Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C13F4NRQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13F4NRQ
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 51 arm-level events and 8 molecular subtypes across 80 patients, 91 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- 2q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 4p 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 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 7q gain cnv correlated to 'METHLYATION_CNMF'.

- 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'.

- 9q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- 12p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 12q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 14q gain cnv correlated to 'CN_CNMF'.

- 17q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

- 20p gain cnv correlated to 'CN_CNMF'.

- 20q gain cnv correlated to 'CN_CNMF'.

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

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

- 1p loss cnv correlated to 'CN_CNMF'.

- 1q loss cnv correlated to 'CN_CNMF', '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'.

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

- 8p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 9p loss cnv correlated to 'METHLYATION_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- 15q loss cnv correlated to 'METHLYATION_CNMF'.

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

- xp loss cnv correlated to 'METHLYATION_CNMF'.

- 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 51 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, 91 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 | 39 (49%) | 41 | 0.00025 (0.00319) | 0.00433 (0.0376) | 0.00019 (0.00258) | 0.00023 (0.00303) | 2e-05 (0.000355) | 3e-05 (0.00051) | 0.0104 (0.077) | 2e-05 (0.000355)
6q gain | 16 (20%) | 64 | 0.0058 (0.0473) | 0.00238 (0.0237) | 0.00035 (0.00408) | 0.00112 (0.0124) | 0.00026 (0.00321) | 0.00034 (0.00408) | 0.00352 (0.0326) | 0.0001 (0.00146)
8p gain | 33 (41%) | 47 | 0.00135 (0.0145) | 0.001 (0.0113) | 0.00259 (0.0252) | 0.00412 (0.0367) | 0.0196 (0.123) | 0.0152 (0.105) | 0.0378 (0.191) | 0.0137 (0.0965)
8q gain | 53 (66%) | 27 | 1e-05 (0.000204) | 1e-05 (0.000204) | 6e-05 (0.000979) | 1e-05 (0.000204) | 9e-05 (0.00136) | 1e-05 (0.000204) | 2e-05 (0.000355) | 0.00011 (0.00155)
3p loss | 43 (54%) | 37 | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204)
3q loss | 43 (54%) | 37 | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204) | 1e-05 (0.000204)
6q loss | 17 (21%) | 63 | 8e-05 (0.00126) | 0.00414 (0.0367) | 0.0495 (0.222) | 0.00503 (0.0419) | 0.0988 (0.363) | 0.23 (0.507) | 0.0388 (0.191) | 0.00152 (0.0159)
8p loss | 9 (11%) | 71 | 0.0296 (0.17) | 0.345 (0.616) | 0.0357 (0.191) | 0.0244 (0.146) | 0.227 (0.507) | 0.28 (0.541) | 0.165 (0.433) | 0.0178 (0.121)
1q loss | 3 (4%) | 77 | 0.0376 (0.191) | 0.167 (0.435) | 0.218 (0.506) | 0.324 (0.601) | 0.429 (0.698) | 0.046 (0.215) | 0.0912 (0.348) | 0.0322 (0.18)
