This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 76 arm-level results and 10 molecular subtypes across 413 patients, 78 significant findings detected with Q value < 0.25.
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2p gain cnv correlated to 'MRNASEQ_CNMF'.
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2q gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
8p gain cnv correlated to 'CN_CNMF'.
-
8q gain cnv correlated to 'CN_CNMF'.
-
11p gain cnv correlated to 'CN_CNMF'.
-
11q gain cnv correlated to 'CN_CNMF'.
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13q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16p gain cnv correlated to 'CN_CNMF'.
-
16q gain cnv correlated to 'CN_CNMF'.
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17q gain cnv correlated to 'MRNASEQ_CNMF'.
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20p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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1p loss cnv correlated to 'CN_CNMF'.
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4p loss cnv correlated to 'CN_CNMF'.
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4q loss cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.
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9p loss cnv correlated to 'CN_CNMF'.
-
9q loss cnv correlated to 'CN_CNMF'.
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11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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12p loss cnv correlated to 'CN_CNMF'.
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12q loss cnv correlated to 'CN_CNMF'.
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14q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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18q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'CN_CNMF'.
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21q 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 76 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 78 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 |
||
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 | |
20q gain | 0 (0%) | 146 |
1.24e-11 (8.7e-09) |
1.89e-13 (1.34e-10) |
9.42e-47 (6.83e-44) |
1.06e-09 (7.39e-07) |
0.000362 (0.235) |
1.58e-06 (0.00108) |
2.61e-13 (1.85e-10) |
3.58e-11 (2.51e-08) |
0.103 (1.00) |
0.429 (1.00) |
13q gain | 0 (0%) | 202 |
2.95e-06 (0.002) |
3.32e-05 (0.0221) |
2.95e-33 (2.13e-30) |
0.000267 (0.174) |
0.0188 (1.00) |
0.0051 (1.00) |
1.71e-06 (0.00117) |
7.16e-05 (0.0474) |
0.045 (1.00) |
0.466 (1.00) |
14q loss | 0 (0%) | 319 |
2.09e-07 (0.000144) |
1.18e-06 (0.000814) |
1.58e-22 (1.14e-19) |
1.2e-06 (0.000822) |
0.00838 (1.00) |
0.0266 (1.00) |
1.5e-06 (0.00103) |
8.78e-05 (0.0579) |
0.532 (1.00) |
0.194 (1.00) |
17p loss | 0 (0%) | 249 |
1.75e-05 (0.0117) |
3.05e-05 (0.0204) |
4.44e-23 (3.2e-20) |
2.31e-07 (0.000159) |
0.0615 (1.00) |
0.0393 (1.00) |
2.65e-06 (0.0018) |
8.2e-06 (0.00554) |
0.147 (1.00) |
0.0464 (1.00) |
18p loss | 0 (0%) | 204 |
2.81e-13 (1.99e-10) |
2.92e-10 (2.04e-07) |
2.44e-46 (1.77e-43) |
5.15e-13 (3.64e-10) |
0.00169 (1.00) |
0.000495 (0.32) |
6.98e-15 (4.98e-12) |
5.87e-09 (4.08e-06) |
0.251 (1.00) |
0.497 (1.00) |
18q loss | 0 (0%) | 188 |
1.92e-12 (1.36e-09) |
3.83e-10 (2.67e-07) |
8.88e-46 (6.42e-43) |
3.62e-15 (2.58e-12) |
0.0162 (1.00) |
0.00138 (0.865) |
4.47e-14 (3.17e-11) |
1.36e-08 (9.46e-06) |
0.0612 (1.00) |
0.499 (1.00) |
7p gain | 0 (0%) | 213 |
0.00124 (0.78) |
0.00375 (1.00) |
1.92e-15 (1.37e-12) |
9.14e-05 (0.0602) |
0.374 (1.00) |
0.0397 (1.00) |
1.09e-07 (7.52e-05) |
2.85e-05 (0.0191) |
0.425 (1.00) |
0.958 (1.00) |
20p gain | 0 (0%) | 225 |
0.00142 (0.887) |
1.47e-06 (0.00101) |
4.29e-20 (3.08e-17) |
0.0127 (1.00) |
0.0344 (1.00) |
0.0371 (1.00) |
3.35e-05 (0.0223) |
0.000197 (0.129) |
0.174 (1.00) |
0.0758 (1.00) |
7q gain | 0 (0%) | 238 |
0.00476 (1.00) |
0.0236 (1.00) |
7.05e-11 (4.93e-08) |
0.00278 (1.00) |
0.65 (1.00) |
0.072 (1.00) |
3.01e-06 (0.00204) |
0.000186 (0.122) |
0.474 (1.00) |
0.752 (1.00) |
15q loss | 0 (0%) | 314 |
0.0193 (1.00) |
0.0122 (1.00) |
9.29e-22 (6.68e-19) |
0.00458 (1.00) |
0.0803 (1.00) |
0.393 (1.00) |
4.07e-05 (0.0271) |
7.35e-05 (0.0486) |
0.488 (1.00) |
0.0435 (1.00) |
8p loss | 0 (0%) | 320 |
0.000317 (0.206) |
0.00156 (0.977) |
7.76e-17 (5.56e-14) |
0.00104 (0.657) |
0.282 (1.00) |
0.0412 (1.00) |
0.141 (1.00) |
0.0665 (1.00) |
0.2 (1.00) |
0.356 (1.00) |
11p loss | 0 (0%) | 391 |
0.47 (1.00) |
0.0674 (1.00) |
8.34e-05 (0.055) |
0.000281 (0.183) |
0.439 (1.00) |
0.248 (1.00) |
0.0489 (1.00) |
0.0184 (1.00) |
0.0401 (1.00) |
