Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1DR2V1X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2V1X
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 80 patients, 95 significant findings detected with P value < 0.05 and Q value < 0.25.

- 2p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 2q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 4p gain cnv correlated to 'CN_CNMF'.

- 4q gain cnv correlated to 'CN_CNMF'.

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

- 6q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 12p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 12q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 13q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 20q gain cnv correlated to 'MRNASEQ_CNMF'.

- 21q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 22q gain cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- xp gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- xq gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 1p loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 1q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' 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'.

- 5q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

- 9p loss cnv correlated to 'CN_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- xp loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- xq loss cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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, 95 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
6p gain | 38 (48%) | 42 | 0.0416 (0.179) | 0.0067 (0.0496) | 0.00034 (0.00389) | 0.00013 (0.00168) | 2e-05 (0.000308) | 1e-05 (0.000174) | 0.00027 (0.00318) | 1e-05 (0.000174)
8p gain | 39 (49%) | 41 | 1e-05 (0.000174) | 0.00011 (0.00147) | 0.00108 (0.0105) | 6e-05 (0.000857) | 0.00275 (0.0239) | 0.00052 (0.00562) | 0.0316 (0.154) | 0.00826 (0.056)
8q gain | 53 (66%) | 27 | 1e-05 (0.000174) | 2e-05 (0.000308) | 0.00017 (0.00212) | 1e-05 (0.000174) | 2e-05 (0.000308) | 1e-05 (0.000174) | 0.00995 (0.0643) | 6e-05 (0.000857)
3p loss | 43 (54%) | 37 | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174)
3q loss | 43 (54%) | 37 | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174) | 1e-05 (0.000174)
6q gain | 16 (20%) | 64 | 0.604 (0.781) | 0.0144 (0.0822) | 0.0191 (0.105) | 0.00101 (0.0101) | 0.00089 (0.00913) | 0.0002 (0.00242) | 0.0101 (0.0643) | 0.00089 (0.00913)
6q loss | 17 (21%) | 63 | 1e-05 (0.000174) | 0.0105 (0.0658) | 0.19 (0.412) | 0.00465 (0.0365) | 0.12 (0.341) | 0.228 (0.452) | 0.0337 (0.159) | 0.00384 (0.0307)
13q gain | 6 (8%) | 74 | 0.0251 (0.132) | 0.683 (0.83) | 0.878 (0.942) | 0.751 (0.88) | 0.914 (0.964) | 0.519 (0.705) | 0.00156 (0.0139) | 0.00777 (0.0553)
17q gain | 9 (11%) | 71 | 0.00146 (0.0133) | 0.223 (0.45) | 0.33 (0.531) | 0.306 (0.513) | 0.532 (0.719) | 0.0283 (0.145) | 0.281 (0.496) | 0.0383 (0.169)
16q loss | 16 (20%) | 64 | 0.0218 (0.116) | 0.0277 (0.144) | 0.154 (0.377) | 0.0131 (0.0772) | 0.195 (0.415) | 0.126 (0.346) | 0.0692 (0.255) | 0.161 (0.385)
