Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C11G0JKF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C11G0JKF
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 57 arm-level results and 8 molecular subtypes across 66 patients, 59 significant findings detected with Q value < 0.25.

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

- 4q gain cnv correlated to 'MRNASEQ_CNMF'.

- 11p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'MRNASEQ_CNMF'.

- 16q gain cnv correlated to 'MRNASEQ_CNMF'.

- Xq gain cnv correlated to 'MRNASEQ_CNMF'.

- 1p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 2p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 2q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 6p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 6q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 8q loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 10q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 13q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 16q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 17p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 57 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 59 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test
2p loss | 0 (0%) | 23 | 0.0828 (1.00) | 2.89e-06 (0.00127) | 8.31e-09 (3.77e-06) | 2.26e-07 (0.000102) | 0.0679 (1.00) | 0.000592 (0.236) | 0.0107 (1.00) | 1.05e-05 (0.00458)
2q loss | 0 (0%) | 23 | 0.0828 (1.00) | 2.89e-06 (0.00127) | 8.31e-09 (3.77e-06) | 2.26e-07 (0.000102) | 0.0679 (1.00) | 0.000592 (0.236) | 0.0107 (1.00) | 1.05e-05 (0.00458)
17p loss | 0 (0%) | 21 | 0.158 (1.00) | 8.78e-07 (0.000392) | 2.61e-09 (1.19e-06) | 3e-07 (0.000135) | 0.0256 (1.00) | 0.000255 (0.104) | 0.0305 (1.00) | 2.11e-05 (0.00913)
17q loss | 0 (0%) | 21 | 0.158 (1.00) | 8.78e-07 (0.000392) | 2.61e-09 (1.19e-06) | 3e-07 (0.000135) | 0.0256 (1.00) | 0.000255 (0.104) | 0.0305 (1.00) | 2.11e-05 (0.00913)
1p loss | 0 (0%) | 18 | 0.342 (1.00) | 8.27e-05 (0.035) | 8.26e-06 (0.0036) | 1.79e-05 (0.00777) | 0.0572 (1.00) | 0.00103 (0.404) | 0.106 (1.00) | 0.000454 (0.182)
1q loss | 0 (0%) | 19 | 0.32 (1.00) | 0.000139 (0.0576) | 3.11e-05 (0.0133) | 6.59e-05 (0.028) | 0.127 (1.00) | 0.00157 (0.606) | 0.0911 (1.00) | 0.000406 (0.164)
6p loss | 0 (0%) | 19 | 0.32 (1.00) | 0.000139 (0.0576) | 1.26e-06 (0.000559) | 2.67e-05 (0.0115) | 0.127 (1.00) | 0.00157 (0.606) | 0.114 (1.00) | 0.000406 (0.164)
