Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1X63KPN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X63KPN
Overview
Introduction

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

Summary

Testing the association between copy number variation 61 arm-level events and 8 molecular subtypes across 66 patients, 62 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

- 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' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

- 13q loss cnv correlated to 'METHLYATION_CNMF' and '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'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 61 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 62 significant findings detected.

|  | Clinical Features | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
1q loss | 52 (79%) | 14 | 0.474 (1.00) | 1e-05 (0.00488) | 7e-05 (0.0313) | 5e-05 (0.0225) | 0.233 (1.00) | 0.00047 (0.201) | 0.0761 (1.00) | 4e-05 (0.0181)
2p loss | 46 (70%) | 20 | 0.0881 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.083 (1.00) | 1e-05 (0.00488) | 0.0231 (1.00) | 1e-05 (0.00488)
2q loss | 46 (70%) | 20 | 0.0883 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0838 (1.00) | 1e-05 (0.00488) | 0.0225 (1.00) | 1e-05 (0.00488)
10p loss | 48 (73%) | 18 | 0.341 (1.00) | 0.00032 (0.138) | 7e-05 (0.0313) | 1e-05 (0.00488) | 0.274 (1.00) | 0.00017 (0.0739) | 0.00639 (1.00) | 1e-05 (0.00488)
10q loss | 49 (74%) | 17 | 0.25 (1.00) | 0.00018 (0.0781) | 2e-05 (0.0092) | 1e-05 (0.00488) | 0.226 (1.00) | 0.00025 (0.108) | 0.0132 (1.00) | 9e-05 (0.0395)
17p loss | 50 (76%) | 16 | 0.3 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0509 (1.00) | 7e-05 (0.0313) | 0.0251 (1.00) | 2e-05 (0.0092)
17q loss | 50 (76%) | 16 | 0.3 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.0512 (1.00) | 6e-05 (0.0269) | 0.0262 (1.00) | 1e-05 (0.00488)
6p loss | 51 (77%) | 15 | 0.33 (1.00) | 8e-05 (0.0354) | 9e-05 (0.0395) | 1e-05 (0.00488) | 0.353 (1.00) | 0.0012 (0.504) | 0.304 (1.00) | 0.00012 (0.0524)
6q loss | 51 (77%) | 15 | 0.329 (1.00) | 0.00012 (0.0524) | 7e-05 (0.0313) | 1e-05 (0.00488) | 0.352 (1.00) | 0.00111 (0.468) | 0.302 (1.00) | 4e-05 (0.0181)
1p loss | 53 (80%) | 13 | 0.674 (1.00) | 3e-05 (0.0137) | 0.0004 (0.172) | 0.00029 (0.125) | 0.164 (1.00) | 0.00129 (0.538) | 0.0991 (1.00) | 0.00143 (0.595)
4p gain | 24 (36%) | 42 | 0.0553 (1.00) | 1 (1.00) | 3e-05 (0.0137) | 6e-05 (0.0269) | 0.77 (1.00) | 0.00859 (1.00) | 0.775 (1.00) | 0.129 (1.00)
4q gain | 24 (36%) | 42 | 0.0566 (1.00) | 1 (1.00) | 2e-05 (0.0092) | 4e-05 (0.0181) | 0.769 (1.00) | 0.00908 (1.00) | 0.775 (1.00) | 0.127 (1.00)
11p gain | 15 (23%) | 51 | 0.284 (1.00) | 0.677 (1.00) | 3e-05 (0.0137) | 0.00043 (0.184) | 0.87 (1.00) | 0.0271 (1.00) | 0.718 (1.00) | 0.153 (1.00)
11q gain | 15 (23%) | 51 | 0.281 (1.00) | 0.681 (1.00) | 1e-05 (0.00488) | 1e-05 (0.00488) | 0.622 (1.00) | 0.0206 (1.00) | 0.387 (1.00) | 0.0558 (1.00)
16p gain | 21 (32%) | 45 | 0.108 (1.00) | 1 (1.00) | 1e-05 (0.00488) | 7e-05 (0.0313) | 0.158 (1.00) | 0.00501 (1.00) | 0.8 (1.00) | 0.0844 (1.00)
16q gain | 21 (32%) | 45 | 0.106 (1.00) | 1 (1.00) | 2e-05 (0.0092) | 8e-05 (0.0354) | 0.16 (1.00) | 0.00536 (1.00) | 0.801 (1.00) | 0.0843 (1.00)
13q loss | 43 (65%) | 23 | 0.26 (1.00) | 0.00053 (0.226) | 0.00353 (1.00) | 8e-05 (0.0354) | 0.852 (1.00) | 0.197 (1.00) | 0.935 (1.00) | 0.0987 (1.00)
8p loss | 9 (14%) | 57 | 1e-05 (0.00488) | 0.0844 (1.00) | 0.0532 (1.00) | 0.0391 (1.00) | 0.147 (1.00) | 0.466 (1.00) | 0.073 (1.00) | 0.0088 (1.00)
8q loss | 8 (12%) | 58 | 1e-05 (0.00488) | 0.042 (1.00) | 0.134 (1.00) | 0.0715 (1.00) | 0.287 (1.00) | 0.527 (1.00) | 0.171 (1.00) | 0.0497 (1.00)
3p gain | 8 (12%) | 58 | 0.271 (1.00) | 0.532 (1.00) | 0.952 (1.00) | 0.648 (1.00) | 0.517 (1.00) | 0.692 (1.00) | 0.0133 (1.00) | 0.795 (1.00)
3q gain | 8 (12%) | 58 | 0.271 (1.00) | 0.528 (1.00) | 0.952 (1.00) | 0.651 (1.00) | 0.514 (1.00) | 0.691 (1.00) | 0.0134 (1.00) | 0.795 (1.00)
5p gain | 8 (12%) | 58 | 0.427 (1.00) | 0.682 (1.00) | 0.448 (1.00) | 0.448 (1.00) | 0.363 (1.00) | 0.0596 (1.00) | 0.683 (1.00) | 0.314 (1.00)
5q gain | 8 (12%) | 58 | 0.425 (1.00) | 0.679 (1.00) | 0.45 (1.00) | 0.449 (1.00) | 0.363 (1.00) | 0.0616 (1.00) | 0.682 (1.00) | 0.312 (1.00)
7p gain | 24 (36%) | 42 | 0.152 (1.00) | 1 (1.00) | 0.0163 (1.00) | 0.0616 (1.00) | 0.9 (1.00) | 0.117 (1.00) | 0.775 (1.00) | 0.415 (1.00)
7q gain | 24 (36%) | 42 | 0.151 (1.00) | 1 (1.00) | 0.0157 (1.00) | 0.0613 (1.00) | 0.901 (1.00) | 0.119 (1.00) | 0.776 (1.00) | 0.418 (1.00)
8p gain | 17 (26%) | 49 | 0.41 (1.00) | 0.418 (1.00) | 0.0038 (1.00) | 0.0317 (1.00) | 0.464 (1.00) | 0.1 (1.00) | 0.731 (1.00) | 0.301 (1.00)
8q gain | 18 (27%) | 48 | 0.341 (1.00) | 0.378 (1.00) | 0.0012 (0.504) | 0.0104 (1.00) | 0.694 (1.00) | 0.0873 (1.00) | 0.938 (1.00) | 0.191 (1.00)
9p gain | 10 (15%) | 56 | 1 (1.00) | 1 (1.00) | 0.724 (1.00) | 0.814 (1.00) | 0.831 (1.00) | 0.601 (1.00) | 0.219 (1.00) | 0.656 (1.00)
9q gain | 10 (15%) | 56 | 1 (1.00) | 1 (1.00) | 0.724 (1.00) | 0.811 (1.00) | 0.833 (1.00) | 0.601 (1.00) | 0.221 (1.00) | 0.66 (1.00)
10p gain | 4 (6%) | 62 | 0.44 (1.00) | 0.164 (1.00) | 0.515 (1.00) | 0.205 (1.00) | 1 (1.00) | 0.165 (1.00) | 0.588 (1.00) | 0.11 (1.00)
12p gain | 19 (29%) | 47 | 0.482 (1.00) | 0.765 (1.00) | 0.078 (1.00) | 0.157 (1.00) | 1 (1.00) | 0.0672 (1.00) | 0.868 (1.00) | 0.429 (1.00)
12q gain | 20 (30%) | 46 | 0.445 (1.00) | 0.593 (1.00) | 0.146 (1.00) | 0.0829 (1.00) | 0.944 (1.00) | 0.033 (1.00) | 0.941 (1.00) | 0.33 (1.00)
14q gain | 21 (32%) | 45 | 0.107 (1.00) | 0.829 (1.00) | 0.00067 (0.285) | 0.00459 (1.00) | 0.426 (1.00) | 0.057 (1.00) | 0.881 (1.00) | 0.162 (1.00)
15q gain | 21 (32%) | 45 | 0.107 (1.00) | 0.827 (1.00) | 0.00184 (0.76) | 0.0621 (1.00) | 0.755 (1.00) | 0.214 (1.00) | 1 (1.00) | 0.136 (1.00)
18p gain | 17 (26%) | 49 | 0.516 (1.00) | 0.806 (1.00) | 0.00195 (0.803) | 0.0128 (1.00) | 0.938 (1.00) | 0.0496 (1.00) | 0.33 (1.00) | 0.0381 (1.00)
18q gain | 16 (24%) | 50 | 0.64 (1.00) | 0.927 (1.00) | 0.00107 (0.453) | 0.0191 (1.00) | 0.821 (1.00) | 0.0519 (1.00) | 0.416 (1.00) | 0.026 (1.00)
19p gain | 19 (29%) | 47 | 0.484 (1.00) | 0.275 (1.00) | 0.022 (1.00) | 0.00939 (1.00) | 0.661 (1.00) | 0.0386 (1.00) | 0.964 (1.00) | 0.126 (1.00)
19q gain | 17 (26%) | 49 | 0.521 (1.00) | 0.307 (1.00) | 0.00124 (0.518) | 0.00155 (0.643) | 0.412 (1.00) | 0.0477 (1.00) | 0.919 (1.00) | 0.024 (1.00)
20p gain | 20 (30%) | 46 | 0.213 (1.00) | 0.597 (1.00) | 0.0302 (1.00) | 0.0314 (1.00) | 0.707 (1.00) | 0.0312 (1.00) | 0.647 (1.00) | 0.31 (1.00)
20q gain | 21 (32%) | 45 | 0.226 (1.00) | 0.388 (1.00) | 0.0684 (1.00) | 0.0168 (1.00) | 0.676 (1.00) | 0.0371 (1.00) | 0.526 (1.00) | 0.436 (1.00)
21q gain | 4 (6%) | 62 | 0.439 (1.00) | 0.161 (1.00) | 0.512 (1.00) | 0.106 (1.00) | 0.677 (1.00) | 0.165 (1.00) | 0.497 (1.00) | 0.131 (1.00)
22q gain | 19 (29%) | 47 | 0.901 (1.00) | 0.712 (1.00) | 0.0699 (1.00) | 0.363 (1.00) | 0.551 (1.00) | 0.023 (1.00) | 1 (1.00) | 0.251 (1.00)
xq gain | 6 (9%) | 60 | 1 (1.00) | 0.722 (1.00) | 0.0067 (1.00) | 0.122 (1.00) | 0.263 (1.00) | 0.117 (1.00) | 0.51 (1.00) | 0.0247 (1.00)
3p loss | 9 (14%) | 57 | 0.0371 (1.00) | 0.895 (1.00) | 0.0657 (1.00) | 0.00331 (1.00) | 0.904 (1.00) | 0.204 (1.00) | 0.0291 (1.00) | 0.0699 (1.00)
3q loss | 8 (12%) | 58 | 0.0217 (1.00) | 0.369 (1.00) | 0.0254 (1.00) | 0.0017 (0.704) | 0.575 (1.00) | 0.178 (1.00) | 0.00532 (1.00) | 0.0245 (1.00)
5p loss | 10 (15%) | 56 | 0.0999 (1.00) | 0.252 (1.00) | 0.00067 (0.285) | 0.0187 (1.00) | 0.426 (1.00) | 0.0134 (1.00) | 0.635 (1.00) | 0.0307 (1.00)
5q loss | 10 (15%) | 56 | 0.0983 (1.00) | 0.251 (1.00) | 0.00074 (0.314) | 0.0189 (1.00) | 0.428 (1.00) | 0.0153 (1.00) | 0.633 (1.00) | 0.0319 (1.00)
9p loss | 10 (15%) | 56 | 1 (1.00) | 0.9 (1.00) | 0.0649 (1.00) | 0.0162 (1.00) | 0.912 (1.00) | 0.598 (1.00) | 0.922 (1.00) | 0.498 (1.00)
9q loss | 10 (15%) | 56 | 1 (1.00) | 0.902 (1.00) | 0.0643 (1.00) | 0.0156 (1.00) | 0.913 (1.00) | 0.601 (1.00) | 0.922 (1.00) | 0.5 (1.00)
11p loss | 7 (11%) | 59 | 0.627 (1.00) | 0.573 (1.00) | 0.111 (1.00) | 0.317 (1.00) | 0.203 (1.00) | 0.938 (1.00) | 0.401 (1.00) | 0.334 (1.00)
11q loss | 7 (11%) | 59 | 0.628 (1.00) | 0.572 (1.00) | 0.11 (1.00) | 0.314 (1.00) | 0.204 (1.00) | 0.939 (1.00) | 0.402 (1.00) | 0.334 (1.00)
16p loss | 4 (6%) | 62 | 0.686 (1.00) | 0.517 (1.00) | 0.0231 (1.00) | 0.0373 (1.00) | 0.683 (1.00) | 0.0869 (1.00) | 0.496 (1.00) | 0.807 (1.00)
16q loss | 5 (8%) | 61 | 0.72 (1.00) | 0.388 (1.00) | 0.00583 (1.00) | 0.00748 (1.00) | 0.427 (1.00) | 0.0481 (1.00) | 0.195 (1.00) | 0.521 (1.00)
18p loss | 8 (12%) | 58 | 0.677 (1.00) | 0.0963 (1.00) | 0.315 (1.00) | 0.211 (1.00) | 0.719 (1.00) | 0.949 (1.00) | 0.884 (1.00) | 0.892 (1.00)
18q loss | 10 (15%) | 56 | 0.623 (1.00) | 0.0791 (1.00) | 0.442 (1.00) | 0.278 (1.00) | 0.575 (1.00) | 0.864 (1.00) | 0.495 (1.00) | 0.613 (1.00)
19q loss | 3 (5%) | 63 | 0.645 (1.00) | 0.767 (1.00) | 0.765 (1.00) | 0.826 (1.00) | 0.513 (1.00) | 0.866 (1.00) | 0.81 (1.00) | 0.767 (1.00)
20p loss | 4 (6%) | 62 | 0.305 (1.00) | 0.807 (1.00) | 0.208 (1.00) | 0.212 (1.00) | 0.453 (1.00) | 0.659 (1.00) | 0.245 (1.00) | 0.272 (1.00)
20q loss | 3 (5%) | 63 | 1 (1.00) | 0.416 (1.00) | 0.227 (1.00) | 0.0578 (1.00) | 0.295 (1.00) | 0.828 (1.00) | 0.188 (1.00) | 0.538 (1.00)
21q loss | 35 (53%) | 31 | 0.775 (1.00) | 0.0103 (1.00) | 0.25 (1.00) | 0.195 (1.00) | 1 (1.00) | 0.128 (1.00) | 0.78 (1.00) | 0.289 (1.00)
22q loss | 8 (12%) | 58 | 0.83 (1.00) | 0.133 (1.00) | 0.249 (1.00) | 0.234 (1.00) | 0.898 (1.00) | 0.217 (1.00) | 0.762 (1.00) | 0.61 (1.00)
xq loss | 39 (59%) | 27 | 0.599 (1.00) | 0.0728 (1.00) | 0.00674 (1.00) | 0.00337 (1.00) | 0.328 (1.00) | 0.00116 (0.488) | 0.0751 (1.00) | 0.0221 (1.00)

