Correlation between copy number variations of arm-level result and molecular subtypes
Testicular Germ Cell Tumors (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1FB51WH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1FB51WH
Overview
Introduction

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

Summary

Testing the association between copy number variation 72 arm-level events and 8 molecular subtypes across 150 patients, 66 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'MRNASEQ_CNMF'.

- 6q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 8p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 8q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 15q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

- 19p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 19q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 22q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 10q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 11p loss cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

- 14q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

- 17p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- xq 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 72 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 66 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | 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
19p loss | 50 (33%) | 100 | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548)
19q loss | 53 (35%) | 97 | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548)
17q gain | 51 (34%) | 99 | 0.00016 (0.0798) | 7e-05 (0.0353) | 1e-05 (0.00548) | 1e-05 (0.00548) | 0.00034 (0.167) | 0.00041 (0.2) | 8e-05 (0.0402) | 0.00299 (1.00)
22q loss | 45 (30%) | 105 | 0.00268 (1.00) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 0.00249 (1.00) | 2e-05 (0.0103) | 5e-05 (0.0254) | 0.00055 (0.264)
17p gain | 40 (27%) | 110 | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 1e-05 (0.00548) | 0.00147 (0.684) | 0.00053 (0.255) | 0.00063 (0.3) | 0.00209 (0.961)
11q loss | 115 (77%) | 35 | 1e-05 (0.00548) | 0.123 (1.00) | 0.0001 (0.0502) | 2e-05 (0.0103) | 0.00019 (0.0944) | 0.00673 (1.00) | 0.00803 (1.00) | 0.0168 (1.00)
22q gain | 38 (25%) | 112 | 1e-05 (0.00548) | 0.00138 (0.644) | 2e-05 (0.0103) | 1e-05 (0.00548) | 0.052 (1.00) | 0.00276 (1.00) | 0.0208 (1.00) | 0.00137 (0.641)
