Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C10P0X6T
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10P0X6T
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, 75 significant findings detected with Q value < 0.25.

- 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' and 'MRNASEQ_CNMF'.

- 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' and 'MRNASEQ_CHIERARCHICAL'.

- 16q gain cnv correlated to 'CN_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_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', 'CN_CNMF', and 'MRNASEQ_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', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 15q loss cnv correlated to 'CN_CNMF'.

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

- 18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', '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, 75 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 | 267 (65%) | 146 | 1.18e-11 (8.21e-09) | 9.69e-15 (6.82e-12) | 9.42e-47 (6.77e-44) | 1.06e-09 (7.32e-07) | 0.00104 (0.649) | 1.24e-05 (0.00826) | 3.95e-16 (2.8e-13) | 5.98e-18 (4.25e-15) | 0.103 (1.00) | 0.429 (1.00)
14q loss | 94 (23%) | 319 | 9.75e-08 (6.68e-05) | 2.1e-06 (0.00142) | 1.58e-22 (1.13e-19) | 1.2e-06 (0.000814) | 0.000251 (0.163) | 0.00308 (1.00) | 1.54e-07 (0.000105) | 1.76e-06 (0.00119) | 0.532 (1.00) | 0.194 (1.00)
18p loss | 209 (51%) | 204 | 2.04e-14 (1.43e-11) | 6.47e-10 (4.46e-07) | 2.44e-46 (1.75e-43) | 5.15e-13 (3.6e-10) | 0.00081 (0.511) | 8.24e-05 (0.0541) | 5.92e-13 (4.13e-10) | 4.6e-14 (3.23e-11) | 0.251 (1.00) | 0.497 (1.00)
13q gain | 211 (51%) | 202 | 1.08e-05 (0.00717) | 4.14e-05 (0.0274) | 2.95e-33 (2.11e-30) | 0.000267 (0.173) | 0.101 (1.00) | 0.0212 (1.00) | 8.39e-07 (0.000572) | 8.46e-06 (0.00567) | 0.045 (1.00) | 0.466 (1.00)
18q loss | 225 (54%) | 188 | 1.4e-13 (9.83e-11) | 1.62e-09 (1.12e-06) | 8.88e-46 (6.36e-43) | 3.62e-15 (2.55e-12) | 0.00975 (1.00) | 0.000662 (0.419) | 1.01e-11 (7.05e-09) | 1.74e-15 (1.23e-12) | 0.0612 (1.00) | 0.499 (1.00)
17p loss | 164 (40%) | 249 | 4.44e-06 (0.00299) | 5.88e-05 (0.0388) | 4.44e-23 (3.18e-20) | 2.31e-07 (0.000158) | 0.028 (1.00) | 0.0336 (1.00) | 0.00041 (0.264) | 5.09e-05 (0.0336) | 0.147 (1.00) | 0.0464 (1.00)
7p gain | 200 (48%) | 213 | 0.0012 (0.745) | 0.00141 (0.877) | 1.92e-15 (1.35e-12) | 9.14e-05 (0.0599) | 0.316 (1.00) | 0.0199 (1.00) | 1.22e-06 (0.000829) | 7.19e-05 (0.0473) | 0.425 (1.00) | 0.958 (1.00)
20p gain | 188 (46%) | 225 | 0.00223 (1.00) | 5.92e-06 (0.00398) | 4.29e-20 (3.05e-17) | 0.0127 (1.00) | 0.0229 (1.00) | 0.0648 (1.00) | 8.67e-06 (0.0058) | 3.55e-07 (0.000242) | 0.174 (1.00) | 0.0758 (1.00)
8p loss | 93 (23%) | 320 | 0.000293 (0.189) | 0.00823 (1.00) | 7.76e-17 (5.51e-14) | 0.00104 (0.649) | 0.229 (1.00) | 0.0337 (1.00) | 0.000218 (0.142) | 0.0025 (1.00) | 0.2 (1.00) | 0.356 (1.00)
7q gain | 175 (42%) | 238 | 0.00419 (1.00) | 0.0146 (1.00) | 7.05e-11 (4.88e-08) | 0.00278 (1.00) | 0.667 (1.00) | 0.0751 (1.00) | 0.000163 (0.106) | 0.000453 (0.291) | 0.474 (1.00) | 0.752 (1.00)
16p gain | 67 (16%) | 346 | 0.0127 (1.00) | 0.0111 (1.00) | 1.08e-14 (7.62e-12) | 0.138 (1.00) | 0.258 (1.00) | 0.0488 (1.00) | 0.00986 (1.00) | 9.94e-05 (0.065) | 0.126 (1.00) | 0.0474 (1.00)
11p loss | 22 (5%) | 391 | 0.494 (1.00) | 0.106 (1.00) | 8.34e-05 (0.0547) | 0.000281 (0.182) | 0.727 (1.00) | 0.514 (1.00) | 0.929 (1.00) | 0.64 (1.00) | 0.0401 (1.00) | 0.162 (1.00)
11q loss | 27 (7%) | 386 | 0.365 (1.00) | 0.0666 (1.00) | 7.92e-06 (0.00532) | 9.61e-06 (0.00641) | 0.652 (1.00) | 0.594 (1.00) | 0.663 (1.00) | 1 (1.00) | 0.358 (1.00) | 0.202 (1.00)
