Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
13 July 2018 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

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

Summary

Testing the association between copy number variation 51 arm-level events and 10 molecular subtypes across 80 patients, 118 significant findings detected with P value < 0.05 and Q value < 0.25.

- 4p gain cnv correlated to 'CN_CNMF'.

- 4q gain cnv correlated to 'CN_THRESHOLDED_CNMF'.

- 6p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 6q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 8p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 8q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 11q gain cnv correlated to 'MIR_MATURE_CHIERARCHICAL'.

- 12p gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 12q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 13q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 14q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 17p gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 20p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 20q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', and 'CN_CNMF'.

- 21q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', and 'CN_CNMF'.

- 22q gain cnv correlated to 'LINCRNA_CNMF'.

- xp gain cnv correlated to 'MIR_MATURE_CNMF' and 'METHYLATION_CNMF'.

- xq gain cnv correlated to 'MIR_MATURE_CNMF' and 'METHYLATION_CNMF'.

- 1p loss cnv correlated to 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', and 'CN_THRESHOLDED_CNMF'.

- 1q loss cnv correlated to 'MIR_MATURE_CHIERARCHICAL'.

- 3p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 3q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 6q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 8p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', and 'METHYLATION_CNMF'.

- 9p loss cnv correlated to 'MRNA_CNMF' and 'CN_THRESHOLDED_CNMF'.

- 9q loss cnv correlated to 'MRNA_CNMF'.

- 15q loss cnv correlated to 'CN_CNMF' and 'CN_THRESHOLDED_CNMF'.

- 16q loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CNMF'.

- 19p loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 19q loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- xp loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- xq loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 118 significant findings detected.