0.162 (1.00) |
11q loss | 0 (0%) | 386 |
0.372 (1.00) |
0.0387 (1.00) |
7.92e-06 (0.00536) |
9.61e-06 (0.00647) |
0.384 (1.00) |
0.6 (1.00) |
0.207 (1.00) |
0.129 (1.00) |
0.358 (1.00) |
0.202 (1.00) |
2p gain | 0 (0%) | 373 |
0.156 (1.00) |
0.0378 (1.00) |
0.00409 (1.00) |
0.046 (1.00) |
0.0492 (1.00) |
0.393 (1.00) |
0.000386 (0.25) |
0.0199 (1.00) |
0.508 (1.00) |
0.355 (1.00) |
2q gain | 0 (0%) | 374 |
0.0985 (1.00) |
0.0352 (1.00) |
0.000173 (0.113) |
0.00235 (1.00) |
0.0311 (1.00) |
0.393 (1.00) |
0.00109 (0.69) |
0.0384 (1.00) |
0.529 (1.00) |
0.405 (1.00) |
8p gain | 0 (0%) | 333 |
0.925 (1.00) |
0.785 (1.00) |
9.22e-06 (0.00621) |
0.0562 (1.00) |
0.117 (1.00) |
0.383 (1.00) |
0.175 (1.00) |
0.0327 (1.00) |
0.615 (1.00) |
0.571 (1.00) |
8q gain | 0 (0%) | 251 |
0.751 (1.00) |
0.612 (1.00) |
9.39e-12 (6.62e-09) |
0.000666 (0.427) |
0.751 (1.00) |
0.021 (1.00) |
0.0072 (1.00) |
0.127 (1.00) |
0.0986 (1.00) |
0.154 (1.00) |
11p gain | 0 (0%) | 395 |
0.151 (1.00) |
0.00135 (0.852) |
0.000314 (0.205) |
0.000575 (0.371) |
0.575 (1.00) |
0.804 (1.00) |
0.871 (1.00) |
0.889 (1.00) |
0.634 (1.00) |
0.882 (1.00) |
11q gain | 0 (0%) | 391 |
0.0301 (1.00) |
0.00227 (1.00) |
3.72e-06 (0.00252) |
0.00141 (0.886) |
0.265 (1.00) |
0.808 (1.00) |
0.151 (1.00) |
0.22 (1.00) |
0.386 (1.00) |
0.693 (1.00) |
16p gain | 0 (0%) | 346 |
0.013 (1.00) |
0.0038 (1.00) |
1.08e-14 (7.71e-12) |
0.138 (1.00) |
0.64 (1.00) |
0.0329 (1.00) |
0.051 (1.00) |
0.18 (1.00) |
0.126 (1.00) |
0.0474 (1.00) |
16q gain | 0 (0%) | 347 |
0.0139 (1.00) |
0.00644 (1.00) |
1.44e-16 (1.03e-13) |
0.136 (1.00) |
0.65 (1.00) |
0.0199 (1.00) |
0.051 (1.00) |
0.18 (1.00) |
0.314 (1.00) |
0.232 (1.00) |
17q gain | 0 (0%) | 365 |
0.0929 (1.00) |
0.0202 (1.00) |
0.000913 (0.581) |
0.00739 (1.00) |
0.866 (1.00) |
0.197 (1.00) |
1.16e-05 (0.0078) |
0.015 (1.00) |
0.0581 (1.00) |
0.753 (1.00) |
1p loss | 0 (0%) | 362 |
0.00489 (1.00) |
0.000765 (0.489) |
7.09e-08 (4.91e-05) |
0.00329 (1.00) |
0.576 (1.00) |
0.698 (1.00) |
0.0984 (1.00) |
0.286 (1.00) |
0.18 (1.00) |
0.274 (1.00) |
4p loss | 0 (0%) | 329 |
0.00469 (1.00) |
0.0521 (1.00) |
1.05e-11 (7.4e-09) |
0.00299 (1.00) |
0.241 (1.00) |
0.708 (1.00) |
0.000754 (0.483) |
0.000599 (0.385) |
0.083 (1.00) |
0.29 (1.00) |
4q loss | 0 (0%) | 345 |
0.00736 (1.00) |
0.0381 (1.00) |
2.26e-10 (1.58e-07) |
0.00223 (1.00) |
0.175 (1.00) |
0.427 (1.00) |
0.00348 (1.00) |
0.0158 (1.00) |
0.00266 (1.00) |
0.0359 (1.00) |
5q loss | 0 (0%) | 375 |
0.126 (1.00) |
0.0563 (1.00) |
1.11e-05 (0.00749) |
0.293 (1.00) |
0.191 (1.00) |
0.234 (1.00) |
0.00763 (1.00) |
0.105 (1.00) |
0.551 (1.00) |
0.48 (1.00) |
9p loss | 0 (0%) | 386 |
0.875 (1.00) |
0.11 (1.00) |
4.4e-05 (0.0292) |
0.0746 (1.00) |
0.133 (1.00) |
0.33 (1.00) |
0.0424 (1.00) |
0.105 (1.00) |
0.53 (1.00) |
0.744 (1.00) |
9q loss | 0 (0%) | 387 |
0.348 (1.00) |
0.124 (1.00) |
2.55e-06 (0.00174) |
0.000619 (0.397) |
0.133 (1.00) |
0.33 (1.00) |
0.000898 (0.572) |
0.036 (1.00) |
0.114 (1.00) |
0.675 (1.00) |
12p loss | 0 (0%) | 392 |
0.0909 (1.00) |
0.11 (1.00) |
7.1e-05 (0.0471) |
0.207 (1.00) |
0.463 (1.00) |
0.922 (1.00) |
0.0802 (1.00) |
0.0817 (1.00) |
0.72 (1.00) |
0.208 (1.00) |
12q loss | 0 (0%) | 393 |
0.17 (1.00) |
0.124 (1.00) |
0.000101 (0.0666) |
0.153 (1.00) |
0.805 (1.00) |
0.88 (1.00) |
0.0161 (1.00) |
0.04 (1.00) |
0.411 (1.00) |
0.362 (1.00) |
20p loss | 0 (0%) | 380 |
0.0132 (1.00) |
0.00713 (1.00) |
8.88e-08 (6.14e-05) |
0.0514 (1.00) |
0.614 (1.00) |
0.472 (1.00) |
0.353 (1.00) |
0.308 (1.00) |
0.906 (1.00) |
0.53 (1.00) |
21q loss | 0 (0%) | 342 |
0.00266 (1.00) |
0.00486 (1.00) |
2.6e-06 (0.00177) |
0.258 (1.00) |
0.524 (1.00) |
0.572 (1.00) |
0.122 (1.00) |
0.342 (1.00) |
0.0731 (1.00) |
0.608 (1.00) |
22q loss | 0 (0%) | 332 |
0.000916 (0.582) |
0.000455 (0.294) |
1.06e-11 (7.46e-09) |
0.0894 (1.00) |
0.341 (1.00) |
0.138 (1.00) |
0.00972 (1.00) |
0.0011 (0.695) |
0.624 (1.00) |
0.123 (1.00) |
1p gain | 0 (0%) | 402 |
0.576 (1.00) |
0.909 (1.00) |
0.275 (1.00) |
0.384 (1.00) |
0.425 (1.00) |
0.683 (1.00) |
0.46 (1.00) |
1 (1.00) |
||
1q gain | 0 (0%) | 366 |
0.0531 (1.00) |
0.732 (1.00) |
0.0788 (1.00) |
0.307 (1.00) |
0.38 (1.00) |
0.0481 (1.00) |
0.12 (1.00) |
0.299 (1.00) |
0.437 (1.00) |
0.837 (1.00) |
3p gain | 0 (0%) | 393 |
0.397 (1.00) |
0.382 (1.00) |
0.071 (1.00) |
0.367 (1.00) |
0.623 (1.00) |
0.721 (1.00) |
0.974 (1.00) |
0.676 (1.00) |
0.626 (1.00) |
0.184 (1.00) |
3q gain | 0 (0%) | 383 |
0.482 (1.00) |
0.0458 (1.00) |
0.000969 (0.614) |
0.22 (1.00) |
0.833 (1.00) |
0.752 (1.00) |
0.415 (1.00) |
0.635 (1.00) |
0.357 (1.00) |
0.824 (1.00) |
4p gain | 0 (0%) | 410 |
0.746 (1.00) |