xq loss | 13 (16%) | 67 | 0.273 (0.496) | 0.0155 (0.0862) | 0.218 (0.45) | 0.146 (0.366) | 0.649 (0.804) | 0.384 (0.577) | 0.00788 (0.0553) | 0.00313 (0.0256)
2p gain | 10 (12%) | 70 | 0.0286 (0.145) | 0.549 (0.737) | 0.0591 (0.228) | 0.117 (0.341) | 0.224 (0.45) | 0.851 (0.92) | 0.706 (0.843) | 0.00312 (0.0256)
2q gain | 8 (10%) | 72 | 0.0107 (0.0658) | 0.222 (0.45) | 0.0538 (0.222) | 0.111 (0.332) | 0.0593 (0.228) | 0.194 (0.415) | 0.298 (0.506) | 8e-05 (0.0011)
11p gain | 10 (12%) | 70 | 0.00824 (0.056) | 0.163 (0.385) | 0.73 (0.867) | 0.383 (0.577) | 0.646 (0.804) | 0.309 (0.513) | 0.134 (0.358) | 0.00638 (0.0482)
17p gain | 8 (10%) | 72 | 0.00035 (0.00389) | 0.26 (0.487) | 0.457 (0.653) | 0.217 (0.45) | 0.602 (0.781) | 0.058 (0.228) | 0.189 (0.412) | 0.0396 (0.172)
21q gain | 14 (18%) | 66 | 0.033 (0.157) | 0.168 (0.392) | 0.0695 (0.255) | 0.0135 (0.0785) | 0.373 (0.569) | 0.296 (0.505) | 0.151 (0.374) | 0.106 (0.332)
22q gain | 5 (6%) | 75 | 0.134 (0.358) | 0.123 (0.344) | 0.107 (0.332) | 0.0718 (0.261) | 0.128 (0.346) | 0.246 (0.469) | 0.00313 (0.0256) | 0.033 (0.157)
xp gain | 10 (12%) | 70 | 0.19 (0.412) | 0.0363 (0.168) | 0.796 (0.886) | 0.14 (0.358) | 0.0533 (0.222) | 0.374 (0.569) | 0.0369 (0.168) | 0.0985 (0.331)
xq gain | 9 (11%) | 71 | 0.26 (0.487) | 0.111 (0.332) | 0.629 (0.789) | 0.02 (0.108) | 0.0551 (0.223) | 0.102 (0.332) | 0.0984 (0.331) | 0.0316 (0.154)
1p loss | 19 (24%) | 61 | 0.303 (0.512) | 0.262 (0.487) | 0.0785 (0.283) | 0.663 (0.813) | 0.967 (1.00) | 0.279 (0.496) | 0.0149 (0.0837) | 0.0302 (0.151)
1q loss | 3 (4%) | 77 | 0.382 (0.577) | 0.179 (0.406) | 0.162 (0.385) | 0.325 (0.531) | 0.192 (0.414) | 0.0457 (0.193) | 0.167 (0.392) | 0.012 (0.0714)
xp loss | 12 (15%) | 68 | 0.185 (0.412) | 0.0551 (0.223) | 0.406 (0.603) | 0.265 (0.491) | 0.927 (0.971) | 0.58 (0.769) | 0.0368 (0.168) | 0.0112 (0.0678)
4p gain | 7 (9%) | 73 | 0.00143 (0.0133) | 0.245 (0.469) | 0.143 (0.361) | 0.12 (0.341) | 0.329 (0.531) | 0.368 (0.568) | 0.326 (0.531) | 0.433 (0.637)
4q gain | 4 (5%) | 76 | 0.00575 (0.0442) | 0.309 (0.513) | 0.0994 (0.331) | 0.345 (0.542) | 0.628 (0.789) | 0.826 (0.901) | 0.789 (0.883) | 0.628 (0.789)
11q gain | 10 (12%) | 70 | 0.099 (0.331) | 0.727 (0.865) | 1 (1.00) | 0.829 (0.901) | 0.699 (0.84) | 0.116 (0.341) | 0.0942 (0.328) | 0.0383 (0.169)
12p gain | 3 (4%) | 77 | 0.141 (0.358) | 0.18 (0.406) | 0.105 (0.332) | 0.0101 (0.0643) | 0.091 (0.322) | 0.271 (0.496) | 0.11 (0.332) | 0.14 (0.358)
12q gain | 3 (4%) | 77 | 0.14 (0.358) | 0.182 (0.406) | 0.105 (0.332) | 0.00919 (0.0613) | 0.0903 (0.322) | 0.274 (0.496) | 0.109 (0.332) | 0.138 (0.358)
20q gain | 9 (11%) | 71 | 0.0691 (0.255) | 0.616 (0.788) | 0.0423 (0.18) | 0.0578 (0.228) | 0.685 (0.831) | 0.156 (0.379) | 0.238 (0.466) | 0.427 (0.63)
5q loss | 3 (4%) | 77 | 0.788 (0.883) | 0.119 (0.341) | 0.246 (0.469) | 0.17 (0.395) | 0.455 (0.652) | 0.871 (0.939) | 0.0385 (0.169) | 0.582 (0.769)