|  | Clinical Features | MRNA CNMF | MRNA CHIERARCHICAL | LINCRNA CNMF | LINCRNA CHIERARCHICAL | MIR MATURE CNMF | MIR MATURE CHIERARCHICAL | CN CNMF | CN THRESHOLDED CNMF | METHYLATION CNMF | METHYLATION CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
6p gain | 40 (50%) | 40 | 0.00864 (0.0572) | 0.00015 (0.00174) | 0.0009 (0.00883) | 5e-05 (0.000671) | 1e-05 (0.000165) | 1e-05 (0.000165) | 2e-05 (0.000309) | 3e-05 (0.000437) | 0.00094 (0.00905) | 1e-05 (0.000165)
8q gain | 54 (68%) | 26 | 0.00541 (0.0411) | 4e-05 (0.000567) | 2e-05 (0.000309) | 1e-05 (0.000165) | 8e-05 (0.000995) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 3e-05 (0.000437) | 1e-05 (0.000165)
3p loss | 42 (52%) | 38 | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165)
3q loss | 44 (55%) | 36 | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165) | 1e-05 (0.000165)
6q gain | 20 (25%) | 60 | 0.136 (0.372) | 0.00057 (0.00593) | 0.00701 (0.049) | 7e-05 (0.000892) | 0.00022 (0.00244) | 5e-05 (0.000671) | 0.00019 (0.00215) | 0.00026 (0.00282) | 0.0032 (0.0268) | 9e-05 (0.00109)
6q loss | 14 (18%) | 66 | 0.0659 (0.258) | 0.00043 (0.00457) | 0.0322 (0.156) | 0.00226 (0.0199) | 0.00065 (0.00663) | 0.075 (0.275) | 6e-05 (0.000785) | 1e-05 (0.000165) | 0.00013 (0.00154) | 0.0122 (0.0767)
xq loss | 12 (15%) | 68 | 0.0212 (0.119) | 0.00259 (0.0224) | 0.00104 (0.00982) | 0.0829 (0.292) | 0.0975 (0.325) | 0.0268 (0.135) | 0.0356 (0.166) | 0.0259 (0.134) | 0.00202 (0.0184) | 0.0183 (0.11)
8p gain | 32 (40%) | 48 | 0.0708 (0.264) | 0.0028 (0.0238) | 0.0987 (0.325) | 0.0246 (0.134) | 0.257 (0.531) | 0.0412 (0.181) | 0.00381 (0.0308) | 0.0757 (0.276) | 0.0268 (0.135) | 0.0235 (0.13)
8p loss | 7 (9%) | 73 | 0.161 (0.413) | 0.00594 (0.0433) | 0.0583 (0.244) | 0.0287 (0.142) | 0.0173 (0.105) | 0.112 (0.348) | 0.0153 (0.0942) | 0.00223 (0.0199) | 0.0469 (0.203) | 0.172 (0.431)
xp loss | 11 (14%) | 69 | 0.0347 (0.164) | 0.008 (0.0537) | 0.00434 (0.0335) | 0.0922 (0.316) | 0.205 (0.48) | 0.0788 (0.283) | 0.0788 (0.283) | 0.058 (0.244) | 0.00763 (0.0519) | 0.0261 (0.134)
20q gain | 9 (11%) | 71 | 0.366 (0.617) | 0.00401 (0.0315) | 0.124 (0.366) | 0.0201 (0.115) | 0.976 (1.00) | 0.489 (0.695) | 0.0251 (0.134) | 0.354 (0.608) | 0.678 (0.822) | 0.511 (0.715)
21q gain | 14 (18%) | 66 | 0.106 (0.337) | 0.00548 (0.0411) | 0.105 (0.337) | 0.0039 (0.0311) | 0.0986 (0.325) | 0.656 (0.815) | 0.0389 (0.176) | 0.495 (0.699) | 0.267 (0.531) | 0.427 (0.662)
1p loss | 18 (22%) | 62 | 0.109 (0.343) | 0.101 (0.329) | 0.417 (0.652) | 0.321 (0.583) | 0.962 (1.00) | 0.0143 (0.0892) | 0.00074 (0.0074) | 1e-05 (0.000165) | 0.068 (0.262) | 0.351 (0.608)
20p gain | 8 (10%) | 72 | 0.703 (0.839) | 0.00579 (0.0428) | 0.0874 (0.303) | 0.041 (0.181) | 1 (1.00) | 0.351 (0.608) | 0.0615 (0.252) | 0.402 (0.632) | 0.338 (0.595) | 0.38 (0.63)
xp gain | 10 (12%) | 70 | 0.896 (0.95) | 0.321 (0.583) | 0.652 (0.815) | 0.402 (0.632) | 0.00923 (0.0603) | 0.453 (0.677) | 0.687 (0.828) | 0.877 (0.95) | 0.00611 (0.0439) | 0.601 (0.786)
xq gain | 9 (11%) | 71 | 0.959 (1.00) | 0.4 (0.632) | 0.397 (0.632) | 0.115 (0.352) | 0.0019 (0.0176) | 0.132 (0.368) | 0.714 (0.848) | 0.794 (0.9) | 0.0251 (0.134) | 0.458 (0.679)
9p loss | 8 (10%) | 72 | 0.026 (0.134) | 0.34 (0.595) | 0.212 (0.481) | 0.0829 (0.292) | 0.194 (0.461) | 0.337 (0.595) | 0.0709 (0.264) | 0.0406 (0.181) | 0.149 (0.392) | 0.1 (0.328)
15q loss | 5 (6%) | 75 | 0.457 (0.679) | 0.481 (0.687) | 0.2 (0.472) | 0.667 (0.815) | 0.215 (0.482) | 1 (1.00) | 0.0322 (0.156) | 0.00762 (0.0519) | 0.656 (0.815) | 0.482 (0.687)
16q loss | 16 (20%) | 64 | 0.128 (0.366) | 0.0902 (0.311) | 0.563 (0.757) | 0.353 (0.608) | 0.238 (0.513) | 0.387 (0.632) | 0.212 (0.481) | 1e-05 (0.000165) | 0.0383 (0.176) | 0.3 (0.56)
19p loss | 3 (4%) | 77 | 0.897 (0.95) | 0.13 (0.366) | 0.818 (0.913) | 0.784 (0.893) | 0.81 (0.91) | 0.129 (0.366) | 0.327 (0.584) | 0.0104 (0.0664) | 0.0652 (0.258) | 0.0335 (0.161)
19q loss | 3 (4%) | 77 | 0.897 (0.95) | 0.128 (0.366) | 0.819 (0.913) | 0.784 (0.893) | 0.809 (0.91) | 0.127 (0.366) | 0.324 (0.584) | 0.0101 (0.0651) | 0.0668 (0.26) | 0.0342 (0.163)
4p gain | 8 (10%) | 72 | 0.113 (0.35) | 0.125 (0.366) | 0.421 (0.656) | 0.375 (0.623) | 0.19 (0.46) | 0.308 (0.568) | 0.0386 (0.176) | 0.0866 (0.302) | 0.129 (0.366) | 0.428 (0.662)
4q gain | 5 (6%) | 75 | 0.0683 (0.262) | 0.482 (0.687) | 0.606 (0.786) | 0.666 (0.815) | 0.469 (0.683) | 0.644 (0.814) | 0.11 (0.343) | 0.00667 (0.0472) | 0.175 (0.437) | 0.262 (0.531)
11q gain | 9 (11%) | 71 | 0.822 (0.913) | 0.448 (0.672) | 0.32 (0.583) | 0.121 (0.365) | 0.248 (0.523) | 0.0419 (0.183) | 0.564 (0.757) | 0.691 (0.829) | 0.678 (0.822) | 0.457 (0.679)
