Correlation between copy number variations of arm-level result and molecular subtypes
Colon/Rectal Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1J96493
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon/Rectal Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1J96493
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 78 arm-level results and 10 molecular subtypes across 575 patients, 89 significant findings detected with Q value < 0.25.

- 2p gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 2q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- 3p gain cnv correlated to 'CN_CNMF'.

- 3q gain cnv correlated to 'CN_CNMF'.

- 6p gain cnv correlated to 'CN_CNMF'.

- 6q gain cnv correlated to 'CN_CNMF'.

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

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

- 8p gain cnv correlated to 'CN_CNMF'.

- 8q gain cnv correlated to 'CN_CNMF'.

- 11p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 11q gain cnv correlated to 'CN_CNMF'.

- 13q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'CN_CNMF'.

- 16q gain cnv correlated to 'CN_CNMF'.

- 17q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- 19p gain cnv correlated to 'CN_CNMF'.

- 20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 4p loss cnv correlated to 'CN_CNMF'.

- 4q loss cnv correlated to 'CN_CNMF'.

- 5q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF'.

- 12p loss cnv correlated to 'CN_CNMF'.

- 12q loss cnv correlated to 'CN_CNMF'.

- 14q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.

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

- 17p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 18q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 19p loss cnv correlated to 'CN_CNMF'.

- 19q loss cnv correlated to 'CN_CNMF'.