9p loss | 8 (10%) | 72 | 0.00138 (0.0131) | 0.127 (0.346) | 0.338 (0.538) | 0.154 (0.377) | 0.336 (0.538) | 0.355 (0.55) | 0.217 (0.45) | 0.293 (0.505)
9q loss | 7 (9%) | 73 | 0.00769 (0.0553) | 0.126 (0.346) | 0.706 (0.843) | 0.239 (0.466) | 0.422 (0.626) | 0.584 (0.769) | 0.151 (0.374) | 0.449 (0.649)
1q gain | 8 (10%) | 72 | 0.814 (0.895) | 0.494 (0.684) | 0.803 (0.887) | 0.803 (0.887) | 0.374 (0.569) | 0.0588 (0.228) | 0.838 (0.908) | 0.952 (0.991)
5p gain | 3 (4%) | 77 | 0.188 (0.412) | 0.179 (0.406) | 0.29 (0.505) | 0.109 (0.332) | 0.281 (0.496) | 0.278 (0.496) | 0.487 (0.679) | 0.77 (0.88)
5q gain | 3 (4%) | 77 | 0.187 (0.412) | 0.18 (0.406) | 0.292 (0.505) | 0.108 (0.332) | 0.281 (0.496) | 0.277 (0.496) | 0.488 (0.679) | 0.772 (0.88)
7p gain | 9 (11%) | 71 | 0.245 (0.469) | 0.403 (0.602) | 1 (1.00) | 0.741 (0.877) | 0.34 (0.539) | 0.181 (0.406) | 0.899 (0.958) | 0.465 (0.662)
7q gain | 8 (10%) | 72 | 0.103 (0.332) | 0.12 (0.341) | 0.957 (0.994) | 0.448 (0.649) | 0.373 (0.569) | 0.33 (0.531) | 0.974 (1.00) | 0.778 (0.883)
9p gain | 5 (6%) | 75 | 0.482 (0.679) | 0.0926 (0.325) | 0.295 (0.505) | 0.225 (0.45) | 0.288 (0.503) | 1 (1.00) | 0.298 (0.506) | 0.566 (0.757)
9q gain | 4 (5%) | 76 | 0.804 (0.887) | 0.162 (0.385) | 0.678 (0.827) | 0.537 (0.723) | 0.33 (0.531) | 0.755 (0.88) | 0.286 (0.502) | 0.473 (0.669)
14q gain | 3 (4%) | 77 | 0.141 (0.358) | 1 (1.00) | 0.104 (0.332) | 0.326 (0.531) | 0.916 (0.964) | 0.592 (0.776) | 0.689 (0.832) | 0.583 (0.769)
16p gain | 4 (5%) | 76 | 1 (1.00) | 0.455 (0.652) | 0.828 (0.901) | 0.438 (0.642) | 0.788 (0.883) | 0.474 (0.669) | 0.387 (0.579) | 0.748 (0.88)
20p gain | 8 (10%) | 72 | 0.0968 (0.331) | 0.28 (0.496) | 0.105 (0.332) | 0.22 (0.45) | 0.927 (0.971) | 0.239 (0.466) | 0.204 (0.432) | 0.119 (0.341)
4q loss | 3 (4%) | 77 | 0.789 (0.883) | 0.771 (0.88) | 0.892 (0.954) | 0.605 (0.781) | 0.916 (0.964) | 0.274 (0.496) | 0.642 (0.803) | 0.309 (0.513)
8p loss | 4 (5%) | 76 | 0.805 (0.887) | 0.756 (0.88) | 0.623 (0.789) | 0.674 (0.824) | 0.447 (0.649) | 0.629 (0.789) | 0.693 (0.836) | 0.345 (0.542)
8q loss | 3 (4%) | 77 | 0.484 (0.679) | 0.66 (0.813) | 1 (1.00) | 0.789 (0.883) | 0.762 (0.88) | 0.772 (0.88) | 0.95 (0.991) | 0.585 (0.769)
12p loss | 3 (4%) | 77 | 0.649 (0.804) | 0.662 (0.813) | 0.242 (0.469) | 0.79 (0.883) | 0.61 (0.781) | 0.52 (0.705) | 0.904 (0.961) | 0.77 (0.88)
13q loss | 3 (4%) | 77 | 0.875 (0.941) | 0.181 (0.406) | 0.352 (0.549) | 0.602 (0.781) | 0.609 (0.781) | 1 (1.00) | 0.489 (0.679) | 0.315 (0.52)
15q loss | 4 (5%) | 76 | 0.343 (0.542) | 0.251 (0.476) | 1 (1.00) | 0.827 (0.901) | 0.448 (0.649) | 0.91 (0.964) | 0.515 (0.703) | 0.629 (0.789)
16p loss | 3 (4%) | 77 | 0.26 (0.487) | 0.5 (0.687) | 0.353 (0.55) | 0.6 (0.781) | 0.761 (0.88) | 1 (1.00) | 1 (1.00) | 1 (1.00)
19p loss | 3 (4%) | 77 | 0.221 (0.45) | 0.0641 (0.244) | 0.503 (0.689) | 1 (1.00) | 0.761 (0.88) | 0.225 (0.45) | 0.124 (0.344) | 0.14 (0.358)
19q loss | 3 (4%) | 77 | 0.224 (0.45) | 0.0649 (0.245) | 0.499 (0.687) | 1 (1.00) | 0.76 (0.88) | 0.228 (0.452) | 0.123 (0.344) | 0.139 (0.358)

'2p gain' versus 'CN_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.14

Table S1. Gene #2: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
2P GAIN MUTATED | 2 | 1 | 5 | 2 | 0 | 0
2P GAIN WILD-TYPE | 20 | 6 | 5 | 29 | 6 | 4

Figure S1. Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.026

Table S2. Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
2P GAIN MUTATED | 1 | 2 | 1 | 6
2P GAIN WILD-TYPE | 17 | 26 | 15 | 6

Figure S2. Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.066

Table S3. Gene #3: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
2Q GAIN MUTATED | 1 | 0 | 5 | 2 | 0 | 0
2Q GAIN WILD-TYPE | 21 | 7 | 5 | 29 | 6 | 4

Figure S3. Get High-res Image Gene #3: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.0011

Table S4. Gene #3: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
2Q GAIN MUTATED | 0 | 2 | 0 | 6
2Q GAIN WILD-TYPE | 18 | 26 | 16 | 6

Figure S4. Get High-res Image Gene #3: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.013

Table S5. Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
4P GAIN MUTATED | 2 | 4 | 1 | 0 | 0 | 0
4P GAIN WILD-TYPE | 20 | 3 | 9 | 31 | 6 | 4

Figure S5. Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.044

Table S6. Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
4Q GAIN MUTATED | 1 | 3 | 0 | 0 | 0 | 0
4Q GAIN WILD-TYPE | 21 | 4 | 10 | 31 | 6 | 4

Figure S6. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.18

Table S7. Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
6P GAIN MUTATED | 7 | 3 | 4 | 21 | 3 | 0
6P GAIN WILD-TYPE | 15 | 4 | 6 | 10 | 3 | 4

Figure S7. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0067 (Fisher's exact test), Q value = 0.05

Table S8. Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
6P GAIN MUTATED | 8 | 7 | 5 | 18
6P GAIN WILD-TYPE | 20 | 7 | 9 | 6

Figure S8. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0039

Table S9. Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
6P GAIN MUTATED | 3 | 5 | 24 | 6
6P GAIN WILD-TYPE | 15 | 10 | 8 | 9

Figure S9. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S10. Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
6P GAIN MUTATED | 8 | 25 | 5
6P GAIN WILD-TYPE | 21 | 8 | 13

Figure S10. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S11. Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
6P GAIN MUTATED | 1 | 3 | 5 | 22 | 6 | 1
6P GAIN WILD-TYPE | 7 | 5 | 6 | 3 | 17 | 4

Figure S11. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S12. Gene #8: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
6P GAIN MUTATED | 4 | 6 | 24 | 4
6P GAIN WILD-TYPE | 13 | 7 | 4 | 18

Figure S12. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0032

Table S13. Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
6P GAIN MUTATED | 7 | 2 | 15 | 0 | 4 | 4 | 3
6P GAIN WILD-TYPE | 13 | 5 | 2 | 9 | 4 | 3 | 3

Figure S13. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S14. Gene #8: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
6P GAIN MUTATED | 6 | 23 | 1 | 5
6P GAIN WILD-TYPE | 12 | 5 | 15 | 7

Figure S14. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.082

Table S15. Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
6Q GAIN MUTATED | 1 | 3 | 3 | 9
6Q GAIN WILD-TYPE | 27 | 11 | 11 | 15

Figure S15. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.1

Table S16. Gene #9: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
6Q GAIN MUTATED | 1 | 1 | 12 | 2
6Q GAIN WILD-TYPE | 17 | 14 | 20 | 13

Figure S16. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.01

Table S17. Gene #9: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
6Q GAIN MUTATED | 1 | 13 | 2
6Q GAIN WILD-TYPE | 28 | 20 | 16