12p gain | 3 (4%) | 77 | 0.271 (0.531) | 0.0713 (0.264) | 0.903 (0.95) | 0.0194 (0.113) | 0.398 (0.632) | 0.54 (0.741) | 0.21 (0.481) | 0.439 (0.664) | 0.267 (0.531) | 0.292 (0.553)
12q gain | 3 (4%) | 77 | 0.271 (0.531) | 0.0714 (0.264) | 0.902 (0.95) | 0.0204 (0.116) | 0.399 (0.632) | 0.538 (0.741) | 0.209 (0.481) | 0.435 (0.664) | 0.267 (0.531) | 0.293 (0.553)
13q gain | 6 (8%) | 74 | 0.736 (0.863) | 0.0251 (0.134) | 0.212 (0.481) | 0.353 (0.608) | 0.383 (0.63) | 0.383 (0.63) | 0.567 (0.757) | 0.154 (0.406) | 0.645 (0.814) | 0.648 (0.814)
14q gain | 3 (4%) | 77 | 0.272 (0.531) | 0.0698 (0.264) | 0.902 (0.95) | 0.0189 (0.112) | 0.67 (0.817) | 0.844 (0.928) | 0.0515 (0.219) | 0.0651 (0.258) | 1 (1.00) | 1 (1.00)
17p gain | 9 (11%) | 71 | 0.147 (0.39) | 0.187 (0.458) | 0.307 (0.567) | 0.0195 (0.113) | 0.805 (0.91) | 0.446 (0.671) | 0.208 (0.481) | 0.237 (0.512) | 0.291 (0.553) | 0.716 (0.848)
22q gain | 6 (8%) | 74 | 0.227 (0.496) | 0.365 (0.616) | 0.0366 (0.17) | 0.136 (0.372) | 0.883 (0.95) | 0.283 (0.547) | 0.564 (0.757) | 0.0617 (0.252) | 0.245 (0.518) | 0.469 (0.683)
1q loss | 4 (5%) | 76 | 0.0958 (0.325) | 0.131 (0.366) | 0.195 (0.461) | 0.217 (0.482) | 0.263 (0.531) | 0.0282 (0.141) | 0.26 (0.531) | 0.159 (0.413) | 0.384 (0.63) | 0.181 (0.446)
9q loss | 7 (9%) | 73 | 0.00365 (0.03) | 0.161 (0.413) | 0.481 (0.687) | 0.232 (0.505) | 0.354 (0.608) | 0.512 (0.716) | 0.243 (0.518) | 0.0633 (0.256) | 0.0657 (0.258) | 0.118 (0.357)
1q gain | 10 (12%) | 70 | 0.895 (0.95) | 0.825 (0.914) | 0.688 (0.828) | 0.555 (0.753) | 0.294 (0.553) | 0.117 (0.357) | 0.18 (0.446) | 0.37 (0.62) | 0.322 (0.583) | 0.437 (0.664)
2p gain | 10 (12%) | 70 | 0.747 (0.866) | 0.554 (0.753) | 0.281 (0.546) | 0.541 (0.741) | 0.932 (0.976) | 0.178 (0.442) | 0.289 (0.553) | 0.827 (0.915) | 0.168 (0.427) | 0.191 (0.461)
2q gain | 8 (10%) | 72 | 0.595 (0.785) | 0.251 (0.527) | 0.129 (0.366) | 0.279 (0.544) | 0.609 (0.786) | 0.0804 (0.287) | 0.503 (0.707) | 0.648 (0.814) | 0.11 (0.343) | 0.134 (0.37)
5p gain | 4 (5%) | 76 | 0.604 (0.786) | 0.757 (0.873) | 0.533 (0.74) | 0.468 (0.683) | 0.217 (0.482) | 0.812 (0.91) | 0.473 (0.686) | 0.721 (0.851) | 0.26 (0.531) | 0.396 (0.632)
5q gain | 4 (5%) | 76 | 0.605 (0.786) | 0.759 (0.873) | 0.534 (0.74) | 0.468 (0.683) | 0.219 (0.483) | 0.811 (0.91) | 0.473 (0.686) | 0.724 (0.851) | 0.26 (0.531) | 0.399 (0.632)
7p gain | 8 (10%) | 72 | 0.215 (0.482) | 0.193 (0.461) | 0.16 (0.413) | 0.445 (0.671) | 0.743 (0.866) | 0.912 (0.957) | 0.869 (0.95) | 0.357 (0.609) | 0.561 (0.757) | 0.543 (0.743)
7q gain | 7 (9%) | 73 | 0.428 (0.662) | 0.0972 (0.325) | 0.295 (0.553) | 0.315 (0.578) | 0.717 (0.848) | 0.634 (0.804) | 0.665 (0.815) | 0.207 (0.481) | 0.159 (0.413) | 0.139 (0.379)
9p gain | 4 (5%) | 76 | 0.883 (0.95) | 0.63 (0.801) | 0.476 (0.687) | 0.362 (0.613) | 0.233 (0.505) | 1 (1.00) | 0.397 (0.632) | 0.962 (1.00) | 0.205 (0.48) | 0.656 (0.815)
9q gain | 3 (4%) | 77 | 0.6 (0.786) | 0.774 (0.887) | 0.104 (0.335) | 0.621 (0.797) | 0.188 (0.46) | 0.842 (0.928) | 0.659 (0.815) | 0.888 (0.95) | 0.375 (0.623) | 0.579 (0.768)
11p gain | 9 (11%) | 71 | 0.745 (0.866) | 0.704 (0.839) | 0.36 (0.612) | 0.194 (0.461) | 0.141 (0.383) | 0.406 (0.637) | 0.588 (0.777) | 0.687 (0.828) | 0.492 (0.698) | 0.902 (0.95)
16p gain | 3 (4%) | 77 | 0.215 (0.482) | 1 (1.00) | 0.615 (0.793) | 1 (1.00) | 1 (1.00) | 0.464 (0.683) | 1 (1.00) | 0.126 (0.366) | 0.271 (0.531) | 0.435 (0.664)
17q gain | 10 (12%) | 70 | 0.327 (0.584) | 0.142 (0.383) | 0.371 (0.621) | 0.0609 (0.252) | 0.624 (0.797) | 0.244 (0.518) | 0.259 (0.531) | 0.223 (0.491) | 0.169 (0.427) | 0.439 (0.664)
4q loss | 3 (4%) | 77 | 0.897 (0.95) | 0.388 (0.632) | 1 (1.00) | 0.702 (0.839) | 0.671 (0.817) | 0.498 (0.701) | 1 (1.00) | 0.125 (0.366) | 0.877 (0.95) | 1 (1.00)
5q loss | 3 (4%) | 77 | 0.894 (0.95) | 1 (1.00) | 0.567 (0.757) | 0.785 (0.893) | 0.609 (0.786) | 0.467 (0.683) | 0.325 (0.584) | 0.889 (0.95) | 0.147 (0.39) | 0.762 (0.875)
11p loss | 3 (4%) | 77 | 0.302 (0.56) | 0.33 (0.585) | 0.744 (0.866) | 0.265 (0.531) | 0.164 (0.419) | 0.724 (0.851) | 0.0507 (0.217) | 0.54 (0.741) | 0.579 (0.768) | 0.293 (0.553)
12p loss | 3 (4%) | 77 | 1 (1.00) | 1 (1.00) | 0.82 (0.913) | 0.787 (0.894) | 0.257 (0.531) | 0.292 (0.553) | 0.663 (0.815) | 0.89 (0.95) | 0.667 (0.815) | 0.577 (0.768)
13q loss | 3 (4%) | 77 | 0.0971 (0.325) | 1 (1.00) | 0.743 (0.866) | 0.482 (0.687) | 0.355 (0.608) | 0.623 (0.797) | 1 (1.00) | 0.126 (0.366) | 0.269 (0.531) | 0.435 (0.664)
16p loss | 7 (9%) | 73 | 0.391 (0.632) | 0.24 (0.514) | 0.625 (0.797) | 0.33 (0.585) | 0.752 (0.87) | 0.857 (0.94) | 0.843 (0.928) | 0.26 (0.531) | 0.608 (0.786) | 0.87 (0.95)
17p loss | 3 (4%) | 77 | 0.302 (0.56) | 0.389 (0.632) | 0.515 (0.718) | 1 (1.00) | 0.55 (0.749) | 0.146 (0.39) | 1 (1.00) | 0.661 (0.815) | 0.874 (0.95) | 0.435 (0.664)

