Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1B56H0C
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/C1B56H0C
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 60 arm-level results and 12 molecular subtypes across 269 patients, 98 significant findings detected with Q value < 0.25.

- 1p gain cnv correlated to 'MRNASEQ_CNMF'.

- 1q gain cnv correlated to 'CN_CNMF'.

- 3q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

- 6p gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 8p gain cnv correlated to 'CN_CNMF'.

- 8q gain cnv correlated to 'CN_CNMF'.

- 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

- 19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 1p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 1q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 3p loss cnv correlated to 'MRNASEQ_CNMF'.

- 3q loss cnv correlated to 'CN_CNMF'.

- 4p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- 4q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 6q loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 13q loss cnv correlated to 'CN_CNMF'.

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

- 22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 60 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 98 significant findings detected.

|  | Molecular subtypes | MRNA CNMF | MRNA CHIERARCHICAL | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | 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 | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test
1p loss | 0 (0%) | 192 | 0.00361 (1.00) | 8.75e-06 (0.00501) | 1.82e-25 (1.14e-22) | 4.62e-58 (2.92e-55) | 7.62e-05 (0.0424) | 0.0316 (1.00) | 1.99e-14 (1.23e-11) | 1.24e-35 (7.84e-33) | 3.34e-11 (2.03e-08) | 8.75e-08 (5.2e-05) | 1.89e-13 (1.16e-10) | 3.1e-10 (1.88e-07)
19q loss | 0 (0%) | 184 | 0.3 (1.00) | 0.0404 (1.00) | 2.7e-23 (1.68e-20) | 1.12e-43 (7.04e-41) | 0.000312 (0.168) | 0.0815 (1.00) | 1.1e-12 (6.72e-10) | 1.37e-29 (8.6e-27) | 1.54e-07 (9.11e-05) | 6.36e-07 (0.000374) | 6.28e-10 (3.79e-07) | 3.46e-08 (2.08e-05)
7p gain | 0 (0%) | 219 | 0.175 (1.00) | 0.653 (1.00) | 4.04e-26 (2.53e-23) | 8.93e-13 (5.48e-10) | 5.46e-05 (0.0306) | 0.00775 (1.00) | 1.04e-06 (0.000606) | 6.21e-05 (0.0348) | 0.00427 (1.00) | 1.02e-06 (0.000597) | 1.5e-05 (0.00851) | 3.71e-11 (2.25e-08)
10p loss | 0 (0%) | 233 | 0.271 (1.00) | 0.561 (1.00) | 1.42e-15 (8.78e-13) | 4.74e-27 (2.98e-24) | 3.9e-07 (0.00023) | 0.000609 (0.321) | 2.38e-11 (1.45e-08) | 4.53e-05 (0.0255) | 0.00888 (1.00) | 5.81e-07 (0.000342) | 2.19e-13 (1.34e-10) | 1.44e-13 (8.87e-11)
10q loss | 0 (0%) | 231 | 0.271 (1.00) | 0.561 (1.00) | 1.2e-14 (7.44e-12) | 7.62e-25 (4.76e-22) | 1.76e-06 (0.00102) | 0.00094 (0.489) | 2.44e-11 (1.49e-08) | 7.54e-05 (0.042) | 0.00631 (1.00) | 2.13e-07 (0.000126) | 2.11e-12 (1.29e-09) | 7.12e-14 (4.39e-11)
20q gain | 0 (0%) | 249 |  |  | 6.77e-07 (0.000397) | 6.38e-08 (3.8e-05) | 0.000123 (0.0678) | 0.237 (1.00) | 6.66e-06 (0.00383) | 0.00133 (0.687) | 0.00426 (1.00) | 0.000174 (0.095) | 6.25e-07 (0.000368) | 1.86e-09 (1.12e-06)
7q gain | 0 (0%) | 201 | 0.282 (1.00) | 0.382 (1.00) | 2.57e-23 (1.6e-20) | 2.54e-11 (1.54e-08) | 0.0023 (1.00) | 0.0534 (1.00) | 1.65e-05 (0.00939) | 0.000223 (0.121) | 0.01 (1.00) | 0.000939 (0.489) | 0.000266 (0.145) | 1.79e-08 (1.08e-05)