Figure S17. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0091

Table S18. Gene #9: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
6Q GAIN MUTATED | 0 | 0 | 3 | 12 | 1 | 0
6Q GAIN WILD-TYPE | 8 | 8 | 8 | 13 | 22 | 5

Figure S18. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0024

Table S19. Gene #9: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
6Q GAIN MUTATED | 1 | 3 | 12 | 0
6Q GAIN WILD-TYPE | 16 | 10 | 16 | 22

Figure S19. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.064

Table S20. Gene #9: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
6Q GAIN MUTATED | 1 | 0 | 7 | 0 | 2 | 1 | 3
6Q GAIN WILD-TYPE | 19 | 7 | 10 | 9 | 6 | 6 | 3

Figure S20. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0091

Table S21. Gene #9: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
6Q GAIN MUTATED | 1 | 12 | 0 | 1
6Q GAIN WILD-TYPE | 17 | 16 | 16 | 11

Figure S21. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S22. Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
8P GAIN MUTATED | 12 | 6 | 9 | 5 | 5 | 2
8P GAIN WILD-TYPE | 10 | 1 | 1 | 26 | 1 | 2

Figure S22. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0015

Table S23. Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
8P GAIN MUTATED | 23 | 3 | 6 | 7
8P GAIN WILD-TYPE | 5 | 11 | 8 | 17

Figure S23. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.011

Table S24. Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
8P GAIN MUTATED | 12 | 9 | 7 | 11
8P GAIN WILD-TYPE | 6 | 6 | 25 | 4

Figure S24. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00086

Table S25. Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
8P GAIN MUTATED | 23 | 8 | 8
8P GAIN WILD-TYPE | 6 | 25 | 10

Figure S25. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.024

Table S26. Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
8P GAIN MUTATED | 5 | 5 | 3 | 7 | 18 | 1
8P GAIN WILD-TYPE | 3 | 3 | 8 | 18 | 5 | 4

Figure S26. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0056

Table S27. Gene #12: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
8P GAIN MUTATED | 13 | 2 | 9 | 15
8P GAIN WILD-TYPE | 4 | 11 | 19 | 7

Figure S27. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.15

Table S28. Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
8P GAIN MUTATED | 15 | 5 | 6 | 1 | 4 | 4 | 3
8P GAIN WILD-TYPE | 5 | 2 | 11 | 8 | 4 | 3 | 3

Figure S28. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00826 (Fisher's exact test), Q value = 0.056

Table S29. Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
8P GAIN MUTATED | 14 | 8 | 10 | 6
8P GAIN WILD-TYPE | 4 | 20 | 6 | 6

Figure S29. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S30. Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
8Q GAIN MUTATED | 18 | 6 | 10 | 9 | 6 | 4
8Q GAIN WILD-TYPE | 4 | 1 | 0 | 22 | 0 | 0

Figure S30. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S31. Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
8Q GAIN MUTATED | 27 | 5 | 10 | 11
8Q GAIN WILD-TYPE | 1 | 9 | 4 | 13

Figure S31. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0021

Table S32. Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
8Q GAIN MUTATED | 15 | 12 | 12 | 14
8Q GAIN WILD-TYPE | 3 | 3 | 20 | 1

Figure S32. 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 = 0.00017

Table S33. 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 S33. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S34. Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
8Q GAIN MUTATED | 7 | 7 | 3 | 12 | 22 | 2
8Q GAIN WILD-TYPE | 1 | 1 | 8 | 13 | 1 | 3

Figure S34. 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 = 0.00017

Table S35. Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
8Q GAIN MUTATED | 16 | 3 | 14 | 20
8Q GAIN WILD-TYPE | 1 | 10 | 14 | 2

Figure S35. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00995 (Fisher's exact test), Q value = 0.064

Table S36. Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
8Q GAIN MUTATED | 19 | 6 | 8 | 4 | 5 | 4 | 5
8Q GAIN WILD-TYPE | 1 | 1 | 9 | 5 | 3 | 3 | 1

Figure S36. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00086

Table S37. Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
8Q GAIN MUTATED | 18 | 12 | 14 | 7
8Q GAIN WILD-TYPE | 0 | 16 | 2 | 5

