Correlation between copy number variations of arm-level result and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1D50K84
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/C1D50K84
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 68 arm-level results and 8 molecular subtypes across 77 patients, 50 significant findings detected with Q value < 0.25.

- 4p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 4q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 5p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 5q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

- 9p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 9q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 10p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 10q gain cnv correlated to 'MRNASEQ_CNMF'.

- 12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 12q gain cnv correlated to 'CN_CNMF'.

- 14q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 16q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 19p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 19q gain cnv correlated to 'CN_CNMF'.

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

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

- Xq gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- 9p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 17p loss cnv correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 50 significant findings detected.

|  | Molecular subtypes | 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 | Chi-square 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
4p gain | 0 (0%) | 50 | 6.88e-06 (0.0035) | 0.022 (1.00) | 4.18e-06 (0.00215) | 5.16e-06 (0.00264) | 0.388 (1.00) | 0.47 (1.00) | 0.774 (1.00) | 0.62 (1.00)
4q gain | 0 (0%) | 52 | 2.02e-05 (0.0101) | 0.0473 (1.00) | 3.01e-05 (0.0149) | 8.09e-06 (0.0041) | 0.775 (1.00) | 0.856 (1.00) | 1 (1.00) | 0.85 (1.00)
5p gain | 0 (0%) | 30 | 2.08e-06 (0.00107) | 0.00469 (1.00) | 1.87e-06 (0.000964) | 2.4e-06 (0.00124) | 1 (1.00) | 0.796 (1.00) | 1 (1.00) | 0.666 (1.00)
5q gain | 0 (0%) | 32 | 3.07e-05 (0.0151) | 0.00202 (0.924) | 1.16e-05 (0.00583) | 7.13e-07 (0.000371) | 0.374 (1.00) | 0.928 (1.00) | 0.374 (1.00) | 0.381 (1.00)
7q gain | 0 (0%) | 40 | 8.43e-06 (0.00426) | 0.00805 (1.00) | 1.63e-08 (8.53e-06) | 4.72e-06 (0.00241) | 1 (1.00) | 0.861 (1.00) | 1 (1.00) | 0.725 (1.00)
9p gain | 0 (0%) | 65 | 7.38e-06 (0.00375) | 0.00205 (0.936) | 0.00037 (0.178) | 0.000143 (0.0693) | 0.204 (1.00) | 0.183 (1.00) | 0.204 (1.00) | 0.221 (1.00)
10p gain | 0 (0%) | 57 | 3.26e-05 (0.016) | 0.0356 (1.00) | 3.15e-05 (0.0155) | 0.00018 (0.0871) | 1 (1.00) | 0.624 (1.00) | 1 (1.00) | 0.886 (1.00)
12p gain | 0 (0%) | 25 | 3.46e-07 (0.000181) | 0.0653 (1.00) | 1.31e-05 (0.00655) | 0.000423 (0.202) | 0.355 (1.00) | 0.601 (1.00) | 0.355 (1.00) | 0.373 (1.00)