0.473 (1.00) |
0.248 (1.00) |
0.0788 (1.00) |
0.208 (1.00) |
0.0334 (1.00) |
||||
4q gain | 0 (0%) | 408 |
0.842 (1.00) |
1 (1.00) |
0.199 (1.00) |
0.493 (1.00) |
0.579 (1.00) |
0.335 (1.00) |
||||
5p gain | 0 (0%) | 374 |
0.29 (1.00) |
0.0418 (1.00) |
0.00223 (1.00) |
0.0236 (1.00) |
0.631 (1.00) |
0.881 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.685 (1.00) |
0.53 (1.00) |
5q gain | 0 (0%) | 392 |
0.657 (1.00) |
0.564 (1.00) |
0.0391 (1.00) |
0.188 (1.00) |
0.429 (1.00) |
0.293 (1.00) |
0.749 (1.00) |
0.578 (1.00) |
1 (1.00) |
0.948 (1.00) |
6p gain | 0 (0%) | 363 |
0.17 (1.00) |
0.0116 (1.00) |
0.0267 (1.00) |
0.675 (1.00) |
0.711 (1.00) |
0.443 (1.00) |
0.0367 (1.00) |
0.268 (1.00) |
0.513 (1.00) |
0.246 (1.00) |
6q gain | 0 (0%) | 368 |
0.312 (1.00) |
0.0248 (1.00) |
0.0317 (1.00) |
0.352 (1.00) |
0.554 (1.00) |
0.433 (1.00) |
0.156 (1.00) |
0.621 (1.00) |
0.441 (1.00) |
0.309 (1.00) |
9p gain | 0 (0%) | 367 |
0.0335 (1.00) |
0.213 (1.00) |
0.28 (1.00) |
0.433 (1.00) |
0.0664 (1.00) |
0.179 (1.00) |
0.879 (1.00) |
0.76 (1.00) |
0.767 (1.00) |
0.763 (1.00) |
9q gain | 0 (0%) | 374 |
0.0915 (1.00) |
0.0775 (1.00) |
0.0641 (1.00) |
0.113 (1.00) |
0.0174 (1.00) |
0.034 (1.00) |
0.362 (1.00) |
0.659 (1.00) |
0.0589 (1.00) |
0.635 (1.00) |
10p gain | 0 (0%) | 395 |
0.65 (1.00) |
0.625 (1.00) |
0.104 (1.00) |
0.0477 (1.00) |
0.428 (1.00) |
0.917 (1.00) |
0.904 (1.00) |
0.466 (1.00) |
0.761 (1.00) |
0.941 (1.00) |
10q gain | 0 (0%) | 406 |
0.114 (1.00) |
0.042 (1.00) |
0.837 (1.00) |
0.861 (1.00) |
0.933 (1.00) |
0.219 (1.00) |
0.202 (1.00) |
0.151 (1.00) |
||
12p gain | 0 (0%) | 347 |
0.248 (1.00) |
0.71 (1.00) |
0.00442 (1.00) |
0.0146 (1.00) |
0.888 (1.00) |
0.813 (1.00) |
0.361 (1.00) |
0.682 (1.00) |
0.069 (1.00) |
0.21 (1.00) |
12q gain | 0 (0%) | 353 |
0.248 (1.00) |
0.542 (1.00) |
0.00181 (1.00) |
0.00291 (1.00) |
0.791 (1.00) |
0.669 (1.00) |
0.27 (1.00) |
0.691 (1.00) |
0.0121 (1.00) |
0.268 (1.00) |
14q gain | 0 (0%) | 398 |
0.485 (1.00) |
0.443 (1.00) |
0.0566 (1.00) |
0.276 (1.00) |
0.221 (1.00) |
0.309 (1.00) |
0.145 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.805 (1.00) |
15q gain | 0 (0%) | 408 |
0.0732 (1.00) |
0.683 (1.00) |
0.07 (1.00) |
0.0333 (1.00) |
0.783 (1.00) |
0.481 (1.00) |
0.473 (1.00) |
0.427 (1.00) |
||
17p gain | 0 (0%) | 404 |
0.618 (1.00) |
0.893 (1.00) |
0.454 (1.00) |
0.23 (1.00) |
0.0316 (1.00) |
0.225 (1.00) |
0.737 (1.00) |
0.891 (1.00) |
||
18p gain | 0 (0%) | 398 |
0.118 (1.00) |
0.637 (1.00) |
0.00548 (1.00) |
0.0139 (1.00) |
0.75 (1.00) |
0.968 (1.00) |
0.171 (1.00) |
0.0581 (1.00) |
0.144 (1.00) |
0.388 (1.00) |
18q gain | 0 (0%) | 404 |
0.0232 (1.00) |
0.0303 (1.00) |
0.52 (1.00) |
0.158 (1.00) |
0.142 (1.00) |
0.267 (1.00) |
0.274 (1.00) |
0.327 (1.00) |
||
19p gain | 0 (0%) | 379 |
0.142 (1.00) |
0.24 (1.00) |
0.00554 (1.00) |
0.0512 (1.00) |
0.294 (1.00) |
0.0782 (1.00) |
0.321 (1.00) |
0.481 (1.00) |
0.588 (1.00) |
0.573 (1.00) |
19q gain | 0 (0%) | 372 |
0.0718 (1.00) |
0.104 (1.00) |
0.437 (1.00) |
0.0666 (1.00) |
0.124 (1.00) |
0.0183 (1.00) |
0.145 (1.00) |
0.297 (1.00) |
0.924 (1.00) |
0.942 (1.00) |
21q gain | 0 (0%) | 402 |
0.194 (1.00) |
0.195 (1.00) |
0.0858 (1.00) |
0.339 (1.00) |
0.358 (1.00) |
0.275 (1.00) |
0.282 (1.00) |
0.73 (1.00) |
0.704 (1.00) |
0.684 (1.00) |
Xq gain | 0 (0%) | 401 |
0.487 (1.00) |
0.777 (1.00) |
0.0331 (1.00) |
0.631 (1.00) |
0.171 (1.00) |
0.344 (1.00) |
0.446 (1.00) |
0.765 (1.00) |
0.352 (1.00) |
0.41 (1.00) |
1q loss | 0 (0%) | 395 |
0.452 (1.00) |
0.135 (1.00) |
0.0103 (1.00) |
0.269 (1.00) |
0.66 (1.00) |
0.791 (1.00) |
0.151 (1.00) |
0.196 (1.00) |
0.941 (1.00) |
0.44 (1.00) |
2p loss | 0 (0%) | 409 |
0.572 (1.00) |
0.111 (1.00) |
0.433 (1.00) |
0.662 (1.00) |
0.132 (1.00) |
|||||
2q loss | 0 (0%) | 407 |
1 (1.00) |
0.156 (1.00) |
0.601 (1.00) |
0.298 (1.00) |
0.245 (1.00) |
0.175 (1.00) |
0.0588 (1.00) |
|||
3p loss | 0 (0%) | 386 |
0.253 (1.00) |
0.104 (1.00) |
0.00251 (1.00) |
0.252 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.458 (1.00) |
0.556 (1.00) |
0.212 (1.00) |
0.143 (1.00) |
3q loss | 0 (0%) | 401 |
0.415 (1.00) |
0.564 (1.00) |
0.224 (1.00) |
1 (1.00) |
0.0158 (1.00) |
0.261 (1.00) |
0.267 (1.00) |
0.683 (1.00) |
0.423 (1.00) |
0.822 (1.00) |
5p loss | 0 (0%) | 388 |
0.875 (1.00) |
0.172 (1.00) |
0.00176 (1.00) |
0.102 (1.00) |
0.478 (1.00) |
0.704 (1.00) |
0.126 (1.00) |
0.416 (1.00) |
0.841 (1.00) |
0.907 (1.00) |
6p loss | 0 (0%) | 401 |
0.54 (1.00) |
0.251 (1.00) |
0.00285 (1.00) |
1 (1.00) |
0.722 (1.00) |
0.942 (1.00) |
0.666 (1.00) |
0.45 (1.00) |
0.642 (1.00) |
0.624 (1.00) |
6q loss | 0 (0%) | 392 |
0.943 (1.00) |