6q loss | 0 (0%) | 19 | 0.32 (1.00) | 0.000139 (0.0576) | 1.26e-06 (0.000559) | 2.67e-05 (0.0115) | 0.127 (1.00) | 0.00157 (0.606) | 0.114 (1.00) | 0.000406 (0.164)
10p loss | 0 (0%) | 22 | 0.261 (1.00) | 0.00329 (1.00) | 2.51e-06 (0.00111) | 3.03e-06 (0.00133) | 0.391 (1.00) | 0.0506 (1.00) | 0.02 (1.00) | 0.000119 (0.0493)
10q loss | 0 (0%) | 22 | 0.261 (1.00) | 0.00329 (1.00) | 2.51e-06 (0.00111) | 3.03e-06 (0.00133) | 0.391 (1.00) | 0.0506 (1.00) | 0.02 (1.00) | 0.000119 (0.0493)
Xq loss | 0 (0%) | 33 | 0.713 (1.00) | 9.23e-05 (0.0386) | 7.96e-05 (0.0337) | 0.000217 (0.0884) | 0.019 (1.00) | 0.00208 (0.792) | 0.0983 (1.00) | 0.00108 (0.424)
4p gain | 0 (0%) | 48 | 0.383 (1.00) | 0.934 (1.00) | 4.56e-05 (0.0194) | 0.000161 (0.0662) | 0.239 (1.00) | 0.1 (1.00) | 0.938 (1.00) | 0.0477 (1.00)
11p gain | 0 (0%) | 53 | 0.517 (1.00) | 0.599 (1.00) | 0.000287 (0.116) | 0.000156 (0.0643) | 0.5 (1.00) | 0.186 (1.00) | 0.717 (1.00) | 0.0361 (1.00)
11q gain | 0 (0%) | 52 | 0.606 (1.00) | 0.613 (1.00) | 8.33e-05 (0.0352) | 2.78e-05 (0.0119) | 0.698 (1.00) | 0.186 (1.00) | 0.855 (1.00) | 0.0192 (1.00)
4q gain | 0 (0%) | 49 | 0.362 (1.00) | 0.806 (1.00) | 0.000173 (0.0707) | 0.000784 (0.31) | 0.144 (1.00) | 0.0977 (1.00) | 0.784 (1.00) | 0.0913 (1.00)
16p gain | 0 (0%) | 51 | 0.556 (1.00) | 1 (1.00) | 9.21e-05 (0.0386) | 0.000936 (0.37) | 0.137 (1.00) | 0.106 (1.00) | 0.909 (1.00) | 0.0318 (1.00)
16q gain | 0 (0%) | 51 | 0.556 (1.00) | 1 (1.00) | 9.21e-05 (0.0386) | 0.000936 (0.37) | 0.137 (1.00) | 0.106 (1.00) | 0.909 (1.00) | 0.0318 (1.00)
Xq gain | 0 (0%) | 57 | 1 (1.00) | 1 (1.00) | 8.84e-05 (0.0371) | 0.00417 (1.00) | 0.294 (1.00) | 0.341 (1.00) | 0.683 (1.00) | 0.00452 (1.00)
8p loss | 0 (0%) | 57 | 8.11e-08 (3.67e-05) | 0.0857 (1.00) | 0.0531 (1.00) | 0.0036 (1.00) | 0.148 (1.00) | 0.341 (1.00) | 0.0757 (1.00) | 0.12 (1.00)
8q loss | 0 (0%) | 58 | 5.86e-07 (0.000262) | 0.0437 (1.00) | 0.134 (1.00) | 0.00434 (1.00) | 0.291 (1.00) | 0.586 (1.00) | 0.165 (1.00) | 0.224 (1.00)
13q loss | 0 (0%) | 29 | 0.116 (1.00) | 0.00191 (0.732) | 0.00123 (0.48) | 0.000506 (0.202) | 0.743 (1.00) | 0.036 (1.00) | 0.933 (1.00) | 0.206 (1.00)
16q loss | 0 (0%) | 62 | 0.685 (1.00) | 0.302 (1.00) | 0.00219 (0.828) | 8.58e-05 (0.0361) | 0.678 (1.00) | 0.452 (1.00) | 0.461 (1.00) | 1 (1.00)
3p gain | 0 (0%) | 61 | 0.721 (1.00) | 1 (1.00) | 1 (1.00) | 0.942 (1.00) | 0.15 (1.00) | 0.134 (1.00) | 0.119 (1.00) | 0.616 (1.00)
3q gain | 0 (0%) | 61 | 0.721 (1.00) | 1 (1.00) | 1 (1.00) | 0.942 (1.00) | 0.15 (1.00) | 0.134 (1.00) | 0.119 (1.00) | 0.616 (1.00)
5p gain | 0 (0%) | 61 | 0.549 (1.00) | 1 (1.00) | 1 (1.00) | 0.839 (1.00) | 0.857 (1.00) | 0.134 (1.00) | 0.757 (1.00) | 0.398 (1.00)
5q gain | 0 (0%) | 61 | 0.549 (1.00) | 1 (1.00) | 1 (1.00) | 0.839 (1.00) | 0.857 (1.00) | 0.134 (1.00) | 0.757 (1.00) | 0.398 (1.00)
7p gain | 0 (0%) | 48 | 0.383 (1.00) | 0.934 (1.00) | 0.00906 (1.00) | 0.0191 (1.00) | 0.197 (1.00) | 1 (1.00) | 0.696 (1.00) | 0.27 (1.00)
7q gain | 0 (0%) | 48 | 0.383 (1.00) | 0.934 (1.00) | 0.00906 (1.00) | 0.0191 (1.00) | 0.197 (1.00) | 1 (1.00) | 0.696 (1.00) | 0.27 (1.00)
8p gain | 0 (0%) | 53 | 0.274 (1.00) | 0.599 (1.00) | 0.0276 (1.00) | 0.0848 (1.00) | 0.177 (1.00) | 1 (1.00) | 0.493 (1.00) | 0.16 (1.00)
8q gain | 0 (0%) | 52 | 0.157 (1.00) | 0.613 (1.00) | 0.00994 (1.00) | 0.0317 (1.00) | 0.387 (1.00) | 1 (1.00) | 0.633 (1.00) | 0.0886 (1.00)
9p gain | 0 (0%) | 58 | 1 (1.00) | 0.779 (1.00) | 0.911 (1.00) | 0.841 (1.00) | 0.804 (1.00) | 0.298 (1.00) | 0.443 (1.00) | 0.823 (1.00)
9q gain | 0 (0%) | 58 | 1 (1.00) | 0.779 (1.00) | 0.911 (1.00) | 0.841 (1.00) | 0.804 (1.00) | 0.298 (1.00) | 0.443 (1.00) | 0.823 (1.00)
12p gain | 0 (0%) | 52 | 0.688 (1.00) | 1 (1.00) | 0.0129 (1.00) | 0.0542 (1.00) | 0.698 (1.00) | 1 (1.00) | 0.995 (1.00) | 0.26 (1.00)
12q gain | 0 (0%) | 53 | 0.764 (1.00) | 0.772 (1.00) | 0.0135 (1.00) | 0.0191 (1.00) | 0.86 (1.00) | 0.675 (1.00) | 0.968 (1.00) | 0.374 (1.00)
14q gain | 0 (0%) | 50 | 0.34 (1.00) | 0.928 (1.00) | 0.000706 (0.28) | 0.00332 (1.00) | 0.261 (1.00) | 0.436 (1.00) | 0.986 (1.00) | 0.146 (1.00)
15q gain | 0 (0%) | 52 | 0.224 (1.00) | 0.664 (1.00) | 0.00113 (0.441) | 0.00646 (1.00) | 0.287 (1.00) | 0.671 (1.00) | 0.775 (1.00) | 0.169 (1.00)
18p gain | 0 (0%) | 52 | 0.475 (1.00) | 0.562 (1.00) | 0.0062 (1.00) | 0.0191 (1.00) | 0.806 (1.00) | 0.386 (1.00) | 0.495 (1.00) | 0.0755 (1.00)
18q gain | 0 (0%) | 53 | 0.671 (1.00) | 0.772 (1.00) | 0.00409 (1.00) | 0.0183 (1.00) | 0.926 (1.00) | 1 (1.00) | 0.717 (1.00) | 0.108 (1.00)
19p gain | 0 (0%) | 55 | 0.867 (1.00) | 0.904 (1.00) | 0.00206 (0.788) | 0.00219 (0.828) | 0.29 (1.00) | 0.337 (1.00) | 0.977 (1.00) | 0.0694 (1.00)
19q gain | 0 (0%) | 57 | 0.713 (1.00) | 0.712 (1.00) | 0.00269 (1.00) | 0.00372 (1.00) | 0.397 (1.00) | 0.341 (1.00) | 0.974 (1.00) | 0.0444 (1.00)