16q loss | 16 (20%) | 64 | 0.0213 (0.132) | 0.131 (0.399) | 0.0943 (0.35) | 0.0127 (0.0929) | 0.824 (0.947) | 0.127 (0.392) | 0.145 (0.425) | 0.0469 (0.215)
xq loss | 13 (16%) | 67 | 0.153 (0.43) | 0.0191 (0.123) | 0.212 (0.506) | 0.146 (0.425) | 0.222 (0.506) | 0.386 (0.661) | 0.018 (0.121) | 0.0464 (0.215)
2p gain | 10 (12%) | 70 | 0.319 (0.597) | 1 (1.00) | 0.0381 (0.191) | 0.115 (0.377) | 0.108 (0.365) | 0.851 (0.959) | 0.552 (0.813) | 0.0327 (0.18)
9q gain | 5 (6%) | 75 | 0.514 (0.771) | 0.0372 (0.191) | 0.839 (0.952) | 0.84 (0.952) | 0.35 (0.621) | 0.749 (0.931) | 0.0185 (0.122) | 0.758 (0.931)
21q gain | 14 (18%) | 66 | 0.00322 (0.0306) | 0.197 (0.479) | 0.104 (0.365) | 0.0135 (0.0965) | 0.869 (0.976) | 0.298 (0.568) | 0.128 (0.393) | 0.468 (0.723)
xq gain | 9 (11%) | 71 | 0.66 (0.89) | 0.281 (0.541) | 0.0242 (0.146) | 0.0195 (0.123) | 0.108 (0.365) | 0.104 (0.365) | 0.434 (0.698) | 0.0885 (0.344)
11p loss | 3 (4%) | 77 | 0.0371 (0.191) | 0.234 (0.507) | 0.0429 (0.204) | 0.109 (0.365) | 0.232 (0.507) | 0.152 (0.43) | 0.216 (0.506) | 0.186 (0.459)
1q gain | 8 (10%) | 72 | 0.717 (0.928) | 0.716 (0.928) | 0.704 (0.921) | 0.8 (0.931) | 0.212 (0.506) | 0.0587 (0.247) | 1 (1.00) | 0.0383 (0.191)
2q gain | 8 (10%) | 72 | 0.395 (0.665) | 0.716 (0.928) | 0.0556 (0.244) | 0.11 (0.365) | 0.277 (0.541) | 0.194 (0.474) | 0.346 (0.616) | 0.00756 (0.0605)
4p gain | 7 (9%) | 73 | 0.0267 (0.158) | 0.279 (0.541) | 0.153 (0.43) | 0.12 (0.38) | 0.885 (0.986) | 0.367 (0.637) | 0.873 (0.976) | 0.23 (0.507)
7q gain | 8 (10%) | 72 | 0.0563 (0.244) | 0.0309 (0.175) | 0.889 (0.988) | 0.445 (0.699) | 0.315 (0.595) | 0.328 (0.602) | 0.261 (0.541) | 0.673 (0.9)
12p gain | 3 (4%) | 77 | 0.159 (0.433) | 0.441 (0.698) | 0.088 (0.344) | 0.00999 (0.0755) | 0.795 (0.931) | 0.274 (0.541) | 1 (1.00) | 0.279 (0.541)
12q gain | 3 (4%) | 77 | 0.161 (0.433) | 0.441 (0.698) | 0.0882 (0.344) | 0.00979 (0.0754) | 0.796 (0.931) | 0.275 (0.541) | 1 (1.00) | 0.279 (0.541)
14q gain | 3 (4%) | 77 | 0.0377 (0.191) | 0.441 (0.698) | 0.588 (0.832) | 0.327 (0.602) | 0.796 (0.931) | 0.597 (0.832) | 1 (1.00) | 0.765 (0.931)
17q gain | 9 (11%) | 71 | 0.217 (0.506) | 1 (1.00) | 0.422 (0.694) | 0.308 (0.584) | 0.254 (0.537) | 0.0286 (0.167) | 0.267 (0.541) | 0.632 (0.866)
20p gain | 8 (10%) | 72 | 0.00923 (0.0724) | 0.566 (0.831) | 0.389 (0.661) | 0.219 (0.506) | 0.279 (0.541) | 0.237 (0.508) | 0.793 (0.931) | 0.843 (0.953)
20q gain | 9 (11%) | 71 | 0.00175 (0.0178) | 0.541 (0.802) | 0.146 (0.425) | 0.0569 (0.244) | 0.18 (0.449) | 0.157 (0.432) | 0.903 (0.995) | 0.779 (0.931)
1p loss | 19 (24%) | 61 | 0.00479 (0.0407) | 0.0508 (0.225) | 0.785 (0.931) | 0.665 (0.892) | 0.366 (0.637) | 0.277 (0.541) | 0.268 (0.541) | 0.0764 (0.312)
9p loss | 8 (10%) | 72 | 0.109 (0.365) | 0.0414 (0.199) | 0.345 (0.616) | 0.153 (0.43) | 0.187 (0.46) | 0.353 (0.622) | 0.171 (0.438) | 0.791 (0.931)
15q loss | 4 (5%) | 76 | 0.156 (0.432) | 0.0482 (0.219) | 0.831 (0.947) | 0.825 (0.947) | 1 (1.00) | 0.911 (0.999) | 1 (1.00) | 0.7 (0.921)
xp loss | 12 (15%) | 68 | 0.342 (0.616) | 0.0393 (0.191) | 0.323 (0.601) | 0.267 (0.541) | 0.48 (0.736) | 0.581 (0.832) | 0.0691 (0.288) | 0.134 (0.403)