19p gain | 0 (0%) | 252 |  |  | 1.33e-07 (7.89e-05) | 1.82e-08 (1.09e-05) | 0.0248 (1.00) | 0.0472 (1.00) | 0.000122 (0.0673) | 8.41e-05 (0.0466) | 0.00944 (1.00) | 0.00157 (0.803) | 5.01e-05 (0.0281) | 3.92e-08 (2.35e-05)
19q gain | 0 (0%) | 257 |  |  | 1.32e-05 (0.00755) | 2.38e-06 (0.00138) | 0.0226 (1.00) | 0.383 (1.00) | 0.00144 (0.743) | 0.00296 (1.00) | 0.0169 (1.00) | 0.00567 (1.00) | 1.68e-05 (0.00954) | 2.44e-06 (0.00141)
20p gain | 0 (0%) | 249 |  |  | 6.77e-07 (0.000397) | 5.31e-08 (3.17e-05) | 0.00427 (1.00) | 0.384 (1.00) | 0.000553 (0.295) | 0.0418 (1.00) | 0.0873 (1.00) | 0.00144 (0.744) | 7.42e-06 (0.00426) | 1.21e-07 (7.19e-05)
4p loss | 0 (0%) | 251 | 0.415 (1.00) | 0.0907 (1.00) | 0.000564 (0.3) | 1.03e-06 (0.000602) | 0.725 (1.00) | 0.628 (1.00) | 0.000408 (0.219) | 2.96e-06 (0.00171) | 0.000452 (0.242) | 0.85 (1.00) | 0.00912 (1.00) | 0.15 (1.00)
4q loss | 0 (0%) | 241 | 0.839 (1.00) | 0.404 (1.00) | 0.000572 (0.304) | 9.78e-06 (0.00558) | 0.612 (1.00) | 0.634 (1.00) | 0.000283 (0.154) | 6.26e-05 (0.035) | 0.000734 (0.386) | 0.887 (1.00) | 0.000559 (0.298) | 0.0563 (1.00)
11p loss | 0 (0%) | 244 | 0.815 (1.00) | 0.106 (1.00) | 2.14e-08 (1.28e-05) | 0.000216 (0.118) | 0.0298 (1.00) | 0.612 (1.00) | 0.00718 (1.00) | 0.00904 (1.00) | 0.00341 (1.00) | 0.647 (1.00) | 0.000168 (0.0924) | 0.123 (1.00)
22q loss | 0 (0%) | 249 | 1 (1.00) | 0.0879 (1.00) | 1.97e-05 (0.0111) | 2.38e-05 (0.0134) | 7.62e-05 (0.0424) | 0.0711 (1.00) | 0.000595 (0.314) | 0.00146 (0.75) | 0.00996 (1.00) | 0.254 (1.00) | 0.000762 (0.4) | 0.00776 (1.00)
10p gain | 0 (0%) | 245 |  |  | 7.42e-05 (0.0414) | 2.02e-06 (0.00117) | 0.136 (1.00) | 0.414 (1.00) | 0.964 (1.00) | 0.0523 (1.00) | 0.731 (1.00) | 0.554 (1.00) | 0.0939 (1.00) | 0.229 (1.00)
1q loss | 0 (0%) | 259 | 0.0889 (1.00) | 0.0202 (1.00) | 0.0502 (1.00) | 0.000172 (0.0943) | 0.0176 (1.00) | 1 (1.00) | 0.0353 (1.00) | 0.000107 (0.0592) | 0.000584 (0.309) | 0.854 (1.00) | 0.00249 (1.00) | 0.0869 (1.00)
1p gain | 0 (0%) | 261 |  |  | 0.0133 (1.00) | 0.00765 (1.00) | 0.0748 (1.00) | 0.74 (1.00) | 0.00022 (0.12) | 0.0317 (1.00) | 0.278 (1.00) | 0.017 (1.00) | 0.0064 (1.00) | 0.00323 (1.00)
1q gain | 0 (0%) | 259 |  |  | 0.000349 (0.187) | 0.0123 (1.00) | 0.464 (1.00) | 1 (1.00) | 0.0999 (1.00) | 0.279 (1.00) | 0.39 (1.00) | 0.252 (1.00) | 0.0331 (1.00) | 0.125 (1.00)
3q gain | 0 (0%) | 266 |  |  | 0.171 (1.00) | 0.211 (1.00) |  |  | 0.0655 (1.00) | 0.387 (1.00) | 0.239 (1.00) | 0.372 (1.00) | 0.000322 (0.173) | 0.0321 (1.00)
6p gain | 0 (0%) | 266 |  |  | 0.0146 (1.00) | 0.626 (1.00) |  |  | 0.0655 (1.00) | 0.387 (1.00) | 0.203 (1.00) | 0.0795 (1.00) | 1.81e-16 (1.13e-13) | 0.196 (1.00)
8p gain | 0 (0%) | 252 |  |  | 0.000308 (0.166) | 0.0761 (1.00) | 0.117 (1.00) | 0.783 (1.00) | 0.201 (1.00) | 0.405 (1.00) | 0.281 (1.00) | 0.843 (1.00) | 0.315 (1.00) | 0.155 (1.00)
8q gain | 0 (0%) | 247 |  |  | 3.05e-05 (0.0172) | 0.0158 (1.00) | 0.0251 (1.00) | 0.414 (1.00) | 0.11 (1.00) | 0.0624 (1.00) | 0.0975 (1.00) | 0.702 (1.00) | 0.29 (1.00) | 0.00865 (1.00)
3p loss | 0 (0%) | 259 |  |  | 0.00226 (1.00) | 0.178 (1.00) | 0.00225 (1.00) | 0.0705 (1.00) | 0.000305 (0.165) | 0.00866 (1.00) | 0.0613 (1.00) | 0.305 (1.00) | 0.0233 (1.00) | 0.0371 (1.00)
3q loss | 0 (0%) | 256 | 0.175 (1.00) | 0.561 (1.00) | 5.87e-06 (0.00338) | 0.0504 (1.00) | 0.0798 (1.00) | 0.0472 (1.00) | 0.0405 (1.00) | 0.074 (1.00) | 0.214 (1.00) | 0.472 (1.00) | 0.42 (1.00) | 0.0494 (1.00)