0.732 (1.00) |
0.0743 (1.00) |
0.697 (1.00) |
0.332 (1.00) |
0.871 (1.00) |
1 (1.00) |
0.845 (1.00) |
0.864 (1.00) |
1 (1.00) |
8q loss | 0 (0%) | 405 |
0.403 (1.00) |
0.777 (1.00) |
0.00966 (1.00) |
0.852 (1.00) |
0.141 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.197 (1.00) |
0.436 (1.00) |
10p loss | 0 (0%) | 391 |
0.67 (1.00) |
0.672 (1.00) |
0.000828 (0.528) |
0.285 (1.00) |
0.201 (1.00) |
0.962 (1.00) |
0.518 (1.00) |
0.352 (1.00) |
0.24 (1.00) |
0.681 (1.00) |
10q loss | 0 (0%) | 389 |
0.606 (1.00) |
0.71 (1.00) |
0.000526 (0.339) |
0.152 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.04 (1.00) |
0.697 (1.00) |
0.393 (1.00) |
13q loss | 0 (0%) | 407 |
0.0209 (1.00) |
0.232 (1.00) |
0.0238 (1.00) |
0.0931 (1.00) |
0.425 (1.00) |
0.464 (1.00) |
0.869 (1.00) |
0.723 (1.00) |
||
16p loss | 0 (0%) | 404 |
0.251 (1.00) |
0.554 (1.00) |
0.305 (1.00) |
0.0298 (1.00) |
0.61 (1.00) |
0.904 (1.00) |
1 (1.00) |
1 (1.00) |
0.711 (1.00) |
1 (1.00) |
16q loss | 0 (0%) | 406 |
0.464 (1.00) |
1 (1.00) |
0.228 (1.00) |
0.199 (1.00) |
0.493 (1.00) |
0.175 (1.00) |
0.17 (1.00) |
|||
17q loss | 0 (0%) | 381 |
0.113 (1.00) |
0.225 (1.00) |
0.00216 (1.00) |
0.22 (1.00) |
0.412 (1.00) |
0.16 (1.00) |
0.0813 (1.00) |
0.109 (1.00) |
0.322 (1.00) |
0.291 (1.00) |
19p loss | 0 (0%) | 399 |
1 (1.00) |
0.319 (1.00) |
0.00275 (1.00) |
0.0957 (1.00) |
0.783 (1.00) |
0.361 (1.00) |
0.00708 (1.00) |
0.0789 (1.00) |
0.693 (1.00) |
0.0876 (1.00) |
19q loss | 0 (0%) | 400 |
0.922 (1.00) |
0.38 (1.00) |
0.0115 (1.00) |
0.0957 (1.00) |
0.906 (1.00) |
0.363 (1.00) |
0.00708 (1.00) |
0.0789 (1.00) |
0.57 (1.00) |
0.0611 (1.00) |
Xq loss | 0 (0%) | 408 |
0.842 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.821 (1.00) |
0.851 (1.00) |
0.14 (1.00) |
P value = 0.000386 (Fisher's exact test), Q value = 0.25
Table S1. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
2P GAIN CNV | 1 | 15 | 5 | 1 |
2P GAIN WILD-TYPE | 30 | 44 | 42 | 53 |
Figure S1. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D3V7.png)
P value = 0.000173 (Fisher's exact test), Q value = 0.11
Table S2. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
2Q GAIN CNV | 28 | 6 | 3 | 2 |
2Q GAIN WILD-TYPE | 142 | 181 | 29 | 22 |
Figure S2. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D4V3.png)
P value = 1.92e-15 (Fisher's exact test), Q value = 1.4e-12
Table S3. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
7P GAIN CNV | 112 | 49 | 23 | 16 |
7P GAIN WILD-TYPE | 58 | 138 | 9 | 8 |
Figure S3. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 9.14e-05 (Fisher's exact test), Q value = 0.06
Table S4. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
7P GAIN CNV | 71 | 38 | 23 |
7P GAIN WILD-TYPE | 34 | 48 | 40 |
Figure S4. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D13V4.png)
P value = 1.09e-07 (Fisher's exact test), Q value = 7.5e-05
Table S5. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
7P GAIN CNV | 19 | 43 | 20 | 11 |
7P GAIN WILD-TYPE | 12 | 16 | 27 | 43 |
Figure S5. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D13V7.png)
P value = 2.85e-05 (Fisher's exact test), Q value = 0.019
Table S6. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
7P GAIN CNV | 13 | 43 | 37 |
7P GAIN WILD-TYPE | 36 | 19 | 43 |
Figure S6. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D13V8.png)
P value = 7.05e-11 (Fisher's exact test), Q value = 4.9e-08
Table S7. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
7Q GAIN CNV | 96 | 45 | 21 | 13 |
7Q GAIN WILD-TYPE | 74 | 142 | 11 | 11 |
Figure S7. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 3.01e-06 (Fisher's exact test), Q value = 0.002
Table S8. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
7Q GAIN CNV | 16 | 39 | 18 | 10 |
7Q GAIN WILD-TYPE | 15 | 20 | 29 | 44 |
Figure S8. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D14V7.png)
P value = 0.000186 (Fisher's exact test), Q value = 0.12
Table S9. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
7Q GAIN CNV | 12 | 39 | 32 |
7Q GAIN WILD-TYPE | 37 | 23 | 48 |
Figure S9. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D14V8.png)
P value = 9.22e-06 (Fisher's exact test), Q value = 0.0062
Table S10. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
8P GAIN CNV | 23 | 32 | 12 | 13 |
8P GAIN WILD-TYPE | 147 | 155 | 20 | 11 |
Figure S10. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 9.39e-12 (Fisher's exact test), Q value = 6.6e-09
Table S11. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
8Q GAIN CNV | 78 | 45 | 17 | 22 |
8Q GAIN WILD-TYPE | 92 | 142 | 15 | 2 |
Figure S11. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 0.000314 (Fisher's exact test), Q value = 0.2
