Correlation between copy number variations of arm-level result and molecular subtypes
Thymoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1B8572M
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/C1B8572M
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 50 arm-level events and 8 molecular subtypes across 123 patients, 112 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'CN_CNMF'.

- 1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

- 9p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 9q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 15q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

- 3q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 6p 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', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 12p loss cnv correlated to 'METHLYATION_CNMF'.

- 12q loss cnv correlated to 'METHLYATION_CNMF'.

- 13q loss cnv correlated to 'CN_CNMF'.

- 16q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 19p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 19q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 21q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 50 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, 112 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 gain | 22 (18%) | 101 | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004)
7p gain | 16 (13%) | 107 | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 0.00016 (0.0522) | 1e-05 (0.004) | 2e-05 (0.00706)
7q gain | 16 (13%) | 107 | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 2e-05 (0.00706) | 0.00011 (0.0364) | 1e-05 (0.004) | 4e-05 (0.0136)
14q gain | 13 (11%) | 110 | 1e-05 (0.004) | 2e-05 (0.00706) | 1e-05 (0.004) | 4e-05 (0.0136) | 0.00019 (0.0614) | 6e-05 (0.0202) | 1e-05 (0.004) | 2e-05 (0.00706)
6p loss | 20 (16%) | 103 | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 4e-05 (0.0136) | 1e-05 (0.004) | 1e-05 (0.004)
6q loss | 19 (15%) | 104 | 1e-05 (0.004) | 1e-05 (0.004) | 1e-05 (0.004) | 2e-05 (0.00706) | 2e-05 (0.00706) | 0.00028 (0.0885) | 1e-05 (0.004) | 7e-05 (0.0234)
3p loss | 12 (10%) | 111 | 1e-05 (0.004) | 1e-05 (0.004) | 0.00058 (0.173) | 0.00038 (0.117) | 0.00073 (0.212) | 0.0044 (1.00) | 1e-05 (0.004) | 0.00045 (0.137)
8p gain | 12 (10%) | 111 | 0.00037 (0.115) | 0.0215 (1.00) | 0.00041 (0.126) | 0.0001 (0.0332) | 0.00072 (0.211) | 0.00172 (0.471) | 0.00023 (0.0734) | 0.00037 (0.115)
8q gain | 12 (10%) | 111 | 0.00023 (0.0734) | 0.0216 (1.00) | 0.00035 (0.11) | 0.00013 (0.0428) | 0.00077 (0.223) | 0.00169 (0.465) | 0.00019 (0.0614) | 0.00052 (0.156)
9q gain | 11 (9%) | 112 | 1e-05 (0.004) | 0.00012 (0.0396) | 0.00035 (0.11) | 0.00044 (0.135) | 0.0106 (1.00) | 0.00595 (1.00) | 0.00491 (1.00) | 0.00079 (0.228)
5p gain | 11 (9%) | 112 | 1e-05 (0.004) | 2e-05 (0.00706) | 0.00115 (0.327) | 0.00108 (0.308) | 0.00072 (0.211) | 0.0133 (1.00) | 2e-05 (0.00706) | 0.00184 (0.502)