6q loss | 0 (0%) | 237 |  |  | 0.000158 (0.087) | 0.02 (1.00) | 0.223 (1.00) | 0.879 (1.00) | 0.497 (1.00) | 0.199 (1.00) | 0.0015 (0.771) | 0.561 (1.00) | 0.703 (1.00) | 0.105 (1.00)
9p loss | 0 (0%) | 220 | 0.0519 (1.00) | 0.653 (1.00) | 9.12e-06 (0.00522) | 0.0243 (1.00) | 0.0489 (1.00) | 0.0519 (1.00) | 0.866 (1.00) | 0.422 (1.00) | 0.827 (1.00) | 0.236 (1.00) | 0.604 (1.00) | 0.448 (1.00)
13q loss | 0 (0%) | 238 | 1 (1.00) | 0.0138 (1.00) | 6.34e-19 (3.94e-16) | 0.0642 (1.00) | 0.0968 (1.00) | 0.939 (1.00) | 0.395 (1.00) | 0.159 (1.00) | 0.632 (1.00) | 0.613 (1.00) | 0.665 (1.00) | 0.187 (1.00)
3p gain | 0 (0%) | 266 |  |  | 1 (1.00) | 0.839 (1.00) |  |  | 0.397 (1.00) | 0.245 (1.00) | 0.239 (1.00) | 0.372 (1.00) | 0.00083 (0.434) | 0.551 (1.00)
4p gain | 0 (0%) | 265 |  |  | 0.0221 (1.00) | 0.309 (1.00) | 0.531 (1.00) | 1 (1.00) | 0.269 (1.00) | 1 (1.00) | 0.483 (1.00) | 0.145 (1.00) | 0.0183 (1.00) | 0.515 (1.00)
9p gain | 0 (0%) | 263 |  |  | 0.0471 (1.00) | 0.298 (1.00) | 0.322 (1.00) | 0.531 (1.00) | 0.333 (1.00) | 0.861 (1.00) | 0.614 (1.00) | 0.34 (1.00) | 0.0728 (1.00) | 0.322 (1.00)
9q gain | 0 (0%) | 260 |  |  | 0.00848 (1.00) | 0.0902 (1.00) | 0.173 (1.00) | 1 (1.00) | 0.0393 (1.00) | 0.355 (1.00) | 0.215 (1.00) | 0.576 (1.00) | 0.0344 (1.00) | 0.341 (1.00)
11p gain | 0 (0%) | 258 |  |  | 0.859 (1.00) | 0.29 (1.00) | 0.11 (1.00) | 0.68 (1.00) | 0.207 (1.00) | 0.0113 (1.00) | 0.336 (1.00) | 0.87 (1.00) | 0.0687 (1.00) | 0.192 (1.00)
11q gain | 0 (0%) | 254 |  |  | 0.303 (1.00) | 0.241 (1.00) | 0.0267 (1.00) | 0.196 (1.00) | 0.318 (1.00) | 0.0498 (1.00) | 0.519 (1.00) | 0.666 (1.00) | 0.155 (1.00) | 0.0491 (1.00)
12p gain | 0 (0%) | 256 |  |  | 0.000763 (0.4) | 0.3 (1.00) | 0.565 (1.00) | 1 (1.00) | 0.0341 (1.00) | 0.0486 (1.00) | 0.247 (1.00) | 0.0839 (1.00) | 0.00257 (1.00) | 0.0441 (1.00)
12q gain | 0 (0%) | 264 |  |  | 0.0979 (1.00) | 1 (1.00) | 0.286 (1.00) | 0.721 (1.00) | 0.166 (1.00) | 0.22 (1.00) | 0.405 (1.00) | 0.146 (1.00) | 0.0181 (1.00) | 0.0519 (1.00)
18p gain | 0 (0%) | 262 |  |  | 0.234 (1.00) | 0.669 (1.00) | 0.0925 (1.00) | 0.771 (1.00) | 0.159 (1.00) | 0.248 (1.00) | 0.516 (1.00) | 0.796 (1.00) | 0.919 (1.00) | 0.681 (1.00)
18q gain | 0 (0%) | 265 |  |  | 0.15 (1.00) | 0.23 (1.00) | 0.053 (1.00) | 1 (1.00) | 0.021 (1.00) | 0.196 (1.00) | 0.667 (1.00) | 0.305 (1.00) | 0.767 (1.00) | 0.515 (1.00)
21q gain | 0 (0%) | 263 |  |  | 0.0808 (1.00) | 0.0789 (1.00) | 0.114 (1.00) | 0.465 (1.00) | 0.119 (1.00) | 0.0954 (1.00) | 0.298 (1.00) | 0.452 (1.00) | 0.188 (1.00) | 0.0761 (1.00)
2p loss | 0 (0%) | 263 |  |  | 0.00518 (1.00) | 1 (1.00) | 0.202 (1.00) | 1 (1.00) | 0.0208 (1.00) | 0.178 (1.00) | 0.62 (1.00) | 0.452 (1.00) | 0.563 (1.00) | 0.864 (1.00)
2q loss | 0 (0%) | 265 |  |  | 0.0522 (1.00) | 0.798 (1.00) | 0.378 (1.00) | 1 (1.00) | 0.331 (1.00) | 0.273 (1.00) | 0.503 (1.00) | 0.708 (1.00) | 0.849 (1.00) | 0.383 (1.00)
5p loss | 0 (0%) | 256 | 1 (1.00) | 0.042 (1.00) | 0.00429 (1.00) | 0.203 (1.00) | 0.611 (1.00) | 1 (1.00) | 0.881 (1.00) | 0.445 (1.00) | 0.35 (1.00) | 0.702 (1.00) | 0.0521 (1.00) | 0.806 (1.00)
5q loss | 0 (0%) | 258 | 0.415 (1.00) | 0.00228 (1.00) | 0.00181 (0.923) | 0.165 (1.00) | 0.0203 (1.00) | 1 (1.00) | 0.177 (1.00) | 0.179 (1.00) | 0.28 (1.00) | 0.405 (1.00) | 0.00128 (0.661) | 0.35 (1.00)