'4p gain' versus 'CN_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.18

Table S1. Gene #4: '4p gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
4P GAIN MUTATED | 0 | 6 | 2 | 0 | 0
4P GAIN WILD-TYPE | 18 | 15 | 35 | 2 | 2

Figure S1. Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #7: 'CN_CNMF'

'4q gain' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.047

Table S2. Gene #5: '4q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
4Q GAIN MUTATED | 0 | 3 | 0 | 1 | 0 | 0 | 1 | 0
4Q GAIN WILD-TYPE | 16 | 4 | 22 | 11 | 2 | 14 | 4 | 2

Figure S2. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.057

Table S3. Gene #8: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
6P GAIN MUTATED | 4 | 3 | 22 | 9 | 2
6P GAIN WILD-TYPE | 7 | 8 | 7 | 12 | 6

Figure S3. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0017

Table S4. Gene #8: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
6P GAIN MUTATED | 5 | 8 | 22 | 5
6P GAIN WILD-TYPE | 10 | 7 | 5 | 18

Figure S4. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'LINCRNA_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0088

Table S5. Gene #8: '6p gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
6P GAIN MUTATED | 5 | 3 | 13 | 4 | 15
6P GAIN WILD-TYPE | 13 | 4 | 15 | 7 | 1

Figure S5. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'6p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S6. Gene #8: '6p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
6P GAIN MUTATED | 4 | 17 | 6 | 13
6P GAIN WILD-TYPE | 17 | 7 | 14 | 2

Figure S6. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'6p gain' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S7. Gene #8: '6p gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
6P GAIN MUTATED | 1 | 8 | 7 | 22 | 2
6P GAIN WILD-TYPE | 12 | 13 | 11 | 2 | 2

Figure S7. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'6p gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S8. Gene #8: '6p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
6P GAIN MUTATED | 2 | 7 | 4 | 16 | 11
6P GAIN WILD-TYPE | 19 | 13 | 4 | 1 | 3

Figure S8. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S9. Gene #8: '6p gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
6P GAIN MUTATED | 4 | 7 | 29 | 0 | 0
6P GAIN WILD-TYPE | 14 | 14 | 8 | 2 | 2

Figure S9. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'CN_CNMF'

'6p gain' versus 'CN_THRESHOLDED_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S10. Gene #8: '6p gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
6P GAIN MUTATED | 3 | 2 | 16 | 10 | 2 | 2 | 3 | 2
6P GAIN WILD-TYPE | 13 | 5 | 6 | 2 | 0 | 12 | 2 | 0

Figure S10. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6p gain' versus 'METHYLATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.009

Table S11. Gene #8: '6p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
6P GAIN MUTATED | 8 | 7 | 6 | 19
6P GAIN WILD-TYPE | 20 | 6 | 10 | 4

Figure S11. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'6p gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S12. Gene #8: '6p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
6P GAIN MUTATED | 9 | 10 | 21
6P GAIN WILD-TYPE | 31 | 5 | 4

Figure S12. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0059

Table S13. Gene #9: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
6Q GAIN MUTATED | 1 | 5 | 13 | 1
6Q GAIN WILD-TYPE | 14 | 10 | 14 | 22

Figure S13. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'LINCRNA_CNMF'

P value = 0.00701 (Fisher's exact test), Q value = 0.049

Table S14. Gene #9: '6q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
6Q GAIN MUTATED | 2 | 2 | 7 | 0 | 9
6Q GAIN WILD-TYPE | 16 | 5 | 21 | 11 | 7

Figure S14. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'6q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00089

Table S15. Gene #9: '6q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
6Q GAIN MUTATED | 0 | 13 | 2 | 5
6Q GAIN WILD-TYPE | 21 | 11 | 18 | 10

Figure S15. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'6q gain' versus 'MIR_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0024

Table S16. Gene #9: '6q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
6Q GAIN MUTATED | 0 | 1 | 5 | 13 | 1
6Q GAIN WILD-TYPE | 13 | 20 | 13 | 11 | 3

Figure S16. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'6q gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S17. Gene #9: '6q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
6Q GAIN MUTATED | 0 | 2 | 2 | 8 | 8
6Q GAIN WILD-TYPE | 21 | 18 | 6 | 9 | 6

Figure S17. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0022

Table S18. Gene #9: '6q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
6Q GAIN MUTATED | 1 | 1 | 18 | 0 | 0
6Q GAIN WILD-TYPE | 17 | 20 | 19 | 2 | 2

Figure S18. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #7: 'CN_CNMF'

'6q gain' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0028

Table S19. Gene #9: '6q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
6Q GAIN MUTATED | 1 | 0 | 8 | 7 | 1 | 0 | 1 | 2
6Q GAIN WILD-TYPE | 15 | 7 | 14 | 5 | 1 | 14 | 4 | 0

Figure S19. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6q gain' versus 'METHYLATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.027

Table S20. Gene #9: '6q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
6Q GAIN MUTATED | 1 | 4 | 5 | 10
6Q GAIN WILD-TYPE | 27 | 9 | 11 | 13

Figure S20. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'6q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S21. Gene #9: '6q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
6Q GAIN MUTATED | 2 | 6 | 12
6Q GAIN WILD-TYPE | 38 | 9 | 13

Figure S21. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.024

Table S22. Gene #12: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
8P GAIN MUTATED | 6 | 7 | 4 | 15
8P GAIN WILD-TYPE | 9 | 8 | 23 | 8

Figure S22. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.13

Table S23. Gene #12: '8p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
8P GAIN MUTATED | 11 | 5 | 12 | 4
8P GAIN WILD-TYPE | 10 | 19 | 8 | 11

Figure S23. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'8p gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.18