16p gain | 0 (0%) | 38 | 2.06e-11 (1.08e-08) | 0.00389 (1.00) | 2.66e-05 (0.0132) | 3.13e-07 (0.000164) | 0.561 (1.00) | 0.435 (1.00) | 1 (1.00) | 0.358 (1.00)
16q gain | 0 (0%) | 39 | 5.11e-11 (2.68e-08) | 0.00282 (1.00) | 5.78e-05 (0.0283) | 1.67e-06 (0.000866) | 0.561 (1.00) | 0.435 (1.00) | 1 (1.00) | 0.358 (1.00)
7p gain | 0 (0%) | 39 | 0.000577 (0.274) | 0.0269 (1.00) | 1.11e-05 (0.00559) | 0.000373 (0.179) | 0.774 (1.00) | 0.928 (1.00) | 0.774 (1.00) | 1 (1.00)
9q gain | 0 (0%) | 61 | 1.13e-05 (0.00566) | 0.00585 (1.00) | 0.00054 (0.257) | 4.17e-05 (0.0205) | 0.436 (1.00) | 0.564 (1.00) | 0.436 (1.00) | 0.747 (1.00)
14q gain | 0 (0%) | 61 | 0.00167 (0.764) | 0.0895 (1.00) | 6.6e-05 (0.0323) | 9.01e-05 (0.0438) | 0.00109 (0.514) | 0.00155 (0.713) | 0.00109 (0.514) | 0.00282 (1.00)
19p gain | 0 (0%) | 35 | 8.31e-05 (0.0405) | 0.0412 (1.00) | 0.00304 (1.00) | 0.000204 (0.0987) | 0.774 (1.00) | 0.738 (1.00) | 0.774 (1.00) | 0.62 (1.00)
20p gain | 0 (0%) | 39 | 2.87e-06 (0.00148) | 0.14 (1.00) | 2.57e-05 (0.0128) | 0.00251 (1.00) | 0.00887 (1.00) | 0.0103 (1.00) | 0.0428 (1.00) | 0.0125 (1.00)
20q gain | 0 (0%) | 36 | 1.7e-06 (0.000881) | 0.0354 (1.00) | 1.94e-05 (0.00968) | 0.000838 (0.396) | 0.0798 (1.00) | 0.0876 (1.00) | 0.0798 (1.00) | 0.035 (1.00)
Xq gain | 0 (0%) | 56 | 0.000212 (0.102) | 0.136 (1.00) | 5.7e-07 (0.000297) | 0.00513 (1.00) | 1 (1.00) | 0.839 (1.00) | 0.528 (1.00) | 1 (1.00)
9p loss | 0 (0%) | 66 | 0.00143 (0.667) | 0.0229 (1.00) | 6.94e-05 (0.0339) | 7.88e-06 (0.004) | 0.0265 (1.00) | 0.183 (1.00) | 0.0265 (1.00) | 0.0563 (1.00)
10q gain | 0 (0%) | 58 | 0.0011 (0.514) | 0.0907 (1.00) | 0.000405 (0.194) | 0.00165 (0.757) | 0.486 (1.00) | 0.437 (1.00) | 0.486 (1.00) | 0.787 (1.00)
12q gain | 0 (0%) | 24 | 5.92e-06 (0.00302) | 0.355 (1.00) | 0.00146 (0.676) | 0.011 (1.00) | 1 (1.00) | 0.436 (1.00) | 1 (1.00) | 0.383 (1.00)
19q gain | 0 (0%) | 37 | 2.32e-05 (0.0115) | 0.0134 (1.00) | 0.00297 (1.00) | 0.000576 (0.274) | 0.385 (1.00) | 0.507 (1.00) | 0.385 (1.00) | 0.387 (1.00)
17p loss | 0 (0%) | 59 | 0.00302 (1.00) | 0.000815 (0.385) | 0.000211 (0.102) | 0.00144 (0.669) | 0.711 (1.00) | 0.257 (1.00) | 0.711 (1.00) | 0.473 (1.00)
1q gain | 0 (0%) | 72 | 0.306 (1.00) | 0.258 (1.00) | 0.339 (1.00) | 0.057 (1.00) | 1 (1.00) | 0.651 (1.00) | 1 (1.00) | 0.631 (1.00)
2p gain | 0 (0%) | 71 | 0.0175 (1.00) | 0.0952 (1.00) | 0.24 (1.00) | 0.0181 (1.00) | 0.579 (1.00) | 0.291 (1.00) | 0.579 (1.00) | 0.278 (1.00)
2q gain | 0 (0%) | 72 | 0.306 (1.00) | 0.0371 (1.00) | 0.185 (1.00) | 0.057 (1.00) | 1 (1.00) |  | 1 (1.00) |
3p gain | 0 (0%) | 69 | 0.201 (1.00) | 0.303 (1.00) | 0.386 (1.00) | 0.521 (1.00) | 0.386 (1.00) | 0.447 (1.00) | 0.386 (1.00) | 0.521 (1.00)