4q gain | 4 (5%) | 76 | 0.155 (0.432) | 0.269 (0.541) | 0.399 (0.67) | 0.344 (0.616) | 0.424 (0.694) | 0.824 (0.947) | 1 (1.00) | 0.227 (0.507)
5p gain | 3 (4%) | 77 | 0.161 (0.433) | 0.443 (0.698) | 0.781 (0.931) | 0.108 (0.365) | 0.793 (0.931) | 0.276 (0.541) | 1 (1.00) | 0.215 (0.506)
5q gain | 3 (4%) | 77 | 0.162 (0.433) | 0.437 (0.698) | 0.784 (0.931) | 0.108 (0.365) | 0.795 (0.931) | 0.274 (0.541) | 1 (1.00) | 0.214 (0.506)
7p gain | 9 (11%) | 71 | 0.164 (0.433) | 0.126 (0.392) | 1 (1.00) | 0.74 (0.931) | 0.661 (0.89) | 0.18 (0.449) | 0.643 (0.871) | 0.781 (0.931)
9p gain | 6 (8%) | 74 | 0.236 (0.508) | 0.178 (0.449) | 0.405 (0.674) | 0.642 (0.871) | 0.743 (0.931) | 1 (1.00) | 0.126 (0.392) | 0.918 (1.00)
11p gain | 9 (11%) | 71 | 0.165 (0.433) | 0.542 (0.802) | 1 (1.00) | 0.739 (0.931) | 0.252 (0.536) | 0.234 (0.507) | 1 (1.00) | 0.702 (0.921)
11q gain | 10 (12%) | 70 | 0.317 (0.596) | 0.829 (0.947) | 0.909 (0.999) | 0.829 (0.947) | 0.134 (0.403) | 0.118 (0.378) | 1 (1.00) | 0.701 (0.921)
13q gain | 6 (8%) | 74 | 0.106 (0.365) | 1 (1.00) | 0.735 (0.931) | 0.751 (0.931) | 0.488 (0.736) | 0.519 (0.774) | 0.406 (0.674) | 0.118 (0.378)
16p gain | 4 (5%) | 76 | 1 (1.00) | 0.436 (0.698) | 1 (1.00) | 0.438 (0.698) | 0.338 (0.615) | 0.474 (0.73) | 0.83 (0.947) | 1 (1.00)
17p gain | 8 (10%) | 72 | 0.0806 (0.323) | 0.801 (0.931) | 0.394 (0.665) | 0.22 (0.506) | 0.355 (0.622) | 0.0586 (0.247) | 0.484 (0.736) | 0.703 (0.921)
22q gain | 6 (8%) | 74 | 0.108 (0.365) | 0.643 (0.871) | 0.151 (0.43) | 0.222 (0.506) | 0.488 (0.736) | 0.175 (0.443) | 1 (1.00) | 0.118 (0.378)
xp gain | 10 (12%) | 70 | 0.389 (0.661) | 0.093 (0.35) | 0.111 (0.367) | 0.141 (0.42) | 0.337 (0.615) | 0.375 (0.649) | 0.377 (0.649) | 0.27 (0.541)
4q loss | 3 (4%) | 77 | 1 (1.00) | 0.79 (0.931) | 0.591 (0.832) | 0.604 (0.832) | 0.795 (0.931) | 0.276 (0.541) | 0.406 (0.674) | 0.489 (0.736)
5q loss | 3 (4%) | 77 | 0.449 (0.701) | 0.107 (0.365) | 0.0893 (0.344) | 0.169 (0.437) | 0.599 (0.832) | 0.871 (0.976) | 0.298 (0.568) | 0.893 (0.988)
8q loss | 3 (4%) | 77 | 0.789 (0.931) | 0.603 (0.832) | 1 (1.00) | 0.792 (0.931) | 1 (1.00) | 0.773 (0.931) | 0.784 (0.931) | 0.893 (0.988)
9q loss | 7 (9%) | 73 | 0.165 (0.433) | 0.0754 (0.311) | 0.596 (0.832) | 0.24 (0.514) | 0.0943 (0.35) | 0.581 (0.832) | 0.0805 (0.323) | 0.422 (0.694)
12p loss | 3 (4%) | 77 | 0.788 (0.931) | 0.606 (0.832) | 1 (1.00) | 0.792 (0.931) | 1 (1.00) | 0.52 (0.774) | 0.593 (0.832) | 1 (1.00)
13q loss | 3 (4%) | 77 | 1 (1.00) | 0.172 (0.438) | 0.592 (0.832) | 0.604 (0.832) | 1 (1.00) | 1 (1.00) | 0.785 (0.931) | 0.488 (0.736)
16p loss | 3 (4%) | 77 | 1 (1.00) | 0.443 (0.698) | 0.587 (0.832) | 0.601 (0.832) | 1 (1.00) | 1 (1.00) | 0.784 (0.931) | 0.355 (0.622)
19p loss | 3 (4%) | 77 | 0.452 (0.701) | 0.603 (0.832) | 0.784 (0.931) | 1 (1.00) | 0.598 (0.832) | 0.228 (0.507) | 0.785 (0.931) | 0.691 (0.921)
19q loss | 3 (4%) | 77 | 0.452 (0.701) | 0.604 (0.832) | 0.781 (0.931) | 1 (1.00) | 0.598 (0.832) | 0.228 (0.507) | 0.789 (0.931) | 0.693 (0.921)