Figure S37. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.056

Table S38. Gene #16: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
11P GAIN MUTATED | 4 | 0 | 5 | 1 | 0 | 0
11P GAIN WILD-TYPE | 18 | 7 | 5 | 30 | 6 | 4

Figure S38. Get High-res Image Gene #16: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00638 (Fisher's exact test), Q value = 0.048

Table S39. Gene #16: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
11P GAIN MUTATED | 0 | 3 | 1 | 5
11P GAIN WILD-TYPE | 18 | 25 | 15 | 7

Figure S39. Get High-res Image Gene #16: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.17

Table S40. Gene #17: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
11Q GAIN MUTATED | 0 | 3 | 1 | 4
11Q GAIN WILD-TYPE | 18 | 25 | 15 | 8

Figure S40. Get High-res Image Gene #17: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.064

Table S41. Gene #18: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
12P GAIN MUTATED | 0 | 0 | 3
12P GAIN WILD-TYPE | 29 | 33 | 15

Figure S41. Get High-res Image Gene #18: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.061

Table S42. Gene #19: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
12Q GAIN MUTATED | 0 | 0 | 3
12Q GAIN WILD-TYPE | 29 | 33 | 15

Figure S42. Get High-res Image Gene #19: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.13

Table S43. Gene #20: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
13Q GAIN MUTATED | 1 | 0 | 4 | 1 | 0 | 0
13Q GAIN WILD-TYPE | 21 | 7 | 6 | 30 | 6 | 4

Figure S43. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.014

Table S44. Gene #20: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
13Q GAIN MUTATED | 1 | 0 | 0 | 0 | 1 | 4 | 0
13Q GAIN WILD-TYPE | 19 | 7 | 17 | 9 | 7 | 3 | 6

Figure S44. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00777 (Fisher's exact test), Q value = 0.055

Table S45. Gene #20: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
13Q GAIN MUTATED | 0 | 2 | 0 | 4
13Q GAIN WILD-TYPE | 18 | 26 | 16 | 8

Figure S45. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0039

Table S46. Gene #23: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
17P GAIN MUTATED | 1 | 0 | 6 | 1 | 0 | 0
17P GAIN WILD-TYPE | 21 | 7 | 4 | 30 | 6 | 4

Figure S46. Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.17

Table S47. Gene #23: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
17P GAIN MUTATED | 0 | 3 | 1 | 4
17P GAIN WILD-TYPE | 18 | 25 | 15 | 8

Figure S47. Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.013

Table S48. Gene #24: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
17Q GAIN MUTATED | 1 | 0 | 6 | 2 | 0 | 0
17Q GAIN WILD-TYPE | 21 | 7 | 4 | 29 | 6 | 4

Figure S48. Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.14

Table S49. Gene #24: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
17Q GAIN MUTATED | 3 | 0 | 6 | 0
17Q GAIN WILD-TYPE | 14 | 13 | 22 | 22

Figure S49. Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.17

Table S50. Gene #24: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
17Q GAIN MUTATED | 0 | 4 | 1 | 4
17Q GAIN WILD-TYPE | 18 | 24 | 15 | 8

Figure S50. Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.18

Table S51. Gene #26: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
20Q GAIN MUTATED | 1 | 4 | 1 | 3
20Q GAIN WILD-TYPE | 17 | 11 | 31 | 12

Figure S51. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.16

Table S52. Gene #27: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
21Q GAIN MUTATED | 5 | 1 | 5 | 2 | 0 | 1
21Q GAIN WILD-TYPE | 17 | 6 | 5 | 29 | 6 | 3

Figure S52. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.078

Table S53. Gene #27: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
21Q GAIN MUTATED | 5 | 2 | 7
21Q GAIN WILD-TYPE | 24 | 31 | 11

Figure S53. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.026

Table S54. Gene #28: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
22Q GAIN MUTATED | 0 | 1 | 0 | 0 | 1 | 3 | 0
22Q GAIN WILD-TYPE | 20 | 6 | 17 | 9 | 7 | 4 | 6

Figure S54. Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.16

Table S55. Gene #28: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
22Q GAIN MUTATED | 0 | 2 | 0 | 3
22Q GAIN WILD-TYPE | 18 | 26 | 16 | 9

Figure S55. Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.17

Table S56. Gene #29: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
XP GAIN MUTATED | 1 | 1 | 5 | 3
XP GAIN WILD-TYPE | 27 | 13 | 9 | 21