2q gain | 39 (9%) | 374 | 0.0577 (1.00) | 0.0512 (1.00) | 0.000173 (0.112) | 0.00235 (1.00) | 0.121 (1.00) | 0.589 (1.00) | 0.00294 (1.00) | 0.00261 (1.00) | 0.529 (1.00) | 0.405 (1.00)
8p gain | 80 (19%) | 333 | 1 (1.00) | 0.988 (1.00) | 9.22e-06 (0.00616) | 0.0562 (1.00) | 0.25 (1.00) | 0.162 (1.00) | 0.47 (1.00) | 0.849 (1.00) | 0.615 (1.00) | 0.571 (1.00)
8q gain | 162 (39%) | 251 | 0.793 (1.00) | 0.151 (1.00) | 9.39e-12 (6.55e-09) | 0.000666 (0.421) | 0.65 (1.00) | 0.0565 (1.00) | 0.15 (1.00) | 0.136 (1.00) | 0.0986 (1.00) | 0.154 (1.00)
11p gain | 18 (4%) | 395 | 0.15 (1.00) | 0.0019 (1.00) | 0.000314 (0.203) | 0.000575 (0.367) | 1 (1.00) | 0.605 (1.00) | 0.00559 (1.00) | 0.0421 (1.00) | 0.634 (1.00) | 0.882 (1.00)
11q gain | 22 (5%) | 391 | 0.0297 (1.00) | 0.00397 (1.00) | 3.72e-06 (0.00251) | 0.00141 (0.877) | 0.299 (1.00) | 0.677 (1.00) | 0.00062 (0.394) | 0.0098 (1.00) | 0.386 (1.00) | 0.693 (1.00)
16q gain | 66 (16%) | 347 | 0.0138 (1.00) | 0.0185 (1.00) | 1.44e-16 (1.02e-13) | 0.136 (1.00) | 0.181 (1.00) | 0.0488 (1.00) | 0.00285 (1.00) | 0.000408 (0.263) | 0.314 (1.00) | 0.232 (1.00)
1p loss | 51 (12%) | 362 | 0.00249 (1.00) | 0.000927 (0.582) | 7.09e-08 (4.87e-05) | 0.00329 (1.00) | 0.71 (1.00) | 0.597 (1.00) | 0.00432 (1.00) | 0.00144 (0.895) | 0.18 (1.00) | 0.274 (1.00)
4p loss | 84 (20%) | 329 | 0.00199 (1.00) | 0.0369 (1.00) | 1.05e-11 (7.31e-09) | 0.00299 (1.00) | 0.157 (1.00) | 0.255 (1.00) | 0.00875 (1.00) | 0.0234 (1.00) | 0.083 (1.00) | 0.29 (1.00)
4q loss | 68 (16%) | 345 | 0.0047 (1.00) | 0.0161 (1.00) | 2.26e-10 (1.56e-07) | 0.00223 (1.00) | 0.11 (1.00) | 0.231 (1.00) | 0.0388 (1.00) | 0.217 (1.00) | 0.00266 (1.00) | 0.0359 (1.00)
5q loss | 38 (9%) | 375 | 0.0926 (1.00) | 0.122 (1.00) | 1.11e-05 (0.00741) | 0.293 (1.00) | 0.381 (1.00) | 0.284 (1.00) | 0.0297 (1.00) | 0.0743 (1.00) | 0.551 (1.00) | 0.48 (1.00)
9p loss | 27 (7%) | 386 | 0.874 (1.00) | 0.197 (1.00) | 4.4e-05 (0.0291) | 0.0746 (1.00) | 0.241 (1.00) | 0.177 (1.00) | 0.301 (1.00) | 0.807 (1.00) | 0.53 (1.00) | 0.744 (1.00)
9q loss | 26 (6%) | 387 | 0.358 (1.00) | 0.171 (1.00) | 2.55e-06 (0.00172) | 0.000619 (0.394) | 0.241 (1.00) | 0.177 (1.00) | 0.0587 (1.00) | 0.371 (1.00) | 0.114 (1.00) | 0.675 (1.00)
12p loss | 21 (5%) | 392 | 0.097 (1.00) | 0.126 (1.00) | 7.1e-05 (0.0468) | 0.207 (1.00) | 0.53 (1.00) | 0.972 (1.00) | 0.282 (1.00) | 0.762 (1.00) | 0.72 (1.00) | 0.208 (1.00)
12q loss | 20 (5%) | 393 | 0.19 (1.00) | 0.154 (1.00) | 0.000101 (0.0662) | 0.153 (1.00) | 0.706 (1.00) | 0.939 (1.00) | 0.446 (1.00) | 0.818 (1.00) | 0.411 (1.00) | 0.362 (1.00)
15q loss | 99 (24%) | 314 | 0.00753 (1.00) | 0.00873 (1.00) | 9.29e-22 (6.62e-19) | 0.00458 (1.00) | 0.0541 (1.00) | 0.597 (1.00) | 0.0437 (1.00) | 0.000451 (0.289) | 0.488 (1.00) | 0.0435 (1.00)
20p loss | 33 (8%) | 380 | 0.0135 (1.00) | 0.00818 (1.00) | 8.88e-08 (6.09e-05) | 0.0514 (1.00) | 0.756 (1.00) | 0.645 (1.00) | 0.0631 (1.00) | 0.0393 (1.00) | 0.906 (1.00) | 0.53 (1.00)
21q loss | 71 (17%) | 342 | 0.0103 (1.00) | 0.00693 (1.00) | 2.6e-06 (0.00175) | 0.258 (1.00) | 0.605 (1.00) | 0.827 (1.00) | 0.103 (1.00) | 0.0245 (1.00) | 0.0731 (1.00) | 0.608 (1.00)
22q loss | 81 (20%) | 332 | 0.000473 (0.303) | 0.000623 (0.395) | 1.06e-11 (7.37e-09) | 0.0894 (1.00) | 0.0623 (1.00) | 0.0152 (1.00) | 0.0621 (1.00) | 0.0011 (0.687) | 0.624 (1.00) | 0.123 (1.00)
1p gain | 11 (3%) | 402 |  |  | 0.576 (1.00) | 0.909 (1.00) | 0.0365 (1.00) | 0.234 (1.00) | 1 (1.00) | 0.0783 (1.00) | 0.46 (1.00) | 1 (1.00)