6p loss | 0 (0%) | 259 |  |  | 0.122 (1.00) | 0.00747 (1.00) | 0.096 (1.00) | 0.806 (1.00) | 0.233 (1.00) | 1 (1.00) | 0.452 (1.00) | 0.0877 (1.00) | 0.662 (1.00) | 0.00806 (1.00)
8p loss | 0 (0%) | 263 |  |  | 0.0176 (1.00) | 0.0588 (1.00) | 0.232 (1.00) | 0.465 (1.00) | 0.333 (1.00) | 0.419 (1.00) | 0.614 (1.00) | 0.193 (1.00) | 0.307 (1.00) | 0.0455 (1.00)
8q loss | 0 (0%) | 265 |  |  | 0.15 (1.00) | 0.00404 (1.00) | 0.792 (1.00) | 1 (1.00) | 0.269 (1.00) | 1 (1.00) | 0.483 (1.00) | 0.088 (1.00) | 0.72 (1.00) | 0.0352 (1.00)
9q loss | 0 (0%) | 262 |  |  | 0.0997 (1.00) | 0.032 (1.00) | 0.954 (1.00) | 0.299 (1.00) | 0.508 (1.00) | 0.00883 (1.00) | 0.0343 (1.00) | 0.796 (1.00) | 0.00901 (1.00) | 0.387 (1.00)
11q loss | 0 (0%) | 262 |  |  | 0.0182 (1.00) | 0.328 (1.00) | 0.026 (1.00) | 1 (1.00) | 0.0157 (1.00) | 0.248 (1.00) | 0.344 (1.00) | 0.796 (1.00) | 0.0122 (1.00) | 0.681 (1.00)
12p loss | 0 (0%) | 265 |  |  | 0.338 (1.00) | 0.714 (1.00) | 0.343 (1.00) | 1 (1.00) | 0.557 (1.00) | 0.803 (1.00) | 0.973 (1.00) | 0.221 (1.00) | 0.0144 (1.00) | 0.811 (1.00)
12q loss | 0 (0%) | 258 |  |  | 0.0096 (1.00) | 0.121 (1.00) | 0.364 (1.00) | 0.323 (1.00) | 0.127 (1.00) | 0.354 (1.00) | 0.368 (1.00) | 0.151 (1.00) | 0.233 (1.00) | 0.54 (1.00)
14q loss | 0 (0%) | 241 |  |  | 0.0195 (1.00) | 0.000572 (0.304) | 0.0719 (1.00) | 0.282 (1.00) | 0.0134 (1.00) | 0.11 (1.00) | 0.0035 (1.00) | 0.00522 (1.00) | 0.0492 (1.00) | 0.161 (1.00)
15q loss | 0 (0%) | 253 |  |  | 0.317 (1.00) | 0.000974 (0.505) | 0.513 (1.00) | 0.0371 (1.00) | 0.765 (1.00) | 0.00483 (1.00) | 0.494 (1.00) | 0.916 (1.00) | 0.24 (1.00) | 0.693 (1.00)
16p loss | 0 (0%) | 266 |  |  | 0.0693 (1.00) | 0.626 (1.00) | 0.286 (1.00) | 0.317 (1.00) | 1 (1.00) | 1 (1.00) | 0.573 (1.00) | 0.146 (1.00) | 0.911 (1.00) | 0.124 (1.00)
16q loss | 0 (0%) | 262 |  |  | 0.0406 (1.00) | 0.0277 (1.00) | 0.0694 (1.00) | 0.353 (1.00) | 0.159 (1.00) | 0.248 (1.00) | 0.764 (1.00) | 0.142 (1.00) | 0.28 (1.00) | 0.198 (1.00)
17p loss | 0 (0%) | 265 |  |  | 0.171 (1.00) | 0.125 (1.00) | 0.197 (1.00) | 1 (1.00) | 0.021 (1.00) | 0.196 (1.00) | 0.496 (1.00) | 0.305 (1.00) | 0.209 (1.00) | 0.218 (1.00)
18p loss | 0 (0%) | 248 | 0.344 (1.00) | 0.212 (1.00) | 0.024 (1.00) | 0.0101 (1.00) | 0.664 (1.00) | 0.131 (1.00) | 0.747 (1.00) | 0.367 (1.00) | 0.0744 (1.00) | 0.208 (1.00) | 0.32 (1.00) | 0.116 (1.00)
18q loss | 0 (0%) | 249 | 0.0889 (1.00) | 0.0468 (1.00) | 0.0188 (1.00) | 0.000854 (0.446) | 0.282 (1.00) | 0.234 (1.00) | 0.518 (1.00) | 0.0879 (1.00) | 0.0778 (1.00) | 0.529 (1.00) | 0.255 (1.00) | 0.179 (1.00)
19p loss | 0 (0%) | 262 | 0.615 (1.00) | 0.117 (1.00) | 0.525 (1.00) | 0.135 (1.00) | 1 (1.00) | 0.0683 (1.00) | 0.299 (1.00) | 0.097 (1.00) | 0.101 (1.00) | 0.403 (1.00) | 0.184 (1.00) | 0.681 (1.00)
20p loss | 0 (0%) | 266 |  |  | 0.312 (1.00) | 0.626 (1.00) | 0.792 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.308 (1.00) | 0.641 (1.00) | 0.76 (1.00) | 0.76 (1.00)
21q loss | 0 (0%) | 258 |  |  | 0.0989 (1.00) | 0.674 (1.00) | 0.399 (1.00) | 0.68 (1.00) | 0.437 (1.00) | 0.179 (1.00) | 0.105 (1.00) | 0.00783 (1.00) | 0.347 (1.00) | 0.454 (1.00)
Xq loss | 0 (0%) | 263 |  |  | 0.0471 (1.00) | 0.298 (1.00) | 0.637 (1.00) | 0.353 (1.00) | 0.333 (1.00) | 0.419 (1.00) | 0.182 (1.00) | 0.00209 (1.00) | 0.589 (1.00) | 0.0761 (1.00)