Table S12. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
11P GAIN CNV | 16 | 1 | 1 | 0 |
11P GAIN WILD-TYPE | 154 | 186 | 31 | 24 |
Figure S12. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D21V3.png)
P value = 3.72e-06 (Fisher's exact test), Q value = 0.0025
Table S13. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
11Q GAIN CNV | 19 | 0 | 2 | 1 |
11Q GAIN WILD-TYPE | 151 | 187 | 30 | 23 |
Figure S13. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D22V3.png)
P value = 2.95e-06 (Fisher's exact test), Q value = 0.002
Table S14. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
13Q GAIN CNV | 10 | 46 | 7 | 14 |
13Q GAIN WILD-TYPE | 21 | 16 | 23 | 9 |
Figure S14. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D25V1.png)
P value = 3.32e-05 (Fisher's exact test), Q value = 0.022
Table S15. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
13Q GAIN CNV | 34 | 11 | 32 |
13Q GAIN WILD-TYPE | 22 | 33 | 14 |
Figure S15. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D25V2.png)
P value = 2.95e-33 (Fisher's exact test), Q value = 2.1e-30
Table S16. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
13Q GAIN CNV | 143 | 42 | 11 | 15 |
13Q GAIN WILD-TYPE | 27 | 145 | 21 | 9 |
Figure S16. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D25V3.png)
P value = 0.000267 (Fisher's exact test), Q value = 0.17
Table S17. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
13Q GAIN CNV | 70 | 35 | 26 |
13Q GAIN WILD-TYPE | 35 | 51 | 37 |
Figure S17. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D25V4.png)
P value = 1.71e-06 (Fisher's exact test), Q value = 0.0012
Table S18. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
13Q GAIN CNV | 19 | 40 | 20 | 11 |
13Q GAIN WILD-TYPE | 12 | 19 | 27 | 43 |
Figure S18. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D25V7.png)
P value = 7.16e-05 (Fisher's exact test), Q value = 0.047
Table S19. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
13Q GAIN CNV | 11 | 39 | 40 |
13Q GAIN WILD-TYPE | 38 | 23 | 40 |
Figure S19. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D25V8.png)
P value = 1.08e-14 (Fisher's exact test), Q value = 7.7e-12
Table S20. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
16P GAIN CNV | 56 | 5 | 5 | 1 |
16P GAIN WILD-TYPE | 114 | 182 | 27 | 23 |
Figure S20. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D28V3.png)
P value = 1.44e-16 (Fisher's exact test), Q value = 1e-13
Table S21. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
16Q GAIN CNV | 58 | 4 | 3 | 1 |
16Q GAIN WILD-TYPE | 112 | 183 | 29 | 23 |
Figure S21. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D29V3.png)
P value = 1.16e-05 (Fisher's exact test), Q value = 0.0078
Table S22. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
17Q GAIN CNV | 4 | 16 | 0 | 2 |
17Q GAIN WILD-TYPE | 27 | 43 | 47 | 52 |
Figure S22. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D31V7.png)
P value = 1.47e-06 (Fisher's exact test), Q value = 0.001
Table S23. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
20P GAIN CNV | 37 | 8 | 28 |
20P GAIN WILD-TYPE | 19 | 36 | 18 |
Figure S23. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D36V2.png)
P value = 4.29e-20 (Fisher's exact test), Q value = 3.1e-17
Table S24. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
20P GAIN CNV | 98 | 44 | 31 | 15 |
20P GAIN WILD-TYPE | 72 | 143 | 1 | 9 |
Figure S24. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 3.35e-05 (Fisher's exact test), Q value = 0.022
Table S25. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
20P GAIN CNV | 15 | 31 | 20 | 7 |
20P GAIN WILD-TYPE | 16 | 28 | 27 | 47 |
Figure S25. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D36V7.png)
P value = 0.000197 (Fisher's exact test), Q value = 0.13
Table S26. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
20P GAIN CNV | 7 | 29 | 37 |
20P GAIN WILD-TYPE | 42 | 33 | 43 |
Figure S26. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D36V8.png)
P value = 1.24e-11 (Fisher's exact test), Q value = 8.7e-09
Table S27. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
20Q GAIN CNV | 10 | 58 | 12 | 19 |
20Q GAIN WILD-TYPE | 21 | 4 | 18 | 4 |
Figure S27. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D37V1.png)
P value = 1.89e-13 (Fisher's exact test), Q value = 1.3e-10
Table S28. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
20Q GAIN CNV | 48 | 10 | 41 |
20Q GAIN WILD-TYPE | 8 | 34 | 5 |
Figure S28. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D37V2.png)
P value = 9.42e-47 (Fisher's exact test), Q value = 6.8e-44
Table S29. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
20Q GAIN CNV | 160 | 54 | 32 | 21 |
20Q GAIN WILD-TYPE | 10 | 133 | 0 | 3 |
Figure S29. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 1.06e-09 (Fisher's exact test), Q value = 7.4e-07
Table S30. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
20Q GAIN CNV | 89 | 37 | 33 |
20Q GAIN WILD-TYPE | 16 | 49 | 30 |
Figure S30. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D37V4.png)
P value = 0.000362 (Fisher's exact test), Q value = 0.23
Table S31. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 81 | 135 | 26 | 83 |
20Q GAIN CNV | 58 | 92 | 19 | 36 |
20Q GAIN WILD-TYPE | 23 | 43 | 7 | 47 |
Figure S31. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'
![](D37V5.png)
P value = 1.58e-06 (Fisher's exact test), Q value = 0.0011
Table S32. Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
20Q GAIN CNV | 11 | 21 | 50 | 123 |
20Q GAIN WILD-TYPE | 15 | 35 | 13 | 57 |
Figure S32. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D37V6.png)
P value = 2.61e-13 (Fisher's exact test), Q value = 1.8e-10
Table S33. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
20Q GAIN CNV | 19 | 53 | 30 | 11 |
20Q GAIN WILD-TYPE | 12 | 6 | 17 | 43 |
Figure S33. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 3.58e-11 (Fisher's exact test), Q value = 2.5e-08
Table S34. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
20Q GAIN CNV | 9 | 49 | 55 |
20Q GAIN WILD-TYPE | 40 | 13 | 25 |
Figure S34. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 7.09e-08 (Fisher's exact test), Q value = 4.9e-05
Table S35. Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
1P LOSS CNV | 36 | 6 | 8 | 1 |
1P LOSS WILD-TYPE | 134 | 181 | 24 | 23 |
Figure S35. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D40V3.png)
P value = 1.05e-11 (Fisher's exact test), Q value = 7.4e-09
Table S36. Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
4P LOSS CNV | 56 | 11 | 13 | 4 |
4P LOSS WILD-TYPE | 114 | 176 | 19 | 20 |
Figure S36. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D46V3.png)
P value = 2.26e-10 (Fisher's exact test), Q value = 1.6e-07
Table S37. Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
4Q LOSS CNV | 49 | 8 | 9 | 2 |
4Q LOSS WILD-TYPE | 121 | 179 | 23 | 22 |
Figure S37. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D47V3.png)
P value = 1.11e-05 (Fisher's exact test), Q value = 0.0075
Table S38. Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
5Q LOSS CNV | 27 | 4 | 3 | 4 |
5Q LOSS WILD-TYPE | 143 | 183 | 29 | 20 |
Figure S38. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D49V3.png)
P value = 0.000317 (Fisher's exact test), Q value = 0.21
Table S39. Gene #52: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
8P LOSS CNV | 2 | 24 | 3 | 9 |
8P LOSS WILD-TYPE | 29 | 38 | 27 | 14 |
Figure S39. Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D52V1.png)
P value = 7.76e-17 (Fisher's exact test), Q value = 5.6e-14
Table S40. Gene #52: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
8P LOSS CNV | 73 | 11 | 3 | 6 |
8P LOSS WILD-TYPE | 97 | 176 | 29 | 18 |
Figure S40. Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D52V3.png)
P value = 4.4e-05 (Fisher's exact test), Q value = 0.029
Table S41. Gene #54: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
9P LOSS CNV | 19 | 2 | 5 | 1 |
9P LOSS WILD-TYPE | 151 | 185 | 27 | 23 |
Figure S41. Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D54V3.png)
P value = 2.55e-06 (Fisher's exact test), Q value = 0.0017
Table S42. Gene #55: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
9Q LOSS CNV | 21 | 1 | 4 | 0 |
9Q LOSS WILD-TYPE | 149 | 186 | 28 | 24 |
Figure S42. Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 8.34e-05 (Fisher's exact test), Q value = 0.055
Table S43. Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
11P LOSS CNV | 14 | 2 | 6 | 0 |
11P LOSS WILD-TYPE | 156 | 185 | 26 | 24 |
Figure S43. Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D58V3.png)
P value = 0.000281 (Fisher's exact test), Q value = 0.18
Table S44. Gene #58: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
11P LOSS CNV | 10 | 0 | 0 |
11P LOSS WILD-TYPE | 95 | 86 | 63 |
Figure S44. Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D58V4.png)
P value = 7.92e-06 (Fisher's exact test), Q value = 0.0054
Table S45. Gene #59: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
11Q LOSS CNV | 19 | 2 | 6 | 0 |
11Q LOSS WILD-TYPE | 151 | 185 | 26 | 24 |
Figure S45. Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D59V3.png)
P value = 9.61e-06 (Fisher's exact test), Q value = 0.0065
Table S46. Gene #59: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
11Q LOSS CNV | 14 | 0 | 0 |