- 20p loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 89 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
| 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
20q gain | 0 (0%) | 172 | 1.23e-18 (9.18e-16) | 2.68e-17 (1.99e-14) | 2.22e-46 (1.68e-43) | 9.04e-13 (6.64e-10) | 0.000311 (0.209) | 0.000133 (0.0909) | 9.03e-18 (6.72e-15) | 1.13e-13 (8.32e-11) | 0.463 (1.00) | 0.101 (1.00)
13q gain | 0 (0%) | 261 | 1e-07 (7.24e-05) | 2.44e-05 (0.0169) | 1.62e-37 (1.23e-34) | 1.71e-08 (1.24e-05) | 0.0129 (1.00) | 0.0683 (1.00) | 8.54e-09 (6.2e-06) | 6.4e-07 (0.000455) | 0.01 (1.00) | 0.45 (1.00)
20p gain | 0 (0%) | 287 | 6.06e-05 (0.0416) | 6.71e-09 (4.88e-06) | 4.25e-22 (3.19e-19) | 7.67e-05 (0.0526) | 0.00725 (1.00) | 0.0222 (1.00) | 3.2e-07 (0.000229) | 3.2e-07 (0.000229) | 0.625 (1.00) | 0.472 (1.00)
14q loss | 0 (0%) | 432 | 4.76e-06 (0.00334) | 2.49e-07 (0.000178) | 1.12e-31 (8.43e-29) | 1.97e-07 (0.000142) | 0.000364 (0.244) | 0.012 (1.00) | 1.73e-07 (0.000124) | 0.000705 (0.468) | 0.114 (1.00) | 0.709 (1.00)
18p loss | 0 (0%) | 251 | 9.87e-15 (7.29e-12) | 8.51e-12 (6.23e-09) | 4.26e-47 (3.23e-44) | 4.33e-19 (3.24e-16) | 0.012 (1.00) | 0.015 (1.00) | 5.39e-16 (3.99e-13) | 2.73e-11 (2e-08) | 0.065 (1.00) | 0.787 (1.00)
18q loss | 0 (0%) | 223 | 1.42e-12 (1.04e-09) | 1.96e-11 (1.44e-08) | 6.8e-51 (5.16e-48) | 8.03e-21 (6.02e-18) | 0.0241 (1.00) | 0.0948 (1.00) | 3.96e-16 (2.93e-13) | 3.68e-09 (2.68e-06) | 0.00938 (1.00) | 0.378 (1.00)
7p gain | 0 (0%) | 285 | 0.000443 (0.297) | 0.00887 (1.00) | 1.89e-21 (1.42e-18) | 7.29e-07 (0.000518) | 0.22 (1.00) | 0.0313 (1.00) | 3.72e-08 (2.69e-05) | 9.54e-05 (0.0653) | 0.0703 (1.00) | 0.0304 (1.00)
7q gain | 0 (0%) | 320 | 0.000644 (0.428) | 0.0134 (1.00) | 6.95e-16 (5.14e-13) | 8.61e-06 (0.00601) | 0.777 (1.00) | 0.18 (1.00) | 8.79e-07 (0.000623) | 1.24e-05 (0.00862) | 0.245 (1.00) | 0.155 (1.00)
17p loss | 0 (0%) | 323 | 0.000242 (0.164) | 0.00165 (1.00) | 5.49e-22 (4.12e-19) | 2.44e-07 (0.000175) | 0.317 (1.00) | 0.486 (1.00) | 3.25e-06 (0.00228) | 0.000795 (0.527) | 0.027 (1.00) | 0.497 (1.00)
2p gain | 0 (0%) | 515 | 0.0169 (1.00) | 0.00499 (1.00) | 0.00816 (1.00) | 0.000256 (0.172) | 0.0735 (1.00) | 0.357 (1.00) | 0.000224 (0.152) | 0.000137 (0.0937) | 0.216 (1.00) | 0.0209 (1.00)
11p gain | 0 (0%) | 536 | 0.063 (1.00) | 0.654 (1.00) | 1.71e-05 (0.0119) | 0.000214 (0.146) | 0.826 (1.00) | 0.764 (1.00) | 0.0491 (1.00) | 0.000153 (0.104) | 0.246 (1.00) | 0.882 (1.00)
2q gain | 0 (0%) | 516 | 0.00368 (1.00) | 0.00391 (1.00) | 0.00101 (0.664) | 5.82e-06 (0.00407) | 0.209 (1.00) | 0.806 (1.00) | 0.000234 (0.158) | 0.000824 (0.546) | 0.251 (1.00) | 0.0504 (1.00)
17q gain | 0 (0%) | 508 | 0.0455 (1.00) | 0.0639 (1.00) | 0.000269 (0.181) | 0.00143 (0.938) | 0.649 (1.00) | 0.0748 (1.00) | 1.47e-05 (0.0102) | 0.00195 (1.00) | 0.0785 (1.00) | 0.354 (1.00)
1p loss | 0 (0%) | 507 | 0.0784 (1.00) | 0.00327 (1.00) | 7.55e-06 (0.00528) | 3.84e-05 (0.0264) | 0.984 (1.00) | 0.821 (1.00) | 0.0764 (1.00) | 0.00823 (1.00) | 0.193 (1.00) | 0.62 (1.00)
9q loss | 0 (0%) | 538 | 0.0484 (1.00) | 0.0135 (1.00) | 1.95e-06 (0.00138) | 3.42e-05 (0.0236) | 0.692 (1.00) | 0.209 (1.00) | 0.0214 (1.00) | 0.0167 (1.00) | 0.0491 (1.00) | 0.82 (1.00)
15q loss | 0 (0%) | 419 | 0.0144 (1.00) | 0.0117 (1.00) | 2.09e-24 (1.57e-21) | 0.0158 (1.00) | 0.303 (1.00) | 0.832 (1.00) | 1.19e-05 (0.00829) | 0.000572 (0.381) | 0.368 (1.00) | 0.246 (1.00)
3p gain | 0 (0%) | 539 | 0.126 (1.00) | 0.433 (1.00) | 0.000181 (0.123) | 0.257 (1.00) | 0.374 (1.00) | 0.77 (1.00) | 0.26 (1.00) | 0.885 (1.00) | 0.208 (1.00) | 0.366 (1.00)
3q gain | 0 (0%) | 522 | 0.22 (1.00) | 0.0947 (1.00) | 2.49e-06 (0.00175) | 0.0353 (1.00) | 0.215 (1.00) | 0.655 (1.00) | 0.075 (1.00) | 0.588 (1.00) | 0.111 (1.00) | 0.544 (1.00)
6p gain | 0 (0%) | 498 | 0.246 (1.00) | 0.00492 (1.00) | 1.55e-06 (0.00109) | 0.401 (1.00) | 0.704 (1.00) | 0.12 (1.00) | 0.0227 (1.00) | 0.227 (1.00) | 0.848 (1.00) | 0.392 (1.00)
6q gain | 0 (0%) | 504 | 0.375 (1.00) | 0.0199 (1.00) | 7.47e-07 (0.000531) | 0.159 (1.00) | 0.317 (1.00) | 0.0418 (1.00) | 0.0607 (1.00) | 0.575 (1.00) | 0.749 (1.00) | 0.251 (1.00)
8p gain | 0 (0%) | 467 | 0.946 (1.00) | 0.746 (1.00) | 1e-08 (7.27e-06) | 0.433 (1.00) | 0.28 (1.00) | 0.215 (1.00) | 0.181 (1.00) | 0.44 (1.00) | 0.49 (1.00) | 0.891 (1.00)
8q gain | 0 (0%) | 340 | 0.0693 (1.00) | 0.621 (1.00) | 1.06e-33 (7.98e-31) | 0.00942 (1.00) | 0.15 (1.00) | 0.33 (1.00) | 0.0011 (0.721) | 0.0265 (1.00) | 0.459 (1.00) | 0.633 (1.00)
11q gain | 0 (0%) | 536 | 0.102 (1.00) | 0.0316 (1.00) | 1.33e-06 (0.000939) | 0.000911 (0.601) | 0.497 (1.00) | 0.651 (1.00) | 0.0356 (1.00) | 0.00526 (1.00) | 0.559 (1.00) | 0.406 (1.00)