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.19

Table S1. Gene #1: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
1Q GAIN MUTATED | 2 | 1 | 0 | 4 | 1 | 0
1Q GAIN WILD-TYPE | 3 | 11 | 16 | 12 | 14 | 10

Figure S1. Get High-res Image Gene #1: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.19

Table S2. Gene #2: '2p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
2P GAIN MUTATED | 2 | 5 | 3
2P GAIN WILD-TYPE | 28 | 10 | 32

Figure S2. Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.18

Table S3. Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
2P GAIN MUTATED | 0 | 5 | 0 | 2 | 1 | 2
2P GAIN WILD-TYPE | 5 | 7 | 16 | 14 | 14 | 8

Figure S3. Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00756 (Fisher's exact test), Q value = 0.06

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
2Q GAIN MUTATED | 0 | 5 | 0 | 2 | 0 | 1
2Q GAIN WILD-TYPE | 5 | 7 | 16 | 14 | 15 | 9

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

'4p gain' versus 'CN_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.16

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
4P GAIN MUTATED | 5 | 2 | 0
4P GAIN WILD-TYPE | 17 | 34 | 22

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

'6p gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0032

Table S6. Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S6. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.038

Table S7. Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
6P GAIN MUTATED | 10 | 8 | 21
6P GAIN WILD-TYPE | 23 | 10 | 8

Figure S7. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0026

Table S8. Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S8. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.003

Table S9. Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S9. 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 = 0.00035

Table S10. Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
6P GAIN MUTATED | 11 | 4 | 24
6P GAIN WILD-TYPE | 23 | 13 | 5

Figure S10. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00051

Table S11. 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 | 5
6P GAIN WILD-TYPE | 13 | 7 | 4 | 17

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

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.077

Table S12. Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
6P GAIN MUTATED | 11 | 20 | 5
6P GAIN WILD-TYPE | 21 | 8 | 9