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S1. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
1P GAIN CNV | 8 | 0 | 0
1P GAIN WILD-TYPE | 86 | 78 | 97

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.000349 (Fisher's exact test), Q value = 0.19

Table S2. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
1Q GAIN CNV | 0 | 4 | 6 | 0
1Q GAIN WILD-TYPE | 52 | 53 | 48 | 106

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000322 (Chi-square test), Q value = 0.17

Table S3. Gene #4: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
3Q GAIN CNV | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 0
3Q GAIN WILD-TYPE | 44 | 46 | 35 | 71 | 27 | 31 | 3 | 8

Figure S3. Get High-res Image Gene #4: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.81e-16 (Chi-square test), Q value = 1.1e-13

Table S4. Gene #6: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
6P GAIN CNV | 0 | 1 | 0 | 0 | 0 | 0 | 2 | 0
6P GAIN WILD-TYPE | 44 | 47 | 35 | 71 | 27 | 31 | 2 | 8

Figure S4. Get High-res Image Gene #6: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 4.04e-26 (Fisher's exact test), Q value = 2.5e-23

Table S5. Gene #7: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
7P GAIN CNV | 2 | 41 | 4 | 3
7P GAIN WILD-TYPE | 50 | 16 | 50 | 103

Figure S5. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 8.93e-13 (Fisher's exact test), Q value = 5.5e-10

Table S6. Gene #7: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
7P GAIN CNV | 16 | 27 | 4 | 2
7P GAIN WILD-TYPE | 106 | 15 | 62 | 32

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

'7p gain' versus 'RPPA_CNMF'

P value = 5.46e-05 (Fisher's exact test), Q value = 0.031

Table S7. Gene #7: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
7P GAIN CNV | 9 | 23 | 8 | 5
7P GAIN WILD-TYPE | 43 | 39 | 60 | 69

Figure S7. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00061

Table S8. Gene #7: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
7P GAIN CNV | 33 | 11 | 6
7P GAIN WILD-TYPE | 61 | 67 | 91

Figure S8. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.21e-05 (Fisher's exact test), Q value = 0.035

Table S9. Gene #7: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
7P GAIN CNV | 3 | 40 | 7
7P GAIN WILD-TYPE | 33 | 101 | 85

Figure S9. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.02e-06 (Fisher's exact test), Q value = 6e-04

Table S10. Gene #7: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
7P GAIN CNV | 9 | 33 | 8
7P GAIN WILD-TYPE | 5 | 112 | 101

Figure S10. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.0085

Table S11. Gene #7: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
7P GAIN CNV | 6 | 21 | 8 | 5 | 1 | 8 | 1 | 0
7P GAIN WILD-TYPE | 38 | 27 | 27 | 66 | 26 | 23 | 3 | 8

Figure S11. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.71e-11 (Fisher's exact test), Q value = 2.2e-08

Table S12. Gene #7: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
7P GAIN CNV | 25 | 16 | 9
7P GAIN WILD-TYPE | 17 | 89 | 112

Figure S12. Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2.57e-23 (Fisher's exact test), Q value = 1.6e-20

Table S13. Gene #8: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
7Q GAIN CNV | 5 | 46 | 6 | 11
7Q GAIN WILD-TYPE | 47 | 11 | 48 | 95

Figure S13. Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.54e-11 (Fisher's exact test), Q value = 1.5e-08

Table S14. Gene #8: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
7Q GAIN CNV | 25 | 30 | 9 | 3
7Q GAIN WILD-TYPE | 97 | 12 | 57 | 31

Figure S14. Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.0094

Table S15. Gene #8: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
7Q GAIN CNV | 39 | 17 | 12
7Q GAIN WILD-TYPE | 55 | 61 | 85

Figure S15. Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.12

Table S16. Gene #8: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
7Q GAIN CNV | 6 | 50 | 12
7Q GAIN WILD-TYPE | 30 | 91 | 80

Figure S16. Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000266 (Chi-square test), Q value = 0.14

Table S17. Gene #8: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
7Q GAIN CNV | 7 | 23 | 12 | 9 | 5 | 11 | 1 | 0
7Q GAIN WILD-TYPE | 37 | 25 | 23 | 62 | 22 | 20 | 3 | 8

Figure S17. Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.79e-08 (Fisher's exact test), Q value = 1.1e-05

Table S18. Gene #8: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
7Q GAIN CNV | 27 | 21 | 20
7Q GAIN WILD-TYPE | 15 | 84 | 101

Figure S18. Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.000308 (Fisher's exact test), Q value = 0.17

Table S19. Gene #9: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
8P GAIN CNV | 6 | 4 | 7 | 0
8P GAIN WILD-TYPE | 46 | 53 | 47 | 106

Figure S19. Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.017

Table S20. Gene #10: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
8Q GAIN CNV | 8 | 6 | 8 | 0
8Q GAIN WILD-TYPE | 44 | 51 | 46 | 106

Figure S20. Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.041

Table S21. Gene #13: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
10P GAIN CNV | 12 | 3 | 7 | 2
10P GAIN WILD-TYPE | 40 | 54 | 47 | 104

Figure S21. Get High-res Image Gene #13: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0012

Table S22. Gene #13: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
10P GAIN CNV | 23 | 0 | 0 | 1
10P GAIN WILD-TYPE | 99 | 42 | 66 | 33

Figure S22. Get High-res Image Gene #13: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 7.9e-05

Table S23. Gene #20: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
19P GAIN CNV | 1 | 14 | 1 | 1
19P GAIN WILD-TYPE | 51 | 43 | 53 | 105

Figure S23. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1.82e-08 (Fisher's exact test), Q value = 1.1e-05

Table S24. Gene #20: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
19P GAIN CNV | 4 | 13 | 0 | 0
19P GAIN WILD-TYPE | 118 | 29 | 66 | 34

Figure S24. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.067

Table S25. Gene #20: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
19P GAIN CNV | 14 | 2 | 1
19P GAIN WILD-TYPE | 80 | 76 | 96

Figure S25. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.41e-05 (Fisher's exact test), Q value = 0.047

Table S26. Gene #20: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
19P GAIN CNV | 0 | 17 | 0
19P GAIN WILD-TYPE | 36 | 124 | 92

Figure S26. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.01e-05 (Chi-square test), Q value = 0.028

Table S27. Gene #20: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
19P GAIN CNV | 2 | 11 | 0 | 2 | 0 | 1 | 1 | 0
19P GAIN WILD-TYPE | 42 | 37 | 35 | 69 | 27 | 30 | 3 | 8

Figure S27. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.92e-08 (Fisher's exact test), Q value = 2.3e-05

Table S28. Gene #20: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
19P GAIN CNV | 12 | 4 | 1
19P GAIN WILD-TYPE | 30 | 101 | 120

Figure S28. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0075

Table S29. Gene #21: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
19Q GAIN CNV | 0 | 10 | 1 | 1
19Q GAIN WILD-TYPE | 52 | 47 | 53 | 105