16p gain | 0 (0%) | 479 | 0.0975 (1.00) | 0.0844 (1.00) | 1.26e-16 (9.37e-14) | 0.0108 (1.00) | 0.941 (1.00) | 0.0295 (1.00) | 0.0228 (1.00) | 0.136 (1.00) | 0.577 (1.00) | 0.347 (1.00)
16q gain | 0 (0%) | 479 | 0.0433 (1.00) | 0.0683 (1.00) | 3.02e-18 (2.25e-15) | 0.00391 (1.00) | 0.991 (1.00) | 0.0182 (1.00) | 0.0198 (1.00) | 0.0602 (1.00) | 0.465 (1.00) | 0.277 (1.00)
19p gain | 0 (0%) | 523 | 0.167 (1.00) | 0.228 (1.00) | 5.84e-05 (0.0401) | 0.0236 (1.00) | 0.598 (1.00) | 0.0285 (1.00) | 0.423 (1.00) | 0.474 (1.00) | 0.718 (1.00) | 0.745 (1.00)
4p loss | 0 (0%) | 453 | 0.106 (1.00) | 0.105 (1.00) | 5.5e-11 (4.01e-08) | 0.0036 (1.00) | 0.693 (1.00) | 0.889 (1.00) | 0.0062 (1.00) | 0.0572 (1.00) | 0.045 (1.00) | 0.769 (1.00)
4q loss | 0 (0%) | 462 | 0.0962 (1.00) | 0.0638 (1.00) | 3.18e-12 (2.33e-09) | 0.00168 (1.00) | 0.606 (1.00) | 0.81 (1.00) | 0.00213 (1.00) | 0.0535 (1.00) | 0.0122 (1.00) | 0.564 (1.00)
5q loss | 0 (0%) | 515 | 0.0163 (1.00) | 0.0917 (1.00) | 5.53e-07 (0.000394) | 0.0816 (1.00) | 0.186 (1.00) | 0.812 (1.00) | 0.0211 (1.00) | 0.0985 (1.00) | 0.963 (1.00) | 0.579 (1.00)
8p loss | 0 (0%) | 430 | 0.0117 (1.00) | 0.00463 (1.00) | 1.14e-18 (8.53e-16) | 0.000373 (0.25) | 0.28 (1.00) | 0.0393 (1.00) | 0.11 (1.00) | 0.152 (1.00) | 0.515 (1.00) | 0.73 (1.00)
9p loss | 0 (0%) | 536 | 0.564 (1.00) | 0.12 (1.00) | 2.9e-05 (0.02) | 0.00158 (1.00) | 0.247 (1.00) | 0.147 (1.00) | 0.102 (1.00) | 0.0221 (1.00) | 0.127 (1.00) | 1 (1.00)
10q loss | 0 (0%) | 529 | 0.34 (1.00) | 0.568 (1.00) | 1.44e-06 (0.00101) | 0.153 (1.00) | 0.0204 (1.00) | 0.772 (1.00) | 0.102 (1.00) | 0.231 (1.00) | 0.714 (1.00) | 0.811 (1.00)
12p loss | 0 (0%) | 542 | 0.114 (1.00) | 0.264 (1.00) | 5.42e-07 (0.000387) | 0.258 (1.00) | 0.694 (1.00) | 0.373 (1.00) | 0.201 (1.00) | 0.46 (1.00) | 0.541 (1.00) | 0.222 (1.00)
12q loss | 0 (0%) | 547 | 0.131 (1.00) | 0.0524 (1.00) | 1.11e-06 (0.000784) | 0.522 (1.00) | 0.885 (1.00) | 0.619 (1.00) | 0.143 (1.00) | 0.189 (1.00) | 0.616 (1.00) | 0.681 (1.00)
19p loss | 0 (0%) | 555 | 0.49 (1.00) | 0.598 (1.00) | 1.46e-05 (0.0102) | 0.0244 (1.00) | 0.579 (1.00) | 0.705 (1.00) | 0.00155 (1.00) | 0.00289 (1.00) | 0.235 (1.00) | 0.371 (1.00)
19q loss | 0 (0%) | 557 | 0.49 (1.00) | 0.598 (1.00) | 0.000235 (0.159) | 0.0965 (1.00) | 0.625 (1.00) | 0.912 (1.00) | 0.00155 (1.00) | 0.00289 (1.00) | 0.424 (1.00) | 0.0976 (1.00)
20p loss | 0 (0%) | 528 | 0.169 (1.00) | 0.18 (1.00) | 4.56e-07 (0.000326) | 0.039 (1.00) | 0.77 (1.00) | 0.365 (1.00) | 0.577 (1.00) | 0.391 (1.00) | 0.554 (1.00) | 0.486 (1.00)
21q loss | 0 (0%) | 461 | 0.0588 (1.00) | 0.319 (1.00) | 3.64e-05 (0.0251) | 0.0555 (1.00) | 0.328 (1.00) | 0.31 (1.00) | 0.235 (1.00) | 0.392 (1.00) | 0.118 (1.00) | 0.342 (1.00)
22q loss | 0 (0%) | 453 | 0.0679 (1.00) | 0.0038 (1.00) | 7.8e-14 (5.75e-11) | 0.352 (1.00) | 0.419 (1.00) | 0.264 (1.00) | 0.0676 (1.00) | 0.0646 (1.00) | 0.0662 (1.00) | 0.1 (1.00)
1p gain | 0 (0%) | 560 | 0.406 (1.00) | 0.102 (1.00) | 0.932 (1.00) | 0.497 (1.00) | 0.497 (1.00) | 0.128 (1.00) | 0.178 (1.00) | 0.33 (1.00) | 0.111 (1.00) | 0.911 (1.00)
1q gain | 0 (0%) | 495 | 0.484 (1.00) | 0.855 (1.00) | 0.0158 (1.00) | 0.926 (1.00) | 0.255 (1.00) | 0.15 (1.00) | 0.128 (1.00) | 0.0758 (1.00) | 0.0729 (1.00) | 0.978 (1.00)
4p gain | 0 (0%) | 569 |  |  | 0.0622 (1.00) | 0.226 (1.00) | 0.184 (1.00) | 0.339 (1.00) |  |  | 0.137 (1.00) | 0.0525 (1.00)
4q gain | 0 (0%) | 568 | 0.704 (1.00) | 1 (1.00) | 0.25 (1.00) | 0.787 (1.00) | 0.732 (1.00) | 0.645 (1.00) |  |  | 0.383 (1.00) | 0.809 (1.00)
5p gain | 0 (0%) | 515 | 0.113 (1.00) | 0.708 (1.00) | 0.0015 (0.985) | 0.178 (1.00) | 0.795 (1.00) | 0.863 (1.00) | 0.401 (1.00) | 0.4 (1.00) | 0.784 (1.00) | 0.354 (1.00)
5q gain | 0 (0%) | 542 | 0.457 (1.00) | 0.534 (1.00) | 0.00356 (1.00) | 0.356 (1.00) | 0.742 (1.00) | 0.557 (1.00) | 0.73 (1.00) | 0.446 (1.00) | 0.818 (1.00) | 0.483 (1.00)
9p gain | 0 (0%) | 496 | 0.42 (1.00) | 0.843 (1.00) | 0.178 (1.00) | 0.79 (1.00) | 0.91 (1.00) | 0.204 (1.00) | 0.539 (1.00) | 0.855 (1.00) | 0.78 (1.00) | 0.781 (1.00)
9q gain | 0 (0%) | 511 | 0.476 (1.00) | 0.923 (1.00) | 0.214 (1.00) | 0.433 (1.00) | 0.612 (1.00) | 0.0336 (1.00) | 0.989 (1.00) | 0.691 (1.00) | 0.408 (1.00) | 0.739 (1.00)
10p gain | 0 (0%) | 547 | 0.137 (1.00) | 0.846 (1.00) | 0.00981 (1.00) | 0.0125 (1.00) | 0.673 (1.00) | 0.857 (1.00) | 0.617 (1.00) | 0.0446 (1.00) | 0.616 (1.00) | 0.496 (1.00)
10q gain | 0 (0%) | 562 | 0.691 (1.00) | 0.589 (1.00) | 0.193 (1.00) | 0.0437 (1.00) | 0.597 (1.00) | 0.288 (1.00) | 0.448 (1.00) | 0.0762 (1.00) | 0.694 (1.00) | 0.902 (1.00)
12p gain | 0 (0%) | 482 | 0.362 (1.00) | 0.818 (1.00) | 0.256 (1.00) | 0.0171 (1.00) | 0.629 (1.00) | 0.205 (1.00) | 0.0232 (1.00) | 0.0134 (1.00) | 0.22 (1.00) | 0.112 (1.00)