Figure S56. Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.17

Table S57. Gene #29: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
XP GAIN MUTATED | 0 | 1 | 4 | 0 | 3 | 1 | 0
XP GAIN WILD-TYPE | 20 | 6 | 13 | 9 | 5 | 6 | 6

Figure S57. Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.11

Table S58. Gene #30: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
XQ GAIN MUTATED | 0 | 5 | 4
XQ GAIN WILD-TYPE | 29 | 28 | 14

Figure S58. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.15

Table S59. Gene #30: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
XQ GAIN MUTATED | 0 | 5 | 0 | 3
XQ GAIN WILD-TYPE | 18 | 23 | 16 | 9

Figure S59. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.084

Table S60. Gene #31: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
1P LOSS MUTATED | 6 | 1 | 3 | 0 | 5 | 4 | 0
1P LOSS WILD-TYPE | 14 | 6 | 14 | 9 | 3 | 3 | 6

Figure S60. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.15

Table S61. Gene #31: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
1P LOSS MUTATED | 1 | 7 | 8 | 3
1P LOSS WILD-TYPE | 17 | 21 | 8 | 9

Figure S61. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.19

Table S62. Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
1Q LOSS MUTATED | 0 | 0 | 0 | 3
1Q LOSS WILD-TYPE | 17 | 13 | 28 | 19

Figure S62. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.071

Table S63. Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
1Q LOSS MUTATED | 0 | 0 | 3 | 0
1Q LOSS WILD-TYPE | 18 | 28 | 13 | 12

Figure S63. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S64. Gene #33: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
3P LOSS MUTATED | 17 | 7 | 8 | 2 | 6 | 3
3P LOSS WILD-TYPE | 5 | 0 | 2 | 29 | 0 | 1

Figure S64. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S65. Gene #33: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
3P LOSS MUTATED | 28 | 3 | 10 | 2
3P LOSS WILD-TYPE | 0 | 11 | 4 | 22

Figure S65. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S66. Gene #33: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
3P LOSS MUTATED | 18 | 10 | 2 | 13
3P LOSS WILD-TYPE | 0 | 5 | 30 | 2

Figure S66. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S67. Gene #33: '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 S67. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S68. Gene #33: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
3P LOSS MUTATED | 8 | 5 | 2 | 2 | 23 | 3
3P LOSS WILD-TYPE | 0 | 3 | 9 | 23 | 0 | 2

Figure S68. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S69. Gene #33: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
3P LOSS MUTATED | 17 | 1 | 3 | 22
3P LOSS WILD-TYPE | 0 | 12 | 25 | 0

Figure S69. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S70. Gene #33: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
3P LOSS MUTATED | 20 | 6 | 2 | 4 | 5 | 2 | 3
3P LOSS WILD-TYPE | 0 | 1 | 15 | 5 | 3 | 5 | 3

Figure S70. Get High-res Image Gene #33: '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 = 0.00017

Table S71. Gene #33: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
3P LOSS MUTATED | 17 | 3 | 16 | 6
3P LOSS WILD-TYPE | 1 | 25 | 0 | 6

Figure S71. Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S72. Gene #34: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
3Q LOSS MUTATED | 17 | 7 | 8 | 2 | 6 | 3
3Q LOSS WILD-TYPE | 5 | 0 | 2 | 29 | 0 | 1

Figure S72. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S73. Gene #34: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
3Q LOSS MUTATED | 28 | 3 | 10 | 2
3Q LOSS WILD-TYPE | 0 | 11 | 4 | 22

Figure S73. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S74. Gene #34: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
3Q LOSS MUTATED | 18 | 10 | 2 | 13
3Q LOSS WILD-TYPE | 0 | 5 | 30 | 2

Figure S74. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S75. Gene #34: '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 S75. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S76. Gene #34: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
3Q LOSS MUTATED | 8 | 5 | 2 | 2 | 23 | 3
3Q LOSS WILD-TYPE | 0 | 3 | 9 | 23 | 0 | 2

Figure S76. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S77. Gene #34: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
3Q LOSS MUTATED | 17 | 1 | 3 | 22
3Q LOSS WILD-TYPE | 0 | 12 | 25 | 0

Figure S77. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S78. Gene #34: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
3Q LOSS MUTATED | 20 | 6 | 2 | 4 | 5 | 2 | 3
3Q LOSS WILD-TYPE | 0 | 1 | 15 | 5 | 3 | 5 | 3