3q gain | 0 (0%) | 67 | 0.305 (1.00) | 0.361 (1.00) | 0.0771 (1.00) | 0.911 (1.00) | 1 (1.00) | 0.776 (1.00) | 1 (1.00) | 0.877 (1.00)
6p gain | 0 (0%) | 66 | 0.105 (1.00) | 0.943 (1.00) | 0.18 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
6q gain | 0 (0%) | 66 | 0.121 (1.00) | 0.545 (1.00) | 0.368 (1.00) | 0.385 (1.00) | 0.436 (1.00) | 0.564 (1.00) | 0.436 (1.00) | 0.747 (1.00)
8p gain | 0 (0%) | 50 | 0.00376 (1.00) | 0.156 (1.00) | 0.0822 (1.00) | 0.111 (1.00) | 0.355 (1.00) | 0.331 (1.00) | 0.758 (1.00) | 0.541 (1.00)
8q gain | 0 (0%) | 46 | 0.00836 (1.00) | 0.395 (1.00) | 0.225 (1.00) | 0.292 (1.00) | 0.763 (1.00) | 0.675 (1.00) | 1 (1.00) | 0.845 (1.00)
11q gain | 0 (0%) | 74 | 0.304 (1.00) | 0.367 (1.00) | 0.15 (1.00) | 0.47 (1.00) | 1 (1.00) |  | 1 (1.00) |
13q gain | 0 (0%) | 72 | 0.726 (1.00) | 0.231 (1.00) | 0.00364 (1.00) | 0.317 (1.00) | 0.617 (1.00) | 0.799 (1.00) | 0.617 (1.00) | 0.812 (1.00)
15q gain | 0 (0%) | 68 | 0.00684 (1.00) | 0.0333 (1.00) | 0.0042 (1.00) | 0.00144 (0.667) | 0.112 (1.00) | 0.564 (1.00) | 0.112 (1.00) | 0.282 (1.00)
21q gain | 0 (0%) | 55 | 0.00117 (0.547) | 0.0184 (1.00) | 0.0104 (1.00) | 0.00095 (0.447) | 0.355 (1.00) | 0.325 (1.00) | 0.121 (1.00) | 0.248 (1.00)
1p loss | 0 (0%) | 58 | 0.0288 (1.00) | 0.0931 (1.00) | 0.14 (1.00) | 0.0534 (1.00) | 0.326 (1.00) | 0.15 (1.00) | 0.326 (1.00) | 0.285 (1.00)
1q loss | 0 (0%) | 65 | 0.199 (1.00) | 0.199 (1.00) | 0.873 (1.00) | 0.67 (1.00) | 0.217 (1.00) | 0.269 (1.00) | 0.217 (1.00) | 0.139 (1.00)
2p loss | 0 (0%) | 68 | 0.0543 (1.00) | 0.042 (1.00) | 0.725 (1.00) | 1 (1.00) | 0.386 (1.00) | 0.223 (1.00) | 0.386 (1.00) | 0.0969 (1.00)
2q loss | 0 (0%) | 70 | 0.00633 (1.00) | 0.00356 (1.00) | 0.454 (1.00) | 0.623 (1.00) | 0.158 (1.00) | 0.0824 (1.00) | 0.158 (1.00) | 0.042 (1.00)
3p loss | 0 (0%) | 64 | 0.366 (1.00) | 0.0662 (1.00) | 0.0858 (1.00) | 0.0678 (1.00) | 1 (1.00) | 0.317 (1.00) | 1 (1.00) | 0.404 (1.00)
3q loss | 0 (0%) | 63 | 0.0294 (1.00) | 0.0264 (1.00) | 0.0558 (1.00) | 0.00425 (1.00) | 0.678 (1.00) | 0.524 (1.00) | 0.678 (1.00) | 0.712 (1.00)
4p loss | 0 (0%) | 70 | 0.0326 (1.00) | 0.028 (1.00) | 0.00133 (0.617) | 0.00398 (1.00) | 1 (1.00) | 0.651 (1.00) | 1 (1.00) | 0.631 (1.00)
4q loss | 0 (0%) | 68 | 0.0057 (1.00) | 0.0253 (1.00) | 0.00156 (0.718) | 0.00357 (1.00) | 1 (1.00) | 0.651 (1.00) | 1 (1.00) | 0.631 (1.00)
5p loss | 0 (0%) | 70 | 0.772 (1.00) | 0.0883 (1.00) | 0.113 (1.00) | 0.0025 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
5q loss | 0 (0%) | 71 | 0.833 (1.00) | 0.0968 (1.00) | 0.017 (1.00) | 0.00906 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
6p loss | 0 (0%) | 71 | 0.211 (1.00) | 0.182 (1.00) | 0.755 (1.00) | 0.649 (1.00) | 0.447 (1.00) |  | 0.447 (1.00) |
6q loss | 0 (0%) | 71 | 0.211 (1.00) | 0.533 (1.00) | 0.755 (1.00) | 1 (1.00) | 0.194 (1.00) |  | 0.194 (1.00) |