12q gain | 0 (0%) | 497 | 0.315 (1.00) | 0.721 (1.00) | 0.0986 (1.00) | 0.00193 (1.00) | 0.91 (1.00) | 0.339 (1.00) | 0.0353 (1.00) | 0.0154 (1.00) | 0.222 (1.00) | 0.166 (1.00)
14q gain | 0 (0%) | 556 | 0.495 (1.00) | 0.55 (1.00) | 0.0301 (1.00) | 0.709 (1.00) | 0.724 (1.00) | 0.397 (1.00) | 0.0605 (1.00) | 0.048 (1.00) | 1 (1.00) | 0.371 (1.00)
15q gain | 0 (0%) | 568 |  |  | 0.515 (1.00) | 0.882 (1.00) | 0.133 (1.00) | 0.131 (1.00) | 1 (1.00) | 0.244 (1.00) | 0.87 (1.00) | 0.374 (1.00)
17p gain | 0 (0%) | 562 | 0.78 (1.00) | 0.00605 (1.00) | 1 (1.00) | 0.85 (1.00) | 0.552 (1.00) | 0.721 (1.00) | 0.0157 (1.00) | 0.009 (1.00) | 0.694 (1.00) | 0.902 (1.00)
18p gain | 0 (0%) | 554 | 0.192 (1.00) | 0.0168 (1.00) | 0.00061 (0.406) | 0.00955 (1.00) | 0.514 (1.00) | 0.897 (1.00) | 0.133 (1.00) | 0.391 (1.00) | 0.568 (1.00) | 0.397 (1.00)
18q gain | 0 (0%) | 563 |  |  | 0.172 (1.00) | 0.00729 (1.00) | 0.648 (1.00) | 0.468 (1.00) | 0.122 (1.00) | 0.858 (1.00) | 0.105 (1.00) | 0.134 (1.00)
19q gain | 0 (0%) | 514 | 0.0123 (1.00) | 0.0249 (1.00) | 0.0122 (1.00) | 0.0715 (1.00) | 0.233 (1.00) | 0.0383 (1.00) | 0.507 (1.00) | 0.512 (1.00) | 0.832 (1.00) | 0.495 (1.00)
21q gain | 0 (0%) | 556 | 0.436 (1.00) | 0.381 (1.00) | 0.00268 (1.00) | 0.709 (1.00) | 0.48 (1.00) | 0.0895 (1.00) | 0.619 (1.00) | 0.834 (1.00) | 0.686 (1.00) | 0.143 (1.00)
22q gain | 0 (0%) | 568 | 0.691 (1.00) | 0.00605 (1.00) | 0.234 (1.00) | 0.466 (1.00) | 0.685 (1.00) | 0.47 (1.00) | 0.689 (1.00) | 0.499 (1.00) | 0.459 (1.00) | 0.596 (1.00)
Xq gain | 0 (0%) | 558 | 0.147 (1.00) | 0.735 (1.00) | 0.0167 (1.00) | 0.338 (1.00) | 0.244 (1.00) | 0.313 (1.00) | 0.846 (1.00) | 1 (1.00) | 0.482 (1.00) | 0.705 (1.00)
1q loss | 0 (0%) | 550 | 0.558 (1.00) | 0.0215 (1.00) | 0.0823 (1.00) | 0.0315 (1.00) | 0.825 (1.00) | 0.949 (1.00) | 0.158 (1.00) | 0.324 (1.00) | 0.425 (1.00) | 0.725 (1.00)
2p loss | 0 (0%) | 565 | 1 (1.00) | 0.435 (1.00) | 0.0735 (1.00) |  | 0.0168 (1.00) | 0.658 (1.00) |  |  | 0.0151 (1.00) | 0.0133 (1.00)
2q loss | 0 (0%) | 567 | 0.741 (1.00) | 0.444 (1.00) | 0.548 (1.00) |  | 0.157 (1.00) | 0.299 (1.00) |  |  | 0.0584 (1.00) | 0.0455 (1.00)
3p loss | 0 (0%) | 540 | 0.938 (1.00) | 0.53 (1.00) | 0.831 (1.00) | 0.835 (1.00) | 0.703 (1.00) | 0.536 (1.00) | 0.441 (1.00) | 0.157 (1.00) | 0.105 (1.00) | 0.729 (1.00)
3q loss | 0 (0%) | 558 | 0.618 (1.00) | 0.816 (1.00) | 0.757 (1.00) | 0.0157 (1.00) | 0.0903 (1.00) | 0.398 (1.00) | 0.385 (1.00) | 0.184 (1.00) | 0.74 (1.00) | 0.772 (1.00)
5p loss | 0 (0%) | 541 | 0.291 (1.00) | 0.433 (1.00) | 0.000544 (0.364) | 0.0341 (1.00) | 0.556 (1.00) | 0.449 (1.00) | 0.234 (1.00) | 0.0352 (1.00) | 0.969 (1.00) | 0.829 (1.00)
6p loss | 0 (0%) | 557 | 0.117 (1.00) | 0.0742 (1.00) | 0.026 (1.00) | 0.277 (1.00) | 0.611 (1.00) | 0.641 (1.00) | 0.89 (1.00) | 0.601 (1.00) | 0.602 (1.00) | 0.923 (1.00)
6q loss | 0 (0%) | 542 | 0.457 (1.00) | 0.338 (1.00) | 0.0983 (1.00) | 1 (1.00) | 0.132 (1.00) | 0.145 (1.00) | 0.737 (1.00) | 0.677 (1.00) | 0.262 (1.00) | 0.298 (1.00)
7q loss | 0 (0%) | 572 |  |  | 0.212 (1.00) |  | 0.834 (1.00) | 1 (1.00) |  |  | 0.764 (1.00) | 1 (1.00)
8q loss | 0 (0%) | 563 | 0.603 (1.00) | 0.639 (1.00) | 0.0828 (1.00) | 0.58 (1.00) | 0.0237 (1.00) | 0.533 (1.00) | 1 (1.00) | 0.828 (1.00) | 0.159 (1.00) | 0.271 (1.00)
10p loss | 0 (0%) | 535 | 0.704 (1.00) | 0.401 (1.00) | 0.000862 (0.57) | 0.419 (1.00) | 0.053 (1.00) | 0.682 (1.00) | 0.409 (1.00) | 0.532 (1.00) | 0.132 (1.00) | 0.591 (1.00)
11p loss | 0 (0%) | 535 | 0.797 (1.00) | 1 (1.00) | 0.00977 (1.00) | 0.706 (1.00) | 0.322 (1.00) | 0.201 (1.00) | 0.0716 (1.00) | 0.0838 (1.00) | 0.113 (1.00) | 0.359 (1.00)
11q loss | 0 (0%) | 524 | 0.975 (1.00) | 0.858 (1.00) | 0.00166 (1.00) | 0.232 (1.00) | 0.731 (1.00) | 0.292 (1.00) | 0.0997 (1.00) | 0.509 (1.00) | 0.129 (1.00) | 0.835 (1.00)
13q loss | 0 (0%) | 563 | 0.324 (1.00) | 0.108 (1.00) | 0.0495 (1.00) | 0.226 (1.00) | 0.0716 (1.00) | 0.108 (1.00) | 0.236 (1.00) | 0.668 (1.00) | 0.726 (1.00) | 0.403 (1.00)
16p loss | 0 (0%) | 560 | 0.256 (1.00) | 0.598 (1.00) | 0.0995 (1.00) | 0.226 (1.00) | 0.561 (1.00) | 0.646 (1.00) | 0.589 (1.00) | 0.601 (1.00) | 1 (1.00) | 0.911 (1.00)
16q loss | 0 (0%) | 558 | 0.0131 (1.00) | 0.506 (1.00) | 0.00221 (1.00) | 0.492 (1.00) | 0.459 (1.00) | 0.748 (1.00) | 0.0911 (1.00) | 0.121 (1.00) | 0.134 (1.00) | 0.257 (1.00)
17q loss | 0 (0%) | 530 | 0.762 (1.00) | 0.558 (1.00) | 0.0023 (1.00) | 0.857 (1.00) | 0.576 (1.00) | 0.587 (1.00) | 0.101 (1.00) | 0.105 (1.00) | 0.116 (1.00) | 0.635 (1.00)
Xq loss | 0 (0%) | 564 | 0.765 (1.00) | 0.839 (1.00) | 0.339 (1.00) | 0.446 (1.00) | 0.108 (1.00) | 0.495 (1.00) | 0.0157 (1.00) | 0.0674 (1.00) | 0.515 (1.00) | 0.652 (1.00)