1q gain | 47 (11%) | 366 | 0.0527 (1.00) | 0.604 (1.00) | 0.0788 (1.00) | 0.307 (1.00) | 0.567 (1.00) | 0.181 (1.00) | 0.0943 (1.00) | 0.931 (1.00) | 0.437 (1.00) | 0.837 (1.00)
2p gain | 40 (10%) | 373 | 0.0975 (1.00) | 0.0566 (1.00) | 0.00409 (1.00) | 0.046 (1.00) | 0.141 (1.00) | 0.488 (1.00) | 0.0059 (1.00) | 0.00433 (1.00) | 0.508 (1.00) | 0.355 (1.00)
3p gain | 20 (5%) | 393 | 0.378 (1.00) | 0.43 (1.00) | 0.071 (1.00) | 0.367 (1.00) | 0.715 (1.00) | 0.175 (1.00) | 0.464 (1.00) | 0.86 (1.00) | 0.626 (1.00) | 0.184 (1.00)
3q gain | 30 (7%) | 383 | 0.458 (1.00) | 0.0551 (1.00) | 0.000969 (0.607) | 0.22 (1.00) | 0.393 (1.00) | 0.444 (1.00) | 0.178 (1.00) | 0.585 (1.00) | 0.357 (1.00) | 0.824 (1.00)
4p gain | 3 (1%) | 410 |  |  | 0.746 (1.00) | 0.473 (1.00) | 0.225 (1.00) | 0.214 (1.00) |  |  | 0.208 (1.00) | 0.0334 (1.00)
4q gain | 5 (1%) | 408 |  |  | 0.842 (1.00) | 1 (1.00) | 1 (1.00) | 0.832 (1.00) |  |  | 0.579 (1.00) | 0.335 (1.00)
5p gain | 39 (9%) | 374 | 0.286 (1.00) | 0.0479 (1.00) | 0.00223 (1.00) | 0.0236 (1.00) | 0.513 (1.00) | 0.987 (1.00) | 0.341 (1.00) | 0.338 (1.00) | 0.685 (1.00) | 0.53 (1.00)
5q gain | 21 (5%) | 392 | 0.656 (1.00) | 0.319 (1.00) | 0.0391 (1.00) | 0.188 (1.00) | 0.369 (1.00) | 0.345 (1.00) | 1 (1.00) | 0.427 (1.00) | 1 (1.00) | 0.948 (1.00)
6p gain | 50 (12%) | 363 | 0.516 (1.00) | 0.0107 (1.00) | 0.0267 (1.00) | 0.675 (1.00) | 0.619 (1.00) | 0.955 (1.00) | 0.299 (1.00) | 0.732 (1.00) | 0.513 (1.00) | 0.246 (1.00)
6q gain | 45 (11%) | 368 | 0.334 (1.00) | 0.0267 (1.00) | 0.0317 (1.00) | 0.352 (1.00) | 0.877 (1.00) | 0.847 (1.00) | 0.443 (1.00) | 0.943 (1.00) | 0.441 (1.00) | 0.309 (1.00)
9p gain | 46 (11%) | 367 | 0.0317 (1.00) | 0.262 (1.00) | 0.28 (1.00) | 0.433 (1.00) | 0.0817 (1.00) | 0.13 (1.00) | 0.0783 (1.00) | 0.35 (1.00) | 0.767 (1.00) | 0.763 (1.00)
9q gain | 39 (9%) | 374 | 0.0568 (1.00) | 0.305 (1.00) | 0.0641 (1.00) | 0.113 (1.00) | 0.017 (1.00) | 0.0254 (1.00) | 0.595 (1.00) | 0.875 (1.00) | 0.0589 (1.00) | 0.635 (1.00)
10p gain | 18 (4%) | 395 | 0.669 (1.00) | 0.55 (1.00) | 0.104 (1.00) | 0.0477 (1.00) | 0.951 (1.00) | 0.696 (1.00) | 0.826 (1.00) | 0.45 (1.00) | 0.761 (1.00) | 0.941 (1.00)
10q gain | 7 (2%) | 406 |  |  | 0.114 (1.00) | 0.042 (1.00) | 0.877 (1.00) | 0.615 (1.00) |  |  | 0.202 (1.00) | 0.151 (1.00)
12p gain | 66 (16%) | 347 | 0.361 (1.00) | 0.0912 (1.00) | 0.00442 (1.00) | 0.0146 (1.00) | 0.537 (1.00) | 0.574 (1.00) | 0.146 (1.00) | 0.561 (1.00) | 0.069 (1.00) | 0.21 (1.00)
12q gain | 60 (15%) | 353 | 0.245 (1.00) | 0.19 (1.00) | 0.00181 (1.00) | 0.00291 (1.00) | 0.417 (1.00) | 0.546 (1.00) | 0.208 (1.00) | 0.874 (1.00) | 0.0121 (1.00) | 0.268 (1.00)
14q gain | 15 (4%) | 398 | 0.484 (1.00) | 0.45 (1.00) | 0.0566 (1.00) | 0.276 (1.00) | 0.0499 (1.00) | 0.367 (1.00) | 0.306 (1.00) | 0.503 (1.00) | 1 (1.00) | 0.805 (1.00)
15q gain | 5 (1%) | 408 |  |  | 0.0732 (1.00) | 0.683 (1.00) | 0.0374 (1.00) | 0.0636 (1.00) |  |  | 0.473 (1.00) | 0.427 (1.00)
17p gain | 9 (2%) | 404 |  |  | 0.618 (1.00) | 0.893 (1.00) | 0.626 (1.00) | 0.0996 (1.00) |  |  | 0.737 (1.00) | 0.891 (1.00)
17q gain | 48 (12%) | 365 | 0.0898 (1.00) | 0.0218 (1.00) | 0.000913 (0.574) | 0.00739 (1.00) | 0.25 (1.00) | 0.185 (1.00) | 0.000475 (0.304) | 0.00605 (1.00) | 0.0581 (1.00) | 0.753 (1.00)
18p gain | 15 (4%) | 398 | 0.117 (1.00) | 0.828 (1.00) | 0.00548 (1.00) | 0.0139 (1.00) | 0.334 (1.00) | 0.603 (1.00) | 0.216 (1.00) | 0.0234 (1.00) | 0.144 (1.00) | 0.388 (1.00)
18q gain | 9 (2%) | 404 |  |  | 0.0232 (1.00) | 0.0303 (1.00) | 0.0747 (1.00) | 0.0666 (1.00) |  |  | 0.274 (1.00) | 0.327 (1.00)