'4p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

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 MUTATED | 4 | 17 | 2 | 1
4P GAIN WILD-TYPE | 15 | 5 | 13 | 9

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
4P GAIN MUTATED | 4 | 14 | 3 | 1 | 1 | 1 | 0
4P GAIN WILD-TYPE | 15 | 2 | 4 | 5 | 9 | 3 | 4

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

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

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 MUTATED | 4 | 17 | 2 | 1
4Q GAIN WILD-TYPE | 15 | 5 | 13 | 9

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

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
4Q GAIN MUTATED | 4 | 14 | 3 | 1 | 1 | 1 | 0
4Q GAIN WILD-TYPE | 15 | 2 | 4 | 5 | 9 | 3 | 4

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

'11p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S5. Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
11P GAIN MUTATED | 1 | 13 | 1 | 0
11P GAIN WILD-TYPE | 18 | 9 | 14 | 10

Figure S5. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.18

Table S6. Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
11P GAIN MUTATED | 1 | 11 | 1 | 1 | 1 | 0 | 0
11P GAIN WILD-TYPE | 18 | 5 | 6 | 5 | 9 | 4 | 4

Figure S6. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S7. Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
11Q GAIN MUTATED | 1 | 14 | 0 | 0
11Q GAIN WILD-TYPE | 18 | 8 | 15 | 10

Figure S7. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S8. Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
11Q GAIN MUTATED | 1 | 12 | 1 | 1 | 0 | 0 | 0
11Q GAIN WILD-TYPE | 18 | 4 | 6 | 5 | 10 | 4 | 4

Figure S8. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
16P GAIN MUTATED | 4 | 16 | 1 | 0
16P GAIN WILD-TYPE | 15 | 6 | 14 | 10

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

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S10. Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
16P GAIN MUTATED | 4 | 13 | 2 | 1 | 0 | 1 | 0
16P GAIN WILD-TYPE | 15 | 3 | 5 | 5 | 10 | 3 | 4

Figure S10. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S11. Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
16Q GAIN MUTATED | 4 | 16 | 1 | 0
16Q GAIN WILD-TYPE | 15 | 6 | 14 | 10

Figure S11. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.035

Table S12. Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
16Q GAIN MUTATED | 4 | 13 | 2 | 1 | 0 | 1 | 0
16Q GAIN WILD-TYPE | 15 | 3 | 5 | 5 | 10 | 3 | 4

Figure S12. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S13. Gene #31: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
1P LOSS MUTATED | 17 | 32 | 4
1P LOSS WILD-TYPE | 1 | 3 | 9

Figure S13. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.17

Table S14. Gene #31: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
1P LOSS MUTATED | 19 | 16 | 14 | 4
1P LOSS WILD-TYPE | 0 | 6 | 1 | 6

Figure S14. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S15. Gene #31: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
1P LOSS MUTATED | 19 | 11 | 6 | 4 | 9 | 4 | 0
1P LOSS WILD-TYPE | 0 | 5 | 1 | 2 | 1 | 0 | 4

Figure S15. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S16. Gene #32: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
1Q LOSS MUTATED | 17 | 32 | 3
1Q LOSS WILD-TYPE | 1 | 3 | 10

Figure S16. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S17. Gene #32: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
1Q LOSS MUTATED | 19 | 16 | 14 | 3
1Q LOSS WILD-TYPE | 0 | 6 | 1 | 7

Figure S17. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S18. Gene #32: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
1Q LOSS MUTATED | 19 | 11 | 5 | 3 | 10 | 4 | 0
1Q LOSS WILD-TYPE | 0 | 5 | 2 | 3 | 0 | 0 | 4

Figure S18. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.2

Table S19. Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
1Q LOSS MUTATED | 18 | 8 | 11 | 3 | 4 | 5 | 3
1Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 1 | 0 | 6

Figure S19. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S20. Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
1Q LOSS MUTATED | 14 | 5 | 12 | 2 | 9 | 8 | 2
1Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 0 | 1 | 6

Figure S20. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S21. Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S21. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S22. Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
2P LOSS MUTATED | 19 | 14 | 13 | 0
2P LOSS WILD-TYPE | 0 | 8 | 2 | 10

Figure S22. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S23. Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
2P LOSS MUTATED | 19 | 10 | 4 | 0 | 10 | 3 | 0
2P LOSS WILD-TYPE | 0 | 6 | 3 | 6 | 0 | 1 | 4

Figure S23. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S24. Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
2P LOSS MUTATED | 18 | 7 | 10 | 2 | 3 | 5 | 1
2P LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 2 | 0 | 8

Figure S24. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S25. Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
2P LOSS MUTATED | 14 | 4 | 11 | 1 | 9 | 7 | 0
2P LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 0 | 2 | 8

Figure S25. Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S26. Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S26. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S27. Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
2Q LOSS MUTATED | 19 | 14 | 13 | 0
2Q LOSS WILD-TYPE | 0 | 8 | 2 | 10

Figure S27. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S28. Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
2Q LOSS MUTATED | 19 | 10 | 4 | 0 | 10 | 3 | 0
2Q LOSS WILD-TYPE | 0 | 6 | 3 | 6 | 0 | 1 | 4

Figure S28. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S29. Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
2Q LOSS MUTATED | 18 | 7 | 10 | 2 | 3 | 5 | 1
2Q LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 2 | 0 | 8

Figure S29. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S30. Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
2Q LOSS MUTATED | 14 | 4 | 11 | 1 | 9 | 7 | 0
2Q LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 0 | 2 | 8

Figure S30. Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.035

Table S31. Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
6P LOSS MUTATED | 17 | 30 | 4
6P LOSS WILD-TYPE | 1 | 5 | 9

Figure S31. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S32. Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
6P LOSS MUTATED | 19 | 15 | 14 | 3
6P LOSS WILD-TYPE | 0 | 7 | 1 | 7

Figure S32. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S33. Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
6P LOSS MUTATED | 19 | 11 | 6 | 1 | 10 | 4 | 0
6P LOSS WILD-TYPE | 0 | 5 | 1 | 5 | 0 | 0 | 4

Figure S33. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.052

Table S34. Gene #39: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
6P LOSS MUTATED | 14 | 5 | 11 | 2 | 9 | 8 | 2
6P LOSS WILD-TYPE | 0 | 3 | 2 | 3 | 0 | 1 | 6

Figure S34. Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.052

Table S35. Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
6Q LOSS MUTATED | 17 | 30 | 4
6Q LOSS WILD-TYPE | 1 | 5 | 9

Figure S35. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S36. Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
6Q LOSS MUTATED | 19 | 15 | 14 | 3
6Q LOSS WILD-TYPE | 0 | 7 | 1 | 7

Figure S36. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S37. Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
6Q LOSS MUTATED | 19 | 11 | 6 | 1 | 10 | 4 | 0
6Q LOSS WILD-TYPE | 0 | 5 | 1 | 5 | 0 | 0 | 4

Figure S37. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S38. Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
6Q LOSS MUTATED | 14 | 5 | 11 | 2 | 9 | 8 | 2
6Q LOSS WILD-TYPE | 0 | 3 | 2 | 3 | 0 | 1 | 6

Figure S38. Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S39. Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S39. Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S40. Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S40. Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S41. Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
10P LOSS MUTATED | 17 | 27 | 4
10P LOSS WILD-TYPE | 1 | 8 | 9

Figure S41. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

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

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

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

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
10P LOSS MUTATED | 19 | 8 | 6 | 2 | 10 | 3 | 0
10P LOSS WILD-TYPE | 0 | 8 | 1 | 4 | 0 | 1 | 4