Figure S12. Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
6P GAIN MUTATED | 1 | 5 | 8 | 15 | 1 | 6
6P GAIN WILD-TYPE | 4 | 7 | 8 | 1 | 14 | 4

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

'6q gain' versus 'CN_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.047

Table S14. Gene #9: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
6Q GAIN MUTATED | 1 | 13 | 2
6Q GAIN WILD-TYPE | 21 | 23 | 20

Figure S14. Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.024

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
6Q GAIN MUTATED | 1 | 5 | 10
6Q GAIN WILD-TYPE | 32 | 13 | 19

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0041

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

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

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

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.012

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 = 0.00026 (Fisher's exact test), Q value = 0.0032

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
6Q GAIN MUTATED | 2 | 1 | 13
6Q GAIN WILD-TYPE | 32 | 16 | 16

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

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0041

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 = 0.00352 (Fisher's exact test), Q value = 0.033

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
6Q GAIN MUTATED | 1 | 8 | 5
6Q GAIN WILD-TYPE | 31 | 20 | 9

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 = 1e-04 (Fisher's exact test), Q value = 0.0015

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
6Q GAIN MUTATED | 0 | 1 | 2 | 10 | 0 | 1
6Q GAIN WILD-TYPE | 5 | 11 | 14 | 6 | 15 | 9

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.18

Table S22. Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
7Q GAIN MUTATED | 4 | 4 | 0
7Q GAIN WILD-TYPE | 29 | 14 | 29

Figure S22. Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.014

Table S23. Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
8P GAIN MUTATED | 14 | 7 | 12
8P GAIN WILD-TYPE | 8 | 29 | 10

Figure S23. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.011

Table S24. Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
8P GAIN MUTATED | 21 | 7 | 5
8P GAIN WILD-TYPE | 12 | 11 | 24

Figure S24. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.025

Table S25. Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
8P GAIN MUTATED | 17 | 9 | 7
8P GAIN WILD-TYPE | 13 | 6 | 28

Figure S25. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.037

Table S26. Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
8P GAIN MUTATED | 18 | 7 | 8
8P GAIN WILD-TYPE | 11 | 26 | 10

Figure S26. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.12

Table S27. Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
8P GAIN MUTATED | 20 | 6 | 7
8P GAIN WILD-TYPE | 14 | 11 | 22

Figure S27. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.11

Table S28. 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 | 10 | 2 | 8 | 13
8P GAIN WILD-TYPE | 7 | 11 | 20 | 9

Figure S28. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.19

Table S29. Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
8P GAIN MUTATED | 18 | 7 | 7
8P GAIN WILD-TYPE | 14 | 21 | 7

Figure S29. Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.097

Table S30. Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
8P GAIN MUTATED | 1 | 8 | 2 | 6 | 8 | 7
8P GAIN WILD-TYPE | 4 | 4 | 14 | 10 | 7 | 3

Figure S30. 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 = 2e-04

Table S31. Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S31. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S32. Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S32. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00098

Table S33. Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S33. 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 = 2e-04

Table S34. 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 S34. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0014

Table S35. Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
8Q GAIN MUTATED | 31 | 9 | 13
8Q GAIN WILD-TYPE | 3 | 8 | 16

Figure S35. 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 = 2e-04

Table S36. 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 S36. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S37. Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
8Q GAIN MUTATED | 30 | 10 | 11
8Q GAIN WILD-TYPE | 2 | 18 | 3

Figure S37. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S38. Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
8Q GAIN MUTATED | 5 | 10 | 4 | 9 | 13 | 10
8Q GAIN WILD-TYPE | 0 | 2 | 12 | 7 | 2 | 0

Figure S38. Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.19

Table S39. Gene #15: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
9Q GAIN MUTATED | 0 | 3 | 2
9Q GAIN WILD-TYPE | 33 | 15 | 27

Figure S39. Get High-res Image Gene #15: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.12

