)
P value = 4.42e-05 (Fisher's exact test), Q value = 0.029
Table S50. Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
13Q LOSS CNV | 63 | 13 | 48 |
13Q LOSS WILD-TYPE | 154 | 113 | 118 |
Figure S50. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D64V2.png)
P value = 4.3e-13 (Fisher's exact test), Q value = 2.9e-10
Table S51. Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
13Q LOSS CNV | 68 | 20 | 50 |
13Q LOSS WILD-TYPE | 93 | 194 | 138 |
Figure S51. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D64V5.png)
P value = 4.49e-07 (Fisher's exact test), Q value = 3e-04
Table S52. Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
14Q LOSS CNV | 47 | 52 | 15 |
14Q LOSS WILD-TYPE | 125 | 118 | 152 |
Figure S52. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D65V1.png)
P value = 8.63e-34 (Fisher's exact test), Q value = 6e-31
Table S53. Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
14Q LOSS CNV | 85 | 4 | 32 |
14Q LOSS WILD-TYPE | 76 | 210 | 156 |
Figure S53. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D65V5.png)
P value = 5.43e-05 (Fisher's exact test), Q value = 0.035
Table S54. Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 170 | 167 |
15Q LOSS CNV | 17 | 34 | 8 |
15Q LOSS WILD-TYPE | 155 | 136 | 159 |
Figure S54. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D66V1.png)
P value = 0.000315 (Fisher's exact test), Q value = 0.2
Table S55. Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 217 | 126 | 166 |
15Q LOSS CNV | 23 | 5 | 31 |
15Q LOSS WILD-TYPE | 194 | 121 | 135 |
Figure S55. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D66V2.png)
P value = 4.06e-06 (Fisher's exact test), Q value = 0.0027
Table S56. Gene #66: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 179 | 130 |
15Q LOSS CNV | 6 | 20 | 29 |
15Q LOSS WILD-TYPE | 157 | 159 | 101 |
Figure S56. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'
![](D66V4.png)
P value = 6.26e-06 (Fisher's exact test), Q value = 0.0041
Table S57. Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
15Q LOSS CNV | 35 | 13 | 14 |
15Q LOSS WILD-TYPE | 126 | 201 | 174 |
Figure S57. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D66V5.png)
P value = 0.000258 (Fisher's exact test), Q value = 0.17
Table S58. Gene #66: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 20 | 24 | 27 |
15Q LOSS CNV | 1 | 2 | 0 | 9 |
15Q LOSS WILD-TYPE | 37 | 18 | 24 | 18 |
Figure S58. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'
![](D66V6.png)
P value = 5.94e-06 (Fisher's exact test), Q value = 0.0039
Table S59. Gene #69: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
17P LOSS CNV | 20 | 2 | 14 |
17P LOSS WILD-TYPE | 141 | 212 | 174 |
Figure S59. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D69V5.png)
P value = 0.000148 (Fisher's exact test), Q value = 0.095
Table S60. Gene #78: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 161 | 214 | 188 |
22Q LOSS CNV | 60 | 43 | 37 |
22Q LOSS WILD-TYPE | 101 | 171 | 151 |
Figure S60. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'
![](D78V5.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = GBM-TP.transferedmergedcluster.txt
-
Number of patients = 563
-
Number of significantly arm-level cnvs = 79
-
Number of molecular subtypes = 10
-
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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.