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

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.074

Table S44. Gene #45: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
10P LOSS MUTATED | 18 | 6 | 11 | 2 | 4 | 4 | 3
10P LOSS WILD-TYPE | 0 | 5 | 1 | 4 | 1 | 1 | 6

Figure S44. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S45. Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
10P LOSS MUTATED | 14 | 3 | 12 | 2 | 9 | 6 | 2
10P LOSS WILD-TYPE | 0 | 5 | 1 | 3 | 0 | 3 | 6

Figure S45. Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.078

Table S46. Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
10Q LOSS MUTATED | 17 | 28 | 4
10Q LOSS WILD-TYPE | 1 | 7 | 9

Figure S46. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S47. Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
10Q LOSS MUTATED | 19 | 13 | 14 | 3
10Q LOSS WILD-TYPE | 0 | 9 | 1 | 7

Figure S47. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S48. Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
10Q LOSS MUTATED | 19 | 8 | 6 | 2 | 10 | 4 | 0
10Q LOSS WILD-TYPE | 0 | 8 | 1 | 4 | 0 | 0 | 4

Figure S48. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.11

Table S49. Gene #46: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
10Q LOSS MUTATED | 18 | 7 | 11 | 2 | 4 | 4 | 3
10Q LOSS WILD-TYPE | 0 | 4 | 1 | 4 | 1 | 1 | 6

Figure S49. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S50. Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
10Q LOSS MUTATED | 14 | 4 | 12 | 2 | 9 | 6 | 2
10Q LOSS WILD-TYPE | 0 | 4 | 1 | 3 | 0 | 3 | 6

Figure S50. Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.23

Table S51. Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
13Q LOSS MUTATED | 11 | 29 | 3
13Q LOSS WILD-TYPE | 7 | 6 | 10

Figure S51. Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.035

Table S52. Gene #49: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
13Q LOSS MUTATED | 15 | 10 | 5 | 0 | 10 | 3 | 0
13Q LOSS WILD-TYPE | 4 | 6 | 2 | 6 | 0 | 1 | 4

Figure S52. Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S53. Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
17P LOSS MUTATED | 17 | 31 | 2
17P LOSS WILD-TYPE | 1 | 4 | 11

Figure S53. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S54. Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
17P LOSS MUTATED | 19 | 16 | 14 | 1
17P LOSS WILD-TYPE | 0 | 6 | 1 | 9

Figure S54. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S55. Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
17P LOSS MUTATED | 19 | 11 | 6 | 0 | 10 | 4 | 0
17P LOSS WILD-TYPE | 0 | 5 | 1 | 6 | 0 | 0 | 4

Figure S55. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S56. Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
17P LOSS MUTATED | 18 | 8 | 11 | 3 | 3 | 5 | 2
17P LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 2 | 0 | 7

Figure S56. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S57. Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
17P LOSS MUTATED | 14 | 5 | 12 | 2 | 9 | 7 | 1
17P LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 0 | 2 | 7

Figure S57. Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S58. Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
17Q LOSS MUTATED | 17 | 31 | 2
17Q LOSS WILD-TYPE | 1 | 4 | 11

Figure S58. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S59. Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
17Q LOSS MUTATED | 19 | 16 | 14 | 1
17Q LOSS WILD-TYPE | 0 | 6 | 1 | 9

Figure S59. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S60. Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
17Q LOSS MUTATED | 19 | 11 | 6 | 0 | 10 | 4 | 0
17Q LOSS WILD-TYPE | 0 | 5 | 1 | 6 | 0 | 0 | 4

Figure S60. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S61. Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
17Q LOSS MUTATED | 18 | 8 | 11 | 3 | 3 | 5 | 2
17Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 2 | 0 | 7

Figure S61. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S62. Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 14 | 8 | 13 | 5 | 9 | 9 | 8
17Q LOSS MUTATED | 14 | 5 | 12 | 2 | 9 | 7 | 1
17Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 0 | 2 | 7

Figure S62. Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

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

- Number of patients = 66

- Number of significantly arm-level cnvs = 61

- 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

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] 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle