Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1668B3H
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1668B3H
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

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.

- 2p gain cnv correlated to 'MRNASEQ_CNMF'.

- 2q gain cnv correlated to 'CN_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 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'.

- 13q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'CN_CNMF'.

- 16q gain cnv correlated to 'CN_CNMF'.

- 17q gain cnv correlated to 'MRNASEQ_CNMF'.

- 20p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 1p loss cnv correlated to 'CN_CNMF'.

- 4p loss cnv correlated to 'CN_CNMF'.

- 4q loss cnv correlated to 'CN_CNMF'.

- 5q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 12p loss cnv correlated to 'CN_CNMF'.

- 12q loss cnv correlated to 'CN_CNMF'.

- 14q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 15q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 17p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 18q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 20p loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

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)

'2p gain' versus 'MRNASEQ_CNMF'

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'

'2q gain' versus 'CN_CNMF'

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'

'7p gain' versus 'CN_CNMF'

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'

'7p gain' versus 'METHLYATION_CNMF'

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'

'7p gain' versus 'MRNASEQ_CNMF'

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'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

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'

'7q gain' versus 'CN_CNMF'

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'

'7q gain' versus 'MRNASEQ_CNMF'

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'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

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'

'8p gain' versus 'CN_CNMF'

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'

'8q gain' versus 'CN_CNMF'

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'

'11p gain' versus 'CN_CNMF'

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'

'11q gain' versus 'CN_CNMF'

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'

'13q gain' versus 'MRNA_CNMF'

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'

'13q gain' versus 'MRNA_CHIERARCHICAL'

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'

'13q gain' versus 'CN_CNMF'

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'

'13q gain' versus 'METHLYATION_CNMF'

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'

'13q gain' versus 'MRNASEQ_CNMF'

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'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

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'

'16p gain' versus 'CN_CNMF'

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'

'16q gain' versus 'CN_CNMF'

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'

'17q gain' versus 'MRNASEQ_CNMF'

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'

'20p gain' versus 'MRNA_CHIERARCHICAL'

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'

'20p gain' versus 'CN_CNMF'

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'

'20p gain' versus 'MRNASEQ_CNMF'

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'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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'

'20q gain' versus 'MRNA_CNMF'

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'

'20q gain' versus 'MRNA_CHIERARCHICAL'

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'

'20q gain' versus 'CN_CNMF'

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'

'20q gain' versus 'METHLYATION_CNMF'

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'

'20q gain' versus 'RPPA_CNMF'

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'

'20q gain' versus 'RPPA_CHIERARCHICAL'

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'

'20q gain' versus 'MRNASEQ_CNMF'

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'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

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'

'1p loss' versus 'CN_CNMF'

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'

'4p loss' versus 'CN_CNMF'

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'

'4q loss' versus 'CN_CNMF'

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'

'5q loss' versus 'CN_CNMF'

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'

'8p loss' versus 'MRNA_CNMF'

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'

'8p loss' versus 'CN_CNMF'

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'

'9p loss' versus 'CN_CNMF'

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'

'9q loss' versus 'CN_CNMF'

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'

'11p loss' versus 'CN_CNMF'

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'

'11p loss' versus 'METHLYATION_CNMF'

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'

'11q loss' versus 'CN_CNMF'

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'

'11q loss' versus 'METHLYATION_CNMF'

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'

'12p loss' versus 'CN_CNMF'

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'

'12q loss' versus 'CN_CNMF'

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'

'14q loss' versus 'MRNA_CNMF'

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'

'14q loss' versus 'MRNA_CHIERARCHICAL'

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'

'14q loss' versus 'CN_CNMF'

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'

'14q loss' versus 'METHLYATION_CNMF'

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'

'14q loss' versus 'MRNASEQ_CNMF'

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'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

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'

'15q loss' versus 'CN_CNMF'

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'

'15q loss' versus 'MRNASEQ_CNMF'

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'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

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'

'17p loss' versus 'MRNA_CNMF'

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'

'17p loss' versus 'MRNA_CHIERARCHICAL'

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'

'17p loss' versus 'CN_CNMF'

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'

'17p loss' versus 'METHLYATION_CNMF'

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'

'17p loss' versus 'MRNASEQ_CNMF'

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'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

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'

'18p loss' versus 'MRNA_CNMF'

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'

'18p loss' versus 'MRNA_CHIERARCHICAL'

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'

'18p loss' versus 'CN_CNMF'

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'

'18p loss' versus 'METHLYATION_CNMF'

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'

'18p loss' versus 'MRNASEQ_CNMF'

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'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

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'

'18q loss' versus 'MRNA_CNMF'

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'

'18q loss' versus 'MRNA_CHIERARCHICAL'

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'

'18q loss' versus 'CN_CNMF'

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'

'18q loss' versus 'METHLYATION_CNMF'

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'

'18q loss' versus 'MRNASEQ_CNMF'

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'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

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'

'20p loss' versus 'CN_CNMF'

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'

'21q loss' versus 'CN_CNMF'

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'

'22q loss' versus 'CN_CNMF'

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'

Methods & Data
Input

- 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

Fisher's exact test

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

Q value calculation

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle