Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1XK8DH1
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/C1XK8DH1
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 49 arm-level events and 8 molecular subtypes across 80 patients, 34 significant findings detected with P value < 0.05 and Q value < 0.25.

- 6p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 6q gain cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 6q 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 49 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, 34 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
8q gain | 53 (66%) | 27 | 1e-05 (0.00392) | 1e-05 (0.00392) | 4e-05 (0.0148) | 1e-05 (0.00392) | 5e-05 (0.0183) | 1e-05 (0.00392) | 1e-05 (0.00392) | 5e-05 (0.0183)
3p loss | 43 (54%) | 37 | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392)
3q loss | 43 (54%) | 37 | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392) | 1e-05 (0.00392)
6p gain | 39 (49%) | 41 | 0.00026 (0.0941) | 0.0039 (1.00) | 0.00026 (0.0941) | 0.00027 (0.0972) | 1e-05 (0.00392) | 3e-05 (0.0111) | 0.0031 (1.00) | 5e-05 (0.0183)
6q gain | 16 (20%) | 64 | 0.00579 (1.00) | 0.00251 (0.884) | 0.00037 (0.133) | 0.00088 (0.315) | 4e-05 (0.0148) | 0.00015 (0.0544) | 0.00623 (1.00) | 0.00088 (0.315)
6q loss | 17 (21%) | 63 | 7e-05 (0.0255) | 0.00327 (1.00) | 0.0508 (1.00) | 0.00502 (1.00) | 0.11 (1.00) | 0.0294 (1.00) | 0.00433 (1.00) | 0.00252 (0.885)
1q gain | 8 (10%) | 72 | 0.715 (1.00) | 0.714 (1.00) | 0.701 (1.00) | 0.803 (1.00) | 0.206 (1.00) | 0.156 (1.00) | 0.314 (1.00) | 0.826 (1.00)
2p gain | 10 (12%) | 70 | 0.315 (1.00) | 1 (1.00) | 0.0377 (1.00) | 0.116 (1.00) | 0.117 (1.00) | 0.199 (1.00) | 0.658 (1.00) | 0.00819 (1.00)
2q gain | 8 (10%) | 72 | 0.393 (1.00) | 0.715 (1.00) | 0.0549 (1.00) | 0.111 (1.00) | 0.312 (1.00) | 0.0163 (1.00) | 0.422 (1.00) | 0.00247 (0.872)
4p gain | 7 (9%) | 73 | 0.0273 (1.00) | 0.282 (1.00) | 0.151 (1.00) | 0.12 (1.00) | 0.775 (1.00) | 0.548 (1.00) | 0.365 (1.00) | 0.296 (1.00)
4q gain | 4 (5%) | 76 | 0.159 (1.00) | 0.271 (1.00) | 0.398 (1.00) | 0.344 (1.00) | 0.329 (1.00) | 0.808 (1.00) | 0.512 (1.00) | 0.302 (1.00)
5p gain | 3 (4%) | 77 | 0.161 (1.00) | 0.442 (1.00) | 0.784 (1.00) | 0.108 (1.00) | 1 (1.00) | 0.0756 (1.00) | 1 (1.00) | 0.842 (1.00)
5q gain | 3 (4%) | 77 | 0.163 (1.00) | 0.439 (1.00) | 0.782 (1.00) | 0.108 (1.00) | 1 (1.00) | 0.0762 (1.00) | 1 (1.00) | 0.838 (1.00)
7p gain | 9 (11%) | 71 | 0.163 (1.00) | 0.127 (1.00) | 1 (1.00) | 0.742 (1.00) | 0.658 (1.00) | 0.221 (1.00) | 0.895 (1.00) | 0.433 (1.00)
7q gain | 8 (10%) | 72 | 0.0556 (1.00) | 0.0303 (1.00) | 0.89 (1.00) | 0.448 (1.00) | 0.273 (1.00) | 0.359 (1.00) | 0.689 (1.00) | 0.268 (1.00)
8p gain | 33 (41%) | 47 | 0.00111 (0.395) | 0.00111 (0.395) | 0.00253 (0.885) | 0.00435 (1.00) | 0.0407 (1.00) | 0.0202 (1.00) | 0.0322 (1.00) | 0.0257 (1.00)
9p gain | 6 (8%) | 74 | 0.233 (1.00) | 0.176 (1.00) | 0.402 (1.00) | 0.638 (1.00) | 0.741 (1.00) | 0.907 (1.00) | 0.087 (1.00) | 0.937 (1.00)
9q gain | 5 (6%) | 75 | 0.51 (1.00) | 0.0378 (1.00) | 0.838 (1.00) | 0.839 (1.00) | 0.342 (1.00) | 0.974 (1.00) | 0.00797 (1.00) | 0.719 (1.00)
11p gain | 9 (11%) | 71 | 0.166 (1.00) | 0.539 (1.00) | 1 (1.00) | 0.74 (1.00) | 0.272 (1.00) | 0.245 (1.00) | 0.546 (1.00) | 0.281 (1.00)
11q gain | 10 (12%) | 70 | 0.317 (1.00) | 0.829 (1.00) | 0.909 (1.00) | 0.83 (1.00) | 0.146 (1.00) | 0.172 (1.00) | 0.544 (1.00) | 0.285 (1.00)
12p gain | 3 (4%) | 77 | 0.162 (1.00) | 0.442 (1.00) | 0.0906 (1.00) | 0.0102 (1.00) | 1 (1.00) | 0.00996 (1.00) | 1 (1.00) | 0.125 (1.00)
12q gain | 3 (4%) | 77 | 0.161 (1.00) | 0.44 (1.00) | 0.0885 (1.00) | 0.00952 (1.00) | 1 (1.00) | 0.00994 (1.00) | 1 (1.00) | 0.125 (1.00)
13q gain | 6 (8%) | 74 | 0.105 (1.00) | 1 (1.00) | 0.737 (1.00) | 0.753 (1.00) | 0.645 (1.00) | 0.105 (1.00) | 1 (1.00) | 0.0605 (1.00)
14q gain | 3 (4%) | 77 | 0.0378 (1.00) | 0.441 (1.00) | 0.589 (1.00) | 0.329 (1.00) | 1 (1.00) | 0.185 (1.00) | 1 (1.00) | 0.729 (1.00)
16p gain | 4 (5%) | 76 | 1 (1.00) | 0.439 (1.00) | 1 (1.00) | 0.438 (1.00) | 0.413 (1.00) | 0.0264 (1.00) | 0.38 (1.00) | 1 (1.00)
17p gain | 8 (10%) | 72 | 0.0809 (1.00) | 0.803 (1.00) | 0.389 (1.00) | 0.22 (1.00) | 0.392 (1.00) | 0.00993 (1.00) | 0.543 (1.00) | 0.283 (1.00)
17q gain | 9 (11%) | 71 | 0.218 (1.00) | 1 (1.00) | 0.422 (1.00) | 0.311 (1.00) | 0.271 (1.00) | 0.0179 (1.00) | 0.412 (1.00) | 0.353 (1.00)
20p gain | 8 (10%) | 72 | 0.00937 (1.00) | 0.569 (1.00) | 0.39 (1.00) | 0.219 (1.00) | 0.31 (1.00) | 0.18 (1.00) | 0.317 (1.00) | 0.695 (1.00)
20q gain | 9 (11%) | 71 | 0.00203 (0.719) | 0.539 (1.00) | 0.144 (1.00) | 0.0566 (1.00) | 0.247 (1.00) | 0.247 (1.00) | 0.414 (1.00) | 0.911 (1.00)
21q gain | 14 (18%) | 66 | 0.00309 (1.00) | 0.196 (1.00) | 0.104 (1.00) | 0.0129 (1.00) | 0.926 (1.00) | 0.165 (1.00) | 0.527 (1.00) | 0.162 (1.00)
22q gain | 6 (8%) | 74 | 0.106 (1.00) | 0.644 (1.00) | 0.153 (1.00) | 0.221 (1.00) | 0.645 (1.00) | 0.00656 (1.00) | 0.729 (1.00) | 0.059 (1.00)