11p loss | 98 (65%) | 52 | 0.00865 (1.00) | 0.183 (1.00) | 0.00048 (0.232) | 0.00052 (0.251) | 0.00047 (0.227) | 0.00046 (0.223) | 0.00501 (1.00) | 0.017 (1.00)
15q loss | 29 (19%) | 121 | 0.0063 (1.00) | 3e-05 (0.0154) | 1e-05 (0.00548) | 1e-05 (0.00548) | 0.0107 (1.00) | 0.00273 (1.00) | 0.00067 (0.318) | 0.0011 (0.516)
8p gain | 110 (73%) | 40 | 0.0637 (1.00) | 0.00548 (1.00) | 3e-05 (0.0154) | 0.00023 (0.114) | 0.062 (1.00) | 0.0266 (1.00) | 0.0153 (1.00) | 0.0658 (1.00)
8q gain | 111 (74%) | 39 | 0.0203 (1.00) | 0.00322 (1.00) | 0.00013 (0.0651) | 0.00025 (0.123) | 0.00464 (1.00) | 0.00328 (1.00) | 0.00813 (1.00) | 0.00665 (1.00)
15q gain | 51 (34%) | 99 | 0.0499 (1.00) | 0.00215 (0.987) | 1e-05 (0.00548) | 3e-05 (0.0154) | 0.0189 (1.00) | 0.011 (1.00) | 0.0262 (1.00) | 0.0203 (1.00)
19p gain | 36 (24%) | 114 | 0.00983 (1.00) | 4e-05 (0.0204) | 7e-05 (0.0353) | 0.00084 (0.396) | 0.0252 (1.00) | 0.0883 (1.00) | 0.369 (1.00) | 0.252 (1.00)
19q gain | 29 (19%) | 121 | 0.0162 (1.00) | 0.00018 (0.0896) | 2e-05 (0.0103) | 0.00059 (0.282) | 0.196 (1.00) | 0.0485 (1.00) | 0.37 (1.00) | 0.22 (1.00)
10p loss | 77 (51%) | 73 | 0.0216 (1.00) | 0.00042 (0.204) | 0.00034 (0.167) | 0.00551 (1.00) | 0.963 (1.00) | 0.447 (1.00) | 0.445 (1.00) | 0.443 (1.00)
10q loss | 72 (48%) | 78 | 0.00858 (1.00) | 6e-05 (0.0304) | 0.00023 (0.114) | 0.00258 (1.00) | 0.363 (1.00) | 0.0765 (1.00) | 0.114 (1.00) | 0.0765 (1.00)
17p loss | 37 (25%) | 113 | 1e-05 (0.00548) | 0.0384 (1.00) | 0.00428 (1.00) | 0.00014 (0.07) | 0.0216 (1.00) | 0.0786 (1.00) | 0.00298 (1.00) | 0.0215 (1.00)
1p gain | 37 (25%) | 113 | 0.00302 (1.00) | 0.00064 (0.304) | 0.00037 (0.181) | 0.00245 (1.00) | 0.0552 (1.00) | 0.16 (1.00) | 0.0042 (1.00) | 0.0332 (1.00)
6q gain | 23 (15%) | 127 | 0.0234 (1.00) | 0.883 (1.00) | 0.0139 (1.00) | 0.00025 (0.123) | 0.0668 (1.00) | 0.0266 (1.00) | 0.164 (1.00) | 0.0776 (1.00)
9q loss | 58 (39%) | 92 | 0.00032 (0.157) | 0.338 (1.00) | 0.308 (1.00) | 0.0173 (1.00) | 0.676 (1.00) | 0.0338 (1.00) | 0.127 (1.00) | 0.309 (1.00)
14q loss | 20 (13%) | 130 | 0.121 (1.00) | 0.0006 (0.286) | 0.00482 (1.00) | 5e-05 (0.0254) | 0.0538 (1.00) | 0.00484 (1.00) | 0.0112 (1.00) | 0.059 (1.00)
xq loss | 29 (19%) | 121 | 0.00033 (0.162) | 0.00194 (0.894) | 0.162 (1.00) | 0.0966 (1.00) | 0.356 (1.00) | 0.243 (1.00) | 0.0848 (1.00) | 0.157 (1.00)