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.17

Table S1. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
2P GAIN CNV | 28 | 9 | 3
2P GAIN WILD-TYPE | 115 | 104 | 88

Figure S1. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.15

Table S2. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
2P GAIN CNV | 1 | 20 | 4 | 3
2P GAIN WILD-TYPE | 37 | 61 | 52 | 63

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.094

Table S3. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
2P GAIN CNV | 9 | 1 | 18
2P GAIN WILD-TYPE | 86 | 66 | 61

Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 5.82e-06 (Fisher's exact test), Q value = 0.0041

Table S4. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
2Q GAIN CNV | 28 | 8 | 1
2Q GAIN WILD-TYPE | 115 | 105 | 90

Figure S4. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.16

Table S5. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
2Q GAIN CNV | 2 | 19 | 3 | 2
2Q GAIN WILD-TYPE | 36 | 62 | 53 | 64

Figure S5. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.12

Table S6. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
3P GAIN CNV | 25 | 7 | 4 | 0
3P GAIN WILD-TYPE | 175 | 227 | 96 | 41

Figure S6. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.0018

Table S7. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
3Q GAIN CNV | 35 | 7 | 9 | 2
3Q GAIN WILD-TYPE | 165 | 227 | 91 | 39

Figure S7. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0011

Table S8. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
6P GAIN CNV | 46 | 15 | 8 | 8
6P GAIN WILD-TYPE | 154 | 219 | 92 | 33

Figure S8. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00053

Table S9. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
6Q GAIN CNV | 43 | 12 | 8 | 8
6Q GAIN WILD-TYPE | 157 | 222 | 92 | 33

Figure S9. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.89e-21 (Fisher's exact test), Q value = 1.4e-18

Table S10. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
7P GAIN CNV | 144 | 62 | 59 | 25
7P GAIN WILD-TYPE | 56 | 172 | 41 | 16

Figure S10. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 7.29e-07 (Fisher's exact test), Q value = 0.00052

