Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
21 August 2015 | analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1833RB9
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/C1833RB9
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 | 0.00018 (0.00245) | 0.00425 (0.0364) | 0.0002 (0.00255) | 0.0003 (0.0036) | 3e-05 (0.00049) | 1e-05 (0.000185) | 0.0102 (0.0759) | 3e-05 (0.00049)
6q gain | 16 (20%) | 64 | 0.00609 (0.0497) | 0.0024 (0.0239) | 0.00029 (0.00359) | 0.00099 (0.0109) | 0.00019 (0.0025) | 0.00033 (0.00385) | 0.00349 (0.0316) | 0.00011 (0.00155)
8p gain | 33 (41%) | 47 | 0.00134 (0.0144) | 0.00085 (0.00963) | 0.00283 (0.0269) | 0.00381 (0.0338) | 0.0198 (0.126) | 0.0144 (0.0997) | 0.038 (0.188) | 0.014 (0.0984)
8q gain | 53 (66%) | 27 | 1e-05 (0.000185) | 1e-05 (0.000185) | 3e-05 (0.00049) | 1e-05 (0.000185) | 0.00011 (0.00155) | 1e-05 (0.000185) | 1e-05 (0.000185) | 0.0001 (0.00151)
3p loss | 43 (54%) | 37 | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185)
3q loss | 43 (54%) | 37 | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185) | 1e-05 (0.000185)
6q loss | 17 (21%) | 63 | 7e-05 (0.0011) | 0.00343 (0.0316) | 0.0485 (0.22) | 0.00457 (0.0381) | 0.1 (0.366) | 0.228 (0.504) | 0.0394 (0.191) | 0.00196 (0.02)
8p loss | 9 (11%) | 71 | 0.03 (0.172) | 0.345 (0.619) | 0.0376 (0.188) | 0.0229 (0.139) | 0.228 (0.504) | 0.282 (0.543) | 0.161 (0.431) | 0.0186 (0.123)
1q loss | 3 (4%) | 77 | 0.0381 (0.188) | 0.17 (0.434) | 0.218 (0.502) | 0.322 (0.598) | 0.43 (0.695) | 0.0469 (0.217) | 0.0893 (0.343) | 0.0314 (0.173)
16q loss | 16 (20%) | 64 | 0.0213 (0.131) | 0.132 (0.403) | 0.0955 (0.354) | 0.0132 (0.0964) | 0.823 (0.948) | 0.125 (0.389) | 0.144 (0.424) | 0.0477 (0.219)
xq loss | 13 (16%) | 67 | 0.155 (0.431) | 0.019 (0.123) | 0.211 (0.502) | 0.145 (0.424) | 0.221 (0.504) | 0.385 (0.66) | 0.0187 (0.123) | 0.0466 (0.217)
2p gain | 10 (12%) | 70 | 0.317 (0.593) | 1 (1.00) | 0.0377 (0.188) | 0.114 (0.374) | 0.108 (0.366) | 0.85 (0.958) | 0.553 (0.814) | 0.0313 (0.173)
9q gain | 5 (6%) | 75 | 0.509 (0.763) | 0.0372 (0.188) | 0.838 (0.951) | 0.839 (0.951) | 0.351 (0.621) | 0.752 (0.933) | 0.0186 (0.123) | 0.758 (0.933)
21q gain | 14 (18%) | 66 | 0.00283 (0.0269) | 0.199 (0.483) | 0.104 (0.366) | 0.0137 (0.0982) | 0.867 (0.975) | 0.296 (0.567) | 0.126 (0.389) | 0.464 (0.717)
xq gain | 9 (11%) | 71 | 0.66 (0.889) | 0.282 (0.543) | 0.0239 (0.143) | 0.0203 (0.127) | 0.106 (0.366) | 0.103 (0.366) | 0.434 (0.695) | 0.0876 (0.343)
11p loss | 3 (4%) | 77 | 0.0382 (0.188) | 0.235 (0.508) | 0.0441 (0.209) | 0.108 (0.366) | 0.23 (0.504) | 0.152 (0.431) | 0.214 (0.502) | 0.184 (0.456)