19p gain | 34 (8%) | 379 | 0.0744 (1.00) | 0.222 (1.00) | 0.00554 (1.00) | 0.0512 (1.00) | 0.229 (1.00) | 0.233 (1.00) | 0.75 (1.00) | 0.104 (1.00) | 0.588 (1.00) | 0.573 (1.00)
19q gain | 41 (10%) | 372 | 0.0676 (1.00) | 0.0935 (1.00) | 0.437 (1.00) | 0.0666 (1.00) | 0.0262 (1.00) | 0.0721 (1.00) | 0.00506 (1.00) | 0.419 (1.00) | 0.924 (1.00) | 0.942 (1.00)
21q gain | 11 (3%) | 402 | 0.192 (1.00) | 0.295 (1.00) | 0.0858 (1.00) | 0.339 (1.00) | 0.193 (1.00) | 0.48 (1.00) | 0.591 (1.00) | 1 (1.00) | 0.704 (1.00) | 0.684 (1.00)
Xq gain | 12 (3%) | 401 | 0.0689 (1.00) | 0.735 (1.00) | 0.0331 (1.00) | 0.631 (1.00) | 0.133 (1.00) | 0.352 (1.00) | 0.892 (1.00) | 0.225 (1.00) | 0.352 (1.00) | 0.41 (1.00)
1q loss | 18 (4%) | 395 | 0.271 (1.00) | 0.112 (1.00) | 0.0103 (1.00) | 0.269 (1.00) | 0.401 (1.00) | 0.594 (1.00) | 0.345 (1.00) | 0.0298 (1.00) | 0.941 (1.00) | 0.44 (1.00)
2p loss | 4 (1%) | 409 | 0.569 (1.00) | 0.142 (1.00) | 0.433 (1.00) |  |  |  | 0.16 (1.00) | 1 (1.00) | 0.662 (1.00) | 0.132 (1.00)
2q loss | 6 (1%) | 407 | 1 (1.00) | 0.0661 (1.00) | 0.601 (1.00) |  | 0.071 (1.00) | 0.269 (1.00) | 0.0816 (1.00) | 1 (1.00) | 0.175 (1.00) | 0.0588 (1.00)
3p loss | 27 (7%) | 386 | 0.528 (1.00) | 0.2 (1.00) | 0.00251 (1.00) | 0.252 (1.00) | 0.427 (1.00) | 0.972 (1.00) | 0.772 (1.00) | 0.195 (1.00) | 0.212 (1.00) | 0.143 (1.00)
3q loss | 12 (3%) | 401 | 0.816 (1.00) | 0.692 (1.00) | 0.224 (1.00) | 1 (1.00) | 0.124 (1.00) | 0.306 (1.00) | 1 (1.00) | 0.183 (1.00) | 0.423 (1.00) | 0.822 (1.00)
5p loss | 25 (6%) | 388 | 0.659 (1.00) | 0.172 (1.00) | 0.00176 (1.00) | 0.102 (1.00) | 0.725 (1.00) | 0.7 (1.00) | 0.434 (1.00) | 0.477 (1.00) | 0.841 (1.00) | 0.907 (1.00)
6p loss | 12 (3%) | 401 | 0.538 (1.00) | 0.05 (1.00) | 0.00285 (1.00) | 1 (1.00) | 0.755 (1.00) | 1 (1.00) | 0.176 (1.00) | 0.34 (1.00) | 0.642 (1.00) | 0.624 (1.00)
6q loss | 21 (5%) | 392 | 0.943 (1.00) | 0.529 (1.00) | 0.0743 (1.00) | 0.697 (1.00) | 0.165 (1.00) | 0.711 (1.00) | 0.575 (1.00) | 0.314 (1.00) | 0.864 (1.00) | 1 (1.00)
8q loss | 8 (2%) | 405 | 0.402 (1.00) | 0.735 (1.00) | 0.00966 (1.00) | 0.852 (1.00) | 0.273 (1.00) | 0.726 (1.00) | 0.0514 (1.00) | 0.0381 (1.00) | 0.197 (1.00) | 0.436 (1.00)
10p loss | 22 (5%) | 391 | 0.63 (1.00) | 0.692 (1.00) | 0.000828 (0.522) | 0.285 (1.00) | 0.109 (1.00) | 0.638 (1.00) | 0.255 (1.00) | 0.0842 (1.00) | 0.24 (1.00) | 0.681 (1.00)
10q loss | 24 (6%) | 389 | 0.373 (1.00) | 0.569 (1.00) | 0.000526 (0.336) | 0.152 (1.00) | 0.135 (1.00) | 0.949 (1.00) | 0.303 (1.00) | 0.0297 (1.00) | 0.697 (1.00) | 0.393 (1.00)
13q loss | 6 (1%) | 407 |  |  | 0.0209 (1.00) | 0.232 (1.00) | 0.038 (1.00) | 0.0214 (1.00) |  |  | 0.869 (1.00) | 0.723 (1.00)
16p loss | 9 (2%) | 404 | 0.249 (1.00) | 0.571 (1.00) | 0.305 (1.00) | 0.0298 (1.00) | 0.528 (1.00) | 1 (1.00) | 0.383 (1.00) | 0.317 (1.00) | 0.711 (1.00) | 1 (1.00)
16q loss | 7 (2%) | 406 | 0.462 (1.00) | 0.917 (1.00) | 0.228 (1.00) |  |  |  | 0.649 (1.00) | 0.558 (1.00) | 0.175 (1.00) | 0.17 (1.00)
17q loss | 32 (8%) | 381 | 0.116 (1.00) | 0.134 (1.00) | 0.00216 (1.00) | 0.22 (1.00) | 0.622 (1.00) | 0.411 (1.00) | 0.903 (1.00) | 0.367 (1.00) | 0.322 (1.00) | 0.291 (1.00)
19p loss | 14 (3%) | 399 | 1 (1.00) | 0.339 (1.00) | 0.00275 (1.00) | 0.0957 (1.00) | 0.127 (1.00) | 0.123 (1.00) | 0.464 (1.00) | 0.34 (1.00) | 0.693 (1.00) | 0.0876 (1.00)
19q loss | 13 (3%) | 400 | 0.922 (1.00) | 0.435 (1.00) | 0.0115 (1.00) | 0.0957 (1.00) | 0.584 (1.00) | 0.196 (1.00) | 0.428 (1.00) | 0.558 (1.00) | 0.57 (1.00) | 0.0611 (1.00)
Xq loss | 5 (1%) | 408 |  |  | 0.842 (1.00) | 1 (1.00) | 0.389 (1.00) | 0.673 (1.00) |  |  | 0.851 (1.00) | 0.14 (1.00)