1q gain | 61 (41%) | 89 | 0.438 (1.00) | 0.664 (1.00) | 0.825 (1.00) | 0.0593 (1.00) | 0.125 (1.00) | 1 (1.00) | 0.753 (1.00) | 0.318 (1.00)
2p gain | 46 (31%) | 104 | 0.0137 (1.00) | 0.00927 (1.00) | 0.0162 (1.00) | 0.167 (1.00) | 0.0592 (1.00) | 0.0874 (1.00) | 0.0835 (1.00) | 0.18 (1.00)
2q gain | 42 (28%) | 108 | 0.116 (1.00) | 0.0331 (1.00) | 0.277 (1.00) | 0.746 (1.00) | 0.501 (1.00) | 0.278 (1.00) | 0.128 (1.00) | 0.759 (1.00)
3p gain | 27 (18%) | 123 | 0.0228 (1.00) | 0.4 (1.00) | 0.00724 (1.00) | 0.00662 (1.00) | 0.0624 (1.00) | 0.0189 (1.00) | 0.0378 (1.00) | 0.134 (1.00)
3q gain | 36 (24%) | 114 | 0.00735 (1.00) | 0.181 (1.00) | 0.0311 (1.00) | 0.0321 (1.00) | 0.192 (1.00) | 0.166 (1.00) | 0.284 (1.00) | 0.698 (1.00)
4p gain | 3 (2%) | 147 | 0.636 (1.00) | 0.197 (1.00) | 1 (1.00) | 0.681 (1.00) |  |  |  |
5p gain | 6 (4%) | 144 | 0.672 (1.00) | 0.0254 (1.00) | 0.0112 (1.00) | 0.00818 (1.00) | 0.018 (1.00) | 0.351 (1.00) | 0.018 (1.00) | 0.251 (1.00)
5q gain | 3 (2%) | 147 | 0.777 (1.00) | 0.0588 (1.00) | 0.0356 (1.00) | 0.0417 (1.00) |  |  |  |
6p gain | 28 (19%) | 122 | 0.00055 (0.264) | 0.752 (1.00) | 0.0129 (1.00) | 0.00081 (0.383) | 0.00434 (1.00) | 0.00192 (0.887) | 0.0386 (1.00) | 0.0293 (1.00)
7p gain | 121 (81%) | 29 | 0.00449 (1.00) | 0.0574 (1.00) | 0.00419 (1.00) | 0.00832 (1.00) | 0.128 (1.00) | 0.114 (1.00) | 0.187 (1.00) | 0.583 (1.00)
7q gain | 105 (70%) | 45 | 0.547 (1.00) | 0.069 (1.00) | 0.00476 (1.00) | 0.0121 (1.00) | 0.106 (1.00) | 0.038 (1.00) | 0.028 (1.00) | 0.105 (1.00)
9p gain | 16 (11%) | 134 | 0.235 (1.00) | 0.335 (1.00) | 0.158 (1.00) | 0.297 (1.00) | 0.614 (1.00) | 0.0994 (1.00) | 0.321 (1.00) | 0.737 (1.00)
9q gain | 17 (11%) | 133 | 0.152 (1.00) | 0.5 (1.00) | 1 (1.00) | 0.0792 (1.00) | 1 (1.00) | 1 (1.00) | 0.66 (1.00) | 0.301 (1.00)
10p gain | 6 (4%) | 144 | 0.583 (1.00) | 0.0929 (1.00) | 0.322 (1.00) | 0.345 (1.00) |  |  |  |
10q gain | 8 (5%) | 142 | 0.595 (1.00) | 0.387 (1.00) | 0.369 (1.00) | 0.225 (1.00) |  |  |  |
11p gain | 10 (7%) | 140 | 0.273 (1.00) | 0.183 (1.00) | 0.165 (1.00) | 0.0514 (1.00) | 0.614 (1.00) | 0.561 (1.00) | 0.229 (1.00) | 0.346 (1.00)
11q gain | 4 (3%) | 146 | 0.387 (1.00) | 0.15 (1.00) | 0.0776 (1.00) | 0.013 (1.00) |  |  |  |
12p gain | 146 (97%) | 4 | 0.193 (1.00) | 0.388 (1.00) | 0.809 (1.00) | 0.368 (1.00) | 0.0695 (1.00) | 1 (1.00) | 0.36 (1.00) | 0.9 (1.00)