7q loss | 0 (0%) | 74 | 0.304 (1.00) | 0.0367 (1.00) | 0.15 (1.00) | 0.0441 (1.00) | 1 (1.00) |  | 1 (1.00) |
8p loss | 0 (0%) | 68 | 0.26 (1.00) | 0.382 (1.00) | 0.15 (1.00) | 0.131 (1.00) | 1 (1.00) | 0.373 (1.00) | 1 (1.00) | 0.44 (1.00)
8q loss | 0 (0%) | 71 | 0.274 (1.00) | 0.081 (1.00) | 0.0311 (1.00) | 0.0251 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
9q loss | 0 (0%) | 73 | 0.561 (1.00) | 0.193 (1.00) | 0.248 (1.00) | 0.0924 (1.00) | 0.117 (1.00) | 0.531 (1.00) | 0.117 (1.00) | 0.273 (1.00)
10p loss | 0 (0%) | 69 | 0.178 (1.00) | 0.245 (1.00) | 0.335 (1.00) | 0.311 (1.00) | 0.117 (1.00) | 0.164 (1.00) | 0.117 (1.00) | 0.273 (1.00)
10q loss | 0 (0%) | 71 | 0.52 (1.00) | 0.334 (1.00) | 0.574 (1.00) | 0.416 (1.00) | 0.495 (1.00) |  | 0.495 (1.00) |
11p loss | 0 (0%) | 62 | 0.00906 (1.00) | 0.0546 (1.00) | 0.22 (1.00) | 0.762 (1.00) | 1 (1.00) | 0.182 (1.00) | 1 (1.00) | 0.186 (1.00)
11q loss | 0 (0%) | 64 | 0.00668 (1.00) | 0.0289 (1.00) | 0.179 (1.00) | 0.686 (1.00) | 1 (1.00) | 0.182 (1.00) | 1 (1.00) | 0.186 (1.00)
12p loss | 0 (0%) | 74 | 0.304 (1.00) | 0.0917 (1.00) | 1 (1.00) | 0.259 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
13q loss | 0 (0%) | 54 | 0.00384 (1.00) | 0.0692 (1.00) | 0.191 (1.00) | 0.304 (1.00) | 0.342 (1.00) | 0.77 (1.00) | 0.342 (1.00) | 0.628 (1.00)
14q loss | 0 (0%) | 68 | 0.00284 (1.00) | 0.0195 (1.00) | 0.0911 (1.00) | 0.0861 (1.00) | 0.311 (1.00) | 0.312 (1.00) | 0.311 (1.00) | 0.202 (1.00)
15q loss | 0 (0%) | 66 | 0.295 (1.00) | 0.0351 (1.00) | 0.0333 (1.00) | 0.0435 (1.00) | 0.311 (1.00) | 0.312 (1.00) | 0.311 (1.00) | 0.202 (1.00)
16p loss | 0 (0%) | 73 | 0.108 (1.00) | 0.133 (1.00) | 0.0418 (1.00) | 0.211 (1.00) | 0.447 (1.00) |  | 0.447 (1.00) |
16q loss | 0 (0%) | 73 | 0.108 (1.00) | 0.00786 (1.00) | 0.0418 (1.00) | 0.0116 (1.00) |  |  |  |
17q loss | 0 (0%) | 63 | 0.0294 (1.00) | 0.0358 (1.00) | 0.0105 (1.00) | 0.00425 (1.00) | 0.112 (1.00) | 0.166 (1.00) | 0.112 (1.00) | 0.282 (1.00)
18p loss | 0 (0%) | 53 | 0.115 (1.00) | 0.042 (1.00) | 0.298 (1.00) | 1 (1.00) | 0.52 (1.00) | 0.687 (1.00) | 0.52 (1.00) | 0.338 (1.00)
18q loss | 0 (0%) | 54 | 0.0603 (1.00) | 0.262 (1.00) | 0.292 (1.00) | 0.858 (1.00) | 0.0999 (1.00) | 0.272 (1.00) | 0.0999 (1.00) | 0.153 (1.00)
20p loss | 0 (0%) | 72 | 0.0485 (1.00) | 0.262 (1.00) | 0.0937 (1.00) | 0.0204 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
21q loss | 0 (0%) | 67 | 0.0328 (1.00) | 0.202 (1.00) | 0.29 (1.00) | 0.468 (1.00) | 0.644 (1.00) | 0.688 (1.00) | 0.158 (1.00) | 0.135 (1.00)
22q loss | 0 (0%) | 48 | 0.106 (1.00) | 0.0096 (1.00) | 0.348 (1.00) | 0.262 (1.00) | 0.197 (1.00) | 0.479 (1.00) | 0.197 (1.00) | 0.244 (1.00)
Xq loss | 0 (0%) | 69 | 0.0242 (1.00) | 0.154 (1.00) | 0.587 (1.00) | 0.413 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)