Figure S29. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.0014

Table S30. Gene #21: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
19Q GAIN CNV | 2 | 9 | 0 | 0
19Q GAIN WILD-TYPE | 120 | 33 | 66 | 34

Figure S30. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.68e-05 (Chi-square test), Q value = 0.0095

Table S31. Gene #21: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
19Q GAIN CNV | 0 | 9 | 0 | 2 | 0 | 0 | 1 | 0
19Q GAIN WILD-TYPE | 44 | 39 | 35 | 69 | 27 | 31 | 3 | 8

Figure S31. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.44e-06 (Fisher's exact test), Q value = 0.0014

Table S32. Gene #21: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
19Q GAIN CNV | 9 | 2 | 1
19Q GAIN WILD-TYPE | 33 | 103 | 120

Figure S32. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 6.77e-07 (Fisher's exact test), Q value = 4e-04

Table S33. Gene #22: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
20P GAIN CNV | 2 | 13 | 5 | 0
20P GAIN WILD-TYPE | 50 | 44 | 49 | 106

Figure S33. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 5.31e-08 (Fisher's exact test), Q value = 3.2e-05

Table S34. Gene #22: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
20P GAIN CNV | 3 | 14 | 1 | 2
20P GAIN WILD-TYPE | 119 | 28 | 65 | 32

Figure S34. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.42e-06 (Chi-square test), Q value = 0.0043

Table S35. Gene #22: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
20P GAIN CNV | 0 | 11 | 0 | 3 | 1 | 3 | 2 | 0
20P GAIN WILD-TYPE | 44 | 37 | 35 | 68 | 26 | 28 | 2 | 8

Figure S35. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-07 (Fisher's exact test), Q value = 7.2e-05

Table S36. Gene #22: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
20P GAIN CNV | 13 | 5 | 2
20P GAIN WILD-TYPE | 29 | 100 | 119

Figure S36. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 6.77e-07 (Fisher's exact test), Q value = 4e-04

Table S37. Gene #23: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
20Q GAIN CNV | 2 | 13 | 5 | 0
20Q GAIN WILD-TYPE | 50 | 44 | 49 | 106

Figure S37. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 6.38e-08 (Fisher's exact test), Q value = 3.8e-05

Table S38. Gene #23: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
20Q GAIN CNV | 5 | 14 | 1 | 0
20Q GAIN WILD-TYPE | 117 | 28 | 65 | 34

Figure S38. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.068

Table S39. Gene #23: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
20Q GAIN CNV | 4 | 11 | 2 | 0
20Q GAIN WILD-TYPE | 48 | 51 | 66 | 74

Figure S39. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0038

Table S40. Gene #23: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
20Q GAIN CNV | 17 | 1 | 2
20Q GAIN WILD-TYPE | 77 | 77 | 95

Figure S40. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.095

Table S41. Gene #23: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
20Q GAIN CNV | 5 | 13 | 2
20Q GAIN WILD-TYPE | 9 | 132 | 107

Figure S41. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.25e-07 (Chi-square test), Q value = 0.00037

Table S42. Gene #23: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
20Q GAIN CNV | 1 | 12 | 0 | 1 | 1 | 3 | 2 | 0
20Q GAIN WILD-TYPE | 43 | 36 | 35 | 70 | 26 | 28 | 2 | 8

Figure S42. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.86e-09 (Fisher's exact test), Q value = 1.1e-06

Table S43. Gene #23: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
20Q GAIN CNV | 13 | 7 | 0
20Q GAIN WILD-TYPE | 29 | 98 | 121

Figure S43. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.75e-06 (Fisher's exact test), Q value = 0.005

Table S44. Gene #25: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 7 | 6 | 10 | 4
1P LOSS CNV | 7 | 2 | 0 | 0
1P LOSS WILD-TYPE | 0 | 4 | 10 | 4

Figure S44. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.82e-25 (Fisher's exact test), Q value = 1.1e-22

Table S45. Gene #25: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
1P LOSS CNV | 0 | 0 | 12 | 65
1P LOSS WILD-TYPE | 52 | 57 | 42 | 41

Figure S45. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.62e-58 (Fisher's exact test), Q value = 2.9e-55

Table S46. Gene #25: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
1P LOSS CNV | 1 | 0 | 66 | 7
1P LOSS WILD-TYPE | 121 | 42 | 0 | 27

Figure S46. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 7.62e-05 (Fisher's exact test), Q value = 0.042

Table S47. Gene #25: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
1P LOSS CNV | 8 | 10 | 25 | 34
1P LOSS WILD-TYPE | 44 | 52 | 43 | 40

Figure S47. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.99e-14 (Fisher's exact test), Q value = 1.2e-11

Table S48. Gene #25: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
1P LOSS CNV | 2 | 31 | 44
1P LOSS WILD-TYPE | 92 | 47 | 53

Figure S48. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-35 (Fisher's exact test), Q value = 7.8e-33

Table S49. Gene #25: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
1P LOSS CNV | 36 | 4 | 37
1P LOSS WILD-TYPE | 0 | 137 | 55

Figure S49. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 3.34e-11 (Chi-square test), Q value = 2e-08

Table S50. Gene #25: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
1P LOSS CNV | 6 | 1 | 38 | 12 | 20
1P LOSS WILD-TYPE | 56 | 47 | 51 | 4 | 33

Figure S50. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.75e-08 (Fisher's exact test), Q value = 5.2e-05

Table S51. Gene #25: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
1P LOSS CNV | 0 | 26 | 51
1P LOSS WILD-TYPE | 14 | 119 | 58

Figure S51. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.89e-13 (Chi-square test), Q value = 1.2e-10

Table S52. Gene #25: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
1P LOSS CNV | 0 | 3 | 7 | 31 | 21 | 11 | 0 | 4
1P LOSS WILD-TYPE | 44 | 45 | 28 | 40 | 6 | 20 | 4 | 4