20p gain | 0 (0%) | 52 | 0.224 (1.00) | 0.562 (1.00) | 0.00468 (1.00) | 0.00377 (1.00) | 0.124 (1.00) | 0.671 (1.00) | 0.842 (1.00) | 0.345 (1.00)
20q gain | 0 (0%) | 51 | 0.282 (1.00) | 0.283 (1.00) | 0.00713 (1.00) | 0.00743 (1.00) | 0.17 (1.00) | 1 (1.00) | 0.793 (1.00) | 0.547 (1.00)
21q gain | 0 (0%) | 63 | 0.646 (1.00) | 0.158 (1.00) | 0.327 (1.00) | 0.333 (1.00) | 0.194 (1.00) | 0.361 (1.00) | 0.219 (1.00) | 0.518 (1.00)
22q gain | 0 (0%) | 51 | 0.882 (1.00) | 0.53 (1.00) | 0.0748 (1.00) | 0.196 (1.00) | 0.466 (1.00) | 1 (1.00) | 0.851 (1.00) | 0.693 (1.00)
3p loss | 0 (0%) | 59 | 0.0826 (1.00) | 1 (1.00) | 0.252 (1.00) | 0.00554 (1.00) | 0.481 (1.00) | 0.581 (1.00) | 0.0334 (1.00) | 0.00713 (1.00)
3q loss | 0 (0%) | 60 | 0.0326 (1.00) | 0.621 (1.00) | 0.135 (1.00) | 0.00126 (0.488) | 0.354 (1.00) | 0.585 (1.00) | 0.00901 (1.00) | 0.00208 (0.792)
5p loss | 0 (0%) | 59 | 0.302 (1.00) | 0.141 (1.00) | 0.0329 (1.00) | 0.00478 (1.00) | 0.886 (1.00) | 0.581 (1.00) | 0.587 (1.00) | 0.686 (1.00)
5q loss | 0 (0%) | 59 | 0.302 (1.00) | 0.141 (1.00) | 0.0329 (1.00) | 0.00478 (1.00) | 0.886 (1.00) | 0.581 (1.00) | 0.587 (1.00) | 0.686 (1.00)
9p loss | 0 (0%) | 58 | 1 (1.00) | 0.888 (1.00) | 0.171 (1.00) | 0.579 (1.00) | 1 (1.00) | 0.298 (1.00) | 0.857 (1.00) | 0.424 (1.00)
9q loss | 0 (0%) | 58 | 1 (1.00) | 0.888 (1.00) | 0.171 (1.00) | 0.579 (1.00) | 1 (1.00) | 0.298 (1.00) | 0.857 (1.00) | 0.424 (1.00)
11p loss | 0 (0%) | 61 | 1 (1.00) | 0.696 (1.00) | 0.129 (1.00) | 0.408 (1.00) | 0.12 (1.00) | 1 (1.00) | 0.0446 (1.00) | 0.0252 (1.00)
11q loss | 0 (0%) | 61 | 1 (1.00) | 0.696 (1.00) | 0.129 (1.00) | 0.408 (1.00) | 0.12 (1.00) | 1 (1.00) | 0.0446 (1.00) | 0.0252 (1.00)
16p loss | 0 (0%) | 63 | 1 (1.00) | 0.418 (1.00) | 0.0126 (1.00) | 0.00148 (0.572) | 1 (1.00) | 1 (1.00) | 0.69 (1.00) | 1 (1.00)
18p loss | 0 (0%) | 61 | 0.257 (1.00) | 0.109 (1.00) | 0.0134 (1.00) | 0.0012 (0.468) | 0.12 (1.00) | 1 (1.00) | 0.258 (1.00) | 0.367 (1.00)
18q loss | 0 (0%) | 59 | 0.222 (1.00) | 0.141 (1.00) | 0.0481 (1.00) | 0.0178 (1.00) | 0.203 (1.00) | 1 (1.00) | 0.191 (1.00) | 0.419 (1.00)
21q loss | 0 (0%) | 38 | 1 (1.00) | 0.00704 (1.00) | 0.23 (1.00) | 0.0379 (1.00) | 0.575 (1.00) | 0.722 (1.00) | 0.224 (1.00) | 0.159 (1.00)
22q loss | 0 (0%) | 61 | 0.721 (1.00) | 0.109 (1.00) | 0.745 (1.00) | 0.38 (1.00) | 1 (1.00) | 1 (1.00) | 0.826 (1.00) | 0.67 (1.00)