1q gain | 8 (10%) | 72 | 0.715 (0.926) | 0.714 (0.926) | 0.701 (0.922) | 0.802 (0.933) | 0.211 (0.502) | 0.0575 (0.245) | 1 (1.00) | 0.0378 (0.188)
2q gain | 8 (10%) | 72 | 0.394 (0.664) | 0.715 (0.926) | 0.0549 (0.24) | 0.112 (0.369) | 0.278 (0.543) | 0.195 (0.476) | 0.346 (0.619) | 0.007 (0.056)
4p gain | 7 (9%) | 73 | 0.0278 (0.164) | 0.282 (0.543) | 0.154 (0.431) | 0.121 (0.384) | 0.884 (0.985) | 0.368 (0.639) | 0.873 (0.976) | 0.23 (0.504)
7q gain | 8 (10%) | 72 | 0.0552 (0.24) | 0.0313 (0.173) | 0.89 (0.989) | 0.448 (0.699) | 0.315 (0.593) | 0.328 (0.604) | 0.261 (0.543) | 0.672 (0.899)
12p gain | 3 (4%) | 77 | 0.162 (0.431) | 0.441 (0.695) | 0.0899 (0.343) | 0.0101 (0.0759) | 0.798 (0.933) | 0.278 (0.543) | 1 (1.00) | 0.279 (0.543)
12q gain | 3 (4%) | 77 | 0.161 (0.431) | 0.441 (0.695) | 0.0879 (0.343) | 0.00955 (0.0735) | 0.794 (0.933) | 0.272 (0.543) | 1 (1.00) | 0.282 (0.543)
14q gain | 3 (4%) | 77 | 0.0373 (0.188) | 0.438 (0.695) | 0.592 (0.833) | 0.327 (0.603) | 0.797 (0.933) | 0.596 (0.833) | 1 (1.00) | 0.765 (0.933)
17q gain | 9 (11%) | 71 | 0.218 (0.502) | 1 (1.00) | 0.42 (0.692) | 0.314 (0.593) | 0.253 (0.535) | 0.0292 (0.17) | 0.264 (0.543) | 0.632 (0.866)
20p gain | 8 (10%) | 72 | 0.0092 (0.0722) | 0.567 (0.832) | 0.39 (0.663) | 0.219 (0.502) | 0.278 (0.543) | 0.239 (0.514) | 0.791 (0.933) | 0.844 (0.954)
20q gain | 9 (11%) | 71 | 0.00172 (0.018) | 0.54 (0.798) | 0.144 (0.424) | 0.0581 (0.245) | 0.182 (0.454) | 0.159 (0.431) | 0.905 (0.997) | 0.78 (0.933)
1p loss | 19 (24%) | 61 | 0.00428 (0.0364) | 0.0518 (0.23) | 0.783 (0.933) | 0.662 (0.889) | 0.366 (0.639) | 0.278 (0.543) | 0.265 (0.543) | 0.0762 (0.311)
9p loss | 8 (10%) | 72 | 0.109 (0.366) | 0.0405 (0.194) | 0.348 (0.62) | 0.154 (0.431) | 0.186 (0.457) | 0.353 (0.621) | 0.17 (0.434) | 0.792 (0.933)
15q loss | 4 (5%) | 76 | 0.158 (0.431) | 0.05 (0.224) | 0.832 (0.948) | 0.824 (0.948) | 1 (1.00) | 0.911 (0.999) | 1 (1.00) | 0.696 (0.922)
xp loss | 12 (15%) | 68 | 0.34 (0.617) | 0.0376 (0.188) | 0.323 (0.598) | 0.264 (0.543) | 0.481 (0.736) | 0.579 (0.833) | 0.07 (0.291) | 0.135 (0.406)
4q gain | 4 (5%) | 76 | 0.157 (0.431) | 0.267 (0.543) | 0.397 (0.667) | 0.345 (0.619) | 0.425 (0.695) | 0.824 (0.948) | 1 (1.00) | 0.226 (0.504)
5p gain | 3 (4%) | 77 | 0.161 (0.431) | 0.441 (0.695) | 0.784 (0.933) | 0.107 (0.366) | 0.793 (0.933) | 0.279 (0.543) | 1 (1.00) | 0.216 (0.502)
5q gain | 3 (4%) | 77 | 0.16 (0.431) | 0.439 (0.695) | 0.784 (0.933) | 0.107 (0.366) | 0.797 (0.933) | 0.275 (0.543) | 1 (1.00) | 0.215 (0.502)