Figure S52. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.1e-10 (Fisher's exact test), Q value = 1.9e-07

Table S53. Gene #25: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
1P LOSS CNV | 1 | 19 | 57
1P LOSS WILD-TYPE | 41 | 86 | 64

Figure S53. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.094

Table S54. Gene #26: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
1Q LOSS CNV | 1 | 0 | 9 | 0
1Q LOSS WILD-TYPE | 121 | 42 | 57 | 34

Figure S54. Get High-res Image Gene #26: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S55. Gene #26: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
1Q LOSS CNV | 5 | 0 | 5
1Q LOSS WILD-TYPE | 31 | 141 | 87

Figure S55. Get High-res Image Gene #26: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.16

Table S56. Gene #29: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
3P LOSS CNV | 9 | 1 | 0
3P LOSS WILD-TYPE | 85 | 77 | 97

Figure S56. Get High-res Image Gene #29: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 5.87e-06 (Fisher's exact test), Q value = 0.0034

Table S57. Gene #30: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
3Q LOSS CNV | 8 | 0 | 5 | 0
3Q LOSS WILD-TYPE | 44 | 57 | 49 | 106

Figure S57. Get High-res Image Gene #30: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 6e-04

Table S58. Gene #31: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
4P LOSS CNV | 3 | 0 | 15 | 0
4P LOSS WILD-TYPE | 119 | 42 | 51 | 34

Figure S58. Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000408 (Fisher's exact test), Q value = 0.22

Table S59. Gene #31: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
4P LOSS CNV | 0 | 10 | 8
4P LOSS WILD-TYPE | 94 | 68 | 89

Figure S59. Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.96e-06 (Fisher's exact test), Q value = 0.0017

Table S60. Gene #31: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
4P LOSS CNV | 10 | 2 | 6
4P LOSS WILD-TYPE | 26 | 139 | 86

Figure S60. Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.000452 (Chi-square test), Q value = 0.24

Table S61. Gene #31: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
4P LOSS CNV | 1 | 1 | 6 | 5 | 5
4P LOSS WILD-TYPE | 61 | 47 | 83 | 11 | 48

Figure S61. Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 9.78e-06 (Fisher's exact test), Q value = 0.0056

Table S62. Gene #32: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
4Q LOSS CNV | 9 | 0 | 18 | 1
4Q LOSS WILD-TYPE | 113 | 42 | 48 | 33

Figure S62. Get High-res Image Gene #32: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.000283 (Fisher's exact test), Q value = 0.15

Table S63. Gene #32: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
4Q LOSS CNV | 2 | 16 | 10
4Q LOSS WILD-TYPE | 92 | 62 | 87

Figure S63. Get High-res Image Gene #32: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-05 (Fisher's exact test), Q value = 0.035

Table S64. Gene #32: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
4Q LOSS CNV | 12 | 8 | 8
4Q LOSS WILD-TYPE | 24 | 133 | 84

Figure S64. Get High-res Image Gene #32: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.087

Table S65. Gene #36: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
6Q LOSS CNV | 3 | 9 | 15 | 5
6Q LOSS WILD-TYPE | 49 | 48 | 39 | 101

Figure S65. Get High-res Image Gene #36: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.0052

Table S66. Gene #39: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
9P LOSS CNV | 5 | 18 | 18 | 8
9P LOSS WILD-TYPE | 47 | 39 | 36 | 98

Figure S66. Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 8.8e-13

Table S67. Gene #41: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
10P LOSS CNV | 1 | 28 | 5 | 2
10P LOSS WILD-TYPE | 51 | 29 | 49 | 104

Figure S67. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 4.74e-27 (Fisher's exact test), Q value = 3e-24

Table S68. Gene #41: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
10P LOSS CNV | 1 | 31 | 3 | 0
10P LOSS WILD-TYPE | 121 | 11 | 63 | 34

Figure S68. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 3.9e-07 (Fisher's exact test), Q value = 0.00023

Table S69. Gene #41: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
10P LOSS CNV | 4 | 21 | 3 | 3
10P LOSS WILD-TYPE | 48 | 41 | 65 | 71

Figure S69. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 2.38e-11 (Fisher's exact test), Q value = 1.5e-08

Table S70. Gene #41: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
10P LOSS CNV | 31 | 1 | 4
10P LOSS WILD-TYPE | 63 | 77 | 93

Figure S70. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.53e-05 (Fisher's exact test), Q value = 0.026

Table S71. Gene #41: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
10P LOSS CNV | 1 | 31 | 4
10P LOSS WILD-TYPE | 35 | 110 | 88

Figure S71. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034

Table S72. Gene #41: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
10P LOSS CNV | 8 | 24 | 4
10P LOSS WILD-TYPE | 6 | 121 | 105

Figure S72. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.19e-13 (Chi-square test), Q value = 1.3e-10

Table S73. Gene #41: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
10P LOSS CNV | 0 | 24 | 1 | 4 | 1 | 6 | 0 | 0
10P LOSS WILD-TYPE | 44 | 24 | 34 | 67 | 26 | 25 | 4 | 8

Figure S73. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.44e-13 (Fisher's exact test), Q value = 8.9e-11

Table S74. Gene #41: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
10P LOSS CNV | 23 | 9 | 4
10P LOSS WILD-TYPE | 19 | 96 | 117

Figure S74. Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1.2e-14 (Fisher's exact test), Q value = 7.4e-12

Table S75. Gene #42: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
10Q LOSS CNV | 2 | 28 | 6 | 2
10Q LOSS WILD-TYPE | 50 | 29 | 48 | 104

Figure S75. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 7.62e-25 (Fisher's exact test), Q value = 4.8e-22

Table S76. Gene #42: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
10Q LOSS CNV | 3 | 31 | 3 | 0
10Q LOSS WILD-TYPE | 119 | 11 | 63 | 34

Figure S76. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.001

Table S77. Gene #42: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
10Q LOSS CNV | 5 | 21 | 4 | 3
10Q LOSS WILD-TYPE | 47 | 41 | 64 | 71