Table S11. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
7P GAIN CNV | 102 | 52 | 36
7P GAIN WILD-TYPE | 41 | 61 | 55

Figure S11. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.72e-08 (Fisher's exact test), Q value = 2.7e-05

Table S12. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
7P GAIN CNV | 22 | 61 | 31 | 17
7P GAIN WILD-TYPE | 16 | 20 | 25 | 49

Figure S12. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.54e-05 (Fisher's exact test), Q value = 0.065

Table S13. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
7P GAIN CNV | 53 | 23 | 55
7P GAIN WILD-TYPE | 42 | 44 | 24

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.95e-16 (Fisher's exact test), Q value = 5.1e-13

Table S14. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
7Q GAIN CNV | 126 | 56 | 52 | 21
7Q GAIN WILD-TYPE | 74 | 178 | 48 | 20

Figure S14. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 8.61e-06 (Fisher's exact test), Q value = 0.006

Table S15. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
7Q GAIN CNV | 88 | 47 | 28
7Q GAIN WILD-TYPE | 55 | 66 | 63

Figure S15. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 8.79e-07 (Fisher's exact test), Q value = 0.00062

Table S16. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
7Q GAIN CNV | 17 | 56 | 24 | 16
7Q GAIN WILD-TYPE | 21 | 25 | 32 | 50

Figure S16. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0086

Table S17. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
7Q GAIN CNV | 43 | 18 | 52
7Q GAIN WILD-TYPE | 52 | 49 | 27

Figure S17. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-08 (Fisher's exact test), Q value = 7.3e-06

Table S18. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
8P GAIN CNV | 26 | 29 | 39 | 14
8P GAIN WILD-TYPE | 174 | 205 | 61 | 27

Figure S18. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.06e-33 (Fisher's exact test), Q value = 8e-31

Table S19. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
8Q GAIN CNV | 78 | 44 | 88 | 25
8Q GAIN WILD-TYPE | 122 | 190 | 12 | 16

Figure S19. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.012

Table S20. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
11P GAIN CNV | 26 | 4 | 5 | 4
11P GAIN WILD-TYPE | 174 | 230 | 95 | 37

Figure S20. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.15

Table S21. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
11P GAIN CNV | 20 | 2 | 3
11P GAIN WILD-TYPE | 123 | 111 | 88

Figure S21. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.1

Table S22. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
11P GAIN CNV | 3 | 0 | 12
11P GAIN WILD-TYPE | 92 | 67 | 67

Figure S22. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00094

Table S23. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
11Q GAIN CNV | 24 | 3 | 5 | 7
11Q GAIN WILD-TYPE | 176 | 231 | 95 | 34

Figure S23. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1e-07 (Fisher's exact test), Q value = 7.2e-05

Table S24. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
13Q GAIN CNV | 13 | 46 | 48 | 13
13Q GAIN WILD-TYPE | 32 | 16 | 21 | 26

Figure S24. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.017

Table S25. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 61 | 114 | 40
13Q GAIN CNV | 19 | 76 | 25
13Q GAIN WILD-TYPE | 42 | 38 | 15

Figure S25. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1.62e-37 (Fisher's exact test), Q value = 1.2e-34

Table S26. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
13Q GAIN CNV | 175 | 64 | 56 | 19
13Q GAIN WILD-TYPE | 25 | 170 | 44 | 22

Figure S26. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1.71e-08 (Fisher's exact test), Q value = 1.2e-05

Table S27. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
13Q GAIN CNV | 106 | 46 | 40
13Q GAIN WILD-TYPE | 37 | 67 | 51

Figure S27. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 8.54e-09 (Fisher's exact test), Q value = 6.2e-06

Table S28. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
13Q GAIN CNV | 25 | 57 | 28 | 14
13Q GAIN WILD-TYPE | 13 | 24 | 28 | 52

Figure S28. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-07 (Fisher's exact test), Q value = 0.00046

Table S29. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
13Q GAIN CNV | 53 | 17 | 54
13Q GAIN WILD-TYPE | 42 | 50 | 25

Figure S29. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 9.4e-14

Table S30. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
16P GAIN CNV | 66 | 7 | 16 | 7
16P GAIN WILD-TYPE | 134 | 227 | 84 | 34

Figure S30. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 3.02e-18 (Fisher's exact test), Q value = 2.3e-15

Table S31. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
16Q GAIN CNV | 68 | 6 | 16 | 6
16Q GAIN WILD-TYPE | 132 | 228 | 84 | 35

Figure S31. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.18

Table S32. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
17Q GAIN CNV | 36 | 13 | 15 | 3
17Q GAIN WILD-TYPE | 164 | 221 | 85 | 38

Figure S32. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.01

Table S33. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
17Q GAIN CNV | 5 | 22 | 2 | 2
17Q GAIN WILD-TYPE | 33 | 59 | 54 | 64

Figure S33. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.04

Table S34. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
19P GAIN CNV | 29 | 7 | 10 | 6
19P GAIN WILD-TYPE | 171 | 227 | 90 | 35

Figure S34. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.042

Table S35. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
20P GAIN CNV | 14 | 39 | 47 | 14
20P GAIN WILD-TYPE | 31 | 23 | 22 | 25

Figure S35. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.71e-09 (Fisher's exact test), Q value = 4.9e-06

Table S36. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 61 | 114 | 40
20P GAIN CNV | 13 | 71 | 30
20P GAIN WILD-TYPE | 48 | 43 | 10

Figure S36. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 4.25e-22 (Fisher's exact test), Q value = 3.2e-19

Table S37. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
20P GAIN CNV | 130 | 67 | 52 | 39
20P GAIN WILD-TYPE | 70 | 167 | 48 | 2

Figure S37. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.053

Table S38. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
20P GAIN CNV | 89 | 42 | 37
20P GAIN WILD-TYPE | 54 | 71 | 54