7p gain | 9 (11%) | 71 | 0.165 (0.431) | 0.131 (0.401) | 1 (1.00) | 0.74 (0.933) | 0.661 (0.889) | 0.179 (0.447) | 0.641 (0.872) | 0.782 (0.933)
9p gain | 6 (8%) | 74 | 0.233 (0.507) | 0.179 (0.447) | 0.401 (0.671) | 0.643 (0.872) | 0.748 (0.933) | 1 (1.00) | 0.125 (0.389) | 0.919 (1.00)
11p gain | 9 (11%) | 71 | 0.163 (0.431) | 0.54 (0.798) | 1 (1.00) | 0.738 (0.933) | 0.251 (0.534) | 0.235 (0.508) | 1 (1.00) | 0.706 (0.923)
11q gain | 10 (12%) | 70 | 0.317 (0.593) | 0.83 (0.948) | 0.909 (0.999) | 0.829 (0.948) | 0.135 (0.406) | 0.117 (0.379) | 1 (1.00) | 0.701 (0.922)
13q gain | 6 (8%) | 74 | 0.105 (0.366) | 1 (1.00) | 0.735 (0.933) | 0.752 (0.933) | 0.488 (0.739) | 0.517 (0.77) | 0.408 (0.677) | 0.119 (0.381)
16p gain | 4 (5%) | 76 | 1 (1.00) | 0.436 (0.695) | 1 (1.00) | 0.438 (0.695) | 0.339 (0.617) | 0.472 (0.726) | 0.831 (0.948) | 1 (1.00)
17p gain | 8 (10%) | 72 | 0.0816 (0.326) | 0.803 (0.933) | 0.393 (0.664) | 0.219 (0.502) | 0.352 (0.621) | 0.0582 (0.245) | 0.481 (0.736) | 0.702 (0.922)
22q gain | 6 (8%) | 74 | 0.105 (0.366) | 0.641 (0.872) | 0.15 (0.431) | 0.218 (0.502) | 0.492 (0.741) | 0.175 (0.444) | 1 (1.00) | 0.12 (0.381)
xp gain | 10 (12%) | 70 | 0.388 (0.662) | 0.0907 (0.343) | 0.111 (0.367) | 0.14 (0.418) | 0.337 (0.617) | 0.375 (0.647) | 0.376 (0.647) | 0.265 (0.543)
4q loss | 3 (4%) | 77 | 1 (1.00) | 0.79 (0.933) | 0.589 (0.833) | 0.6 (0.833) | 0.797 (0.933) | 0.274 (0.543) | 0.407 (0.677) | 0.489 (0.739)
5q loss | 3 (4%) | 77 | 0.449 (0.699) | 0.109 (0.366) | 0.0901 (0.343) | 0.169 (0.434) | 0.596 (0.833) | 0.872 (0.976) | 0.298 (0.568) | 0.894 (0.989)
8q loss | 3 (4%) | 77 | 0.788 (0.933) | 0.603 (0.833) | 1 (1.00) | 0.791 (0.933) | 1 (1.00) | 0.773 (0.933) | 0.787 (0.933) | 0.893 (0.989)
9q loss | 7 (9%) | 73 | 0.164 (0.431) | 0.074 (0.305) | 0.592 (0.833) | 0.243 (0.518) | 0.0952 (0.354) | 0.584 (0.833) | 0.0788 (0.318) | 0.418 (0.691)
12p loss | 3 (4%) | 77 | 0.787 (0.933) | 0.607 (0.833) | 1 (1.00) | 0.792 (0.933) | 1 (1.00) | 0.516 (0.77) | 0.592 (0.833) | 1 (1.00)
13q loss | 3 (4%) | 77 | 1 (1.00) | 0.169 (0.434) | 0.592 (0.833) | 0.603 (0.833) | 1 (1.00) | 1 (1.00) | 0.786 (0.933) | 0.487 (0.739)
16p loss | 3 (4%) | 77 | 1 (1.00) | 0.441 (0.695) | 0.59 (0.833) | 0.602 (0.833) | 1 (1.00) | 1 (1.00) | 0.785 (0.933) | 0.355 (0.621)
19p loss | 3 (4%) | 77 | 0.451 (0.7) | 0.605 (0.833) | 0.783 (0.933) | 1 (1.00) | 0.596 (0.833) | 0.229 (0.504) | 0.785 (0.933) | 0.692 (0.919)
19q loss | 3 (4%) | 77 | 0.449 (0.699) | 0.604 (0.833) | 0.781 (0.933) | 1 (1.00) | 0.6 (0.833) | 0.228 (0.504) | 0.786 (0.933) | 0.692 (0.919)