12q gain | 100 (67%) | 50 | 0.566 (1.00) | 0.841 (1.00) | 0.205 (1.00) | 0.339 (1.00) | 0.348 (1.00) | 0.846 (1.00) | 0.986 (1.00) | 0.754 (1.00)
14q gain | 51 (34%) | 99 | 0.253 (1.00) | 0.236 (1.00) | 0.585 (1.00) | 0.396 (1.00) | 0.48 (1.00) | 0.713 (1.00) | 0.71 (1.00) | 0.949 (1.00)
16p gain | 16 (11%) | 134 | 0.012 (1.00) | 0.0797 (1.00) | 0.00425 (1.00) | 0.0172 (1.00) | 0.11 (1.00) | 0.0139 (1.00) | 0.0287 (1.00) | 0.0366 (1.00)
16q gain | 14 (9%) | 136 | 0.00756 (1.00) | 0.139 (1.00) | 0.0101 (1.00) | 0.0489 (1.00) | 0.109 (1.00) | 0.014 (1.00) | 0.0294 (1.00) | 0.0375 (1.00)
18p gain | 4 (3%) | 146 | 0.688 (1.00) | 0.0703 (1.00) | 0.377 (1.00) | 0.783 (1.00) |  |  |  |
20p gain | 34 (23%) | 116 | 0.00544 (1.00) | 0.113 (1.00) | 0.0412 (1.00) | 0.286 (1.00) | 0.101 (1.00) | 0.0838 (1.00) | 0.11 (1.00) | 0.272 (1.00)
20q gain | 40 (27%) | 110 | 0.00668 (1.00) | 0.00584 (1.00) | 0.00685 (1.00) | 0.0532 (1.00) | 0.0624 (1.00) | 0.124 (1.00) | 0.108 (1.00) | 0.15 (1.00)
21q gain | 125 (83%) | 25 | 0.402 (1.00) | 0.273 (1.00) | 0.084 (1.00) | 0.238 (1.00) | 0.0909 (1.00) | 0.215 (1.00) | 0.452 (1.00) | 0.254 (1.00)
xq gain | 22 (15%) | 128 | 0.00187 (0.866) | 0.0177 (1.00) | 0.00082 (0.387) | 0.00363 (1.00) | 0.0209 (1.00) | 0.0494 (1.00) | 0.155 (1.00) | 0.377 (1.00)
1p loss | 18 (12%) | 132 | 0.121 (1.00) | 0.57 (1.00) | 0.649 (1.00) | 0.887 (1.00) | 0.345 (1.00) | 0.352 (1.00) | 0.114 (1.00) | 0.508 (1.00)
1q loss | 8 (5%) | 142 | 0.344 (1.00) | 0.243 (1.00) | 0.291 (1.00) | 0.217 (1.00) | 0.0422 (1.00) | 0.0142 (1.00) | 0.00381 (1.00) | 0.0772 (1.00)
2p loss | 5 (3%) | 145 | 0.862 (1.00) | 0.377 (1.00) | 1 (1.00) | 1 (1.00) | 0.231 (1.00) | 1 (1.00) | 0.207 (1.00) | 0.679 (1.00)
2q loss | 6 (4%) | 144 | 0.444 (1.00) | 0.681 (1.00) | 0.556 (1.00) | 0.901 (1.00) | 0.231 (1.00) | 0.205 (1.00) | 0.702 (1.00) | 0.601 (1.00)
3p loss | 30 (20%) | 120 | 0.935 (1.00) | 0.0303 (1.00) | 0.00151 (0.701) | 0.00342 (1.00) | 0.0195 (1.00) | 0.0364 (1.00) | 0.116 (1.00) | 0.187 (1.00)
3q loss | 22 (15%) | 128 | 0.741 (1.00) | 0.739 (1.00) | 0.0854 (1.00) | 0.0572 (1.00) | 0.0548 (1.00) | 0.184 (1.00) | 0.0867 (1.00) | 0.539 (1.00)
4p loss | 92 (61%) | 58 | 0.63 (1.00) | 0.0455 (1.00) | 0.0312 (1.00) | 0.163 (1.00) | 0.14 (1.00) | 0.139 (1.00) | 0.481 (1.00) | 0.319 (1.00)