Figure S38. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00023

Table S39. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
20P GAIN CNV | 19 | 48 | 26 | 10
20P GAIN WILD-TYPE | 19 | 33 | 30 | 56

Figure S39. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00023

Table S40. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
20P GAIN CNV | 46 | 11 | 46
20P GAIN WILD-TYPE | 49 | 56 | 33

Figure S40. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1.23e-18 (Fisher's exact test), Q value = 9.2e-16

Table S41. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
20Q GAIN CNV | 15 | 61 | 62 | 18
20Q GAIN WILD-TYPE | 30 | 1 | 7 | 21

Figure S41. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.68e-17 (Fisher's exact test), Q value = 2e-14

Table S42. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 61 | 114 | 40
20Q GAIN CNV | 18 | 102 | 36
20Q GAIN WILD-TYPE | 43 | 12 | 4

Figure S42. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 2.22e-46 (Fisher's exact test), Q value = 1.7e-43

Table S43. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
20Q GAIN CNV | 193 | 91 | 79 | 40
20Q GAIN WILD-TYPE | 7 | 143 | 21 | 1

Figure S43. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 9.04e-13 (Fisher's exact test), Q value = 6.6e-10

Table S44. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
20Q GAIN CNV | 128 | 57 | 53
20Q GAIN WILD-TYPE | 15 | 56 | 38

Figure S44. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.21

Table S45. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 115 | 184 | 33 | 119
20Q GAIN CNV | 85 | 141 | 23 | 64
20Q GAIN WILD-TYPE | 30 | 43 | 10 | 55

Figure S45. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.091

Table S46. Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 248 | 92 | 35
20Q GAIN CNV | 62 | 182 | 50 | 19
20Q GAIN WILD-TYPE | 14 | 66 | 42 | 16

Figure S46. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 9.03e-18 (Fisher's exact test), Q value = 6.7e-15

Table S47. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
20Q GAIN CNV | 27 | 74 | 41 | 15
20Q GAIN WILD-TYPE | 11 | 7 | 15 | 51

Figure S47. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-13 (Fisher's exact test), Q value = 8.3e-11

Table S48. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
20Q GAIN CNV | 69 | 19 | 69
20Q GAIN WILD-TYPE | 26 | 48 | 10

Figure S48. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0053

Table S49. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
1P LOSS CNV | 39 | 14 | 6 | 9
1P LOSS WILD-TYPE | 161 | 220 | 94 | 32

Figure S49. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.026

Table S50. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
1P LOSS CNV | 29 | 4 | 6
1P LOSS WILD-TYPE | 114 | 109 | 85

Figure S50. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 5.5e-11 (Fisher's exact test), Q value = 4e-08

Table S51. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
4P LOSS CNV | 70 | 21 | 17 | 14
4P LOSS WILD-TYPE | 130 | 213 | 83 | 27

Figure S51. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 3.18e-12 (Fisher's exact test), Q value = 2.3e-09

Table S52. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
4Q LOSS CNV | 68 | 16 | 17 | 12
4Q LOSS WILD-TYPE | 132 | 218 | 83 | 29

Figure S52. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 5.53e-07 (Fisher's exact test), Q value = 0.00039

Table S53. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
5Q LOSS CNV | 31 | 6 | 17 | 6
5Q LOSS WILD-TYPE | 169 | 228 | 83 | 35

Figure S53. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.14e-18 (Fisher's exact test), Q value = 8.5e-16

Table S54. Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
8P LOSS CNV | 88 | 17 | 31 | 9
8P LOSS WILD-TYPE | 112 | 217 | 69 | 32

Figure S54. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.02

Table S55. Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
9P LOSS CNV | 26 | 4 | 7 | 2
9P LOSS WILD-TYPE | 174 | 230 | 93 | 39

Figure S55. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0014

Table S56. Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
9Q LOSS CNV | 28 | 4 | 3 | 2
9Q LOSS WILD-TYPE | 172 | 230 | 97 | 39

Figure S56. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.024

Table S57. Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
9Q LOSS CNV | 19 | 1 | 2
9Q LOSS WILD-TYPE | 124 | 112 | 89

Figure S57. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.001

Table S58. Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
10Q LOSS CNV | 16 | 6 | 13 | 11
10Q LOSS WILD-TYPE | 184 | 228 | 87 | 30

Figure S58. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 5.42e-07 (Fisher's exact test), Q value = 0.00039

Table S59. Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
12P LOSS CNV | 21 | 2 | 3 | 7
12P LOSS WILD-TYPE | 179 | 232 | 97 | 34

Figure S59. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00078

Table S60. Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
12Q LOSS CNV | 19 | 2 | 1 | 6
12Q LOSS WILD-TYPE | 181 | 232 | 99 | 35

Figure S60. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 4.76e-06 (Fisher's exact test), Q value = 0.0033

Table S61. Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
14Q LOSS CNV | 7 | 28 | 26 | 2
14Q LOSS WILD-TYPE | 38 | 34 | 43 | 37

Figure S61. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.49e-07 (Fisher's exact test), Q value = 0.00018

Table S62. Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 61 | 114 | 40
14Q LOSS CNV | 3 | 42 | 18
14Q LOSS WILD-TYPE | 58 | 72 | 22

Figure S62. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.12e-31 (Fisher's exact test), Q value = 8.4e-29

Table S63. Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
14Q LOSS CNV | 109 | 20 | 6 | 8
14Q LOSS WILD-TYPE | 91 | 214 | 94 | 33

Figure S63. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.97e-07 (Fisher's exact test), Q value = 0.00014

Table S64. Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
14Q LOSS CNV | 53 | 12 | 12
14Q LOSS WILD-TYPE | 90 | 101 | 79

Figure S64. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.000364 (Fisher's exact test), Q value = 0.24