'4p gain' versus 'CN_CNMF'

P value = 6.88e-06 (Fisher's exact test), Q value = 0.0035

Table S1. Gene #6: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
4P GAIN CNV | 1 | 8 | 12 | 6
4P GAIN WILD-TYPE | 28 | 11 | 7 | 4

Figure S1. Get High-res Image Gene #6: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 4.18e-06 (Fisher's exact test), Q value = 0.0021

Table S2. Gene #6: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
4P GAIN CNV | 0 | 7 | 11 | 8
4P GAIN WILD-TYPE | 24 | 5 | 6 | 15

Figure S2. Get High-res Image Gene #6: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.16e-06 (Fisher's exact test), Q value = 0.0026

Table S3. Gene #6: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
4P GAIN CNV | 0 | 13 | 13
4P GAIN WILD-TYPE | 23 | 19 | 8

Figure S3. Get High-res Image Gene #6: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.01

Table S4. Gene #7: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
4Q GAIN CNV | 1 | 7 | 12 | 5
4Q GAIN WILD-TYPE | 28 | 12 | 7 | 5

Figure S4. Get High-res Image Gene #7: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3.01e-05 (Fisher's exact test), Q value = 0.015

Table S5. Gene #7: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
4Q GAIN CNV | 0 | 7 | 9 | 8
4Q GAIN WILD-TYPE | 24 | 5 | 8 | 15

Figure S5. Get High-res Image Gene #7: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.09e-06 (Fisher's exact test), Q value = 0.0041

Table S6. Gene #7: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
4Q GAIN CNV | 0 | 11 | 13
4Q GAIN WILD-TYPE | 23 | 21 | 8

Figure S6. Get High-res Image Gene #7: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0011

Table S7. Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
5P GAIN CNV | 7 | 17 | 16 | 7
5P GAIN WILD-TYPE | 22 | 2 | 3 | 3

Figure S7. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.00096

Table S8. Gene #8: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
5P GAIN CNV | 4 | 9 | 14 | 19
5P GAIN WILD-TYPE | 20 | 3 | 3 | 4

Figure S8. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0012

Table S9. Gene #8: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
5P GAIN CNV | 4 | 26 | 16
5P GAIN WILD-TYPE | 19 | 6 | 5

Figure S9. Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.015

Table S10. Gene #9: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
5Q GAIN CNV | 7 | 16 | 14 | 8
5Q GAIN WILD-TYPE | 22 | 3 | 5 | 2

Figure S10. Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0058

Table S11. Gene #9: '5q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
5Q GAIN CNV | 4 | 9 | 14 | 17
5Q GAIN WILD-TYPE | 20 | 3 | 3 | 6

Figure S11. Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.13e-07 (Fisher's exact test), Q value = 0.00037

Table S12. Gene #9: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
5Q GAIN CNV | 3 | 24 | 17
5Q GAIN WILD-TYPE | 20 | 8 | 4

Figure S12. Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0056

Table S13. Gene #12: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
7P GAIN CNV | 4 | 11 | 13 | 10
7P GAIN WILD-TYPE | 20 | 1 | 4 | 13

Figure S13. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000373 (Fisher's exact test), Q value = 0.18

Table S14. Gene #12: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
7P GAIN CNV | 5 | 16 | 17
7P GAIN WILD-TYPE | 18 | 16 | 4

Figure S14. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 8.43e-06 (Fisher's exact test), Q value = 0.0043