Table S24. Gene #12: '8p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
8P GAIN MUTATED | 13 | 10 | 1 | 4 | 4
8P GAIN WILD-TYPE | 8 | 10 | 7 | 13 | 10

Figure S24. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.031

Table S25. Gene #12: '8p gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
8P GAIN MUTATED | 12 | 11 | 8 | 0 | 1
8P GAIN WILD-TYPE | 6 | 10 | 29 | 2 | 1

Figure S25. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'CN_CNMF'

'8p gain' versus 'METHYLATION_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.14

Table S26. Gene #12: '8p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
8P GAIN MUTATED | 16 | 2 | 8 | 6
8P GAIN WILD-TYPE | 12 | 11 | 8 | 17

Figure S26. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'8p gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.13

Table S27. Gene #12: '8p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
8P GAIN MUTATED | 22 | 4 | 6
8P GAIN WILD-TYPE | 18 | 11 | 19

Figure S27. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.041

Table S28. Gene #13: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
8Q GAIN MUTATED | 10 | 9 | 13 | 14 | 8
8Q GAIN WILD-TYPE | 1 | 2 | 16 | 7 | 0

Figure S28. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00057

Table S29. Gene #13: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
8Q GAIN MUTATED | 15 | 9 | 10 | 20
8Q GAIN WILD-TYPE | 0 | 6 | 17 | 3

Figure S29. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'LINCRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S30. Gene #13: '8q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
8Q GAIN MUTATED | 18 | 0 | 20 | 6 | 10
8Q GAIN WILD-TYPE | 0 | 7 | 8 | 5 | 6

Figure S30. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'8q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S31. Gene #13: '8q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
8Q GAIN MUTATED | 20 | 9 | 18 | 7
8Q GAIN WILD-TYPE | 1 | 15 | 2 | 8

Figure S31. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'8q gain' versus 'MIR_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.001

Table S32. Gene #13: '8q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
8Q GAIN MUTATED | 11 | 20 | 5 | 16 | 2
8Q GAIN WILD-TYPE | 2 | 1 | 13 | 8 | 2

Figure S32. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'8q gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S33. Gene #13: '8q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
8Q GAIN MUTATED | 20 | 18 | 1 | 8 | 7
8Q GAIN WILD-TYPE | 1 | 2 | 7 | 9 | 7

Figure S33. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S34. Gene #13: '8q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
8Q GAIN MUTATED | 16 | 20 | 14 | 2 | 2
8Q GAIN WILD-TYPE | 2 | 1 | 23 | 0 | 0

Figure S34. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'CN_CNMF'

'8q gain' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S35. Gene #13: '8q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
8Q GAIN MUTATED | 15 | 7 | 4 | 8 | 2 | 12 | 5 | 1
8Q GAIN WILD-TYPE | 1 | 0 | 18 | 4 | 0 | 2 | 0 | 1

Figure S35. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'8q gain' versus 'METHYLATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S36. Gene #13: '8q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
8Q GAIN MUTATED | 27 | 3 | 12 | 12
8Q GAIN WILD-TYPE | 1 | 10 | 4 | 11

Figure S36. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'8q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S37. Gene #13: '8q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
8Q GAIN MUTATED | 37 | 5 | 12
8Q GAIN WILD-TYPE | 3 | 10 | 13

Figure S37. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'11q gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.18

Table S38. Gene #17: '11q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
11Q GAIN MUTATED | 0 | 2 | 0 | 5 | 2
11Q GAIN WILD-TYPE | 21 | 18 | 8 | 12 | 12

Figure S38. Get High-res Image Gene #17: '11q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'12p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.11

Table S39. Gene #18: '12p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
12P GAIN MUTATED | 0 | 0 | 3 | 0
12P GAIN WILD-TYPE | 21 | 24 | 17 | 15

Figure S39. Get High-res Image Gene #18: '12p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'12q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.12

Table S40. Gene #19: '12q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
12Q GAIN MUTATED | 0 | 0 | 3 | 0
12Q GAIN WILD-TYPE | 21 | 24 | 17 | 15

Figure S40. Get High-res Image Gene #19: '12q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.13

Table S41. Gene #20: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
13Q GAIN MUTATED | 0 | 3 | 0 | 3
13Q GAIN WILD-TYPE | 15 | 12 | 27 | 20

Figure S41. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.11

Table S42. Gene #21: '14q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
14Q GAIN MUTATED | 0 | 0 | 3 | 0
14Q GAIN WILD-TYPE | 21 | 24 | 17 | 15

Figure S42. Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'17p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.11

Table S43. Gene #23: '17p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
17P GAIN MUTATED | 0 | 4 | 5 | 0
17P GAIN WILD-TYPE | 21 | 20 | 15 | 15

Figure S43. Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00579 (Fisher's exact test), Q value = 0.043

Table S44. Gene #25: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
20P GAIN MUTATED | 0 | 4 | 0 | 4
20P GAIN WILD-TYPE | 15 | 11 | 27 | 19

Figure S44. Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.18

Table S45. Gene #25: '20p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
20P GAIN MUTATED | 0 | 4 | 4 | 0
20P GAIN WILD-TYPE | 21 | 20 | 16 | 15

Figure S45. Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00401 (Fisher's exact test), Q value = 0.031

Table S46. Gene #26: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
20Q GAIN MUTATED | 0 | 4 | 0 | 5
20Q GAIN WILD-TYPE | 15 | 11 | 27 | 18

Figure S46. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.12

Table S47. Gene #26: '20q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
20Q GAIN MUTATED | 0 | 4 | 5 | 0
20Q GAIN WILD-TYPE | 21 | 20 | 15 | 15

Figure S47. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.13

Table S48. Gene #26: '20q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
20Q GAIN MUTATED | 6 | 0 | 3 | 0 | 0
20Q GAIN WILD-TYPE | 12 | 21 | 34 | 2 | 2

Figure S48. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #7: 'CN_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00548 (Fisher's exact test), Q value = 0.041