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.11

Table S1. Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
2Q GAIN MUTATED | 28 | 6 | 3 | 2
2Q GAIN WILD-TYPE | 142 | 181 | 29 | 22

Figure S1. Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.92e-15 (Fisher's exact test), Q value = 1.4e-12

Table S2. Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
7P GAIN MUTATED | 112 | 49 | 23 | 16
7P GAIN WILD-TYPE | 58 | 138 | 9 | 8

Figure S2. Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.14e-05 (Fisher's exact test), Q value = 0.06

Table S3. Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
7P GAIN MUTATED | 71 | 38 | 23
7P GAIN WILD-TYPE | 34 | 48 | 40

Figure S3. Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00083

Table S4. Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
7P GAIN MUTATED | 48 | 18 | 10 | 10
7P GAIN WILD-TYPE | 19 | 40 | 29 | 10

Figure S4. Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.047

Table S5. Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
7P GAIN MUTATED | 16 | 11 | 59
7P GAIN WILD-TYPE | 48 | 7 | 43

Figure S5. Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 7.05e-11 (Fisher's exact test), Q value = 4.9e-08

Table S6. Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
7Q GAIN MUTATED | 96 | 45 | 21 | 13
7Q GAIN WILD-TYPE | 74 | 142 | 11 | 11

Figure S6. Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.11

Table S7. Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
7Q GAIN MUTATED | 40 | 16 | 9 | 10
7Q GAIN WILD-TYPE | 27 | 42 | 30 | 10

Figure S7. Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0062

Table S8. Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
8P GAIN MUTATED | 23 | 32 | 12 | 13
8P GAIN WILD-TYPE | 147 | 155 | 20 | 11

Figure S8. Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 9.39e-12 (Fisher's exact test), Q value = 6.5e-09

Table S9. Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
8Q GAIN MUTATED | 78 | 45 | 17 | 22
8Q GAIN WILD-TYPE | 92 | 142 | 15 | 2