Table S15. Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
7Q GAIN CNV | 4 | 13 | 15 | 5
7Q GAIN WILD-TYPE | 25 | 6 | 4 | 5

Figure S15. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 8.5e-06

Table S16. Gene #13: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
7Q GAIN CNV | 2 | 12 | 13 | 10
7Q GAIN WILD-TYPE | 22 | 0 | 4 | 13

Figure S16. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.72e-06 (Fisher's exact test), Q value = 0.0024

Table S17. Gene #13: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
7Q GAIN CNV | 3 | 16 | 18
7Q GAIN WILD-TYPE | 20 | 16 | 3

Figure S17. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 7.38e-06 (Fisher's exact test), Q value = 0.0037

Table S18. Gene #16: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
9P GAIN CNV | 0 | 1 | 10 | 1
9P GAIN WILD-TYPE | 29 | 18 | 9 | 9

Figure S18. Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

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

Table S19. Gene #16: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
9P GAIN CNV | 0 | 5 | 5 | 1
9P GAIN WILD-TYPE | 24 | 7 | 12 | 22

Figure S19. Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.069

Table S20. Gene #16: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
9P GAIN CNV | 1 | 1 | 9
9P GAIN WILD-TYPE | 22 | 31 | 12

Figure S20. Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0057

Table S21. Gene #17: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
9Q GAIN CNV | 2 | 1 | 12 | 1
9Q GAIN WILD-TYPE | 27 | 18 | 7 | 9

Figure S21. Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.02

Table S22. Gene #17: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
9Q GAIN CNV | 3 | 1 | 11
9Q GAIN WILD-TYPE | 20 | 31 | 10

Figure S22. Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.016

Table S23. Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
10P GAIN CNV | 5 | 1 | 13 | 1
10P GAIN WILD-TYPE | 24 | 18 | 6 | 9

Figure S23. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.016

Table S24. Gene #18: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
10P GAIN CNV | 4 | 10 | 4 | 2
10P GAIN WILD-TYPE | 20 | 2 | 13 | 21

Figure S24. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.087

Table S25. Gene #18: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
10P GAIN CNV | 6 | 2 | 12
10P GAIN WILD-TYPE | 17 | 30 | 9

Figure S25. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.000405 (Fisher's exact test), Q value = 0.19

Table S26. Gene #19: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
10Q GAIN CNV | 5 | 9 | 3 | 2
10Q GAIN WILD-TYPE | 19 | 3 | 14 | 21

Figure S26. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00018

Table S27. Gene #21: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
12P GAIN CNV | 9 | 19 | 16 | 8
12P GAIN WILD-TYPE | 20 | 0 | 3 | 2

Figure S27. Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0066

Table S28. Gene #21: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
12P GAIN CNV | 7 | 12 | 14 | 18
12P GAIN WILD-TYPE | 17 | 0 | 3 | 5

Figure S28. Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000423 (Fisher's exact test), Q value = 0.2

Table S29. Gene #21: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
12P GAIN CNV | 8 | 25 | 18
12P GAIN WILD-TYPE | 15 | 7 | 3

Figure S29. Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 5.92e-06 (Fisher's exact test), Q value = 0.003

Table S30. Gene #22: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
12Q GAIN CNV | 10 | 18 | 17 | 8
12Q GAIN WILD-TYPE | 19 | 1 | 2 | 2

Figure S30. Get High-res Image Gene #22: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.032

Table S31. Gene #24: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
14Q GAIN CNV | 2 | 5 | 8 | 0
14Q GAIN WILD-TYPE | 22 | 7 | 9 | 23

Figure S31. Get High-res Image Gene #24: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.01e-05 (Fisher's exact test), Q value = 0.044

Table S32. Gene #24: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
14Q GAIN CNV | 2 | 2 | 11
14Q GAIN WILD-TYPE | 21 | 30 | 10

Figure S32. Get High-res Image Gene #24: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 2.06e-11 (Fisher's exact test), Q value = 1.1e-08

Table S33. Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
16P GAIN CNV | 3 | 19 | 14 | 3
16P GAIN WILD-TYPE | 26 | 0 | 5 | 7

Figure S33. Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.013

Table S34. Gene #26: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
16P GAIN CNV | 3 | 9 | 13 | 14
16P GAIN WILD-TYPE | 21 | 3 | 4 | 9