Table S49. Gene #27: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
21Q GAIN MUTATED | 1 | 3 | 1 | 9
21Q GAIN WILD-TYPE | 14 | 12 | 26 | 14

Figure S49. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.031

Table S50. Gene #27: '21q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
21Q GAIN MUTATED | 1 | 3 | 9 | 1
21Q GAIN WILD-TYPE | 20 | 21 | 11 | 14

Figure S50. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.18

Table S51. Gene #27: '21q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
21Q GAIN MUTATED | 7 | 3 | 3 | 1 | 0
21Q GAIN WILD-TYPE | 11 | 18 | 34 | 1 | 2

Figure S51. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #7: 'CN_CNMF'

'22q gain' versus 'LINCRNA_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.17

Table S52. Gene #28: '22q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
22Q GAIN MUTATED | 0 | 0 | 6 | 0 | 0
22Q GAIN WILD-TYPE | 18 | 7 | 22 | 11 | 16

Figure S52. Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'xp gain' versus 'MIR_MATURE_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.06

Table S53. Gene #29: 'xp gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
XP GAIN MUTATED | 1 | 0 | 1 | 8 | 0
XP GAIN WILD-TYPE | 12 | 21 | 17 | 16 | 4

Figure S53. Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'xp gain' versus 'METHYLATION_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.044

Table S54. Gene #29: 'xp gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
XP GAIN MUTATED | 1 | 0 | 6 | 3
XP GAIN WILD-TYPE | 27 | 13 | 10 | 20

Figure S54. Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'xq gain' versus 'MIR_MATURE_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.018

Table S55. Gene #30: 'xq gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
XQ GAIN MUTATED | 1 | 0 | 0 | 8 | 0
XQ GAIN WILD-TYPE | 12 | 21 | 18 | 16 | 4

Figure S55. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'xq gain' versus 'METHYLATION_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.13

Table S56. Gene #30: 'xq gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
XQ GAIN MUTATED | 1 | 0 | 5 | 3
XQ GAIN WILD-TYPE | 27 | 13 | 11 | 20

Figure S56. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'1p loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.089

Table S57. Gene #31: '1p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
1P LOSS MUTATED | 9 | 2 | 0 | 6 | 1
1P LOSS WILD-TYPE | 12 | 18 | 8 | 11 | 13

Figure S57. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0074

Table S58. Gene #31: '1p loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
1P LOSS MUTATED | 11 | 2 | 5 | 0 | 0
1P LOSS WILD-TYPE | 7 | 19 | 32 | 2 | 2

Figure S58. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #7: 'CN_CNMF'

'1p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S59. Gene #31: '1p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
1P LOSS MUTATED | 11 | 1 | 2 | 1 | 0 | 0 | 1 | 2
1P LOSS WILD-TYPE | 5 | 6 | 20 | 11 | 2 | 14 | 4 | 0

Figure S59. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'1q loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.14

Table S60. Gene #32: '1q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
1Q LOSS MUTATED | 4 | 0 | 0 | 0 | 0
1Q LOSS WILD-TYPE | 17 | 20 | 8 | 17 | 14

Figure S60. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S61. Gene #33: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
3P LOSS MUTATED | 11 | 7 | 1 | 15 | 8
3P LOSS WILD-TYPE | 0 | 4 | 28 | 6 | 0

Figure S61. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S62. Gene #33: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
3P LOSS MUTATED | 15 | 3 | 1 | 23
3P LOSS WILD-TYPE | 0 | 12 | 26 | 0

Figure S62. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S63. Gene #33: '3p loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
3P LOSS MUTATED | 18 | 0 | 17 | 6 | 1
3P LOSS WILD-TYPE | 0 | 7 | 11 | 5 | 15

Figure S63. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'3p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S64. Gene #33: '3p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
3P LOSS MUTATED | 20 | 1 | 20 | 1
3P LOSS WILD-TYPE | 1 | 23 | 0 | 14

Figure S64. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'3p loss' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S65. Gene #33: '3p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
3P LOSS MUTATED | 11 | 20 | 6 | 3 | 2
3P LOSS WILD-TYPE | 2 | 1 | 12 | 21 | 2

Figure S65. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'3p loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S66. Gene #33: '3p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
3P LOSS MUTATED | 21 | 17 | 0 | 2 | 2
3P LOSS WILD-TYPE | 0 | 3 | 8 | 15 | 12

Figure S66. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S67. Gene #33: '3p loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
3P LOSS MUTATED | 17 | 21 | 1 | 2 | 1
3P LOSS WILD-TYPE | 1 | 0 | 36 | 0 | 1

Figure S67. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #7: 'CN_CNMF'

'3p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S68. Gene #33: '3p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
3P LOSS MUTATED | 15 | 7 | 0 | 0 | 1 | 14 | 5 | 0
3P LOSS WILD-TYPE | 1 | 0 | 22 | 12 | 1 | 0 | 0 | 2

Figure S68. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'3p loss' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S69. Gene #33: '3p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
3P LOSS MUTATED | 28 | 1 | 11 | 2
3P LOSS WILD-TYPE | 0 | 12 | 5 | 21

Figure S69. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'3p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S70. Gene #33: '3p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
3P LOSS MUTATED | 40 | 0 | 2
3P LOSS WILD-TYPE | 0 | 15 | 23

Figure S70. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S71. Gene #34: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
3Q LOSS MUTATED | 11 | 7 | 3 | 15 | 8
3Q LOSS WILD-TYPE | 0 | 4 | 26 | 6 | 0

Figure S71. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S72. Gene #34: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
3Q LOSS MUTATED | 15 | 4 | 2 | 23
3Q LOSS WILD-TYPE | 0 | 11 | 25 | 0

Figure S72. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S73. Gene #34: '3q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
3Q LOSS MUTATED | 18 | 0 | 17 | 7 | 2
3Q LOSS WILD-TYPE | 0 | 7 | 11 | 4 | 14