Figure S77. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.44e-11 (Fisher's exact test), Q value = 1.5e-08

Table S78. Gene #42: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
10Q LOSS CNV | 32 | 1 | 5
10Q LOSS WILD-TYPE | 62 | 77 | 92

Figure S78. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.54e-05 (Fisher's exact test), Q value = 0.042

Table S79. Gene #42: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
10Q LOSS CNV | 1 | 32 | 5
10Q LOSS WILD-TYPE | 35 | 109 | 87

Figure S79. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.13e-07 (Fisher's exact test), Q value = 0.00013

Table S80. Gene #42: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
10Q LOSS CNV | 9 | 24 | 5
10Q LOSS WILD-TYPE | 5 | 121 | 104

Figure S80. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.11e-12 (Chi-square test), Q value = 1.3e-09

Table S81. Gene #42: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
10Q LOSS CNV | 0 | 24 | 1 | 4 | 2 | 6 | 1 | 0
10Q LOSS WILD-TYPE | 44 | 24 | 34 | 67 | 25 | 25 | 3 | 8

Figure S81. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.12e-14 (Fisher's exact test), Q value = 4.4e-11

Table S82. Gene #42: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
10Q LOSS CNV | 24 | 9 | 5
10Q LOSS WILD-TYPE | 18 | 96 | 116

Figure S82. Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2.14e-08 (Fisher's exact test), Q value = 1.3e-05

Table S83. Gene #43: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
11P LOSS CNV | 12 | 2 | 11 | 0
11P LOSS WILD-TYPE | 40 | 55 | 43 | 106

Figure S83. Get High-res Image Gene #43: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.12

Table S84. Gene #43: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
11P LOSS CNV | 21 | 2 | 0 | 2
11P LOSS WILD-TYPE | 101 | 40 | 66 | 32

Figure S84. Get High-res Image Gene #43: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000168 (Chi-square test), Q value = 0.092

Table S85. Gene #43: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
11P LOSS CNV | 3 | 8 | 4 | 5 | 0 | 1 | 3 | 1
11P LOSS WILD-TYPE | 41 | 40 | 31 | 66 | 27 | 30 | 1 | 7

Figure S85. Get High-res Image Gene #43: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 6.34e-19 (Fisher's exact test), Q value = 3.9e-16

Table S86. Gene #47: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
13Q LOSS CNV | 3 | 1 | 27 | 0
13Q LOSS WILD-TYPE | 49 | 56 | 27 | 106

Figure S86. Get High-res Image Gene #47: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 2.7e-23 (Fisher's exact test), Q value = 1.7e-20

Table S87. Gene #56: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
19Q LOSS CNV | 1 | 0 | 20 | 64
19Q LOSS WILD-TYPE | 51 | 57 | 34 | 42

Figure S87. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.12e-43 (Fisher's exact test), Q value = 7e-41

Table S88. Gene #56: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
19Q LOSS CNV | 7 | 2 | 64 | 9
19Q LOSS WILD-TYPE | 115 | 40 | 2 | 25

Figure S88. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.000312 (Fisher's exact test), Q value = 0.17

Table S89. Gene #56: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
19Q LOSS CNV | 8 | 16 | 24 | 37
19Q LOSS WILD-TYPE | 44 | 46 | 44 | 37

Figure S89. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1.1e-12 (Fisher's exact test), Q value = 6.7e-10

Table S90. Gene #56: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
19Q LOSS CNV | 5 | 33 | 47
19Q LOSS WILD-TYPE | 89 | 45 | 50

Figure S90. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-29 (Fisher's exact test), Q value = 8.6e-27

Table S91. Gene #56: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
19Q LOSS CNV | 35 | 9 | 41
19Q LOSS WILD-TYPE | 1 | 132 | 51

Figure S91. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1.54e-07 (Chi-square test), Q value = 9.1e-05

Table S92. Gene #56: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
19Q LOSS CNV | 8 | 6 | 41 | 11 | 19
19Q LOSS WILD-TYPE | 54 | 42 | 48 | 5 | 34

Figure S92. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.36e-07 (Fisher's exact test), Q value = 0.00037

Table S93. Gene #56: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
19Q LOSS CNV | 1 | 30 | 54
19Q LOSS WILD-TYPE | 13 | 115 | 55

Figure S93. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.28e-10 (Chi-square test), Q value = 3.8e-07

Table S94. Gene #56: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
19Q LOSS CNV | 2 | 6 | 9 | 34 | 20 | 11 | 0 | 3
19Q LOSS WILD-TYPE | 42 | 42 | 26 | 37 | 7 | 20 | 4 | 5

Figure S94. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.46e-08 (Fisher's exact test), Q value = 2.1e-05

Table S95. Gene #56: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
19Q LOSS CNV | 3 | 23 | 59
19Q LOSS WILD-TYPE | 39 | 82 | 62

Figure S95. Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.011

Table S96. Gene #59: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
22Q LOSS CNV | 3 | 8 | 9 | 0
22Q LOSS WILD-TYPE | 49 | 49 | 45 | 106

Figure S96. Get High-res Image Gene #59: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.38e-05 (Fisher's exact test), Q value = 0.013

Table S97. Gene #59: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
22Q LOSS CNV | 7 | 11 | 0 | 2
22Q LOSS WILD-TYPE | 115 | 31 | 66 | 32

Figure S97. Get High-res Image Gene #59: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 7.62e-05 (Fisher's exact test), Q value = 0.042

Table S98. Gene #59: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
22Q LOSS CNV | 2 | 14 | 2 | 2
22Q LOSS WILD-TYPE | 50 | 48 | 66 | 72

Figure S98. Get High-res Image Gene #59: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

Methods & Data
Input

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

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

- Number of patients = 269

- Number of significantly arm-level cnvs = 60

- Number of molecular subtypes = 12

- 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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