xq gain | 10 (12%) | 70 | 0.39 (1.00) | 0.0934 (1.00) | 0.108 (1.00) | 0.139 (1.00) | 0.157 (1.00) | 0.0556 (1.00) | 0.367 (1.00) | 0.366 (1.00)
1p loss | 19 (24%) | 61 | 0.0044 (1.00) | 0.0523 (1.00) | 0.781 (1.00) | 0.663 (1.00) | 0.318 (1.00) | 0.00897 (1.00) | 0.461 (1.00) | 0.052 (1.00)
1q loss | 3 (4%) | 77 | 0.0383 (1.00) | 0.169 (1.00) | 0.217 (1.00) | 0.322 (1.00) | 0.42 (1.00) | 0.492 (1.00) | 0.0685 (1.00) | 0.0732 (1.00)
4q loss | 3 (4%) | 77 | 1 (1.00) | 0.791 (1.00) | 0.592 (1.00) | 0.602 (1.00) | 1 (1.00) | 0.612 (1.00) | 0.379 (1.00) | 0.622 (1.00)
5q loss | 3 (4%) | 77 | 0.45 (1.00) | 0.109 (1.00) | 0.0883 (1.00) | 0.17 (1.00) | 0.595 (1.00) | 0.185 (1.00) | 0.204 (1.00) | 0.841 (1.00)
8p loss | 9 (11%) | 71 | 0.0303 (1.00) | 0.344 (1.00) | 0.0371 (1.00) | 0.023 (1.00) | 0.199 (1.00) | 0.163 (1.00) | 0.139 (1.00) | 0.0313 (1.00)
8q loss | 3 (4%) | 77 | 0.786 (1.00) | 0.602 (1.00) | 1 (1.00) | 0.791 (1.00) | 0.795 (1.00) | 1 (1.00) | 1 (1.00) | 0.839 (1.00)
9p loss | 8 (10%) | 72 | 0.109 (1.00) | 0.0415 (1.00) | 0.344 (1.00) | 0.151 (1.00) | 0.184 (1.00) | 0.254 (1.00) | 0.151 (1.00) | 0.399 (1.00)
9q loss | 7 (9%) | 73 | 0.167 (1.00) | 0.0749 (1.00) | 0.593 (1.00) | 0.239 (1.00) | 0.0911 (1.00) | 0.401 (1.00) | 0.0867 (1.00) | 0.155 (1.00)
11p loss | 3 (4%) | 77 | 0.0373 (1.00) | 0.236 (1.00) | 0.0432 (1.00) | 0.108 (1.00) | 0.223 (1.00) | 0.249 (1.00) | 0.283 (1.00) | 0.188 (1.00)
12p loss | 3 (4%) | 77 | 0.788 (1.00) | 0.604 (1.00) | 1 (1.00) | 0.789 (1.00) | 0.792 (1.00) | 1 (1.00) | 0.769 (1.00) | 1 (1.00)
13q loss | 3 (4%) | 77 | 1 (1.00) | 0.17 (1.00) | 0.593 (1.00) | 0.603 (1.00) | 0.794 (1.00) | 0.61 (1.00) | 0.559 (1.00) | 0.626 (1.00)
15q loss | 4 (5%) | 76 | 0.155 (1.00) | 0.0492 (1.00) | 0.83 (1.00) | 0.826 (1.00) | 1 (1.00) | 0.662 (1.00) | 0.814 (1.00) | 0.565 (1.00)
16p loss | 3 (4%) | 77 | 1 (1.00) | 0.437 (1.00) | 0.591 (1.00) | 0.606 (1.00) | 0.794 (1.00) | 0.771 (1.00) | 0.561 (1.00) | 0.625 (1.00)
16q loss | 16 (20%) | 64 | 0.0212 (1.00) | 0.132 (1.00) | 0.0961 (1.00) | 0.013 (1.00) | 0.933 (1.00) | 0.00625 (1.00) | 0.358 (1.00) | 0.242 (1.00)
19p loss | 3 (4%) | 77 | 0.452 (1.00) | 0.604 (1.00) | 0.782 (1.00) | 1 (1.00) | 0.598 (1.00) | 0.00287 (0.999) | 0.561 (1.00) | 0.281 (1.00)
19q loss | 3 (4%) | 77 | 0.454 (1.00) | 0.603 (1.00) | 0.782 (1.00) | 1 (1.00) | 0.597 (1.00) | 0.00257 (0.897) | 0.56 (1.00) | 0.279 (1.00)
xq loss | 12 (15%) | 68 | 0.339 (1.00) | 0.0384 (1.00) | 0.321 (1.00) | 0.266 (1.00) | 0.392 (1.00) | 0.0489 (1.00) | 0.102 (1.00) | 0.0725 (1.00)

'6p gain' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.094

Table S1. Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
6P GAIN MUTATED | 9 | 26 | 4
6P GAIN WILD-TYPE | 13 | 10 | 18

Figure S1. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.094

Table S2. Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
6P GAIN MUTATED | 8 | 5 | 26
6P GAIN WILD-TYPE | 22 | 10 | 9

Figure S2. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.097

Table S3. Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
6P GAIN MUTATED | 9 | 25 | 5
6P GAIN WILD-TYPE | 20 | 8 | 13

Figure S3. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S4. Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 16 | 29
6P GAIN MUTATED | 10 | 4 | 24
6P GAIN WILD-TYPE | 24 | 12 | 5

Figure S4. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.011

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 12 | 18 | 24 | 10 | 7
6P GAIN MUTATED | 2 | 5 | 16 | 5 | 8 | 2
6P GAIN WILD-TYPE | 6 | 7 | 2 | 19 | 2 | 5

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.018

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 20 | 11 | 32 | 10
6P GAIN MUTATED | 2 | 4 | 23 | 6
6P GAIN WILD-TYPE | 18 | 7 | 9 | 4

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.13

Table S7. Gene #9: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
6Q GAIN MUTATED | 1 | 1 | 14
6Q GAIN WILD-TYPE | 29 | 14 | 21

Figure S7. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.015

Table S8. Gene #9: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 16 | 29
6Q GAIN MUTATED | 1 | 1 | 13
6Q GAIN WILD-TYPE | 33 | 15 | 16

Figure S8. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.054

Table S9. Gene #9: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 12 | 18 | 24 | 10 | 7
6Q GAIN MUTATED | 0 | 2 | 10 | 0 | 2 | 1
6Q GAIN WILD-TYPE | 8 | 10 | 8 | 24 | 8 | 6

Figure S9. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S10. Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
8Q GAIN MUTATED | 21 | 12 | 20
8Q GAIN WILD-TYPE | 1 | 24 | 2

Figure S10. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S11. Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
8Q GAIN MUTATED | 31 | 12 | 10
8Q GAIN WILD-TYPE | 2 | 6 | 19

Figure S11. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.015

Table S12. Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
8Q GAIN MUTATED | 27 | 12 | 14
8Q GAIN WILD-TYPE | 3 | 3 | 21

Figure S12. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S13. Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
8Q GAIN MUTATED | 27 | 12 | 14
8Q GAIN WILD-TYPE | 2 | 21 | 4

Figure S13. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.018

Table S14. Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 16 | 29
8Q GAIN MUTATED | 31 | 8 | 13
8Q GAIN WILD-TYPE | 3 | 8 | 16

Figure S14. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S15. Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 12 | 18 | 24 | 10 | 7
8Q GAIN MUTATED | 8 | 2 | 10 | 22 | 4 | 6
8Q GAIN WILD-TYPE | 0 | 10 | 8 | 2 | 6 | 1