Figure S78. Get High-res Image Gene #34: '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 = 0.00017

Table S79. Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
3Q LOSS MUTATED | 17 | 3 | 16 | 6
3Q LOSS WILD-TYPE | 1 | 25 | 0 | 6

Figure S79. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.17

Table S80. Gene #36: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
5Q LOSS MUTATED | 0 | 0 | 0 | 0 | 2 | 1 | 0
5Q LOSS WILD-TYPE | 20 | 7 | 17 | 9 | 6 | 6 | 6

Figure S80. Get High-res Image Gene #36: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S81. Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
6Q LOSS MUTATED | 0 | 7 | 2 | 4 | 4 | 0
6Q LOSS WILD-TYPE | 22 | 0 | 8 | 27 | 2 | 4

Figure S81. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.066

Table S82. Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
6Q LOSS MUTATED | 12 | 1 | 1 | 3
6Q LOSS WILD-TYPE | 16 | 13 | 13 | 21

Figure S82. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.036

Table S83. Gene #37: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
6Q LOSS MUTATED | 12 | 4 | 1
6Q LOSS WILD-TYPE | 17 | 29 | 17

Figure S83. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.16

Table S84. Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
6Q LOSS MUTATED | 10 | 2 | 2 | 2 | 0 | 1 | 0
6Q LOSS WILD-TYPE | 10 | 5 | 15 | 7 | 8 | 6 | 6

Figure S84. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.031

Table S85. Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
6Q LOSS MUTATED | 10 | 3 | 2 | 2
6Q LOSS WILD-TYPE | 8 | 25 | 14 | 10

Figure S85. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.013

Table S86. Gene #40: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
9P LOSS MUTATED | 0 | 2 | 3 | 1 | 0 | 2
9P LOSS WILD-TYPE | 22 | 5 | 7 | 30 | 6 | 2

Figure S86. Get High-res Image Gene #40: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.055

Table S87. Gene #41: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
9Q LOSS MUTATED | 0 | 2 | 3 | 1 | 0 | 1
9Q LOSS WILD-TYPE | 22 | 5 | 7 | 30 | 6 | 3

Figure S87. Get High-res Image Gene #41: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.12

Table S88. Gene #46: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
16Q LOSS MUTATED | 4 | 5 | 1 | 4 | 2 | 0
16Q LOSS WILD-TYPE | 18 | 2 | 9 | 27 | 4 | 4

Figure S88. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.14

Table S89. Gene #46: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
16Q LOSS MUTATED | 10 | 0 | 3 | 3
16Q LOSS WILD-TYPE | 18 | 14 | 11 | 21

Figure S89. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.077

Table S90. Gene #46: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
16Q LOSS MUTATED | 11 | 4 | 1
16Q LOSS WILD-TYPE | 18 | 29 | 17

Figure S90. Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.17

Table S91. Gene #49: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
XP LOSS MUTATED | 4 | 1 | 0 | 1 | 4 | 2 | 0
XP LOSS WILD-TYPE | 16 | 6 | 17 | 8 | 4 | 5 | 6

Figure S91. Get High-res Image Gene #49: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.068

Table S92. Gene #49: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
XP LOSS MUTATED | 2 | 3 | 7 | 0
XP LOSS WILD-TYPE | 16 | 25 | 9 | 12

Figure S92. Get High-res Image Gene #49: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.086

Table S93. Gene #50: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
XQ LOSS MUTATED | 5 | 1 | 6 | 1
XQ LOSS WILD-TYPE | 23 | 13 | 8 | 23

Figure S93. Get High-res Image Gene #50: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00788 (Fisher's exact test), Q value = 0.055

Table S94. Gene #50: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
XQ LOSS MUTATED | 4 | 1 | 0 | 1 | 5 | 2 | 0
XQ LOSS WILD-TYPE | 16 | 6 | 17 | 8 | 3 | 5 | 6

Figure S94. Get High-res Image Gene #50: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.026

Table S95. Gene #50: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
XQ LOSS MUTATED | 2 | 3 | 8 | 0
XQ LOSS WILD-TYPE | 16 | 25 | 8 | 12

Figure S95. Get High-res Image Gene #50: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/22534465/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/22542449/UVM-TP.transferedmergedcluster.txt

- Number of patients = 80

- 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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