Figure S9. Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.2

Table S10. Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
11P GAIN MUTATED | 16 | 1 | 1 | 0
11P GAIN WILD-TYPE | 154 | 186 | 31 | 24

Figure S10. Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.0025

Table S11. Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
11Q GAIN MUTATED | 19 | 0 | 2 | 1
11Q GAIN WILD-TYPE | 151 | 187 | 30 | 23

Figure S11. Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0072

Table S12. Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
13Q GAIN MUTATED | 46 | 10 | 8 | 14
13Q GAIN WILD-TYPE | 17 | 22 | 22 | 9

Figure S12. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'13q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.027

Table S13. Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
13Q GAIN MUTATED | 11 | 30 | 6 | 31
13Q GAIN WILD-TYPE | 33 | 18 | 7 | 12

Figure S13. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 2.95e-33 (Fisher's exact test), Q value = 2.1e-30

Table S14. Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
13Q GAIN MUTATED | 143 | 42 | 11 | 15
13Q GAIN WILD-TYPE | 27 | 145 | 21 | 9

Figure S14. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.17

Table S15. Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
13Q GAIN MUTATED | 70 | 35 | 26
13Q GAIN WILD-TYPE | 35 | 51 | 37

Figure S15. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.39e-07 (Fisher's exact test), Q value = 0.00057

Table S16. Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
13Q GAIN MUTATED | 49 | 18 | 12 | 13
13Q GAIN WILD-TYPE | 18 | 40 | 27 | 7

Figure S16. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.46e-06 (Fisher's exact test), Q value = 0.0057

Table S17. Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
13Q GAIN MUTATED | 17 | 9 | 66
13Q GAIN WILD-TYPE | 47 | 9 | 36

Figure S17. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.08e-14 (Fisher's exact test), Q value = 7.6e-12

Table S18. Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
16P GAIN MUTATED | 56 | 5 | 5 | 1
16P GAIN WILD-TYPE | 114 | 182 | 27 | 23

Figure S18. Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.94e-05 (Fisher's exact test), Q value = 0.065

Table S19. Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
16P GAIN MUTATED | 3 | 6 | 29
16P GAIN WILD-TYPE | 61 | 12 | 73

Figure S19. Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 1.44e-16 (Fisher's exact test), Q value = 1e-13

Table S20. Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
16Q GAIN MUTATED | 58 | 4 | 3 | 1
16Q GAIN WILD-TYPE | 112 | 183 | 29 | 23

Figure S20. Get High-res Image Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.92e-06 (Fisher's exact test), Q value = 0.004

Table S21. Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
20P GAIN MUTATED | 8 | 31 | 8 | 27
20P GAIN WILD-TYPE | 36 | 17 | 5 | 16

Figure S21. Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 4.29e-20 (Fisher's exact test), Q value = 3.1e-17

Table S22. Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
20P GAIN MUTATED | 98 | 44 | 31 | 15
20P GAIN WILD-TYPE | 72 | 143 | 1 | 9

Figure S22. Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.67e-06 (Fisher's exact test), Q value = 0.0058

Table S23. Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
20P GAIN MUTATED | 44 | 14 | 18 | 14
20P GAIN WILD-TYPE | 23 | 44 | 21 | 6

Figure S23. Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.55e-07 (Fisher's exact test), Q value = 0.00024

Table S24. Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
20P GAIN MUTATED | 15 | 8 | 67
20P GAIN WILD-TYPE | 49 | 10 | 35

Figure S24. Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.18e-11 (Fisher's exact test), Q value = 8.2e-09

Table S25. Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
20Q GAIN MUTATED | 59 | 10 | 13 | 19
20Q GAIN WILD-TYPE | 4 | 22 | 17 | 4

Figure S25. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.69e-15 (Fisher's exact test), Q value = 6.8e-12

Table S26. Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
20Q GAIN MUTATED | 10 | 43 | 8 | 40
20Q GAIN WILD-TYPE | 34 | 5 | 5 | 3

Figure S26. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 9.42e-47 (Fisher's exact test), Q value = 6.8e-44

Table S27. Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
20Q GAIN MUTATED | 160 | 54 | 32 | 21
20Q GAIN WILD-TYPE | 10 | 133 | 0 | 3

Figure S27. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 7.3e-07

Table S28. Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
20Q GAIN MUTATED | 89 | 37 | 33
20Q GAIN WILD-TYPE | 16 | 49 | 30

Figure S28. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0083

Table S29. Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 142 | 23 | 48 | 51
20Q GAIN MUTATED | 97 | 10 | 18 | 41
20Q GAIN WILD-TYPE | 45 | 13 | 30 | 10

Figure S29. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.95e-16 (Fisher's exact test), Q value = 2.8e-13

Table S30. Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
20Q GAIN MUTATED | 64 | 17 | 23 | 18
20Q GAIN WILD-TYPE | 3 | 41 | 16 | 2

Figure S30. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.98e-18 (Fisher's exact test), Q value = 4.3e-15

Table S31. Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
20Q GAIN MUTATED | 17 | 12 | 93
20Q GAIN WILD-TYPE | 47 | 6 | 9

Figure S31. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 7.09e-08 (Fisher's exact test), Q value = 4.9e-05

Table S32. Gene #40: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
1P LOSS MUTATED | 36 | 6 | 8 | 1
1P LOSS WILD-TYPE | 134 | 181 | 24 | 23

Figure S32. Get High-res Image Gene #40: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 1.05e-11 (Fisher's exact test), Q value = 7.3e-09