11Q LOSS WILD-TYPE | 91 | 86 | 63 |
Figure S46. Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D59V4.png)
P value = 7.1e-05 (Fisher's exact test), Q value = 0.047
Table S47. Gene #60: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
12P LOSS CNV | 17 | 1 | 3 | 0 |
12P LOSS WILD-TYPE | 153 | 186 | 29 | 24 |
Figure S47. Get High-res Image Gene #60: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D60V3.png)
P value = 0.000101 (Fisher's exact test), Q value = 0.067
Table S48. Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
12Q LOSS CNV | 15 | 1 | 4 | 0 |
12Q LOSS WILD-TYPE | 155 | 186 | 28 | 24 |
Figure S48. Get High-res Image Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D61V3.png)
P value = 2.09e-07 (Fisher's exact test), Q value = 0.00014
Table S49. Gene #63: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
14Q LOSS CNV | 2 | 30 | 1 | 9 |
14Q LOSS WILD-TYPE | 29 | 32 | 29 | 14 |
Figure S49. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D63V1.png)
P value = 1.18e-06 (Fisher's exact test), Q value = 0.00081
Table S50. Gene #63: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
14Q LOSS CNV | 21 | 1 | 20 |
14Q LOSS WILD-TYPE | 35 | 43 | 26 |
Figure S50. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D63V2.png)
P value = 1.58e-22 (Fisher's exact test), Q value = 1.1e-19
Table S51. Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
14Q LOSS CNV | 78 | 8 | 8 | 0 |
14Q LOSS WILD-TYPE | 92 | 179 | 24 | 24 |
Figure S51. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D63V3.png)
P value = 1.2e-06 (Fisher's exact test), Q value = 0.00082
Table S52. Gene #63: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
14Q LOSS CNV | 36 | 6 | 6 |
14Q LOSS WILD-TYPE | 69 | 80 | 57 |
Figure S52. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D63V4.png)
P value = 1.5e-06 (Fisher's exact test), Q value = 0.001
Table S53. Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
14Q LOSS CNV | 8 | 23 | 6 | 1 |
14Q LOSS WILD-TYPE | 23 | 36 | 41 | 53 |
Figure S53. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D63V7.png)
P value = 8.78e-05 (Fisher's exact test), Q value = 0.058
Table S54. Gene #63: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
14Q LOSS CNV | 1 | 20 | 17 |
14Q LOSS WILD-TYPE | 48 | 42 | 63 |
Figure S54. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D63V8.png)
P value = 9.29e-22 (Fisher's exact test), Q value = 6.7e-19
Table S55. Gene #64: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
15Q LOSS CNV | 70 | 9 | 19 | 1 |
15Q LOSS WILD-TYPE | 100 | 178 | 13 | 23 |
Figure S55. Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D64V3.png)
P value = 4.07e-05 (Fisher's exact test), Q value = 0.027
Table S56. Gene #64: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
15Q LOSS CNV | 8 | 20 | 10 | 1 |
15Q LOSS WILD-TYPE | 23 | 39 | 37 | 53 |
Figure S56. Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D64V7.png)
P value = 7.35e-05 (Fisher's exact test), Q value = 0.049
Table S57. Gene #64: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
15Q LOSS CNV | 1 | 20 | 18 |
15Q LOSS WILD-TYPE | 48 | 42 | 62 |
Figure S57. Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D64V8.png)
P value = 1.75e-05 (Fisher's exact test), Q value = 0.012
Table S58. Gene #67: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
17P LOSS CNV | 7 | 38 | 5 | 13 |
17P LOSS WILD-TYPE | 24 | 24 | 25 | 10 |
Figure S58. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D67V1.png)
P value = 3.05e-05 (Fisher's exact test), Q value = 0.02
Table S59. Gene #67: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
17P LOSS CNV | 29 | 7 | 27 |
17P LOSS WILD-TYPE | 27 | 37 | 19 |
Figure S59. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D67V2.png)
P value = 4.44e-23 (Fisher's exact test), Q value = 3.2e-20
Table S60. Gene #67: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
17P LOSS CNV | 109 | 26 | 16 | 13 |
17P LOSS WILD-TYPE | 61 | 161 | 16 | 11 |
Figure S60. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D67V3.png)
P value = 2.31e-07 (Fisher's exact test), Q value = 0.00016
Table S61. Gene #67: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
17P LOSS CNV | 61 | 19 | 17 |
17P LOSS WILD-TYPE | 44 | 67 | 46 |
Figure S61. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D67V4.png)
P value = 2.65e-06 (Fisher's exact test), Q value = 0.0018
Table S62. Gene #67: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
17P LOSS CNV | 14 | 36 | 14 | 8 |
17P LOSS WILD-TYPE | 17 | 23 | 33 | 46 |
Figure S62. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D67V7.png)
P value = 8.2e-06 (Fisher's exact test), Q value = 0.0055