Table S40. Gene #15: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
9Q GAIN MUTATED | 0 | 2 | 3
9Q GAIN WILD-TYPE | 32 | 26 | 11

Figure S40. Get High-res Image Gene #15: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.075

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 = 0.00979 (Fisher's exact test), Q value = 0.075

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'

'14q gain' versus 'CN_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.19

Table S43. Gene #21: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
14Q GAIN MUTATED | 0 | 0 | 3
14Q GAIN WILD-TYPE | 22 | 36 | 19

Figure S43. Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.17

Table S44. 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 S44. Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.072

Table S45. Gene #25: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
20P GAIN MUTATED | 0 | 2 | 6
20P GAIN WILD-TYPE | 22 | 34 | 16

Figure S45. Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.018

Table S46. Gene #26: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
20Q GAIN MUTATED | 0 | 2 | 7
20Q GAIN WILD-TYPE | 22 | 34 | 15

Figure S46. Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.031

Table S47. Gene #27: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
21Q GAIN MUTATED | 3 | 2 | 9
21Q GAIN WILD-TYPE | 19 | 34 | 13

Figure S47. 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 = 0.097

Table S48. 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 S48. Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.15

Table S49. Gene #30: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
XQ GAIN MUTATED | 0 | 3 | 6
XQ GAIN WILD-TYPE | 30 | 12 | 29

Figure S49. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.12

Table S50. 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 S50. Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.041

Table S51. Gene #31: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
1P LOSS MUTATED | 2 | 6 | 11
1P LOSS WILD-TYPE | 20 | 30 | 11

Figure S51. Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.19

Table S52. Gene #32: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
1Q LOSS MUTATED | 0 | 0 | 3
1Q LOSS WILD-TYPE | 22 | 36 | 19

Figure S52. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.21

Table S53. 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 S53. Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.18

Table S54. Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
1Q LOSS MUTATED | 0 | 0 | 0 | 0 | 3 | 0
1Q LOSS WILD-TYPE | 5 | 12 | 16 | 16 | 12 | 10

Figure S54. 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 = 2e-04

Table S55. Gene #33: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S55. 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 = 2e-04

Table S56. Gene #33: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S56. 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 = 2e-04

Table S57. Gene #33: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S57. 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 = 2e-04

Table S58. 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 S58. 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 = 2e-04

Table S59. Gene #33: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
3P LOSS MUTATED | 29 | 12 | 2
3P LOSS WILD-TYPE | 5 | 5 | 27

Figure S59. 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 = 2e-04

Table S60. 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 S60. 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 = 2e-04

Table S61. Gene #33: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
3P LOSS MUTATED | 29 | 4 | 9
3P LOSS WILD-TYPE | 3 | 24 | 5

Figure S61. 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 = 2e-04

Table S62. Gene #33: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
3P LOSS MUTATED | 5 | 7 | 4 | 1 | 15 | 10
3P LOSS WILD-TYPE | 0 | 5 | 12 | 15 | 0 | 0

Figure S62. 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 = 2e-04

Table S63. Gene #34: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S63. 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 = 2e-04

Table S64. Gene #34: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S64. 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 = 2e-04

Table S65. Gene #34: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S65. 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 = 2e-04

Table S66. 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 S66. 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 = 2e-04

Table S67. Gene #34: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
3Q LOSS MUTATED | 29 | 12 | 2
3Q LOSS WILD-TYPE | 5 | 5 | 27

Figure S67. 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 = 2e-04

Table S68. 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 S68. 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 = 2e-04

Table S69. Gene #34: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
3Q LOSS MUTATED | 29 | 4 | 9
3Q LOSS WILD-TYPE | 3 | 24 | 5

Figure S69. 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 = 2e-04

Table S70. Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
3Q LOSS MUTATED | 5 | 7 | 4 | 1 | 15 | 10
3Q LOSS WILD-TYPE | 0 | 5 | 12 | 15 | 0 | 0

Figure S70. Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0013

Table S71. Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S71. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.037

Table S72. Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
6Q LOSS MUTATED | 13 | 2 | 2
6Q LOSS WILD-TYPE | 20 | 16 | 27