4q loss | 108 (72%) | 42 | 0.0669 (1.00) | 0.0108 (1.00) | 0.0108 (1.00) | 0.0122 (1.00) | 0.12 (1.00) | 0.107 (1.00) | 0.626 (1.00) | 0.508 (1.00)
5p loss | 103 (69%) | 47 | 0.113 (1.00) | 0.208 (1.00) | 0.115 (1.00) | 0.132 (1.00) | 0.53 (1.00) | 0.125 (1.00) | 0.237 (1.00) | 0.308 (1.00)
5q loss | 101 (67%) | 49 | 0.059 (1.00) | 0.0627 (1.00) | 0.014 (1.00) | 0.00338 (1.00) | 0.501 (1.00) | 0.0486 (1.00) | 0.103 (1.00) | 0.154 (1.00)
6p loss | 13 (9%) | 137 | 0.265 (1.00) | 0.037 (1.00) | 0.161 (1.00) | 0.0142 (1.00) | 0.925 (1.00) | 0.563 (1.00) | 0.546 (1.00) | 0.705 (1.00)
6q loss | 16 (11%) | 134 | 0.121 (1.00) | 0.0094 (1.00) | 0.0449 (1.00) | 0.00103 (0.484) | 0.95 (1.00) | 0.626 (1.00) | 0.763 (1.00) | 0.788 (1.00)
8p loss | 12 (8%) | 138 | 0.356 (1.00) | 0.0507 (1.00) | 0.0105 (1.00) | 0.0474 (1.00) | 0.422 (1.00) | 0.281 (1.00) | 0.0553 (1.00) | 0.327 (1.00)
8q loss | 5 (3%) | 145 | 0.188 (1.00) | 0.0239 (1.00) | 0.0022 (1.00) | 0.0125 (1.00) |  |  |  |
9p loss | 63 (42%) | 87 | 0.0328 (1.00) | 1 (1.00) | 0.868 (1.00) | 0.437 (1.00) | 0.436 (1.00) | 0.548 (1.00) | 0.285 (1.00) | 0.594 (1.00)
13q loss | 113 (75%) | 37 | 0.0441 (1.00) | 0.289 (1.00) | 0.0323 (1.00) | 0.0014 (0.652) | 0.132 (1.00) | 0.134 (1.00) | 0.00608 (1.00) | 0.0413 (1.00)
16p loss | 44 (29%) | 106 | 0.149 (1.00) | 0.0068 (1.00) | 0.0808 (1.00) | 0.262 (1.00) | 0.107 (1.00) | 0.287 (1.00) | 0.396 (1.00) | 0.179 (1.00)
16q loss | 51 (34%) | 99 | 0.0785 (1.00) | 0.0662 (1.00) | 0.232 (1.00) | 0.484 (1.00) | 0.0772 (1.00) | 0.286 (1.00) | 0.397 (1.00) | 0.352 (1.00)
17q loss | 16 (11%) | 134 | 0.00567 (1.00) | 0.129 (1.00) | 0.0197 (1.00) | 0.028 (1.00) | 0.0773 (1.00) | 0.0483 (1.00) | 0.0157 (1.00) | 0.0752 (1.00)
18p loss | 116 (77%) | 34 | 0.692 (1.00) | 0.0753 (1.00) | 0.0443 (1.00) | 0.243 (1.00) | 0.124 (1.00) | 0.0989 (1.00) | 0.0844 (1.00) | 0.108 (1.00)
18q loss | 122 (81%) | 28 | 0.0855 (1.00) | 0.317 (1.00) | 0.0663 (1.00) | 0.124 (1.00) | 0.0556 (1.00) | 0.0677 (1.00) | 0.0114 (1.00) | 0.0105 (1.00)
20p loss | 30 (20%) | 120 | 0.235 (1.00) | 0.188 (1.00) | 0.199 (1.00) | 0.171 (1.00) | 0.702 (1.00) | 0.136 (1.00) | 0.268 (1.00) | 0.159 (1.00)
20q loss | 15 (10%) | 135 | 0.586 (1.00) | 0.49 (1.00) | 0.199 (1.00) | 0.27 (1.00) | 0.295 (1.00) | 0.12 (1.00) | 0.101 (1.00) | 0.393 (1.00)

