Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1RF5SD5
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/C1RF5SD5
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 45 arm-level results and 10 molecular subtypes across 494 patients, 132 significant findings detected with Q value < 0.25.

- 1q gain cnv correlated to 'CN_CNMF'.

- 4p gain cnv correlated to 'CN_CNMF'.

- 4q gain cnv correlated to 'CN_CNMF'.

- 5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11q gain cnv correlated to 'CN_CNMF'.

- 12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 13q gain cnv correlated to 'CN_CNMF'.

- 14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 19p gain cnv correlated to 'CN_CNMF'.

- 19q gain cnv correlated to 'CN_CNMF'.

- 20p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 1p loss cnv correlated to 'CN_CNMF'.

- 2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 8q loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'CN_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF'.

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

- 15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 18p loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 45 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 132 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
7q gain | 0 (0%) | 475 | 1.95e-23 (8.15e-21) | 2.06e-05 (0.00732) | 0.805 (1.00) | 0.00206 (0.543) | 7.11e-05 (0.024) | 1.23e-05 (0.00451) | 0.000332 (0.102) | 2.25e-05 (0.00796) | 7.82e-05 (0.0264) | 1.63e-05 (0.00595)
12p gain | 0 (0%) | 483 | 1.08e-12 (4.45e-10) | 4.68e-06 (0.00176) | 1 (1.00) | 0.0281 (1.00) | 2.32e-05 (0.0082) | 4.9e-06 (0.00184) | 3.75e-05 (0.0131) | 1.29e-05 (0.00474) | 0.000147 (0.0484) | 9.1e-06 (0.00338)
12q gain | 0 (0%) | 482 | 1.34e-12 (5.47e-10) | 1.51e-06 (0.000589) | 1 (1.00) | 0.0281 (1.00) | 7.58e-06 (0.00283) | 1.57e-06 (0.000607) | 1.21e-05 (0.00446) | 3.57e-06 (0.00136) | 5.02e-05 (0.0173) | 2.43e-06 (0.000931)
16p gain | 0 (0%) | 482 | 5.86e-14 (2.42e-11) | 1.21e-05 (0.00446) | 0.795 (1.00) | 0.0363 (1.00) | 0.000225 (0.071) | 4.56e-05 (0.0158) | 0.000181 (0.0591) | 4.67e-05 (0.0162) | 0.000388 (0.117) | 2.42e-05 (0.00851)
17p gain | 0 (0%) | 482 | 1.99e-09 (8.02e-07) | 1.51e-06 (0.000589) | 0.773 (1.00) | 0.0122 (1.00) | 7.58e-06 (0.00283) | 1.57e-06 (0.000607) | 1.21e-05 (0.00446) | 3.57e-06 (0.00136) | 5.02e-05 (0.0173) | 2.43e-06 (0.000931)
17q gain | 0 (0%) | 481 | 3.8e-09 (1.53e-06) | 3.34e-07 (0.000132) | 0.795 (1.00) | 0.0193 (1.00) | 2.22e-06 (0.000855) | 3.35e-07 (0.000132) | 3.86e-06 (0.00145) | 9.76e-07 (0.000383) | 1.69e-05 (0.00617) | 6.38e-07 (0.000251)
2p loss | 0 (0%) | 486 | 5.2e-09 (2.08e-06) | 0.000139 (0.0461) | 1 (1.00) | 0.079 (1.00) | 0.000645 (0.189) | 0.000218 (0.0697) | 6.43e-05 (0.022) | 1.99e-05 (0.00709) | 0.000242 (0.0759) | 1.75e-05 (0.00635)
22q loss | 0 (0%) | 429 | 4.98e-57 (2.08e-54) | 4.44e-05 (0.0155) | 0.0578 (1.00) | 0.244 (1.00) | 6.84e-11 (2.77e-08) | 8.07e-11 (3.26e-08) | 3.24e-05 (0.0114) | 5.3e-06 (0.00198) | 1.56e-07 (6.17e-05) | 3.09e-06 (0.00118)