Table S65. Gene #65: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 115 | 184 | 33 | 119
14Q LOSS CNV | 30 | 64 | 4 | 18
14Q LOSS WILD-TYPE | 85 | 120 | 29 | 101

Figure S65. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.73e-07 (Fisher's exact test), Q value = 0.00012

Table S66. Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
14Q LOSS CNV | 9 | 33 | 10 | 2
14Q LOSS WILD-TYPE | 29 | 48 | 46 | 64

Figure S66. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 2.09e-24 (Fisher's exact test), Q value = 1.6e-21

Table S67. Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
15Q LOSS CNV | 88 | 16 | 26 | 26
15Q LOSS WILD-TYPE | 112 | 218 | 74 | 15

Figure S67. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0083

Table S68. Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
15Q LOSS CNV | 11 | 30 | 13 | 3
15Q LOSS WILD-TYPE | 27 | 51 | 43 | 63

Figure S68. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.16

Table S69. Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
17P LOSS CNV | 14 | 36 | 41 | 10
17P LOSS WILD-TYPE | 31 | 26 | 28 | 29

Figure S69. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 5.49e-22 (Fisher's exact test), Q value = 4.1e-19

Table S70. Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
17P LOSS CNV | 128 | 46 | 57 | 21
17P LOSS WILD-TYPE | 72 | 188 | 43 | 20

Figure S70. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 2.44e-07 (Fisher's exact test), Q value = 0.00018

Table S71. Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
17P LOSS CNV | 86 | 35 | 27
17P LOSS WILD-TYPE | 57 | 78 | 64

Figure S71. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 3.25e-06 (Fisher's exact test), Q value = 0.0023

Table S72. Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
17P LOSS CNV | 21 | 45 | 21 | 11
17P LOSS WILD-TYPE | 17 | 36 | 35 | 55

Figure S72. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 9.87e-15 (Fisher's exact test), Q value = 7.3e-12

Table S73. Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
18P LOSS CNV | 11 | 53 | 52 | 10
18P LOSS WILD-TYPE | 34 | 9 | 17 | 29

Figure S73. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.51e-12 (Fisher's exact test), Q value = 6.2e-09

Table S74. Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 61 | 114 | 40
18P LOSS CNV | 13 | 81 | 32
18P LOSS WILD-TYPE | 48 | 33 | 8

Figure S74. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 4.26e-47 (Fisher's exact test), Q value = 3.2e-44

Table S75. Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
18P LOSS CNV | 176 | 53 | 62 | 33
18P LOSS WILD-TYPE | 24 | 181 | 38 | 8

Figure S75. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 4.33e-19 (Fisher's exact test), Q value = 3.2e-16

Table S76. Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
18P LOSS CNV | 120 | 38 | 35
18P LOSS WILD-TYPE | 23 | 75 | 56

Figure S76. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 5.39e-16 (Fisher's exact test), Q value = 4e-13

Table S77. Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
18P LOSS CNV | 20 | 66 | 33 | 9
18P LOSS WILD-TYPE | 18 | 15 | 23 | 57

Figure S77. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-11 (Fisher's exact test), Q value = 2e-08

Table S78. Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
18P LOSS CNV | 56 | 13 | 59
18P LOSS WILD-TYPE | 39 | 54 | 20

Figure S78. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 1e-09

Table S79. Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 45 | 62 | 69 | 39
18Q LOSS CNV | 15 | 54 | 54 | 12
18Q LOSS WILD-TYPE | 30 | 8 | 15 | 27

Figure S79. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-11 (Fisher's exact test), Q value = 1.4e-08

Table S80. Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 61 | 114 | 40
18Q LOSS CNV | 16 | 86 | 33
18Q LOSS WILD-TYPE | 45 | 28 | 7

Figure S80. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 6.8e-51 (Fisher's exact test), Q value = 5.2e-48

Table S81. Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
18Q LOSS CNV | 180 | 59 | 77 | 36
18Q LOSS WILD-TYPE | 20 | 175 | 23 | 5

Figure S81. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 8.03e-21 (Fisher's exact test), Q value = 6e-18

Table S82. Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 143 | 113 | 91
18Q LOSS CNV | 128 | 45 | 38
18Q LOSS WILD-TYPE | 15 | 68 | 53

Figure S82. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3.96e-16 (Fisher's exact test), Q value = 2.9e-13

Table S83. Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 81 | 56 | 66
18Q LOSS CNV | 26 | 68 | 34 | 11
18Q LOSS WILD-TYPE | 12 | 13 | 22 | 55

Figure S83. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-09 (Fisher's exact test), Q value = 2.7e-06

Table S84. Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 95 | 67 | 79
18Q LOSS CNV | 58 | 19 | 62
18Q LOSS WILD-TYPE | 37 | 48 | 17

Figure S84. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.01

Table S85. Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
19P LOSS CNV | 7 | 1 | 5 | 7
19P LOSS WILD-TYPE | 193 | 233 | 95 | 34

Figure S85. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.16

Table S86. Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
19Q LOSS CNV | 6 | 1 | 6 | 5
19Q LOSS WILD-TYPE | 194 | 233 | 94 | 36

Figure S86. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00033

Table S87. Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
20P LOSS CNV | 27 | 5 | 15 | 0
20P LOSS WILD-TYPE | 173 | 229 | 85 | 41

Figure S87. Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.025

Table S88. Gene #76: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
21Q LOSS CNV | 58 | 28 | 16 | 12
21Q LOSS WILD-TYPE | 142 | 206 | 84 | 29

Figure S88. Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.8e-14 (Fisher's exact test), Q value = 5.7e-11

Table S89. Gene #77: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 200 | 234 | 100 | 41
22Q LOSS CNV | 76 | 20 | 13 | 13
22Q LOSS WILD-TYPE | 124 | 214 | 87 | 28

Figure S89. Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 575

- Number of significantly arm-level cnvs = 78

- Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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