'4p gain' versus 'MRNASEQ_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.019

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
4P GAIN CNV | 3 | 14 | 1 | 0
4P GAIN WILD-TYPE | 16 | 8 | 14 | 10

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000161 (Chi-square test), Q value = 0.066

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
4P GAIN CNV | 1 | 1 | 12 | 0 | 4
4P GAIN WILD-TYPE | 9 | 9 | 5 | 6 | 19

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

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.071

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
4Q GAIN CNV | 3 | 13 | 1 | 0
4Q GAIN WILD-TYPE | 16 | 9 | 14 | 10

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

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.000287 (Fisher's exact test), Q value = 0.12

Table S4. Gene #13: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
11P GAIN CNV | 1 | 11 | 1 | 0
11P GAIN WILD-TYPE | 18 | 11 | 14 | 10

Figure S4. Get High-res Image Gene #13: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000156 (Chi-square test), Q value = 0.064

Table S5. Gene #13: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
11P GAIN CNV | 1 | 1 | 10 | 0 | 1
11P GAIN WILD-TYPE | 9 | 9 | 7 | 6 | 22

Figure S5. Get High-res Image Gene #13: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 8.33e-05 (Fisher's exact test), Q value = 0.035

Table S6. Gene #14: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
11Q GAIN CNV | 1 | 12 | 1 | 0
11Q GAIN WILD-TYPE | 18 | 10 | 14 | 10

Figure S6. Get High-res Image Gene #14: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.78e-05 (Chi-square test), Q value = 0.012

Table S7. Gene #14: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
11Q GAIN CNV | 1 | 1 | 11 | 0 | 1
11Q GAIN WILD-TYPE | 9 | 9 | 6 | 6 | 22

Figure S7. Get High-res Image Gene #14: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 9.21e-05 (Fisher's exact test), Q value = 0.039

Table S8. Gene #19: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
16P GAIN CNV | 3 | 12 | 0 | 0
16P GAIN WILD-TYPE | 16 | 10 | 15 | 10

Figure S8. Get High-res Image Gene #19: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 9.21e-05 (Fisher's exact test), Q value = 0.039

Table S9. Gene #20: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
16Q GAIN CNV | 3 | 12 | 0 | 0
16Q GAIN WILD-TYPE | 16 | 10 | 15 | 10

Figure S9. Get High-res Image Gene #20: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Xq gain' versus 'MRNASEQ_CNMF'

P value = 8.84e-05 (Fisher's exact test), Q value = 0.037

Table S10. Gene #29: 'Xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
XQ GAIN CNV | 0 | 9 | 0 | 0
XQ GAIN WILD-TYPE | 19 | 13 | 15 | 10

Figure S10. Get High-res Image Gene #29: 'Xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 8.27e-05 (Fisher's exact test), Q value = 0.035

Table S11. Gene #30: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
1P LOSS CNV | 16 | 29 | 3
1P LOSS WILD-TYPE | 2 | 6 | 10

Figure S11. Get High-res Image Gene #30: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 8.26e-06 (Fisher's exact test), Q value = 0.0036

Table S12. Gene #30: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
1P LOSS CNV | 19 | 12 | 14 | 3
1P LOSS WILD-TYPE | 0 | 10 | 1 | 7

Figure S12. Get High-res Image Gene #30: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-05 (Chi-square test), Q value = 0.0078

Table S13. Gene #30: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
1P LOSS CNV | 9 | 2 | 9 | 6 | 22
1P LOSS WILD-TYPE | 1 | 8 | 8 | 0 | 1

Figure S13. Get High-res Image Gene #30: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.18