Table S33. Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
4P LOSS MUTATED | 56 | 11 | 13 | 4
4P LOSS WILD-TYPE | 114 | 176 | 19 | 20

Figure S33. Get High-res Image Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 2.26e-10 (Fisher's exact test), Q value = 1.6e-07

Table S34. Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
4Q LOSS MUTATED | 49 | 8 | 9 | 2
4Q LOSS WILD-TYPE | 121 | 179 | 23 | 22

Figure S34. Get High-res Image Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0074

Table S35. Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
5Q LOSS MUTATED | 27 | 4 | 3 | 4
5Q LOSS WILD-TYPE | 143 | 183 | 29 | 20

Figure S35. Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.19

Table S36. Gene #52: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
8P LOSS MUTATED | 24 | 2 | 3 | 9
8P LOSS WILD-TYPE | 39 | 30 | 27 | 14

Figure S36. Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 7.76e-17 (Fisher's exact test), Q value = 5.5e-14

Table S37. Gene #52: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
8P LOSS MUTATED | 73 | 11 | 3 | 6
8P LOSS WILD-TYPE | 97 | 176 | 29 | 18

Figure S37. Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.14

Table S38. Gene #52: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
8P LOSS MUTATED | 25 | 5 | 8 | 9
8P LOSS WILD-TYPE | 42 | 53 | 31 | 11

Figure S38. Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.029

Table S39. Gene #54: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
9P LOSS MUTATED | 19 | 2 | 5 | 1
9P LOSS WILD-TYPE | 151 | 185 | 27 | 23

Figure S39. Get High-res Image Gene #54: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 2.55e-06 (Fisher's exact test), Q value = 0.0017

Table S40. Gene #55: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
9Q LOSS MUTATED | 21 | 1 | 4 | 0
9Q LOSS WILD-TYPE | 149 | 186 | 28 | 24

Figure S40. Get High-res Image Gene #55: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.055

Table S41. Gene #58: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
11P LOSS MUTATED | 14 | 2 | 6 | 0
11P LOSS WILD-TYPE | 156 | 185 | 26 | 24

Figure S41. Get High-res Image Gene #58: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.18

Table S42. Gene #58: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
11P LOSS MUTATED | 10 | 0 | 0
11P LOSS WILD-TYPE | 95 | 86 | 63

Figure S42. Get High-res Image Gene #58: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 7.92e-06 (Fisher's exact test), Q value = 0.0053

Table S43. Gene #59: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
11Q LOSS MUTATED | 19 | 2 | 6 | 0
11Q LOSS WILD-TYPE | 151 | 185 | 26 | 24

Figure S43. Get High-res Image Gene #59: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.61e-06 (Fisher's exact test), Q value = 0.0064

Table S44. Gene #59: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
11Q LOSS MUTATED | 14 | 0 | 0
11Q LOSS WILD-TYPE | 91 | 86 | 63

Figure S44. Get High-res Image Gene #59: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.047

Table S45. Gene #60: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
12P LOSS MUTATED | 17 | 1 | 3 | 0
12P LOSS WILD-TYPE | 153 | 186 | 29 | 24

Figure S45. Get High-res Image Gene #60: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.066

Table S46. Gene #61: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
12Q LOSS MUTATED | 15 | 1 | 4 | 0
12Q LOSS WILD-TYPE | 155 | 186 | 28 | 24

Figure S46. Get High-res Image Gene #61: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

P value = 9.75e-08 (Fisher's exact test), Q value = 6.7e-05

Table S47. Gene #63: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
14Q LOSS MUTATED | 31 | 2 | 1 | 9
14Q LOSS WILD-TYPE | 32 | 30 | 29 | 14

Figure S47. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.1e-06 (Fisher's exact test), Q value = 0.0014

Table S48. Gene #63: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
14Q LOSS MUTATED | 1 | 17 | 5 | 20
14Q LOSS WILD-TYPE | 43 | 31 | 8 | 23

Figure S48. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 1.58e-22 (Fisher's exact test), Q value = 1.1e-19

Table S49. Gene #63: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
14Q LOSS MUTATED | 78 | 8 | 8 | 0
14Q LOSS WILD-TYPE | 92 | 179 | 24 | 24

Figure S49. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00081

Table S50. Gene #63: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
14Q LOSS MUTATED | 36 | 6 | 6
14Q LOSS WILD-TYPE | 69 | 80 | 57

Figure S50. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.16

Table S51. Gene #63: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 64 | 117 | 7 | 76
14Q LOSS MUTATED | 14 | 40 | 0 | 7
14Q LOSS WILD-TYPE | 50 | 77 | 7 | 69

Figure S51. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00011

Table S52. Gene #63: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
14Q LOSS MUTATED | 34 | 4 | 7 | 7
14Q LOSS WILD-TYPE | 33 | 54 | 32 | 13

Figure S52. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0012

Table S53. Gene #63: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
14Q LOSS MUTATED | 6 | 2 | 44
14Q LOSS WILD-TYPE | 58 | 16 | 58

Figure S53. Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 9.29e-22 (Fisher's exact test), Q value = 6.6e-19

Table S54. Gene #64: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
15Q LOSS MUTATED | 70 | 9 | 19 | 1
15Q LOSS WILD-TYPE | 100 | 178 | 13 | 23

Figure S54. Get High-res Image Gene #64: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.003