Figure S15. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S16. Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 29 | 12
8Q GAIN MUTATED | 30 | 10 | 10
8Q GAIN WILD-TYPE | 2 | 19 | 2

Figure S16. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.018

Table S17. Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 20 | 11 | 32 | 10
8Q GAIN MUTATED | 18 | 9 | 13 | 10
8Q GAIN WILD-TYPE | 2 | 2 | 19 | 0

Figure S17. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S18. Gene #32: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
3P LOSS MUTATED | 22 | 2 | 19
3P LOSS WILD-TYPE | 0 | 34 | 3

Figure S18. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S19. Gene #32: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
3P LOSS MUTATED | 33 | 9 | 1
3P LOSS WILD-TYPE | 0 | 9 | 28

Figure S19. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
3P LOSS MUTATED | 30 | 10 | 3
3P LOSS WILD-TYPE | 0 | 5 | 32

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

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S21. Gene #32: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
3P LOSS MUTATED | 29 | 2 | 12
3P LOSS WILD-TYPE | 0 | 31 | 6

Figure S21. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S22. Gene #32: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 16 | 29
3P LOSS MUTATED | 30 | 11 | 2
3P LOSS WILD-TYPE | 4 | 5 | 27

Figure S22. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S23. Gene #32: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 12 | 18 | 24 | 10 | 7
3P LOSS MUTATED | 8 | 1 | 1 | 24 | 2 | 7
3P LOSS WILD-TYPE | 0 | 11 | 17 | 0 | 8 | 0

Figure S23. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S24. Gene #32: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 29 | 12
3P LOSS MUTATED | 30 | 4 | 8
3P LOSS WILD-TYPE | 2 | 25 | 4

Figure S24. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S25. Gene #32: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 20 | 11 | 32 | 10
3P LOSS MUTATED | 20 | 7 | 5 | 10
3P LOSS WILD-TYPE | 0 | 4 | 27 | 0

Figure S25. Get High-res Image Gene #32: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S26. Gene #33: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
3Q LOSS MUTATED | 22 | 2 | 19
3Q LOSS WILD-TYPE | 0 | 34 | 3

Figure S26. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S27. Gene #33: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
3Q LOSS MUTATED | 33 | 9 | 1
3Q LOSS WILD-TYPE | 0 | 9 | 28

Figure S27. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S28. Gene #33: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
3Q LOSS MUTATED | 30 | 10 | 3
3Q LOSS WILD-TYPE | 0 | 5 | 32

Figure S28. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S29. Gene #33: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
3Q LOSS MUTATED | 29 | 2 | 12
3Q LOSS WILD-TYPE | 0 | 31 | 6

Figure S29. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S30. Gene #33: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 16 | 29
3Q LOSS MUTATED | 30 | 11 | 2
3Q LOSS WILD-TYPE | 4 | 5 | 27

Figure S30. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S31. Gene #33: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 12 | 18 | 24 | 10 | 7
3Q LOSS MUTATED | 8 | 1 | 1 | 24 | 2 | 7
3Q LOSS WILD-TYPE | 0 | 11 | 17 | 0 | 8 | 0

Figure S31. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S32. Gene #33: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 29 | 12
3Q LOSS MUTATED | 30 | 4 | 8
3Q LOSS WILD-TYPE | 2 | 25 | 4

Figure S32. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S33. Gene #33: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 20 | 11 | 32 | 10
3Q LOSS MUTATED | 20 | 7 | 5 | 10
3Q LOSS WILD-TYPE | 0 | 4 | 27 | 0

Figure S33. Get High-res Image Gene #33: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.025

Table S34. Gene #36: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
6Q LOSS MUTATED | 12 | 4 | 1
6Q LOSS WILD-TYPE | 10 | 32 | 21

Figure S34. Get High-res Image Gene #36: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 80

- Number of significantly arm-level cnvs = 49

- 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)
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