Figure S73. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'3q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S74. Gene #34: '3q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
3Q LOSS MUTATED | 21 | 1 | 20 | 2
3Q LOSS WILD-TYPE | 0 | 23 | 0 | 13

Figure S74. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'3q loss' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S75. Gene #34: '3q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
3Q LOSS MUTATED | 11 | 21 | 7 | 3 | 2
3Q LOSS WILD-TYPE | 2 | 0 | 11 | 21 | 2

Figure S75. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'3q loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S76. Gene #34: '3q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
3Q LOSS MUTATED | 21 | 18 | 1 | 2 | 2
3Q LOSS WILD-TYPE | 0 | 2 | 7 | 15 | 12

Figure S76. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S77. Gene #34: '3q loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
3Q LOSS MUTATED | 17 | 21 | 2 | 2 | 2
3Q LOSS WILD-TYPE | 1 | 0 | 35 | 0 | 0

Figure S77. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #7: 'CN_CNMF'

'3q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S78. Gene #34: '3q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
3Q LOSS MUTATED | 16 | 7 | 0 | 0 | 2 | 14 | 5 | 0
3Q LOSS WILD-TYPE | 0 | 0 | 22 | 12 | 0 | 0 | 0 | 2

Figure S78. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'3q loss' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S79. Gene #34: '3q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
3Q LOSS MUTATED | 28 | 3 | 11 | 2
3Q LOSS WILD-TYPE | 0 | 10 | 5 | 21

Figure S79. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'3q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S80. Gene #34: '3q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
3Q LOSS MUTATED | 40 | 2 | 2
3Q LOSS WILD-TYPE | 0 | 13 | 23

Figure S80. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0046

Table S81. Gene #37: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
6Q LOSS MUTATED | 6 | 1 | 0 | 7
6Q LOSS WILD-TYPE | 9 | 14 | 27 | 16

Figure S81. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'LINCRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.16

Table S82. Gene #37: '6q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
6Q LOSS MUTATED | 7 | 0 | 6 | 0 | 1
6Q LOSS WILD-TYPE | 11 | 7 | 22 | 11 | 15

Figure S82. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'6q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.02

Table S83. Gene #37: '6q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
6Q LOSS MUTATED | 6 | 0 | 7 | 1
6Q LOSS WILD-TYPE | 15 | 24 | 13 | 14

Figure S83. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'6q loss' versus 'MIR_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0066

Table S84. Gene #37: '6q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
6Q LOSS MUTATED | 4 | 9 | 0 | 1 | 0
6Q LOSS WILD-TYPE | 9 | 12 | 18 | 23 | 4

Figure S84. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00078

Table S85. Gene #37: '6q loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
6Q LOSS MUTATED | 2 | 11 | 1 | 0 | 0
6Q LOSS WILD-TYPE | 16 | 10 | 36 | 2 | 2

Figure S85. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'CN_CNMF'

'6q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S86. Gene #37: '6q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
6Q LOSS MUTATED | 1 | 7 | 0 | 1 | 1 | 0 | 4 | 0
6Q LOSS WILD-TYPE | 15 | 0 | 22 | 11 | 1 | 14 | 1 | 2

Figure S86. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6q loss' versus 'METHYLATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0015

Table S87. Gene #37: '6q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
6Q LOSS MUTATED | 12 | 0 | 0 | 2
6Q LOSS WILD-TYPE | 16 | 13 | 16 | 21

Figure S87. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'6q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.077

Table S88. Gene #37: '6q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
6Q LOSS MUTATED | 12 | 0 | 2
6Q LOSS WILD-TYPE | 28 | 15 | 23

Figure S88. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00594 (Fisher's exact test), Q value = 0.043

Table S89. Gene #38: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
8P LOSS MUTATED | 5 | 0 | 1 | 1
8P LOSS WILD-TYPE | 10 | 15 | 26 | 22

Figure S89. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.14

Table S90. Gene #38: '8p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
8P LOSS MUTATED | 5 | 0 | 1 | 1
8P LOSS WILD-TYPE | 16 | 24 | 19 | 14

Figure S90. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'8p loss' versus 'MIR_MATURE_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.1

Table S91. Gene #38: '8p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
8P LOSS MUTATED | 2 | 5 | 0 | 0 | 0
8P LOSS WILD-TYPE | 11 | 16 | 18 | 24 | 4

Figure S91. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.094

Table S92. Gene #38: '8p loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
8P LOSS MUTATED | 0 | 6 | 1 | 0 | 0
8P LOSS WILD-TYPE | 18 | 15 | 36 | 2 | 2

Figure S92. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #7: 'CN_CNMF'

'8p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.02

Table S93. Gene #38: '8p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
8P LOSS MUTATED | 0 | 4 | 0 | 1 | 0 | 1 | 1 | 0
8P LOSS WILD-TYPE | 16 | 3 | 22 | 11 | 2 | 13 | 4 | 2

Figure S93. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'8p loss' versus 'METHYLATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.2

Table S94. Gene #38: '8p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
8P LOSS MUTATED | 6 | 0 | 0 | 1
8P LOSS WILD-TYPE | 22 | 13 | 16 | 22

Figure S94. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.13

Table S95. Gene #39: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
9P LOSS MUTATED | 4 | 0 | 1 | 3 | 0
9P LOSS WILD-TYPE | 7 | 11 | 28 | 18 | 8

Figure S95. Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.18

Table S96. Gene #39: '9p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
9P LOSS MUTATED | 4 | 1 | 0 | 0 | 0 | 1 | 1 | 1
9P LOSS WILD-TYPE | 12 | 6 | 22 | 12 | 2 | 13 | 4 | 1

Figure S96. Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.03

Table S97. Gene #40: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
9Q LOSS MUTATED | 4 | 0 | 0 | 3 | 0
9Q LOSS WILD-TYPE | 7 | 11 | 29 | 18 | 8

Figure S97. Get High-res Image Gene #40: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.16