9p gain | 11 (9%) | 112 | 1e-05 (0.004) | 0.00016 (0.0522) | 0.00038 (0.117) | 0.00045 (0.137) | 0.01 (1.00) | 0.0064 (1.00) | 0.00478 (1.00) | 0.00107 (0.306)
16q loss | 13 (11%) | 110 | 0.0583 (1.00) | 0.00485 (1.00) | 2e-05 (0.00706) | 1e-05 (0.004) | 0.0595 (1.00) | 2e-05 (0.00706) | 0.00126 (0.35) | 0.00067 (0.198)
5q gain | 9 (7%) | 114 | 1e-05 (0.004) | 2e-05 (0.00706) | 0.00667 (1.00) | 0.00454 (1.00) | 0.00341 (0.883) | 0.0173 (1.00) | 0.00019 (0.0614) | 0.00296 (0.77)
20p gain | 10 (8%) | 113 | 0.00058 (0.173) | 0.0243 (1.00) | 0.00089 (0.256) | 0.0003 (0.0942) | 0.0532 (1.00) | 0.0107 (1.00) | 0.00055 (0.164) | 0.054 (1.00)
20q gain | 10 (8%) | 113 | 0.00064 (0.189) | 0.0246 (1.00) | 0.001 (0.287) | 0.00028 (0.0885) | 0.0531 (1.00) | 0.0109 (1.00) | 0.00049 (0.147) | 0.0547 (1.00)
11p loss | 9 (7%) | 114 | 1e-05 (0.004) | 1e-05 (0.004) | 0.00702 (1.00) | 0.00475 (1.00) | 0.00841 (1.00) | 0.0514 (1.00) | 0.00014 (0.0458) | 0.00831 (1.00)
21q loss | 9 (7%) | 114 | 1e-05 (0.004) | 1e-05 (0.004) | 0.00517 (1.00) | 0.00461 (1.00) | 0.00938 (1.00) | 0.0517 (1.00) | 0.00023 (0.0734) | 0.00838 (1.00)
15q gain | 12 (10%) | 111 | 0.00017 (0.0551) | 6e-05 (0.0202) | 0.0258 (1.00) | 0.016 (1.00) | 0.0146 (1.00) | 0.0207 (1.00) | 0.00141 (0.391) | 0.00532 (1.00)
3q loss | 7 (6%) | 116 | 0.00068 (0.2) | 0.00022 (0.0704) | 0.0243 (1.00) | 0.0221 (1.00) | 0.0326 (1.00) | 0.0851 (1.00) | 0.00218 (0.582) | 0.00902 (1.00)
11q loss | 7 (6%) | 116 | 4e-05 (0.0136) | 4e-05 (0.0136) | 0.0246 (1.00) | 0.00805 (1.00) | 0.0338 (1.00) | 0.111 (1.00) | 0.00222 (0.591) | 0.00852 (1.00)
1p gain | 8 (7%) | 115 | 0.00013 (0.0428) | 0.0211 (1.00) | 0.00678 (1.00) | 0.00254 (0.668) | 0.0217 (1.00) | 0.0215 (1.00) | 0.00344 (0.888) | 0.00661 (1.00)
12p loss | 8 (7%) | 115 | 0.00394 (1.00) | 9e-05 (0.03) | 0.00683 (1.00) | 0.00834 (1.00) | 0.0211 (1.00) | 0.0529 (1.00) | 0.00357 (0.917) | 0.0193 (1.00)
12q loss | 7 (6%) | 116 | 0.00198 (0.535) | 1e-05 (0.004) | 0.00771 (1.00) | 0.00878 (1.00) | 0.0331 (1.00) | 0.122 (1.00) | 0.00197 (0.534) | 0.0357 (1.00)
13q loss | 14 (11%) | 109 | 2e-05 (0.00706) | 0.00586 (1.00) | 0.0662 (1.00) | 0.0405 (1.00) | 0.371 (1.00) | 0.577 (1.00) | 0.0598 (1.00) | 0.35 (1.00)
19p loss | 3 (2%) | 120 | 0.103 (1.00) | 0.35 (1.00) | 0.00121 (0.341) | 0.00044 (0.135) | 0.199 (1.00) | 0.00962 (1.00) | 0.106 (1.00) | 0.06 (1.00)
19q loss | 3 (2%) | 120 | 0.103 (1.00) | 0.347 (1.00) | 0.00123 (0.346) | 0.00045 (0.137) | 0.198 (1.00) | 0.00963 (1.00) | 0.106 (1.00) | 0.0594 (1.00)
22q loss | 13 (11%) | 110 | 1e-05 (0.004) | 0.114 (1.00) | 0.086 (1.00) | 0.0375 (1.00) | 0.111 (1.00) | 0.334 (1.00) | 0.0546 (1.00) | 0.333 (1.00)
3q gain | 5 (4%) | 118 | 0.26 (1.00) | 0.139 (1.00) | 0.178 (1.00) | 0.0422 (1.00) | 0.726 (1.00) | 0.00538 (1.00) | 0.353 (1.00) | 0.171 (1.00)
12p gain | 4 (3%) | 119 | 0.0279 (1.00) | 0.149 (1.00) | 0.00471 (1.00) | 0.00272 (0.71) | 0.172 (1.00) | 0.0273 (1.00) | 0.0449 (1.00) | 0.17 (1.00)
12q gain | 4 (3%) | 119 | 0.0287 (1.00) | 0.146 (1.00) | 0.00447 (1.00) | 0.0027 (0.707) | 0.171 (1.00) | 0.0268 (1.00) | 0.0455 (1.00) | 0.171 (1.00)
17q gain | 7 (6%) | 116 | 0.394 (1.00) | 0.22 (1.00) | 0.0481 (1.00) | 0.0043 (1.00) | 0.77 (1.00) | 0.0682 (1.00) | 0.439 (1.00) | 0.4 (1.00)
18p gain | 3 (2%) | 120 | 0.102 (1.00) | 0.176 (1.00) | 0.0329 (1.00) | 0.0321 (1.00) | 0.197 (1.00) | 0.286 (1.00) | 0.104 (1.00) | 0.503 (1.00)
18q gain | 3 (2%) | 120 | 0.104 (1.00) | 0.177 (1.00) | 0.0331 (1.00) | 0.0319 (1.00) | 0.196 (1.00) | 0.288 (1.00) | 0.105 (1.00) | 0.501 (1.00)
19p gain | 3 (2%) | 120 | 0.0238 (1.00) | 0.175 (1.00) | 0.303 (1.00) | 0.336 (1.00) | 0.198 (1.00) | 0.611 (1.00) | 0.106 (1.00) | 0.302 (1.00)
19q gain | 3 (2%) | 120 | 0.0248 (1.00) | 0.177 (1.00) | 0.304 (1.00) | 0.338 (1.00) | 0.196 (1.00) | 0.609 (1.00) | 0.105 (1.00) | 0.302 (1.00)
21q gain | 3 (2%) | 120 | 0.276 (1.00) | 0.349 (1.00) | 0.486 (1.00) | 0.199 (1.00) | 0.649 (1.00) | 0.341 (1.00) | 0.74 (1.00) | 0.62 (1.00)
22q gain | 5 (4%) | 118 | 0.0355 (1.00) | 0.0319 (1.00) | 0.322 (1.00) | 0.236 (1.00) | 0.323 (1.00) | 0.61 (1.00) | 0.223 (1.00) | 0.683 (1.00)
xq gain | 5 (4%) | 118 | 0.00124 (0.347) | 0.00759 (1.00) | 0.0505 (1.00) | 0.0682 (1.00) | 0.147 (1.00) | 0.271 (1.00) | 0.0117 (1.00) | 0.104 (1.00)
1p loss | 4 (3%) | 119 | 0.00532 (1.00) | 0.00243 (0.642) | 0.0555 (1.00) | 0.126 (1.00) | 0.173 (1.00) | 0.526 (1.00) | 0.0449 (1.00) | 0.301 (1.00)
4p loss | 5 (4%) | 118 | 0.00737 (1.00) | 0.0116 (1.00) | 0.048 (1.00) | 0.0661 (1.00) | 0.325 (1.00) | 0.383 (1.00) | 0.052 (1.00) | 0.264 (1.00)
4q loss | 4 (3%) | 119 | 0.0284 (1.00) | 0.061 (1.00) | 0.136 (1.00) | 0.145 (1.00) | 0.435 (1.00) | 0.114 (1.00) | 0.103 (1.00) | 0.0864 (1.00)
9p loss | 4 (3%) | 119 | 0.25 (1.00) | 0.106 (1.00) | 0.0214 (1.00) | 0.00385 (0.986) | 1 (1.00) | 0.0595 (1.00) | 1 (1.00) | 0.332 (1.00)
10p loss | 3 (2%) | 120 | 0.6 (1.00) | 0.346 (1.00) | 0.0214 (1.00) | 0.0243 (1.00) | 1 (1.00) | 0.0153 (1.00) | 0.741 (1.00) | 0.619 (1.00)
16p loss | 5 (4%) | 118 | 0.128 (1.00) | 0.202 (1.00) | 0.166 (1.00) | 0.12 (1.00) | 0.324 (1.00) | 0.579 (1.00) | 0.224 (1.00) | 0.306 (1.00)
17p loss | 14 (11%) | 109 | 0.0235 (1.00) | 0.00119 (0.337) | 0.0157 (1.00) | 0.00125 (0.349) | 0.372 (1.00) | 0.00209 (0.562) | 0.0279 (1.00) | 0.0616 (1.00)
17q loss | 6 (5%) | 117 | 0.0102 (1.00) | 0.00861 (1.00) | 0.316 (1.00) | 0.155 (1.00) | 0.27 (1.00) | 0.236 (1.00) | 0.0993 (1.00) | 0.437 (1.00)
18p loss | 7 (6%) | 116 | 0.00229 (0.607) | 0.00854 (1.00) | 0.0241 (1.00) | 0.0218 (1.00) | 0.0136 (1.00) | 0.0958 (1.00) | 0.00192 (0.522) | 0.0426 (1.00)
18q loss | 7 (6%) | 116 | 0.00168 (0.464) | 0.00814 (1.00) | 0.0254 (1.00) | 0.0216 (1.00) | 0.014 (1.00) | 0.0953 (1.00) | 0.00217 (0.582) | 0.0431 (1.00)
xq loss | 4 (3%) | 119 | 0.0273 (1.00) | 0.0364 (1.00) | 0.0564 (1.00) | 0.125 (1.00) | 0.026 (1.00) | 0.253 (1.00) | 0.0458 (1.00) | 0.301 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.043

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
1P GAIN MUTATED | 0 | 7 | 1
1P GAIN WILD-TYPE | 65 | 24 | 26

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S2. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
1Q GAIN MUTATED | 3 | 18 | 1
1Q GAIN WILD-TYPE | 62 | 13 | 26

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S3. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
1Q GAIN MUTATED | 2 | 6 | 14 | 0
1Q GAIN WILD-TYPE | 37 | 30 | 10 | 24

Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S4. Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
1Q GAIN MUTATED | 15 | 0 | 7 | 0
1Q GAIN WILD-TYPE | 28 | 30 | 6 | 29

Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S5. Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
1Q GAIN MUTATED | 15 | 0 | 0 | 7
1Q GAIN WILD-TYPE | 29 | 41 | 20 | 3

Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S6. Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
1Q GAIN MUTATED | 21 | 0 | 0 | 1 | 0
1Q GAIN WILD-TYPE | 37 | 61 | 1 | 1 | 1

Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S7. Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
1Q GAIN MUTATED | 7 | 0 | 10 | 5 | 0 | 0
1Q GAIN WILD-TYPE | 20 | 18 | 18 | 2 | 16 | 27

Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S8. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
1Q GAIN MUTATED | 1 | 0 | 21
1Q GAIN WILD-TYPE | 17 | 59 | 25

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S9. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
1Q GAIN MUTATED | 7 | 0 | 15 | 0
1Q GAIN WILD-TYPE | 22 | 33 | 18 | 28

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S10. Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
5P GAIN MUTATED | 0 | 11 | 0
5P GAIN WILD-TYPE | 65 | 20 | 27

Figure S10. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S11. Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
5P GAIN MUTATED | 0 | 2 | 9 | 0
5P GAIN WILD-TYPE | 39 | 34 | 15 | 24

Figure S11. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.21

Table S12. Gene #4: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
5P GAIN MUTATED | 10 | 0 | 0 | 1 | 0
5P GAIN WILD-TYPE | 48 | 61 | 1 | 1 | 1

Figure S12. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S13. Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
5P GAIN MUTATED | 0 | 0 | 11
5P GAIN WILD-TYPE | 18 | 59 | 35

Figure S13. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S14. Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
5Q GAIN MUTATED | 0 | 9 | 0
5Q GAIN WILD-TYPE | 65 | 22 | 27

Figure S14. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S15. Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
5Q GAIN MUTATED | 0 | 1 | 8 | 0
5Q GAIN WILD-TYPE | 39 | 35 | 16 | 24

Figure S15. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.061

Table S16. Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
5Q GAIN MUTATED | 0 | 0 | 9
5Q GAIN WILD-TYPE | 18 | 59 | 37

Figure S16. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S17. Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
7P GAIN MUTATED | 0 | 16 | 0
7P GAIN WILD-TYPE | 65 | 15 | 27

Figure S17. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S18. Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
7P GAIN MUTATED | 1 | 1 | 14 | 0
7P GAIN WILD-TYPE | 38 | 35 | 10 | 24

Figure S18. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S19. Gene #6: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
7P GAIN MUTATED | 16 | 0 | 0 | 0
7P GAIN WILD-TYPE | 27 | 30 | 13 | 29

Figure S19. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S20. Gene #6: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
7P GAIN MUTATED | 16 | 0 | 0 | 0
7P GAIN WILD-TYPE | 28 | 41 | 20 | 10

Figure S20. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S21. Gene #6: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
7P GAIN MUTATED | 15 | 0 | 0 | 1 | 0
7P GAIN WILD-TYPE | 43 | 61 | 1 | 1 | 1

Figure S21. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.052

Table S22. Gene #6: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
7P GAIN MUTATED | 9 | 0 | 7 | 0 | 0 | 0
7P GAIN WILD-TYPE | 18 | 18 | 21 | 7 | 16 | 27

Figure S22. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S23. Gene #6: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
7P GAIN MUTATED | 0 | 0 | 16
7P GAIN WILD-TYPE | 18 | 59 | 30

Figure S23. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S24. Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
7P GAIN MUTATED | 10 | 0 | 6 | 0
7P GAIN WILD-TYPE | 19 | 33 | 27 | 28

Figure S24. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S25. Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
7Q GAIN MUTATED | 0 | 16 | 0
7Q GAIN WILD-TYPE | 65 | 15 | 27

Figure S25. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S26. Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
7Q GAIN MUTATED | 1 | 1 | 14 | 0
7Q GAIN WILD-TYPE | 38 | 35 | 10 | 24

Figure S26. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S27. Gene #7: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
7Q GAIN MUTATED | 16 | 0 | 0 | 0
7Q GAIN WILD-TYPE | 27 | 30 | 13 | 29

Figure S27. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S28. Gene #7: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
7Q GAIN MUTATED | 16 | 0 | 0 | 0
7Q GAIN WILD-TYPE | 28 | 41 | 20 | 10

Figure S28. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S29. Gene #7: '7q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
7Q GAIN MUTATED | 15 | 0 | 0 | 1 | 0
7Q GAIN WILD-TYPE | 43 | 61 | 1 | 1 | 1

Figure S29. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.036

Table S30. Gene #7: '7q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
7Q GAIN MUTATED | 9 | 0 | 7 | 0 | 0 | 0
7Q GAIN WILD-TYPE | 18 | 18 | 21 | 7 | 16 | 27

Figure S30. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S31. Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
7Q GAIN MUTATED | 0 | 0 | 16
7Q GAIN WILD-TYPE | 18 | 59 | 30

Figure S31. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S32. Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
7Q GAIN MUTATED | 10 | 0 | 6 | 0
7Q GAIN WILD-TYPE | 19 | 33 | 27 | 28

Figure S32. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S33. Gene #8: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
8P GAIN MUTATED | 2 | 9 | 1
8P GAIN WILD-TYPE | 63 | 22 | 26

Figure S33. Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.13

Table S34. Gene #8: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
8P GAIN MUTATED | 8 | 0 | 4 | 0
8P GAIN WILD-TYPE | 35 | 30 | 9 | 29

Figure S34. Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.033

Table S35. Gene #8: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
8P GAIN MUTATED | 8 | 0 | 0 | 4
8P GAIN WILD-TYPE | 36 | 41 | 20 | 6

Figure S35. Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.21

Table S36. Gene #8: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
8P GAIN MUTATED | 12 | 0 | 0 | 0 | 0
8P GAIN WILD-TYPE | 46 | 61 | 1 | 2 | 1

Figure S36. Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.073

Table S37. Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
8P GAIN MUTATED | 2 | 0 | 10
8P GAIN WILD-TYPE | 16 | 59 | 36

Figure S37. Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S38. Gene #8: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
8P GAIN MUTATED | 4 | 0 | 8 | 0
8P GAIN WILD-TYPE | 25 | 33 | 25 | 28

Figure S38. Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.073

Table S39. Gene #9: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
8Q GAIN MUTATED | 2 | 9 | 1
8Q GAIN WILD-TYPE | 63 | 22 | 26

Figure S39. Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.11

Table S40. Gene #9: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
8Q GAIN MUTATED | 8 | 0 | 4 | 0
8Q GAIN WILD-TYPE | 35 | 30 | 9 | 29

Figure S40. Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.043

Table S41. Gene #9: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
8Q GAIN MUTATED | 8 | 0 | 0 | 4
8Q GAIN WILD-TYPE | 36 | 41 | 20 | 6

Figure S41. Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.22

Table S42. Gene #9: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
8Q GAIN MUTATED | 12 | 0 | 0 | 0 | 0
8Q GAIN WILD-TYPE | 46 | 61 | 1 | 2 | 1

Figure S42. Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.061

Table S43. Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
8Q GAIN MUTATED | 2 | 0 | 10
8Q GAIN WILD-TYPE | 16 | 59 | 36

Figure S43. Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.16

Table S44. Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
8Q GAIN MUTATED | 4 | 0 | 8 | 0
8Q GAIN WILD-TYPE | 25 | 33 | 25 | 28

Figure S44. Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S45. Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
9P GAIN MUTATED | 0 | 11 | 0
9P GAIN WILD-TYPE | 65 | 20 | 27

Figure S45. Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.052

Table S46. Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
9P GAIN MUTATED | 2 | 0 | 8 | 1
9P GAIN WILD-TYPE | 37 | 36 | 16 | 23

Figure S46. Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.12

Table S47. Gene #10: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
9P GAIN MUTATED | 10 | 0 | 0 | 0
9P GAIN WILD-TYPE | 33 | 30 | 13 | 29

Figure S47. Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S48. Gene #10: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
9P GAIN MUTATED | 10 | 0 | 0 | 0
9P GAIN WILD-TYPE | 34 | 41 | 20 | 10

Figure S48. Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S49. Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
9Q GAIN MUTATED | 0 | 11 | 0
9Q GAIN WILD-TYPE | 65 | 20 | 27

Figure S49. Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.04

Table S50. Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
9Q GAIN MUTATED | 2 | 0 | 8 | 1
9Q GAIN WILD-TYPE | 37 | 36 | 16 | 23

Figure S50. Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.11

Table S51. Gene #11: '9q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
9Q GAIN MUTATED | 10 | 0 | 0 | 0
9Q GAIN WILD-TYPE | 33 | 30 | 13 | 29

Figure S51. Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.13

Table S52. Gene #11: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
9Q GAIN MUTATED | 10 | 0 | 0 | 0
9Q GAIN WILD-TYPE | 34 | 41 | 20 | 10

Figure S52. Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.23

Table S53. Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
9Q GAIN MUTATED | 8 | 0 | 2 | 1
9Q GAIN WILD-TYPE | 21 | 33 | 31 | 27

Figure S53. Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S54. Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
14Q GAIN MUTATED | 0 | 13 | 0
14Q GAIN WILD-TYPE | 65 | 18 | 27

Figure S54. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S55. Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
14Q GAIN MUTATED | 2 | 1 | 10 | 0
14Q GAIN WILD-TYPE | 37 | 35 | 14 | 24

Figure S55. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S56. Gene #14: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
14Q GAIN MUTATED | 13 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 30 | 30 | 13 | 29

Figure S56. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S57. Gene #14: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
14Q GAIN MUTATED | 13 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 31 | 41 | 20 | 10

Figure S57. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.061

Table S58. Gene #14: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
14Q GAIN MUTATED | 12 | 0 | 0 | 1 | 0
14Q GAIN WILD-TYPE | 46 | 61 | 1 | 1 | 1

Figure S58. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.02

Table S59. Gene #14: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
14Q GAIN MUTATED | 10 | 0 | 3 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 17 | 18 | 25 | 7 | 16 | 27

Figure S59. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S60. Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
14Q GAIN MUTATED | 0 | 0 | 13
14Q GAIN WILD-TYPE | 18 | 59 | 33

Figure S60. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S61. Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
14Q GAIN MUTATED | 10 | 0 | 3 | 0
14Q GAIN WILD-TYPE | 19 | 33 | 30 | 28

Figure S61. Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.055

Table S62. Gene #15: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
15Q GAIN MUTATED | 1 | 9 | 2
15Q GAIN WILD-TYPE | 64 | 22 | 25

Figure S62. Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.02

Table S63. Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
15Q GAIN MUTATED | 2 | 1 | 9 | 0
15Q GAIN WILD-TYPE | 37 | 35 | 15 | 24

Figure S63. Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.17

Table S64. Gene #21: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
20P GAIN MUTATED | 1 | 8 | 1
20P GAIN WILD-TYPE | 64 | 23 | 26

Figure S64. Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.094

Table S65. Gene #21: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
20P GAIN MUTATED | 6 | 0 | 0 | 4
20P GAIN WILD-TYPE | 38 | 41 | 20 | 6

Figure S65. Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.16

Table S66. Gene #21: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
20P GAIN MUTATED | 1 | 0 | 9
20P GAIN WILD-TYPE | 17 | 59 | 37

Figure S66. Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.19

Table S67. Gene #22: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
20Q GAIN MUTATED | 1 | 8 | 1
20Q GAIN WILD-TYPE | 64 | 23 | 26

Figure S67. Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.088

Table S68. Gene #22: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
20Q GAIN MUTATED | 6 | 0 | 0 | 4
20Q GAIN WILD-TYPE | 38 | 41 | 20 | 6

Figure S68. Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.15

Table S69. Gene #22: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
20Q GAIN MUTATED | 1 | 0 | 9
20Q GAIN WILD-TYPE | 17 | 59 | 37

Figure S69. Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S70. Gene #27: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
3P LOSS MUTATED | 1 | 10 | 1
3P LOSS WILD-TYPE | 64 | 21 | 26

Figure S70. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S71. Gene #27: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
3P LOSS MUTATED | 0 | 2 | 10 | 0
3P LOSS WILD-TYPE | 39 | 34 | 14 | 24

Figure S71. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.17

Table S72. Gene #27: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
3P LOSS MUTATED | 9 | 0 | 3 | 0
3P LOSS WILD-TYPE | 34 | 30 | 10 | 29

Figure S72. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.12

Table S73. Gene #27: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
3P LOSS MUTATED | 10 | 0 | 0 | 2
3P LOSS WILD-TYPE | 34 | 41 | 20 | 8

Figure S73. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.21

Table S74. Gene #27: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
3P LOSS MUTATED | 12 | 0 | 0 | 0 | 0
3P LOSS WILD-TYPE | 46 | 61 | 1 | 2 | 1

Figure S74. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S75. Gene #27: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
3P LOSS MUTATED | 0 | 0 | 12
3P LOSS WILD-TYPE | 18 | 59 | 34

Figure S75. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S76. Gene #27: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
3P LOSS MUTATED | 7 | 0 | 5 | 0
3P LOSS WILD-TYPE | 22 | 33 | 28 | 28

Figure S76. Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.2

Table S77. Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
3Q LOSS MUTATED | 0 | 6 | 1
3Q LOSS WILD-TYPE | 65 | 25 | 26

Figure S77. Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.07

Table S78. Gene #28: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
3Q LOSS MUTATED | 0 | 1 | 6 | 0
3Q LOSS WILD-TYPE | 39 | 35 | 18 | 24

Figure S78. Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S79. Gene #31: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
6P LOSS MUTATED | 1 | 18 | 1
6P LOSS WILD-TYPE | 64 | 13 | 26

Figure S79. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S80. Gene #31: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
6P LOSS MUTATED | 2 | 3 | 15 | 0
6P LOSS WILD-TYPE | 37 | 33 | 9 | 24

Figure S80. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S81. Gene #31: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
6P LOSS MUTATED | 14 | 0 | 6 | 0
6P LOSS WILD-TYPE | 29 | 30 | 7 | 29

Figure S81. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S82. Gene #31: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
6P LOSS MUTATED | 15 | 0 | 0 | 5
6P LOSS WILD-TYPE | 29 | 41 | 20 | 5

Figure S82. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S83. Gene #31: '6p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
6P LOSS MUTATED | 19 | 0 | 0 | 1 | 0
6P LOSS WILD-TYPE | 39 | 61 | 1 | 1 | 1

Figure S83. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S84. Gene #31: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
6P LOSS MUTATED | 9 | 0 | 8 | 3 | 0 | 0
6P LOSS WILD-TYPE | 18 | 18 | 20 | 4 | 16 | 27

Figure S84. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S85. Gene #31: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
6P LOSS MUTATED | 1 | 0 | 19
6P LOSS WILD-TYPE | 17 | 59 | 27

Figure S85. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S86. Gene #31: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
6P LOSS MUTATED | 10 | 0 | 10 | 0
6P LOSS WILD-TYPE | 19 | 33 | 23 | 28

Figure S86. Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S87. Gene #32: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
6Q LOSS MUTATED | 0 | 17 | 2
6Q LOSS WILD-TYPE | 65 | 14 | 25

Figure S87. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S88. Gene #32: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
6Q LOSS MUTATED | 1 | 3 | 15 | 0
6Q LOSS WILD-TYPE | 38 | 33 | 9 | 24

Figure S88. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S89. Gene #32: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
6Q LOSS MUTATED | 12 | 0 | 7 | 0
6Q LOSS WILD-TYPE | 31 | 30 | 6 | 29

Figure S89. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S90. Gene #32: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
6Q LOSS MUTATED | 13 | 0 | 1 | 5
6Q LOSS WILD-TYPE | 31 | 41 | 19 | 5

Figure S90. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S91. Gene #32: '6q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 58 | 61 | 1 | 2 | 1
6Q LOSS MUTATED | 17 | 1 | 0 | 1 | 0
6Q LOSS WILD-TYPE | 41 | 60 | 1 | 1 | 1