5q gain | 0 (0%) | 480 | 2.84e-18 (1.17e-15) | 4.86e-05 (0.0168) | 1 (1.00) | 0.0281 (1.00) | 0.000231 (0.0729) | 8.87e-05 (0.0296) | 0.000436 (0.131) | 2.79e-05 (0.00979) | 0.00155 (0.422) | 2.13e-05 (0.00756)
7p gain | 0 (0%) | 477 | 1.76e-22 (7.34e-20) | 0.000149 (0.0488) | 0.835 (1.00) | 0.0106 (1.00) | 0.000536 (0.159) | 0.000114 (0.038) | 0.00261 (0.674) | 0.000255 (0.0794) | 0.000527 (0.157) | 0.000184 (0.06)
2q loss | 0 (0%) | 487 | 3.94e-09 (1.58e-06) | 0.000343 (0.105) | 0.839 (1.00) | 0.0521 (1.00) | 0.00153 (0.419) | 0.000675 (0.196) | 0.000219 (0.0697) | 7.85e-05 (0.0264) | 0.000758 (0.218) | 7.02e-05 (0.0239)
15q loss | 0 (0%) | 487 | 0.000653 (0.19) | 0.000343 (0.105) | 0.457 (1.00) | 0.25 (1.00) | 0.00153 (0.419) | 0.000675 (0.196) | 0.000219 (0.0697) | 7.85e-05 (0.0264) | 0.000758 (0.218) | 7.02e-05 (0.0239)
14q gain | 0 (0%) | 486 | 5.2e-09 (2.08e-06) | 0.000139 (0.0461) | 1 (1.00) | 0.25 (1.00) | 0.000645 (0.189) | 0.000218 (0.0697) | 0.00106 (0.303) | 0.000573 (0.17) | 0.00344 (0.864) | 0.000587 (0.173)
16q gain | 0 (0%) | 484 | 6.03e-13 (2.48e-10) | 6.6e-05 (0.0225) | 1 (1.00) | 0.126 (1.00) | 0.00181 (0.491) | 0.000415 (0.125) | 0.0014 (0.388) | 0.000637 (0.187) | 0.00278 (0.712) | 0.0005 (0.15)
5p gain | 0 (0%) | 477 | 7.68e-20 (3.19e-17) | 0.000366 (0.111) | 0.835 (1.00) | 0.107 (1.00) | 0.00286 (0.729) | 0.000995 (0.285) | 0.00357 (0.893) | 0.000204 (0.066) | 0.00688 (1.00) | 0.000131 (0.0435)
20p gain | 0 (0%) | 485 | 1.17e-11 (4.77e-09) | 0.000251 (0.0787) | 1 (1.00) | 0.079 (1.00) | 0.00467 (1.00) | 0.00183 (0.493) | 0.00382 (0.95) | 0.00188 (0.503) | 0.00566 (1.00) | 0.00149 (0.412)
20q gain | 0 (0%) | 485 | 1.17e-11 (4.77e-09) | 0.000251 (0.0787) | 1 (1.00) | 0.079 (1.00) | 0.00467 (1.00) | 0.00183 (0.493) | 0.00382 (0.95) | 0.00188 (0.503) | 0.00566 (1.00) | 0.00149 (0.412)
11q loss | 0 (0%) | 485 | 3.28e-06 (0.00125) | 0.0106 (1.00) | 0.321 (1.00) | 0.794 (1.00) | 0.0185 (1.00) | 0.017 (1.00) | 0.000352 (0.107) | 0.00336 (0.846) | 0.00122 (0.34) | 0.00275 (0.706)
1q gain | 0 (0%) | 473 | 3.68e-06 (0.00139) | 0.0848 (1.00) | 0.00319 (0.808) | 0.0931 (1.00) | 0.0107 (1.00) | 0.00403 (0.99) | 0.233 (1.00) | 0.203 (1.00) | 0.185 (1.00) | 0.0917 (1.00)
4p gain | 0 (0%) | 490 | 1.89e-05 (0.00685) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.0755 (1.00) | 0.0676 (1.00) | 0.129 (1.00) | 0.0942 (1.00)
4q gain | 0 (0%) | 490 | 1.89e-05 (0.00685) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.0755 (1.00) | 0.0676 (1.00) | 0.129 (1.00) | 0.0942 (1.00)
11q gain | 0 (0%) | 490 | 0.000207 (0.0668) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
13q gain | 0 (0%) | 491 | 0.0003 (0.0929) | 0.0585 (1.00) |  |  | 0.0985 (1.00) | 0.0788 (1.00) | 0.207 (1.00) | 0.355 (1.00) | 0.323 (1.00) | 0.27 (1.00)
19p gain | 0 (0%) | 490 | 1.89e-05 (0.00685) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
19q gain | 0 (0%) | 489 | 1.16e-06 (0.000453) | 0.00581 (1.00) | 0.636 (1.00) | 0.0523 (1.00) | 0.0161 (1.00) | 0.0069 (1.00) | 0.00249 (0.648) | 0.0012 (0.338) | 0.00735 (1.00) | 0.00111 (0.316)
1p loss | 0 (0%) | 491 | 0.0003 (0.0929) | 0.582 (1.00) |  |  | 0.493 (1.00) | 0.183 (1.00) | 0.207 (1.00) | 0.355 (1.00) | 0.323 (1.00) | 0.27 (1.00)