Table S14. Gene #30: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
1P LOSS CNV | 5 | 5 | 17 | 21
1P LOSS WILD-TYPE | 7 | 3 | 8 | 0

Figure S14. Get High-res Image Gene #30: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.058

Table S15. Gene #31: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
1Q LOSS CNV | 16 | 28 | 3
1Q LOSS WILD-TYPE | 2 | 7 | 10

Figure S15. Get High-res Image Gene #31: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.013

Table S16. Gene #31: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
1Q LOSS CNV | 19 | 12 | 13 | 3
1Q LOSS WILD-TYPE | 0 | 10 | 2 | 7

Figure S16. Get High-res Image Gene #31: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.59e-05 (Chi-square test), Q value = 0.028

Table S17. Gene #31: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
1Q LOSS CNV | 9 | 2 | 9 | 5 | 22
1Q LOSS WILD-TYPE | 1 | 8 | 8 | 1 | 1

Figure S17. Get High-res Image Gene #31: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000406 (Fisher's exact test), Q value = 0.16

Table S18. Gene #31: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
1Q LOSS CNV | 5 | 5 | 16 | 21
1Q LOSS WILD-TYPE | 7 | 3 | 9 | 0

Figure S18. Get High-res Image Gene #31: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 2.89e-06 (Fisher's exact test), Q value = 0.0013

Table S19. Gene #32: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
2P LOSS CNV | 16 | 26 | 1
2P LOSS WILD-TYPE | 2 | 9 | 12

Figure S19. Get High-res Image Gene #32: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 8.31e-09 (Fisher's exact test), Q value = 3.8e-06

Table S20. Gene #32: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
2P LOSS CNV | 19 | 11 | 13 | 0
2P LOSS WILD-TYPE | 0 | 11 | 2 | 10

Figure S20. Get High-res Image Gene #32: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-07 (Chi-square test), Q value = 1e-04

Table S21. Gene #32: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
2P LOSS CNV | 10 | 0 | 8 | 3 | 22
2P LOSS WILD-TYPE | 0 | 10 | 9 | 3 | 1

Figure S21. Get High-res Image Gene #32: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000592 (Fisher's exact test), Q value = 0.24

Table S22. Gene #32: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
2P LOSS CNV | 1 | 42
2P LOSS WILD-TYPE | 8 | 15

Figure S22. Get High-res Image Gene #32: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0046

Table S23. Gene #32: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
2P LOSS CNV | 3 | 4 | 15 | 21
2P LOSS WILD-TYPE | 9 | 4 | 10 | 0

Figure S23. Get High-res Image Gene #32: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 2.89e-06 (Fisher's exact test), Q value = 0.0013

Table S24. Gene #33: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
2Q LOSS CNV | 16 | 26 | 1
2Q LOSS WILD-TYPE | 2 | 9 | 12

Figure S24. Get High-res Image Gene #33: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 8.31e-09 (Fisher's exact test), Q value = 3.8e-06

Table S25. Gene #33: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
2Q LOSS CNV | 19 | 11 | 13 | 0
2Q LOSS WILD-TYPE | 0 | 11 | 2 | 10

Figure S25. Get High-res Image Gene #33: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-07 (Chi-square test), Q value = 1e-04

Table S26. Gene #33: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
2Q LOSS CNV | 10 | 0 | 8 | 3 | 22
2Q LOSS WILD-TYPE | 0 | 10 | 9 | 3 | 1

Figure S26. Get High-res Image Gene #33: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000592 (Fisher's exact test), Q value = 0.24

Table S27. Gene #33: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
2Q LOSS CNV | 1 | 42
2Q LOSS WILD-TYPE | 8 | 15

Figure S27. Get High-res Image Gene #33: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0046

Table S28. Gene #33: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
2Q LOSS CNV | 3 | 4 | 15 | 21
2Q LOSS WILD-TYPE | 9 | 4 | 10 | 0

Figure S28. Get High-res Image Gene #33: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.058

Table S29. Gene #38: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
6P LOSS CNV | 16 | 28 | 3
6P LOSS WILD-TYPE | 2 | 7 | 10

Figure S29. Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.00056

Table S30. Gene #38: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
6P LOSS CNV | 19 | 12 | 14 | 2
6P LOSS WILD-TYPE | 0 | 10 | 1 | 8

Figure S30. Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-05 (Chi-square test), Q value = 0.011

Table S31. Gene #38: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
6P LOSS CNV | 10 | 2 | 9 | 4 | 22
6P LOSS WILD-TYPE | 0 | 8 | 8 | 2 | 1

Figure S31. Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000406 (Fisher's exact test), Q value = 0.16

Table S32. Gene #38: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
6P LOSS CNV | 5 | 5 | 16 | 21
6P LOSS WILD-TYPE | 7 | 3 | 9 | 0

Figure S32. Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.058

Table S33. Gene #39: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
6Q LOSS CNV | 16 | 28 | 3
6Q LOSS WILD-TYPE | 2 | 7 | 10

Figure S33. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.00056

Table S34. Gene #39: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
6Q LOSS CNV | 19 | 12 | 14 | 2
6Q LOSS WILD-TYPE | 0 | 10 | 1 | 8

Figure S34. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-05 (Chi-square test), Q value = 0.011

Table S35. Gene #39: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
6Q LOSS CNV | 10 | 2 | 9 | 4 | 22
6Q LOSS WILD-TYPE | 0 | 8 | 8 | 2 | 1

Figure S35. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000406 (Fisher's exact test), Q value = 0.16

Table S36. Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
6Q LOSS CNV | 5 | 5 | 16 | 21
6Q LOSS WILD-TYPE | 7 | 3 | 9 | 0

Figure S36. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 8.11e-08 (Fisher's exact test), Q value = 3.7e-05

Table S37. Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
8P LOSS CNV | 0 | 0 | 9
8P LOSS WILD-TYPE | 5 | 47 | 5

Figure S37. Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 5.86e-07 (Fisher's exact test), Q value = 0.00026

Table S38. Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
8Q LOSS CNV | 0 | 0 | 8
8Q LOSS WILD-TYPE | 5 | 47 | 6

Figure S38. Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 2.51e-06 (Fisher's exact test), Q value = 0.0011

Table S39. Gene #44: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
10P LOSS CNV | 19 | 9 | 13 | 3
10P LOSS WILD-TYPE | 0 | 13 | 2 | 7

Figure S39. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.03e-06 (Chi-square test), Q value = 0.0013

Table S40. Gene #44: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
10P LOSS CNV | 10 | 2 | 6 | 4 | 22
10P LOSS WILD-TYPE | 0 | 8 | 11 | 2 | 1

Figure S40. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.049

Table S41. Gene #44: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
10P LOSS CNV | 6 | 3 | 14 | 21
10P LOSS WILD-TYPE | 6 | 5 | 11 | 0

Figure S41. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.51e-06 (Fisher's exact test), Q value = 0.0011

Table S42. Gene #45: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
10Q LOSS CNV | 19 | 9 | 13 | 3
10Q LOSS WILD-TYPE | 0 | 13 | 2 | 7

Figure S42. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.03e-06 (Chi-square test), Q value = 0.0013

Table S43. Gene #45: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
10Q LOSS CNV | 10 | 2 | 6 | 4 | 22
10Q LOSS WILD-TYPE | 0 | 8 | 11 | 2 | 1

Figure S43. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.049

Table S44. Gene #45: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
10Q LOSS CNV | 6 | 3 | 14 | 21
10Q LOSS WILD-TYPE | 6 | 5 | 11 | 0

Figure S44. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000506 (Chi-square test), Q value = 0.2

Table S45. Gene #48: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
13Q LOSS CNV | 10 | 1 | 8 | 2 | 16
13Q LOSS WILD-TYPE | 0 | 9 | 9 | 4 | 7

Figure S45. Get High-res Image Gene #48: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.58e-05 (Chi-square test), Q value = 0.036

Table S46. Gene #50: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
16Q LOSS CNV | 4 | 0 | 0 | 0 | 0
16Q LOSS WILD-TYPE | 6 | 10 | 17 | 6 | 23

Figure S46. Get High-res Image Gene #50: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 8.78e-07 (Fisher's exact test), Q value = 0.00039

Table S47. Gene #51: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
17P LOSS CNV | 16 | 28 | 1
17P LOSS WILD-TYPE | 2 | 7 | 12

Figure S47. Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 2.61e-09 (Fisher's exact test), Q value = 1.2e-06

Table S48. Gene #51: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
17P LOSS CNV | 19 | 12 | 14 | 0
17P LOSS WILD-TYPE | 0 | 10 | 1 | 10

Figure S48. Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-07 (Chi-square test), Q value = 0.00013

Table S49. Gene #51: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
17P LOSS CNV | 10 | 0 | 9 | 4 | 22
17P LOSS WILD-TYPE | 0 | 10 | 8 | 2 | 1

Figure S49. Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000255 (Fisher's exact test), Q value = 0.1

Table S50. Gene #51: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
17P LOSS CNV | 1 | 44
17P LOSS WILD-TYPE | 8 | 13

Figure S50. Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0091

Table S51. Gene #51: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
17P LOSS CNV | 3 | 5 | 16 | 21
17P LOSS WILD-TYPE | 9 | 3 | 9 | 0

Figure S51. Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 8.78e-07 (Fisher's exact test), Q value = 0.00039

Table S52. Gene #52: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
17Q LOSS CNV | 16 | 28 | 1
17Q LOSS WILD-TYPE | 2 | 7 | 12

Figure S52. Get High-res Image Gene #52: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 2.61e-09 (Fisher's exact test), Q value = 1.2e-06

Table S53. Gene #52: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
17Q LOSS CNV | 19 | 12 | 14 | 0
17Q LOSS WILD-TYPE | 0 | 10 | 1 | 10

Figure S53. Get High-res Image Gene #52: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-07 (Chi-square test), Q value = 0.00013

Table S54. Gene #52: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
17Q LOSS CNV | 10 | 0 | 9 | 4 | 22
17Q LOSS WILD-TYPE | 0 | 10 | 8 | 2 | 1

Figure S54. Get High-res Image Gene #52: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000255 (Fisher's exact test), Q value = 0.1

Table S55. Gene #52: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
17Q LOSS CNV | 1 | 44
17Q LOSS WILD-TYPE | 8 | 13

Figure S55. Get High-res Image Gene #52: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0091

Table S56. Gene #52: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
17Q LOSS CNV | 3 | 5 | 16 | 21
17Q LOSS WILD-TYPE | 9 | 3 | 9 | 0

Figure S56. Get High-res Image Gene #52: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Xq loss' versus 'METHLYATION_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.039

Table S57. Gene #57: 'Xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
XQ LOSS CNV | 12 | 21 | 0
XQ LOSS WILD-TYPE | 6 | 14 | 13

Figure S57. Get High-res Image Gene #57: 'Xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Xq loss' versus 'MRNASEQ_CNMF'

P value = 7.96e-05 (Fisher's exact test), Q value = 0.034

Table S58. Gene #57: 'Xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
XQ LOSS CNV | 15 | 8 | 10 | 0
XQ LOSS WILD-TYPE | 4 | 14 | 5 | 10

Figure S58. Get High-res Image Gene #57: 'Xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000217 (Chi-square test), Q value = 0.088

Table S59. Gene #57: 'Xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
XQ LOSS CNV | 7 | 0 | 5 | 3 | 18
XQ LOSS WILD-TYPE | 3 | 10 | 12 | 3 | 5

Figure S59. Get High-res Image Gene #57: 'Xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

- Number of patients = 66

- Number of significantly arm-level cnvs = 57

- Number of molecular subtypes = 8

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

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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