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
1P GAIN MUTATED | 9 | 19 | 9
1P GAIN WILD-TYPE | 61 | 21 | 31

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S2. Gene #11: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
6Q GAIN MUTATED | 8 | 0 | 0 | 11 | 0 | 3 | 1
6Q GAIN WILD-TYPE | 35 | 27 | 12 | 13 | 8 | 20 | 12

Figure S2. Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S3. Gene #14: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
8P GAIN MUTATED | 63 | 26 | 21
8P GAIN WILD-TYPE | 7 | 14 | 19

Figure S3. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S4. Gene #14: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
8P GAIN MUTATED | 37 | 26 | 8 | 14 | 5 | 15 | 5
8P GAIN WILD-TYPE | 6 | 1 | 4 | 10 | 3 | 8 | 8

Figure S4. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.065

Table S5. Gene #15: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
8Q GAIN MUTATED | 62 | 28 | 21
8Q GAIN WILD-TYPE | 8 | 12 | 19

Figure S5. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S6. Gene #15: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
8Q GAIN MUTATED | 40 | 22 | 8 | 15 | 5 | 17 | 4
8Q GAIN WILD-TYPE | 3 | 5 | 4 | 9 | 3 | 6 | 9

Figure S6. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S7. Gene #25: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
15Q GAIN MUTATED | 38 | 8 | 5
15Q GAIN WILD-TYPE | 32 | 32 | 35

Figure S7. Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S8. Gene #25: '15q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
15Q GAIN MUTATED | 26 | 12 | 1 | 4 | 0 | 7 | 1
15Q GAIN WILD-TYPE | 17 | 15 | 11 | 20 | 8 | 16 | 12

Figure S8. Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S9. Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
17P GAIN MUTATED | 9 | 2 | 29
17P GAIN WILD-TYPE | 39 | 42 | 29

Figure S9. Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S10. Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
17P GAIN MUTATED | 3 | 23 | 14
17P GAIN WILD-TYPE | 53 | 26 | 31

Figure S10. Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S11. Gene #28: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
17P GAIN MUTATED | 3 | 19 | 18
17P GAIN WILD-TYPE | 67 | 21 | 22

Figure S11. Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S12. Gene #28: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
17P GAIN MUTATED | 2 | 1 | 5 | 11 | 4 | 12 | 5
17P GAIN WILD-TYPE | 41 | 26 | 7 | 13 | 4 | 11 | 8

Figure S12. Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.08

Table S13. Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
17Q GAIN MUTATED | 13 | 7 | 31
17Q GAIN WILD-TYPE | 35 | 37 | 27

Figure S13. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S14. Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
17Q GAIN MUTATED | 8 | 27 | 16
17Q GAIN WILD-TYPE | 48 | 22 | 29

Figure S14. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S15. Gene #29: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
17Q GAIN MUTATED | 7 | 23 | 21
17Q GAIN WILD-TYPE | 63 | 17 | 19

Figure S15. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S16. Gene #29: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
17Q GAIN MUTATED | 4 | 3 | 6 | 13 | 4 | 15 | 6
17Q GAIN WILD-TYPE | 39 | 24 | 6 | 11 | 4 | 8 | 7

Figure S16. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S17. Gene #29: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
17Q GAIN MUTATED | 1 | 11 | 10 | 3
17Q GAIN WILD-TYPE | 11 | 10 | 6 | 22

Figure S17. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.2

Table S18. Gene #29: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
17Q GAIN MUTATED | 7 | 9 | 9
17Q GAIN WILD-TYPE | 37 | 6 | 6

Figure S18. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S19. Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 22 | 13 | 20 | 19
17Q GAIN MUTATED | 2 | 9 | 3 | 11
17Q GAIN WILD-TYPE | 20 | 4 | 17 | 8

Figure S19. Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S20. Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
19P GAIN MUTATED | 23 | 3 | 10
19P GAIN WILD-TYPE | 33 | 46 | 35

Figure S20. Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S21. Gene #31: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
19P GAIN MUTATED | 28 | 3 | 5
19P GAIN WILD-TYPE | 42 | 37 | 35

Figure S21. Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.09

Table S22. Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
19Q GAIN MUTATED | 20 | 2 | 7
19Q GAIN WILD-TYPE | 36 | 47 | 38

Figure S22. Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S23. Gene #32: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
19Q GAIN MUTATED | 24 | 1 | 4
19Q GAIN WILD-TYPE | 46 | 39 | 36

Figure S23. Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S24. Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
22Q GAIN MUTATED | 9 | 23 | 6
22Q GAIN WILD-TYPE | 39 | 21 | 52

Figure S24. Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S25. Gene #36: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
22Q GAIN MUTATED | 30 | 3 | 5
22Q GAIN WILD-TYPE | 40 | 37 | 35

Figure S25. Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S26. Gene #36: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
22Q GAIN MUTATED | 11 | 19 | 1 | 4 | 1 | 1 | 1
22Q GAIN WILD-TYPE | 32 | 8 | 11 | 20 | 7 | 22 | 12

Figure S26. Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S27. Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
9Q LOSS MUTATED | 11 | 13 | 34
9Q LOSS WILD-TYPE | 37 | 31 | 24