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0378 (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 = 0.0377 (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 = 0.0313 (Fisher's exact test), Q value = 0.17

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 = 0.007 (Fisher's exact test), Q value = 0.056

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 = 0.0278 (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 = 0.00018 (Fisher's exact test), Q value = 0.0024

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 = 0.00425 (Fisher's exact test), Q value = 0.036

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 = 2e-04 (Fisher's exact test), Q value = 0.0025

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 = 3e-04 (Fisher's exact test), Q value = 0.0036

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 = 3e-05 (Fisher's exact test), Q value = 0.00049

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 = 1e-05 (Fisher's exact test), Q value = 0.00019

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 = 0.0102 (Fisher's exact test), Q value = 0.076

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 = 3e-05 (Fisher's exact test), Q value = 0.00049

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 = 0.00609 (Fisher's exact test), Q value = 0.05

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 = 0.0024 (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 = 0.00029 (Fisher's exact test), Q value = 0.0036

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 = 0.00099 (Fisher's exact test), Q value = 0.011

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 = 0.00019 (Fisher's exact test), Q value = 0.0025

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 = 0.00033 (Fisher's exact test), Q value = 0.0038

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 = 0.00349 (Fisher's exact test), Q value = 0.032

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 = 0.00011 (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 = 0.0313 (Fisher's exact test), Q value = 0.17

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 = 0.00134 (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 = 0.00085 (Fisher's exact test), Q value = 0.0096

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 = 0.00283 (Fisher's exact test), Q value = 0.027

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 = 0.00381 (Fisher's exact test), Q value = 0.034

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 = 0.0198 (Fisher's exact test), Q value = 0.13

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 = 0.0144 (Fisher's exact test), Q value = 0.1

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 = 0.038 (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 = 0.014 (Fisher's exact test), Q value = 0.098

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 = 0.00019

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 = 0.00019

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 = 3e-05 (Fisher's exact test), Q value = 0.00049

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 = 0.00019

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

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 = 0.00019

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 = 1e-05 (Fisher's exact test), Q value = 0.00019

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 = 1e-04 (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 = 0.0186 (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 = 0.0101 (Fisher's exact test), Q value = 0.076

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 = 0.00955 (Fisher's exact test), Q value = 0.074

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 = 0.0373 (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 = 0.0292 (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 = 0.0092 (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 = 0.00172 (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 = 0.00283 (Fisher's exact test), Q value = 0.027

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 = 0.0137 (Fisher's exact test), Q value = 0.098

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 = 0.0239 (Fisher's exact test), Q value = 0.14

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 = 0.0203 (Fisher's exact test), Q value = 0.13

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 = 0.00428 (Fisher's exact test), Q value = 0.036

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 = 0.0381 (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 = 0.0469 (Fisher's exact test), Q value = 0.22

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 = 0.0314 (Fisher's exact test), Q value = 0.17

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 7e-05 (Fisher's exact test), Q value = 0.0011

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 = 0.00343 (Fisher's exact test), Q value = 0.032

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 = 0.0485 (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 = 0.00457 (Fisher's exact test), Q value = 0.038

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 = 0.0394 (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 = 0.00196 (Fisher's exact test), Q value = 0.02

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 = 0.03 (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 = 0.0376 (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 = 0.0229 (Fisher's exact test), Q value = 0.14

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 = 0.0186 (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 = 0.0405 (Fisher's exact test), Q value = 0.19

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 = 0.0382 (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 = 0.0441 (Fisher's exact test), Q value = 0.21

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 = 0.05 (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 = 0.0132 (Fisher's exact test), Q value = 0.096

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 = 0.0477 (Fisher's exact test), Q value = 0.22

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 = 0.0376 (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 = 0.019 (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 = 0.0187 (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 = 0.0466 (Fisher's exact test), Q value = 0.22

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/19783310/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/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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