Figure S72. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.22

Table S73. Gene #37: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
6Q LOSS MUTATED | 11 | 2 | 4
6Q LOSS WILD-TYPE | 19 | 13 | 31

Figure S73. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00503 (Fisher's exact test), Q value = 0.042

Table S74. 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 S74. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.19

Table S75. Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
6Q LOSS MUTATED | 12 | 4 | 1
6Q LOSS WILD-TYPE | 20 | 24 | 13

Figure S75. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.016

Table S76. Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
6Q LOSS MUTATED | 3 | 1 | 2 | 2 | 2 | 7
6Q LOSS WILD-TYPE | 2 | 11 | 14 | 14 | 13 | 3

Figure S76. Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.17

Table S77. Gene #38: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
8P LOSS MUTATED | 6 | 2 | 1
8P LOSS WILD-TYPE | 16 | 34 | 21

Figure S77. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.19

Table S78. Gene #38: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
8P LOSS MUTATED | 7 | 0 | 2
8P LOSS WILD-TYPE | 23 | 15 | 33

Figure S78. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.15

Table S79. Gene #38: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
8P LOSS MUTATED | 7 | 2 | 0
8P LOSS WILD-TYPE | 22 | 31 | 18

Figure S79. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.12

Table S80. Gene #38: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
8P LOSS MUTATED | 3 | 1 | 0 | 1 | 3 | 1
8P LOSS WILD-TYPE | 2 | 11 | 16 | 15 | 12 | 9

Figure S80. Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.2

Table S81. Gene #40: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
9P LOSS MUTATED | 6 | 2 | 0
9P LOSS WILD-TYPE | 27 | 16 | 29

Figure S81. Get High-res Image Gene #40: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.19

Table S82. Gene #42: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
11P LOSS MUTATED | 0 | 0 | 3
11P LOSS WILD-TYPE | 22 | 36 | 19

Figure S82. Get High-res Image Gene #42: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.2

Table S83. Gene #42: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
11P LOSS MUTATED | 1 | 2 | 0
11P LOSS WILD-TYPE | 29 | 13 | 35

Figure S83. Get High-res Image Gene #42: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.22

Table S84. Gene #45: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
15Q LOSS MUTATED | 1 | 3 | 0
15Q LOSS WILD-TYPE | 32 | 15 | 29

Figure S84. Get High-res Image Gene #45: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.13

Table S85. Gene #47: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
16Q LOSS MUTATED | 9 | 5 | 2
16Q LOSS WILD-TYPE | 13 | 31 | 20

Figure S85. Get High-res Image Gene #47: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.093

Table S86. Gene #47: '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 S86. Get High-res Image Gene #47: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.21

Table S87. Gene #47: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
16Q LOSS MUTATED | 3 | 2 | 0 | 4 | 4 | 3
16Q LOSS WILD-TYPE | 2 | 10 | 16 | 12 | 11 | 7

Figure S87. Get High-res Image Gene #47: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.19

Table S88. Gene #50: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
XP LOSS MUTATED | 6 | 5 | 1
XP LOSS WILD-TYPE | 27 | 13 | 28

Figure S88. Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.12

Table S89. Gene #51: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
XQ LOSS MUTATED | 6 | 6 | 1
XQ LOSS WILD-TYPE | 27 | 12 | 28

Figure S89. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.12

Table S90. Gene #51: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
XQ LOSS MUTATED | 5 | 2 | 6
XQ LOSS WILD-TYPE | 27 | 26 | 8

Figure S90. Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.21

Table S91. Gene #51: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
XQ LOSS MUTATED | 1 | 1 | 2 | 2 | 7 | 0
XQ LOSS WILD-TYPE | 4 | 11 | 14 | 14 | 8 | 10

Figure S91. Get High-res Image Gene #51: '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/15908355/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/15952300/UVM-TP.transferedmergedcluster.txt

- Number of patients = 80

- Number of significantly arm-level cnvs = 51

- 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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