Figure S27. Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.2

Table S28. Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
10P LOSS MUTATED | 20 | 36 | 21
10P LOSS WILD-TYPE | 36 | 13 | 24

Figure S28. Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S29. Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
10P LOSS MUTATED | 27 | 31 | 19
10P LOSS WILD-TYPE | 43 | 9 | 21

Figure S29. Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S30. Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
10Q LOSS MUTATED | 16 | 36 | 20
10Q LOSS WILD-TYPE | 40 | 13 | 25

Figure S30. Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S31. Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
10Q LOSS MUTATED | 24 | 30 | 18
10Q LOSS WILD-TYPE | 46 | 10 | 22

Figure S31. Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.23

Table S32. Gene #56: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
11P LOSS MUTATED | 54 | 28 | 16
11P LOSS WILD-TYPE | 16 | 12 | 24

Figure S32. Get High-res Image Gene #56: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.23

Table S33. Gene #56: '11p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
11P LOSS MUTATED | 10 | 16 | 4 | 21
11P LOSS WILD-TYPE | 2 | 5 | 12 | 4

Figure S33. Get High-res Image Gene #56: '11p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S34. Gene #56: '11p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
11P LOSS MUTATED | 36 | 11 | 4
11P LOSS WILD-TYPE | 8 | 4 | 11

Figure S34. Get High-res Image Gene #56: '11p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S35. Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
11Q LOSS MUTATED | 30 | 44 | 41
11Q LOSS WILD-TYPE | 18 | 0 | 17

Figure S35. Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.05

Table S36. Gene #57: '11q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
11Q LOSS MUTATED | 62 | 32 | 21
11Q LOSS WILD-TYPE | 8 | 8 | 19

Figure S36. Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S37. Gene #57: '11q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
11Q LOSS MUTATED | 35 | 27 | 11 | 15 | 6 | 18 | 3
11Q LOSS WILD-TYPE | 8 | 0 | 1 | 9 | 2 | 5 | 10

Figure S37. Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.094

Table S38. Gene #57: '11q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
11Q LOSS MUTATED | 9 | 19 | 8 | 25
11Q LOSS WILD-TYPE | 3 | 2 | 8 | 0

Figure S38. Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S39. Gene #59: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
14Q LOSS MUTATED | 0 | 3 | 0 | 5 | 0 | 10 | 2
14Q LOSS WILD-TYPE | 43 | 24 | 12 | 19 | 8 | 13 | 11

Figure S39. Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S40. Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
15Q LOSS MUTATED | 1 | 17 | 11
15Q LOSS WILD-TYPE | 55 | 32 | 34

Figure S40. Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S41. Gene #60: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
15Q LOSS MUTATED | 1 | 13 | 15
15Q LOSS WILD-TYPE | 69 | 27 | 25

Figure S41. Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S42. Gene #60: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
15Q LOSS MUTATED | 0 | 1 | 3 | 7 | 4 | 8 | 6
15Q LOSS WILD-TYPE | 43 | 26 | 9 | 17 | 4 | 15 | 7

Figure S42. Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S43. Gene #63: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
17P LOSS MUTATED | 5 | 23 | 9
17P LOSS WILD-TYPE | 43 | 21 | 49

Figure S43. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.07

Table S44. Gene #63: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
17P LOSS MUTATED | 10 | 16 | 2 | 1 | 0 | 4 | 4
17P LOSS WILD-TYPE | 33 | 11 | 10 | 23 | 8 | 19 | 9

Figure S44. Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S45. Gene #67: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
19P LOSS MUTATED | 12 | 5 | 33
19P LOSS WILD-TYPE | 36 | 39 | 25

Figure S45. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S46. Gene #67: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
19P LOSS MUTATED | 2 | 31 | 17
19P LOSS WILD-TYPE | 54 | 18 | 28

Figure S46. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S47. Gene #67: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
19P LOSS MUTATED | 2 | 27 | 21
19P LOSS WILD-TYPE | 68 | 13 | 19

Figure S47. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S48. Gene #67: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
19P LOSS MUTATED | 0 | 2 | 9 | 12 | 5 | 16 | 6
19P LOSS WILD-TYPE | 43 | 25 | 3 | 12 | 3 | 7 | 7