Table S98. Gene #44: '15q loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
15Q LOSS MUTATED | 3 | 0 | 1 | 0 | 1
15Q LOSS WILD-TYPE | 15 | 21 | 36 | 2 | 1

Figure S98. Get High-res Image Gene #44: '15q loss' versus Molecular Subtype #7: 'CN_CNMF'

'15q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.052

Table S99. Gene #44: '15q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
15Q LOSS MUTATED | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 1
15Q LOSS WILD-TYPE | 13 | 7 | 22 | 12 | 1 | 14 | 5 | 1

Figure S99. Get High-res Image Gene #44: '15q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'16q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S100. Gene #46: '16q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
16Q LOSS MUTATED | 3 | 7 | 1 | 2 | 0 | 1 | 0 | 2
16Q LOSS WILD-TYPE | 13 | 0 | 21 | 10 | 2 | 13 | 5 | 0

Figure S100. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'16q loss' versus 'METHYLATION_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.18

Table S101. Gene #46: '16q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
16Q LOSS MUTATED | 10 | 0 | 3 | 3
16Q LOSS WILD-TYPE | 18 | 13 | 13 | 20

Figure S101. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'19p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.066

Table S102. Gene #48: '19p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
19P LOSS MUTATED | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1
19P LOSS WILD-TYPE | 16 | 7 | 21 | 12 | 1 | 14 | 5 | 1

Figure S102. Get High-res Image Gene #48: '19p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'19p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.16

Table S103. Gene #48: '19p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
19P LOSS MUTATED | 0 | 0 | 3
19P LOSS WILD-TYPE | 40 | 15 | 22

Figure S103. Get High-res Image Gene #48: '19p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'19q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.065

Table S104. Gene #49: '19q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
19Q LOSS MUTATED | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1
19Q LOSS WILD-TYPE | 16 | 7 | 21 | 12 | 1 | 14 | 5 | 1

Figure S104. Get High-res Image Gene #49: '19q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'19q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.16

Table S105. Gene #49: '19q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
19Q LOSS MUTATED | 0 | 0 | 3
19Q LOSS WILD-TYPE | 40 | 15 | 22

Figure S105. Get High-res Image Gene #49: '19q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.16

Table S106. Gene #50: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
XP LOSS MUTATED | 2 | 0 | 2 | 7 | 0
XP LOSS WILD-TYPE | 9 | 11 | 27 | 14 | 8

Figure S106. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.008 (Fisher's exact test), Q value = 0.054

Table S107. Gene #50: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
XP LOSS MUTATED | 0 | 1 | 2 | 8
XP LOSS WILD-TYPE | 15 | 14 | 25 | 15

Figure S107. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'LINCRNA_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.034

Table S108. Gene #50: 'xp loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
XP LOSS MUTATED | 0 | 0 | 7 | 4 | 0
XP LOSS WILD-TYPE | 18 | 7 | 21 | 7 | 16

Figure S108. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'xp loss' versus 'METHYLATION_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.052

Table S109. Gene #50: 'xp loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
XP LOSS MUTATED | 4 | 1 | 6 | 0
XP LOSS WILD-TYPE | 24 | 12 | 10 | 23

Figure S109. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'xp loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.13

Table S110. Gene #50: 'xp loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
XP LOSS MUTATED | 8 | 3 | 0
XP LOSS WILD-TYPE | 32 | 12 | 25

Figure S110. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.12

Table S111. Gene #51: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
XQ LOSS MUTATED | 3 | 0 | 2 | 7 | 0
XQ LOSS WILD-TYPE | 8 | 11 | 27 | 14 | 8

Figure S111. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.022

Table S112. Gene #51: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
XQ LOSS MUTATED | 0 | 1 | 2 | 9
XQ LOSS WILD-TYPE | 15 | 14 | 25 | 14

Figure S112. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'LINCRNA_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0098

Table S113. Gene #51: 'xq loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
XQ LOSS MUTATED | 0 | 0 | 7 | 5 | 0
XQ LOSS WILD-TYPE | 18 | 7 | 21 | 6 | 16

Figure S113. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'xq loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.14

Table S114. Gene #51: 'xq loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
XQ LOSS MUTATED | 8 | 1 | 0 | 2 | 1
XQ LOSS WILD-TYPE | 13 | 19 | 8 | 15 | 13

Figure S114. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.17

Table S115. Gene #51: 'xq loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
XQ LOSS MUTATED | 6 | 3 | 2 | 0 | 1
XQ LOSS WILD-TYPE | 12 | 18 | 35 | 2 | 1

Figure S115. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #7: 'CN_CNMF'

'xq loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.13

Table S116. Gene #51: 'xq loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
XQ LOSS MUTATED | 6 | 2 | 1 | 0 | 0 | 1 | 1 | 1
XQ LOSS WILD-TYPE | 10 | 5 | 21 | 12 | 2 | 13 | 4 | 1

Figure S116. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'xq loss' versus 'METHYLATION_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.018

Table S117. Gene #51: 'xq loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
XQ LOSS MUTATED | 4 | 1 | 7 | 0
XQ LOSS WILD-TYPE | 24 | 12 | 9 | 23

Figure S117. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'xq loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.11

Table S118. Gene #51: 'xq loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
XQ LOSS MUTATED | 9 | 3 | 0
XQ LOSS WILD-TYPE | 31 | 12 | 25

Figure S118. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

- Processed Copy number data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/18c76f9c-e604-4517-bc19-4bda4cb583f6/correlate_genomic_events_all/597ba7df-da6d-44b2-a96c-e44efd0c26c0/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtypes file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/9d897bdb-7a9a-423a-ad17-06f28ae98803/aggregate_clusters_workflow/1d8bac82-5a1d-4cd2-aeb1-8ddd0e1e7a20/call-aggregate_clusters/TCGA-UVM-TP.transposedmergedcluster.txt

- Number of patients = 80

- Number of significantly arm-level cnvs = 51

- Number of molecular subtypes = 10

- Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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