Table S63. Gene #67: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
17P LOSS CNV | 7 | 36 | 29 |
17P LOSS WILD-TYPE | 42 | 26 | 51 |
Figure S63. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D67V8.png)
P value = 2.81e-13 (Fisher's exact test), Q value = 2e-10
Table S64. Gene #69: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
18P LOSS CNV | 5 | 51 | 5 | 16 |
18P LOSS WILD-TYPE | 26 | 11 | 25 | 7 |
Figure S64. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D69V1.png)
P value = 2.92e-10 (Fisher's exact test), Q value = 2e-07
Table S65. Gene #69: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
18P LOSS CNV | 35 | 6 | 36 |
18P LOSS WILD-TYPE | 21 | 38 | 10 |
Figure S65. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D69V2.png)
P value = 2.44e-46 (Fisher's exact test), Q value = 1.8e-43
Table S66. Gene #69: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
18P LOSS CNV | 143 | 26 | 27 | 13 |
18P LOSS WILD-TYPE | 27 | 161 | 5 | 11 |
Figure S66. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 5.15e-13 (Fisher's exact test), Q value = 3.6e-10
Table S67. Gene #69: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
18P LOSS CNV | 81 | 24 | 21 |
18P LOSS WILD-TYPE | 24 | 62 | 42 |
Figure S67. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D69V4.png)
P value = 6.98e-15 (Fisher's exact test), Q value = 5e-12
Table S68. Gene #69: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
18P LOSS CNV | 14 | 49 | 21 | 5 |
18P LOSS WILD-TYPE | 17 | 10 | 26 | 49 |
Figure S68. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D69V7.png)
P value = 5.87e-09 (Fisher's exact test), Q value = 4.1e-06
Table S69. Gene #69: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
18P LOSS CNV | 6 | 42 | 41 |
18P LOSS WILD-TYPE | 43 | 20 | 39 |
Figure S69. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D69V8.png)
P value = 1.92e-12 (Fisher's exact test), Q value = 1.4e-09
Table S70. Gene #70: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
18Q LOSS CNV | 6 | 52 | 6 | 16 |
18Q LOSS WILD-TYPE | 25 | 10 | 24 | 7 |
Figure S70. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D70V1.png)
P value = 3.83e-10 (Fisher's exact test), Q value = 2.7e-07
Table S71. Gene #70: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
18Q LOSS CNV | 36 | 7 | 37 |
18Q LOSS WILD-TYPE | 20 | 37 | 9 |
Figure S71. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D70V2.png)
P value = 8.88e-46 (Fisher's exact test), Q value = 6.4e-43
Table S72. Gene #70: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
18Q LOSS CNV | 149 | 33 | 27 | 16 |
18Q LOSS WILD-TYPE | 21 | 154 | 5 | 8 |
Figure S72. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D70V3.png)
P value = 3.62e-15 (Fisher's exact test), Q value = 2.6e-12
Table S73. Gene #70: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
18Q LOSS CNV | 88 | 28 | 22 |
18Q LOSS WILD-TYPE | 17 | 58 | 41 |
Figure S73. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D70V4.png)
P value = 4.47e-14 (Fisher's exact test), Q value = 3.2e-11
Table S74. Gene #70: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
18Q LOSS CNV | 18 | 51 | 21 | 8 |
18Q LOSS WILD-TYPE | 13 | 8 | 26 | 46 |
Figure S74. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D70V7.png)
P value = 1.36e-08 (Fisher's exact test), Q value = 9.5e-06
Table S75. Gene #70: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
18Q LOSS CNV | 9 | 46 | 43 |
18Q LOSS WILD-TYPE | 40 | 16 | 37 |
Figure S75. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D70V8.png)
P value = 8.88e-08 (Fisher's exact test), Q value = 6.1e-05
Table S76. Gene #73: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
20P LOSS CNV | 27 | 2 | 0 | 4 |
20P LOSS WILD-TYPE | 143 | 185 | 32 | 20 |
Figure S76. Get High-res Image Gene #73: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D73V3.png)
P value = 2.6e-06 (Fisher's exact test), Q value = 0.0018
Table S77. Gene #74: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
21Q LOSS CNV | 40 | 15 | 13 | 3 |
21Q LOSS WILD-TYPE | 130 | 172 | 19 | 21 |
Figure S77. Get High-res Image Gene #74: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D74V3.png)
P value = 1.06e-11 (Fisher's exact test), Q value = 7.5e-09
Table S78. Gene #75: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
22Q LOSS CNV | 56 | 11 | 12 | 2 |
22Q LOSS WILD-TYPE | 114 | 176 | 20 | 22 |
Figure S78. Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D75V3.png)
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
-
Number of patients = 413
-
Number of significantly arm-level cnvs = 76
-
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.