Figure S48. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S49. Gene #67: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
19P LOSS MUTATED | 0 | 15 | 7 | 1
19P LOSS WILD-TYPE | 12 | 6 | 9 | 24

Figure S49. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S50. Gene #67: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
19P LOSS MUTATED | 2 | 14 | 7
19P LOSS WILD-TYPE | 42 | 1 | 8

Figure S50. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S51. Gene #67: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 22 | 13 | 20 | 19
19P LOSS MUTATED | 1 | 11 | 0 | 11
19P LOSS WILD-TYPE | 21 | 2 | 20 | 8

Figure S51. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S52. Gene #67: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 8 | 15 | 11 | 5 | 13 | 11
19P LOSS MUTATED | 0 | 0 | 14 | 6 | 2 | 1 | 0
19P LOSS WILD-TYPE | 11 | 8 | 1 | 5 | 3 | 12 | 11

Figure S52. Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S53. Gene #68: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
19Q LOSS MUTATED | 11 | 7 | 35
19Q LOSS WILD-TYPE | 37 | 37 | 23

Figure S53. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S54. Gene #68: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
19Q LOSS MUTATED | 1 | 34 | 18
19Q LOSS WILD-TYPE | 55 | 15 | 27

Figure S54. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S55. Gene #68: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
19Q LOSS MUTATED | 1 | 30 | 22
19Q LOSS WILD-TYPE | 69 | 10 | 18

Figure S55. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S56. Gene #68: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
19Q LOSS MUTATED | 0 | 1 | 9 | 13 | 5 | 19 | 6
19Q LOSS WILD-TYPE | 43 | 26 | 3 | 11 | 3 | 4 | 7

Figure S56. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S57. Gene #68: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
19Q LOSS MUTATED | 0 | 15 | 6 | 1
19Q LOSS WILD-TYPE | 12 | 6 | 10 | 24

Figure S57. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S58. Gene #68: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
19Q LOSS MUTATED | 2 | 14 | 6
19Q LOSS WILD-TYPE | 42 | 1 | 9

Figure S58. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S59. Gene #68: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 22 | 13 | 20 | 19
19Q LOSS MUTATED | 1 | 11 | 0 | 10
19Q LOSS WILD-TYPE | 21 | 2 | 20 | 9

Figure S59. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S60. Gene #68: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 8 | 15 | 11 | 5 | 13 | 11
19Q LOSS MUTATED | 0 | 0 | 14 | 5 | 2 | 1 | 0
19Q LOSS WILD-TYPE | 11 | 8 | 1 | 6 | 3 | 12 | 11

Figure S60. Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S61. Gene #71: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
22Q LOSS MUTATED | 4 | 28 | 13
22Q LOSS WILD-TYPE | 52 | 21 | 32

Figure S61. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S62. Gene #71: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
22Q LOSS MUTATED | 6 | 23 | 16
22Q LOSS WILD-TYPE | 64 | 17 | 24

Figure S62. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S63. Gene #71: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
22Q LOSS MUTATED | 5 | 1 | 7 | 10 | 4 | 13 | 5
22Q LOSS WILD-TYPE | 38 | 26 | 5 | 14 | 4 | 10 | 8

Figure S63. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S64. Gene #71: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
22Q LOSS MUTATED | 3 | 10 | 6
22Q LOSS WILD-TYPE | 41 | 5 | 9

Figure S64. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S65. Gene #71: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 22 | 13 | 20 | 19
22Q LOSS MUTATED | 0 | 7 | 3 | 9
22Q LOSS WILD-TYPE | 22 | 6 | 17 | 10

Figure S65. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.16

Table S66. Gene #72: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
XQ LOSS MUTATED | 1 | 11 | 17
XQ LOSS WILD-TYPE | 47 | 33 | 41

Figure S66. Get High-res Image Gene #72: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

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

- Number of patients = 150

- Number of significantly arm-level cnvs = 72

- Number of molecular subtypes = 8

- 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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