Table S55. Gene #67: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
17P LOSS MUTATED | 40 | 7 | 5 | 13
17P LOSS WILD-TYPE | 23 | 25 | 25 | 10

Figure S55. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.039

Table S56. Gene #67: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
17P LOSS MUTATED | 7 | 28 | 6 | 24
17P LOSS WILD-TYPE | 37 | 20 | 7 | 19

Figure S56. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 4.44e-23 (Fisher's exact test), Q value = 3.2e-20

Table S57. Gene #67: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
17P LOSS MUTATED | 109 | 26 | 16 | 13
17P LOSS WILD-TYPE | 61 | 161 | 16 | 11

Figure S57. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-07 (Fisher's exact test), Q value = 0.00016

Table S58. Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
17P LOSS MUTATED | 61 | 19 | 17
17P LOSS WILD-TYPE | 44 | 67 | 46

Figure S58. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.09e-05 (Fisher's exact test), Q value = 0.034

Table S59. Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
17P LOSS MUTATED | 15 | 7 | 59
17P LOSS WILD-TYPE | 49 | 11 | 43

Figure S59. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.04e-14 (Fisher's exact test), Q value = 1.4e-11

Table S60. Gene #69: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
18P LOSS MUTATED | 53 | 5 | 5 | 16
18P LOSS WILD-TYPE | 10 | 27 | 25 | 7

Figure S60. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.47e-10 (Fisher's exact test), Q value = 4.5e-07

Table S61. Gene #69: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
18P LOSS MUTATED | 6 | 31 | 8 | 34
18P LOSS WILD-TYPE | 38 | 17 | 5 | 9

Figure S61. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 2.44e-46 (Fisher's exact test), Q value = 1.8e-43

Table S62. Gene #69: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
18P LOSS MUTATED | 143 | 26 | 27 | 13
18P LOSS WILD-TYPE | 27 | 161 | 5 | 11

Figure S62. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.15e-13 (Fisher's exact test), Q value = 3.6e-10

Table S63. Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
18P LOSS MUTATED | 81 | 24 | 21
18P LOSS WILD-TYPE | 24 | 62 | 42

Figure S63. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 8.24e-05 (Fisher's exact test), Q value = 0.054

Table S64. Gene #69: '18p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 142 | 23 | 48 | 51
18P LOSS MUTATED | 85 | 7 | 12 | 26
18P LOSS WILD-TYPE | 57 | 16 | 36 | 25

Figure S64. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.92e-13 (Fisher's exact test), Q value = 4.1e-10

Table S65. Gene #69: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
18P LOSS MUTATED | 57 | 13 | 16 | 15
18P LOSS WILD-TYPE | 10 | 45 | 23 | 5

Figure S65. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.6e-14 (Fisher's exact test), Q value = 3.2e-11

Table S66. Gene #69: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
18P LOSS MUTATED | 12 | 9 | 80
18P LOSS WILD-TYPE | 52 | 9 | 22

Figure S66. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.4e-13 (Fisher's exact test), Q value = 9.8e-11

Table S67. Gene #70: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 63 | 32 | 30 | 23
18Q LOSS MUTATED | 54 | 6 | 6 | 16
18Q LOSS WILD-TYPE | 9 | 26 | 24 | 7

Figure S67. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-09 (Fisher's exact test), Q value = 1.1e-06

Table S68. Gene #70: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 48 | 13 | 43
18Q LOSS MUTATED | 7 | 32 | 9 | 34
18Q LOSS WILD-TYPE | 37 | 16 | 4 | 9

Figure S68. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 8.88e-46 (Fisher's exact test), Q value = 6.4e-43

Table S69. Gene #70: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
18Q LOSS MUTATED | 149 | 33 | 27 | 16
18Q LOSS WILD-TYPE | 21 | 154 | 5 | 8

Figure S69. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.62e-15 (Fisher's exact test), Q value = 2.5e-12

Table S70. Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
18Q LOSS MUTATED | 88 | 28 | 22
18Q LOSS WILD-TYPE | 17 | 58 | 41

Figure S70. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 7e-09

Table S71. Gene #70: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 67 | 58 | 39 | 20
18Q LOSS MUTATED | 57 | 15 | 18 | 16
18Q LOSS WILD-TYPE | 10 | 43 | 21 | 4

Figure S71. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-15 (Fisher's exact test), Q value = 1.2e-12

Table S72. Gene #70: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 18 | 102
18Q LOSS MUTATED | 12 | 11 | 83
18Q LOSS WILD-TYPE | 52 | 7 | 19

Figure S72. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 8.88e-08 (Fisher's exact test), Q value = 6.1e-05

Table S73. Gene #73: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
20P LOSS MUTATED | 27 | 2 | 0 | 4
20P LOSS WILD-TYPE | 143 | 185 | 32 | 20

Figure S73. Get High-res Image Gene #73: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.0018

Table S74. Gene #74: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
21Q LOSS MUTATED | 40 | 15 | 13 | 3
21Q LOSS WILD-TYPE | 130 | 172 | 19 | 21

Figure S74. Get High-res Image Gene #74: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 7.4e-09

Table S75. Gene #75: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
22Q LOSS MUTATED | 56 | 11 | 12 | 2
22Q LOSS WILD-TYPE | 114 | 176 | 20 | 22

Figure S75. Get High-res Image Gene #75: '22q loss mutation analysis' versus Clinical Feature #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