Figure S91. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.088

Table S92. Gene #32: '6q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
6Q LOSS MUTATED | 9 | 0 | 6 | 3 | 1 | 0
6Q LOSS WILD-TYPE | 18 | 18 | 22 | 4 | 15 | 27

Figure S92. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S93. Gene #32: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
6Q LOSS MUTATED | 0 | 0 | 19
6Q LOSS WILD-TYPE | 18 | 59 | 27

Figure S93. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.023

Table S94. Gene #32: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
6Q LOSS MUTATED | 10 | 1 | 8 | 0
6Q LOSS WILD-TYPE | 19 | 32 | 25 | 28

Figure S94. Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S95. Gene #35: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
11P LOSS MUTATED | 0 | 9 | 0
11P LOSS WILD-TYPE | 65 | 22 | 27

Figure S95. Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S96. Gene #35: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
11P LOSS MUTATED | 0 | 1 | 8 | 0
11P LOSS WILD-TYPE | 39 | 35 | 16 | 24

Figure S96. Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.046

Table S97. Gene #35: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
11P LOSS MUTATED | 0 | 0 | 9
11P LOSS WILD-TYPE | 18 | 59 | 37

Figure S97. Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S98. Gene #36: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
11Q LOSS MUTATED | 0 | 7 | 0
11Q LOSS WILD-TYPE | 65 | 24 | 27

Figure S98. Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S99. Gene #36: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
11Q LOSS MUTATED | 0 | 0 | 7 | 0
11Q LOSS WILD-TYPE | 39 | 36 | 17 | 24

Figure S99. Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.03

Table S100. Gene #37: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
12P LOSS MUTATED | 1 | 0 | 7 | 0
12P LOSS WILD-TYPE | 38 | 36 | 17 | 24

Figure S100. Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S101. Gene #38: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
12Q LOSS MUTATED | 0 | 0 | 7 | 0
12Q LOSS WILD-TYPE | 39 | 36 | 17 | 24

Figure S101. Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S102. Gene #39: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
13Q LOSS MUTATED | 0 | 9 | 5
13Q LOSS WILD-TYPE | 65 | 22 | 22

Figure S102. Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S103. Gene #41: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 30 | 13 | 29
16Q LOSS MUTATED | 3 | 1 | 8 | 1
16Q LOSS WILD-TYPE | 40 | 29 | 5 | 28

Figure S103. Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S104. Gene #41: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
16Q LOSS MUTATED | 3 | 1 | 1 | 8
16Q LOSS WILD-TYPE | 41 | 40 | 19 | 2

Figure S104. Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S105. Gene #41: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 27 | 18 | 28 | 7 | 16 | 27
16Q LOSS MUTATED | 1 | 0 | 4 | 6 | 1 | 1
16Q LOSS WILD-TYPE | 26 | 18 | 24 | 1 | 15 | 26

Figure S105. Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.2

Table S106. Gene #41: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 29 | 33 | 33 | 28
16Q LOSS MUTATED | 1 | 1 | 10 | 1
16Q LOSS WILD-TYPE | 28 | 32 | 23 | 27

Figure S106. Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.13

Table S107. Gene #46: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
19P LOSS MUTATED | 0 | 0 | 0 | 3
19P LOSS WILD-TYPE | 44 | 41 | 20 | 7

Figure S107. Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S108. Gene #47: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 44 | 41 | 20 | 10
19Q LOSS MUTATED | 0 | 0 | 0 | 3
19Q LOSS WILD-TYPE | 44 | 41 | 20 | 7

Figure S108. Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S109. Gene #48: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
21Q LOSS MUTATED | 0 | 9 | 0
21Q LOSS WILD-TYPE | 65 | 22 | 27

Figure S109. Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S110. Gene #48: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 36 | 24 | 24
21Q LOSS MUTATED | 0 | 1 | 8 | 0
21Q LOSS WILD-TYPE | 39 | 35 | 16 | 24

Figure S110. Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.073

Table S111. Gene #48: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 59 | 46
21Q LOSS MUTATED | 0 | 0 | 9
21Q LOSS WILD-TYPE | 18 | 59 | 37

Figure S111. Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S112. Gene #49: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 31 | 27
22Q LOSS MUTATED | 0 | 4 | 9
22Q LOSS WILD-TYPE | 65 | 27 | 18

Figure S112. Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 123

- Number of significantly arm-level cnvs = 50

- 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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