3q loss | 0 (0%) | 491 | 0.0003 (0.0929) | 0.0585 (1.00) |  |  | 0.0985 (1.00) | 0.0788 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
8p loss | 0 (0%) | 490 | 1.89e-05 (0.00685) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
8q loss | 0 (0%) | 490 | 1.89e-05 (0.00685) | 0.0149 (1.00) |  |  | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
9p loss | 0 (0%) | 482 | 2.13e-11 (8.66e-09) | 0.0712 (1.00) | 0.56 (1.00) | 0.204 (1.00) | 0.0924 (1.00) | 0.134 (1.00) | 0.0506 (1.00) | 0.0401 (1.00) | 0.0792 (1.00) | 0.0276 (1.00)
9q loss | 0 (0%) | 477 | 1.59e-13 (6.56e-11) | 0.111 (1.00) | 0.209 (1.00) | 0.00396 (0.977) | 0.182 (1.00) | 0.231 (1.00) | 0.0759 (1.00) | 0.0878 (1.00) | 0.108 (1.00) | 0.0555 (1.00)
10p loss | 0 (0%) | 488 | 6.87e-08 (2.73e-05) | 0.0263 (1.00) |  |  | 0.0509 (1.00) | 0.0183 (1.00) | 0.00929 (1.00) | 0.00658 (1.00) | 0.0259 (1.00) | 0.00664 (1.00)
10q loss | 0 (0%) | 489 | 1.16e-06 (0.000453) | 0.0757 (1.00) |  |  | 0.119 (1.00) | 0.0361 (1.00) | 0.0268 (1.00) | 0.0215 (1.00) | 0.0687 (1.00) | 0.0216 (1.00)
11p loss | 0 (0%) | 487 | 7.98e-08 (3.17e-05) | 0.00956 (1.00) | 0.495 (1.00) | 1 (1.00) | 0.00712 (1.00) | 0.0174 (1.00) | 0.00316 (0.804) | 0.00196 (0.522) | 0.00954 (1.00) | 0.00199 (0.528)
18p loss | 0 (0%) | 490 | 0.000207 (0.0668) | 0.22 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.242 (1.00) | 0.121 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.0227 (1.00) | 0.0402 (1.00)
18q loss | 0 (0%) | 490 | 0.000207 (0.0668) | 0.22 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.242 (1.00) | 0.121 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.0227 (1.00) | 0.0402 (1.00)
21q loss | 0 (0%) | 488 | 0.000191 (0.0621) | 0.0973 (1.00) | 0.384 (1.00) | 0.0523 (1.00) | 0.223 (1.00) | 0.226 (1.00) | 0.0684 (1.00) | 0.0841 (1.00) | 0.0892 (1.00) | 0.0459 (1.00)
11p gain | 0 (0%) | 489 | 0.00134 (0.373) | 0.00581 (1.00) |  |  | 0.0161 (1.00) | 0.0069 (1.00) | 0.00249 (0.648) | 0.0012 (0.338) | 0.00735 (1.00) | 0.00111 (0.316)
18p gain | 0 (0%) | 491 | 0.00246 (0.648) | 0.0585 (1.00) |  |  | 0.0985 (1.00) | 0.0788 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
18q gain | 0 (0%) | 491 | 0.00246 (0.648) | 0.0585 (1.00) |  |  | 0.0985 (1.00) | 0.0788 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
21q gain | 0 (0%) | 491 | 0.00246 (0.648) | 0.0585 (1.00) |  |  | 0.0985 (1.00) | 0.0788 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
6q loss | 0 (0%) | 491 | 0.0219 (1.00) | 0.0585 (1.00) |  |  | 0.0985 (1.00) | 0.0788 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
13q loss | 0 (0%) | 483 | 0.0122 (1.00) | 0.0243 (1.00) | 0.0774 (1.00) | 1 (1.00) | 0.0233 (1.00) | 0.0183 (1.00) | 0.00902 (1.00) | 0.00997 (1.00) | 0.00684 (1.00) | 0.0107 (1.00)
17p loss | 0 (0%) | 487 | 0.00118 (0.333) | 0.525 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.786 (1.00) | 0.887 (1.00) | 0.519 (1.00) | 0.493 (1.00) | 0.9 (1.00) | 0.44 (1.00)
19p loss | 0 (0%) | 490 | 0.132 (1.00) | 0.0149 (1.00) | 0.278 (1.00) | 0.364 (1.00) | 0.0444 (1.00) | 0.0219 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)

'1q gain' versus 'CN_CNMF'

P value = 3.68e-06 (Fisher's exact test), Q value = 0.0014

Table S1. Gene #1: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
1Q GAIN CNV | 9 | 11 | 1
1Q GAIN WILD-TYPE | 25 | 372 | 76

Figure S1. Get High-res Image Gene #1: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S2. Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
4P GAIN CNV | 4 | 0 | 0
4P GAIN WILD-TYPE | 30 | 383 | 77

Figure S2. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S3. Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
4Q GAIN CNV | 4 | 0 | 0
4Q GAIN WILD-TYPE | 30 | 383 | 77

Figure S3. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 7.68e-20 (Fisher's exact test), Q value = 3.2e-17

Table S4. Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
5P GAIN CNV | 16 | 1 | 0
5P GAIN WILD-TYPE | 18 | 382 | 77

Figure S4. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000366 (Fisher's exact test), Q value = 0.11

Table S5. Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
5P GAIN CNV | 12 | 3 | 2
5P GAIN WILD-TYPE | 139 | 80 | 258

Figure S5. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.066

Table S6. Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
5P GAIN CNV | 0 | 11 | 6
5P GAIN WILD-TYPE | 155 | 119 | 202

Figure S6. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.044

Table S7. Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
5P GAIN CNV | 6 | 11 | 0
5P GAIN WILD-TYPE | 193 | 117 | 166

Figure S7. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2.84e-18 (Fisher's exact test), Q value = 1.2e-15

Table S8. Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
5Q GAIN CNV | 14 | 0 | 0
5Q GAIN WILD-TYPE | 20 | 383 | 77

Figure S8. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 4.86e-05 (Fisher's exact test), Q value = 0.017

Table S9. Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
5Q GAIN CNV | 12 | 1 | 1
5Q GAIN WILD-TYPE | 139 | 82 | 259

Figure S9. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.073

Table S10. Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
5Q GAIN CNV | 12 | 0 | 0 | 2
5Q GAIN WILD-TYPE | 138 | 55 | 114 | 159

Figure S10. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-05 (Fisher's exact test), Q value = 0.03

Table S11. Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
5Q GAIN CNV | 12 | 2 | 0 | 0
5Q GAIN WILD-TYPE | 120 | 210 | 94 | 42

Figure S11. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000436 (Fisher's exact test), Q value = 0.13

Table S12. Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
5Q GAIN CNV | 11 | 1 | 2
5Q GAIN WILD-TYPE | 139 | 172 | 168

Figure S12. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.0098

Table S13. Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
5Q GAIN CNV | 0 | 11 | 3
5Q GAIN WILD-TYPE | 155 | 119 | 205

Figure S13. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.0076

Table S14. Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
5Q GAIN CNV | 3 | 11 | 0
5Q GAIN WILD-TYPE | 196 | 117 | 166

Figure S14. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.76e-22 (Fisher's exact test), Q value = 7.3e-20

Table S15. Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
7P GAIN CNV | 17 | 0 | 0
7P GAIN WILD-TYPE | 17 | 383 | 77

Figure S15. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.049

Table S16. Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
7P GAIN CNV | 13 | 2 | 2
7P GAIN WILD-TYPE | 138 | 81 | 258

Figure S16. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000536 (Fisher's exact test), Q value = 0.16

Table S17. Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
7P GAIN CNV | 13 | 0 | 1 | 2
7P GAIN WILD-TYPE | 137 | 55 | 113 | 159

Figure S17. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.038

Table S18. Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
7P GAIN CNV | 13 | 2 | 1 | 0
7P GAIN WILD-TYPE | 119 | 210 | 93 | 42

Figure S18. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000255 (Fisher's exact test), Q value = 0.079

Table S19. Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
7P GAIN CNV | 1 | 12 | 4
7P GAIN WILD-TYPE | 154 | 118 | 204

Figure S19. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000527 (Fisher's exact test), Q value = 0.16

Table S20. Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
7P GAIN CNV | 13 | 1 | 3
7P GAIN WILD-TYPE | 150 | 168 | 158

Figure S20. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.06

Table S21. Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
7P GAIN CNV | 4 | 12 | 1
7P GAIN WILD-TYPE | 195 | 116 | 165

Figure S21. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.95e-23 (Fisher's exact test), Q value = 8.1e-21

Table S22. Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
7Q GAIN CNV | 18 | 0 | 1
7Q GAIN WILD-TYPE | 16 | 383 | 76

Figure S22. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.0073

Table S23. Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
7Q GAIN CNV | 15 | 2 | 2
7Q GAIN WILD-TYPE | 136 | 81 | 258

Figure S23. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 7.11e-05 (Fisher's exact test), Q value = 0.024

Table S24. Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
7Q GAIN CNV | 15 | 0 | 1 | 2
7Q GAIN WILD-TYPE | 135 | 55 | 113 | 159

Figure S24. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0045

Table S25. Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
7Q GAIN CNV | 15 | 2 | 1 | 0
7Q GAIN WILD-TYPE | 117 | 210 | 93 | 42

Figure S25. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000332 (Fisher's exact test), Q value = 0.1

Table S26. Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
7Q GAIN CNV | 14 | 2 | 3
7Q GAIN WILD-TYPE | 136 | 171 | 167

Figure S26. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.008

Table S27. Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
7Q GAIN CNV | 1 | 14 | 4
7Q GAIN WILD-TYPE | 154 | 116 | 204

Figure S27. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.82e-05 (Fisher's exact test), Q value = 0.026

Table S28. Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
7Q GAIN CNV | 15 | 1 | 3
7Q GAIN WILD-TYPE | 148 | 168 | 158

Figure S28. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.006

Table S29. Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
7Q GAIN CNV | 4 | 14 | 1
7Q GAIN WILD-TYPE | 195 | 114 | 165

Figure S29. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.067

Table S30. Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11Q GAIN CNV | 3 | 0 | 1
11Q GAIN WILD-TYPE | 31 | 383 | 76

Figure S30. Get High-res Image Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.08e-12 (Fisher's exact test), Q value = 4.4e-10

Table S31. Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
12P GAIN CNV | 10 | 0 | 1
12P GAIN WILD-TYPE | 24 | 383 | 76

Figure S31. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0018

Table S32. Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
12P GAIN CNV | 11 | 0 | 0
12P GAIN WILD-TYPE | 140 | 83 | 260

Figure S32. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0082

Table S33. Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
12P GAIN CNV | 11 | 0 | 0 | 0
12P GAIN WILD-TYPE | 139 | 55 | 114 | 161

Figure S33. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.9e-06 (Fisher's exact test), Q value = 0.0018

Table S34. Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
12P GAIN CNV | 11 | 0 | 0 | 0
12P GAIN WILD-TYPE | 121 | 212 | 94 | 42

Figure S34. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.013

Table S35. Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
12P GAIN CNV | 10 | 0 | 1
12P GAIN WILD-TYPE | 140 | 173 | 169

Figure S35. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0047

Table S36. Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
12P GAIN CNV | 0 | 10 | 1
12P GAIN WILD-TYPE | 155 | 120 | 207

Figure S36. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.048

Table S37. Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
12P GAIN CNV | 10 | 0 | 1
12P GAIN WILD-TYPE | 153 | 169 | 160

Figure S37. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.1e-06 (Fisher's exact test), Q value = 0.0034

Table S38. Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
12P GAIN CNV | 1 | 10 | 0
12P GAIN WILD-TYPE | 198 | 118 | 166

Figure S38. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.34e-12 (Fisher's exact test), Q value = 5.5e-10

Table S39. Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
12Q GAIN CNV | 10 | 0 | 2
12Q GAIN WILD-TYPE | 24 | 383 | 75

Figure S39. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00059

Table S40. Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
12Q GAIN CNV | 12 | 0 | 0
12Q GAIN WILD-TYPE | 139 | 83 | 260

Figure S40. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0028

Table S41. Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
12Q GAIN CNV | 12 | 0 | 0 | 0
12Q GAIN WILD-TYPE | 138 | 55 | 114 | 161

Figure S41. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00061

Table S42. Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
12Q GAIN CNV | 12 | 0 | 0 | 0
12Q GAIN WILD-TYPE | 120 | 212 | 94 | 42

Figure S42. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0045

Table S43. Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
12Q GAIN CNV | 11 | 0 | 1
12Q GAIN WILD-TYPE | 139 | 173 | 169

Figure S43. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0014

Table S44. Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
12Q GAIN CNV | 0 | 11 | 1
12Q GAIN WILD-TYPE | 155 | 119 | 207

Figure S44. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.017

Table S45. Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
12Q GAIN CNV | 11 | 0 | 1
12Q GAIN WILD-TYPE | 152 | 169 | 160

Figure S45. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00093

Table S46. Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
12Q GAIN CNV | 1 | 11 | 0
12Q GAIN WILD-TYPE | 198 | 117 | 166

Figure S46. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S47. Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
13Q GAIN CNV | 3 | 0 | 0
13Q GAIN WILD-TYPE | 31 | 383 | 77

Figure S47. Get High-res Image Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.2e-09 (Fisher's exact test), Q value = 2.1e-06

Table S48. Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
14Q GAIN CNV | 7 | 0 | 1
14Q GAIN WILD-TYPE | 27 | 383 | 76

Figure S48. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.046

Table S49. Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
14Q GAIN CNV | 8 | 0 | 0
14Q GAIN WILD-TYPE | 143 | 83 | 260

Figure S49. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000645 (Fisher's exact test), Q value = 0.19

Table S50. Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
14Q GAIN CNV | 8 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 142 | 55 | 114 | 161

Figure S50. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.07

Table S51. Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
14Q GAIN CNV | 8 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 124 | 212 | 94 | 42

Figure S51. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000573 (Fisher's exact test), Q value = 0.17

Table S52. Gene #13: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
14Q GAIN CNV | 0 | 7 | 1
14Q GAIN WILD-TYPE | 155 | 123 | 207

Figure S52. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.17

Table S53. Gene #13: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
14Q GAIN CNV | 1 | 7 | 0
14Q GAIN WILD-TYPE | 198 | 121 | 166

Figure S53. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 5.86e-14 (Fisher's exact test), Q value = 2.4e-11

Table S54. Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
16P GAIN CNV | 11 | 0 | 1
16P GAIN WILD-TYPE | 23 | 383 | 76

Figure S54. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0045

Table S55. Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
16P GAIN CNV | 11 | 1 | 0
16P GAIN WILD-TYPE | 140 | 82 | 260

Figure S55. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.071

Table S56. Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
16P GAIN CNV | 11 | 0 | 0 | 1
16P GAIN WILD-TYPE | 139 | 55 | 114 | 160

Figure S56. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.016

Table S57. Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
16P GAIN CNV | 11 | 1 | 0 | 0
16P GAIN WILD-TYPE | 121 | 211 | 94 | 42

Figure S57. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.059

Table S58. Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
16P GAIN CNV | 10 | 0 | 2
16P GAIN WILD-TYPE | 140 | 173 | 168

Figure S58. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.67e-05 (Fisher's exact test), Q value = 0.016

Table S59. Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
16P GAIN CNV | 0 | 10 | 2
16P GAIN WILD-TYPE | 155 | 120 | 206

Figure S59. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000388 (Fisher's exact test), Q value = 0.12

Table S60. Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
16P GAIN CNV | 10 | 0 | 2
16P GAIN WILD-TYPE | 153 | 169 | 159

Figure S60. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.0085

Table S61. Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
16P GAIN CNV | 2 | 10 | 0
16P GAIN WILD-TYPE | 197 | 118 | 166

Figure S61. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 6.03e-13 (Fisher's exact test), Q value = 2.5e-10

Table S62. Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
16Q GAIN CNV | 10 | 0 | 0
16Q GAIN WILD-TYPE | 24 | 383 | 77

Figure S62. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.023

Table S63. Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
16Q GAIN CNV | 9 | 1 | 0
16Q GAIN WILD-TYPE | 142 | 82 | 260

Figure S63. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000415 (Fisher's exact test), Q value = 0.12

Table S64. Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
16Q GAIN CNV | 9 | 1 | 0 | 0
16Q GAIN WILD-TYPE | 123 | 211 | 94 | 42

Figure S64. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000637 (Fisher's exact test), Q value = 0.19

Table S65. Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
16Q GAIN CNV | 0 | 8 | 2
16Q GAIN WILD-TYPE | 155 | 122 | 206

Figure S65. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.15

Table S66. Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
16Q GAIN CNV | 2 | 8 | 0
16Q GAIN WILD-TYPE | 197 | 120 | 166

Figure S66. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1.99e-09 (Fisher's exact test), Q value = 8e-07

Table S67. Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
17P GAIN CNV | 9 | 2 | 1
17P GAIN WILD-TYPE | 25 | 381 | 76

Figure S67. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00059

Table S68. Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
17P GAIN CNV | 12 | 0 | 0
17P GAIN WILD-TYPE | 139 | 83 | 260

Figure S68. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0028

Table S69. Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
17P GAIN CNV | 12 | 0 | 0 | 0
17P GAIN WILD-TYPE | 138 | 55 | 114 | 161

Figure S69. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00061

Table S70. Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
17P GAIN CNV | 12 | 0 | 0 | 0
17P GAIN WILD-TYPE | 120 | 212 | 94 | 42

Figure S70. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0045

Table S71. Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
17P GAIN CNV | 11 | 0 | 1
17P GAIN WILD-TYPE | 139 | 173 | 169

Figure S71. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0014

Table S72. Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
17P GAIN CNV | 0 | 11 | 1
17P GAIN WILD-TYPE | 155 | 119 | 207

Figure S72. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.017

Table S73. Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
17P GAIN CNV | 11 | 0 | 1
17P GAIN WILD-TYPE | 152 | 169 | 160

Figure S73. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00093

Table S74. Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
17P GAIN CNV | 1 | 11 | 0
17P GAIN WILD-TYPE | 198 | 117 | 166

Figure S74. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 3.8e-09 (Fisher's exact test), Q value = 1.5e-06

Table S75. Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
17Q GAIN CNV | 9 | 2 | 2
17Q GAIN WILD-TYPE | 25 | 381 | 75

Figure S75. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3.34e-07 (Fisher's exact test), Q value = 0.00013

Table S76. Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
17Q GAIN CNV | 13 | 0 | 0
17Q GAIN WILD-TYPE | 138 | 83 | 260

Figure S76. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.00085

Table S77. Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
17Q GAIN CNV | 13 | 0 | 0 | 0
17Q GAIN WILD-TYPE | 137 | 55 | 114 | 161

Figure S77. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-07 (Fisher's exact test), Q value = 0.00013

Table S78. Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
17Q GAIN CNV | 13 | 0 | 0 | 0
17Q GAIN WILD-TYPE | 119 | 212 | 94 | 42

Figure S78. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 3.86e-06 (Fisher's exact test), Q value = 0.0015

Table S79. Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
17Q GAIN CNV | 12 | 0 | 1
17Q GAIN WILD-TYPE | 138 | 173 | 169

Figure S79. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.76e-07 (Fisher's exact test), Q value = 0.00038

Table S80. Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
17Q GAIN CNV | 0 | 12 | 1
17Q GAIN WILD-TYPE | 155 | 118 | 207

Figure S80. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.0062

Table S81. Gene #17: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
17Q GAIN CNV | 12 | 0 | 1
17Q GAIN WILD-TYPE | 151 | 169 | 160

Figure S81. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.38e-07 (Fisher's exact test), Q value = 0.00025

Table S82. Gene #17: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
17Q GAIN CNV | 1 | 12 | 0
17Q GAIN WILD-TYPE | 198 | 116 | 166

Figure S82. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S83. Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
19P GAIN CNV | 4 | 0 | 0
19P GAIN WILD-TYPE | 30 | 383 | 77

Figure S83. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00045

Table S84. Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
19Q GAIN CNV | 5 | 0 | 0
19Q GAIN WILD-TYPE | 29 | 383 | 77

Figure S84. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.17e-11 (Fisher's exact test), Q value = 4.8e-09

Table S85. Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
20P GAIN CNV | 9 | 0 | 0
20P GAIN WILD-TYPE | 25 | 383 | 77

Figure S85. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.079

Table S86. Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
20P GAIN CNV | 8 | 1 | 0
20P GAIN WILD-TYPE | 143 | 82 | 260

Figure S86. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.17e-11 (Fisher's exact test), Q value = 4.8e-09

Table S87. Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
20Q GAIN CNV | 9 | 0 | 0
20Q GAIN WILD-TYPE | 25 | 383 | 77

Figure S87. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.079

Table S88. Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
20Q GAIN CNV | 8 | 1 | 0
20Q GAIN WILD-TYPE | 143 | 82 | 260

Figure S88. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S89. Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
1P LOSS CNV | 3 | 0 | 0
1P LOSS WILD-TYPE | 31 | 383 | 77

Figure S89. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 5.2e-09 (Fisher's exact test), Q value = 2.1e-06

Table S90. Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
2P LOSS CNV | 7 | 0 | 1
2P LOSS WILD-TYPE | 27 | 383 | 76

Figure S90. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.046

Table S91. Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 143 | 83 | 260

Figure S91. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000645 (Fisher's exact test), Q value = 0.19

Table S92. Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
2P LOSS CNV | 8 | 0 | 0 | 0
2P LOSS WILD-TYPE | 142 | 55 | 114 | 161

Figure S92. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.07

Table S93. Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
2P LOSS CNV | 8 | 0 | 0 | 0
2P LOSS WILD-TYPE | 124 | 212 | 94 | 42

Figure S93. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.022

Table S94. Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 142 | 173 | 170

Figure S94. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0071

Table S95. Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
2P LOSS CNV | 0 | 8 | 0
2P LOSS WILD-TYPE | 155 | 122 | 208

Figure S95. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.076

Table S96. Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 155 | 169 | 161

Figure S96. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0063

Table S97. Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
2P LOSS CNV | 0 | 8 | 0
2P LOSS WILD-TYPE | 199 | 120 | 166

Figure S97. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 1.6e-06

Table S98. Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 27 | 383 | 77

Figure S98. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.1

Table S99. Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 144 | 83 | 260

Figure S99. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.2

Table S100. Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
2Q LOSS CNV | 7 | 0 | 0 | 0
2Q LOSS WILD-TYPE | 125 | 212 | 94 | 42

Figure S100. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.07

Table S101. Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 143 | 173 | 170

Figure S101. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.026

Table S102. Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
2Q LOSS CNV | 0 | 7 | 0
2Q LOSS WILD-TYPE | 155 | 123 | 208

Figure S102. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.22

Table S103. Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 156 | 169 | 161

Figure S103. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.024

Table S104. Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
2Q LOSS CNV | 0 | 7 | 0
2Q LOSS WILD-TYPE | 199 | 121 | 166

Figure S104. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S105. Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
3Q LOSS CNV | 3 | 0 | 0
3Q LOSS WILD-TYPE | 31 | 383 | 77

Figure S105. Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S106. Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
8P LOSS CNV | 4 | 0 | 0
8P LOSS WILD-TYPE | 30 | 383 | 77

Figure S106. Get High-res Image Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S107. Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
8Q LOSS CNV | 4 | 0 | 0
8Q LOSS WILD-TYPE | 30 | 383 | 77

Figure S107. Get High-res Image Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.13e-11 (Fisher's exact test), Q value = 8.7e-09

Table S108. Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
9P LOSS CNV | 10 | 1 | 1
9P LOSS WILD-TYPE | 24 | 382 | 76

Figure S108. Get High-res Image Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.59e-13 (Fisher's exact test), Q value = 6.6e-11

Table S109. Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
9Q LOSS CNV | 13 | 3 | 1
9Q LOSS WILD-TYPE | 21 | 380 | 76

Figure S109. Get High-res Image Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 2.7e-05

Table S110. Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
10P LOSS CNV | 6 | 0 | 0
10P LOSS WILD-TYPE | 28 | 383 | 77

Figure S110. Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00045

Table S111. Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
10Q LOSS CNV | 5 | 0 | 0
10Q LOSS WILD-TYPE | 29 | 383 | 77

Figure S111. Get High-res Image Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 3.2e-05

Table S112. Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11P LOSS CNV | 6 | 0 | 1
11P LOSS WILD-TYPE | 28 | 383 | 76

Figure S112. Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 0.0012

Table S113. Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11Q LOSS CNV | 6 | 2 | 1
11Q LOSS WILD-TYPE | 28 | 381 | 76

Figure S113. Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.11

Table S114. Gene #37: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
11Q LOSS CNV | 8 | 0 | 1
11Q LOSS WILD-TYPE | 142 | 173 | 169

Figure S114. Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000653 (Fisher's exact test), Q value = 0.19

Table S115. Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
15Q LOSS CNV | 4 | 2 | 1
15Q LOSS WILD-TYPE | 30 | 381 | 76

Figure S115. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.1

Table S116. Gene #39: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
15Q LOSS CNV | 7 | 0 | 0
15Q LOSS WILD-TYPE | 144 | 83 | 260

Figure S116. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.2

Table S117. Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
15Q LOSS CNV | 7 | 0 | 0 | 0
15Q LOSS WILD-TYPE | 125 | 212 | 94 | 42

Figure S117. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.07

Table S118. Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
15Q LOSS CNV | 7 | 0 | 0
15Q LOSS WILD-TYPE | 143 | 173 | 170

Figure S118. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.026

Table S119. Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
15Q LOSS CNV | 0 | 7 | 0
15Q LOSS WILD-TYPE | 155 | 123 | 208

Figure S119. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.22

Table S120. Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
15Q LOSS CNV | 7 | 0 | 0
15Q LOSS WILD-TYPE | 156 | 169 | 161

Figure S120. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.024

Table S121. Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
15Q LOSS CNV | 0 | 7 | 0
15Q LOSS WILD-TYPE | 199 | 121 | 166

Figure S121. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.067

Table S122. Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
18P LOSS CNV | 3 | 0 | 1
18P LOSS WILD-TYPE | 31 | 383 | 76

Figure S122. Get High-res Image Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.067

Table S123. Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
18Q LOSS CNV | 3 | 0 | 1
18Q LOSS WILD-TYPE | 31 | 383 | 76

Figure S123. Get High-res Image Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.062

Table S124. Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
21Q LOSS CNV | 4 | 1 | 1
21Q LOSS WILD-TYPE | 30 | 382 | 76

Figure S124. Get High-res Image Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 4.98e-57 (Fisher's exact test), Q value = 2.1e-54

Table S125. Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
22Q LOSS CNV | 8 | 0 | 57
22Q LOSS WILD-TYPE | 26 | 383 | 20

Figure S125. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.44e-05 (Fisher's exact test), Q value = 0.015

Table S126. Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
22Q LOSS CNV | 36 | 7 | 22
22Q LOSS WILD-TYPE | 115 | 76 | 238

Figure S126. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 6.84e-11 (Fisher's exact test), Q value = 2.8e-08

Table S127. Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 150 | 55 | 114 | 161
22Q LOSS CNV | 35 | 5 | 20 | 1
22Q LOSS WILD-TYPE | 115 | 50 | 94 | 160

Figure S127. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.07e-11 (Fisher's exact test), Q value = 3.3e-08

Table S128. Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 132 | 212 | 94 | 42
22Q LOSS CNV | 35 | 7 | 18 | 1
22Q LOSS WILD-TYPE | 97 | 205 | 76 | 41

Figure S128. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.011

Table S129. Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
22Q LOSS CNV | 36 | 16 | 13
22Q LOSS WILD-TYPE | 114 | 157 | 157

Figure S129. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.3e-06 (Fisher's exact test), Q value = 0.002

Table S130. Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
22Q LOSS CNV | 16 | 34 | 15
22Q LOSS WILD-TYPE | 139 | 96 | 193

Figure S130. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 6.2e-05

Table S131. Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
22Q LOSS CNV | 42 | 11 | 12
22Q LOSS WILD-TYPE | 121 | 158 | 149

Figure S131. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.09e-06 (Fisher's exact test), Q value = 0.0012

Table S132. Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
22Q LOSS CNV | 14 | 34 | 17
22Q LOSS WILD-TYPE | 185 | 94 | 149

Figure S132. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Mutation data file = broad_values_by_arm.mutsig.cluster.txt

- Molecular subtypes file = THCA-TP.transferedmergedcluster.txt

- Number of patients = 494

- Number of significantly arm-level cnvs = 45

- 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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)
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