Figure S34. Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.13e-07 (Fisher's exact test), Q value = 0.00016

Table S35. Gene #26: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
16P GAIN CNV | 2 | 19 | 18
16P GAIN WILD-TYPE | 21 | 13 | 3

Figure S35. Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5.11e-11 (Fisher's exact test), Q value = 2.7e-08

Table S36. Gene #27: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
16Q GAIN CNV | 3 | 19 | 13 | 3
16Q GAIN WILD-TYPE | 26 | 0 | 6 | 7

Figure S36. Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 5.78e-05 (Fisher's exact test), Q value = 0.028

Table S37. Gene #27: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
16Q GAIN CNV | 3 | 8 | 13 | 14
16Q GAIN WILD-TYPE | 21 | 4 | 4 | 9

Figure S37. Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.00087

Table S38. Gene #27: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
16Q GAIN CNV | 2 | 19 | 17
16Q GAIN WILD-TYPE | 21 | 13 | 4

Figure S38. Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 8.31e-05 (Fisher's exact test), Q value = 0.04

Table S39. Gene #28: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
19P GAIN CNV | 9 | 10 | 18 | 5
19P GAIN WILD-TYPE | 20 | 9 | 1 | 5

Figure S39. Get High-res Image Gene #28: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.099

Table S40. Gene #28: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
19P GAIN CNV | 10 | 12 | 19
19P GAIN WILD-TYPE | 13 | 20 | 2

Figure S40. Get High-res Image Gene #28: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.012

Table S41. Gene #29: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
19Q GAIN CNV | 8 | 10 | 18 | 4
19Q GAIN WILD-TYPE | 21 | 9 | 1 | 6

Figure S41. Get High-res Image Gene #29: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0015

Table S42. Gene #30: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
20P GAIN CNV | 4 | 16 | 12 | 6
20P GAIN WILD-TYPE | 25 | 3 | 7 | 4

Figure S42. Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.013

Table S43. Gene #30: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
20P GAIN CNV | 3 | 8 | 8 | 18
20P GAIN WILD-TYPE | 21 | 4 | 9 | 5

Figure S43. Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.7e-06 (Fisher's exact test), Q value = 0.00088

Table S44. Gene #31: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
20Q GAIN CNV | 5 | 17 | 13 | 6
20Q GAIN WILD-TYPE | 24 | 2 | 6 | 4

Figure S44. Get High-res Image Gene #31: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.0097

Table S45. Gene #31: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
20Q GAIN CNV | 4 | 10 | 8 | 18
20Q GAIN WILD-TYPE | 20 | 2 | 9 | 5

Figure S45. Get High-res Image Gene #31: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Xq gain' versus 'CN_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.1

Table S46. Gene #33: 'Xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 19 | 19 | 10
XQ GAIN CNV | 1 | 8 | 10 | 2
XQ GAIN WILD-TYPE | 28 | 11 | 9 | 8

Figure S46. Get High-res Image Gene #33: 'Xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'Xq gain' versus 'MRNASEQ_CNMF'

P value = 5.7e-07 (Fisher's exact test), Q value = 3e-04

Table S47. Gene #33: 'Xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
XQ GAIN CNV | 0 | 10 | 6 | 5
XQ GAIN WILD-TYPE | 24 | 2 | 11 | 18

Figure S47. Get High-res Image Gene #33: 'Xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6.94e-05 (Fisher's exact test), Q value = 0.034

Table S48. Gene #49: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
9P LOSS CNV | 10 | 0 | 1 | 0
9P LOSS WILD-TYPE | 14 | 12 | 16 | 23

Figure S48. Get High-res Image Gene #49: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.88e-06 (Fisher's exact test), Q value = 0.004

Table S49. Gene #49: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 32 | 21
9P LOSS CNV | 10 | 0 | 1
9P LOSS WILD-TYPE | 13 | 32 | 20

Figure S49. Get High-res Image Gene #49: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.1

Table S50. Gene #61: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 12 | 17 | 23
17P LOSS CNV | 12 | 0 | 5 | 1
17P LOSS WILD-TYPE | 12 | 12 | 12 | 22

Figure S50. Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

- Number of patients = 77

- Number of significantly arm-level cnvs = 68

- 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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