Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
04 October 2018 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 72 arm-level events and 3 molecular subtypes across 100 patients, 67 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 3p gain cnv correlated to 'METHYLATION_CNMF'.

- 3q gain cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 6p gain cnv correlated to 'METHYLATION_CNMF'.

- 12p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 12q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 13q gain cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 14q gain cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 16p gain cnv correlated to 'METHYLATION_CNMF'.

- 18q gain cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- 20p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 20q gain cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 21q gain cnv correlated to 'METHYLATION_CNMF'.

- 22q gain cnv correlated to 'METHYLATION_CNMF'.

- 1p loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 1q loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 3p loss cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- 4p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 4q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- 5p loss cnv correlated to 'METHYLATION_CNMF'.

- 5q loss cnv correlated to 'METHYLATION_CNMF'.

- 8p loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 8q loss cnv correlated to 'METHYLATION_CNMF'.

- 9p loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 9q loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 10q loss cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- 11p loss cnv correlated to 'METHYLATION_CNMF'.

- 11q loss cnv correlated to 'METHYLATION_CNMF'.

- 12p loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 12q loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 15q loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 16p loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 16q loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 17p loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- 17q loss cnv correlated to 'METHYLATION_CNMF'.

- 18p loss cnv correlated to 'METHYLATION_CNMF'.

- 19p loss cnv correlated to 'METHYLATION_CNMF'.

- 19q loss cnv correlated to 'METHYLATION_CNMF'.

- 22q loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- xp loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- xq loss cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 72 arm-level events and 3 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 67 significant findings detected.

|  | Clinical Features | MRNA CHIERARCHICAL | METHYLATION CNMF | METHYLATION CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test
1q gain | 27 (27%) | 73 | 0.0237 (0.0968) | 1e-05 (0.00216) | 0.0007 (0.0126)
20p gain | 22 (22%) | 78 | 0.0327 (0.124) | 0.00049 (0.0126) | 0.0482 (0.155)
4p loss | 12 (12%) | 88 | 0.0154 (0.0773) | 0.00913 (0.0563) | 0.0176 (0.0793)
4q loss | 12 (12%) | 88 | 0.0151 (0.0773) | 0.0085 (0.054) | 0.0165 (0.0774)
3q gain | 16 (16%) | 84 | 0.248 (0.447) | 0.00526 (0.0437) | 0.00739 (0.0499)
13q gain | 6 (6%) | 94 | 0.753 (0.86) | 0.00065 (0.0126) | 0.00777 (0.0509)
14q gain | 7 (7%) | 93 | 0.46 (0.645) | 0.0039 (0.0366) | 0.034 (0.124)
20q gain | 22 (22%) | 78 | 0.119 (0.283) | 5e-05 (0.0036) | 0.00592 (0.047)
1p loss | 4 (4%) | 96 | 0.122 (0.285) | 0.0036 (0.0353) | 0.0334 (0.124)
1q loss | 3 (3%) | 97 | 0.438 (0.634) | 0.00516 (0.0437) | 0.0352 (0.124)
8p loss | 7 (7%) | 93 | 0.158 (0.341) | 4e-05 (0.0036) | 0.0301 (0.12)
9p loss | 14 (14%) | 86 | 0.283 (0.494) | 0.0144 (0.0758) | 0.00249 (0.0299)
9q loss | 16 (16%) | 84 | 0.127 (0.294) | 0.00733 (0.0499) | 0.011 (0.0658)
12p loss | 4 (4%) | 96 | 0.939 (0.953) | 0.0159 (0.0774) | 0.00651 (0.0485)
12q loss | 4 (4%) | 96 | 0.939 (0.953) | 0.0163 (0.0774) | 0.00677 (0.0487)
15q loss | 13 (13%) | 87 | 0.547 (0.738) | 0.00123 (0.0204) | 0.0001 (0.0054)
16p loss | 6 (6%) | 94 | 0.893 (0.937) | 0.00425 (0.0382) | 0.0455 (0.151)
16q loss | 7 (7%) | 93 | 0.863 (0.927) | 0.00069 (0.0126) | 0.0144 (0.0758)
17p loss | 13 (13%) | 87 | 0.101 (0.27) | 0.00232 (0.0299) | 0.00027 (0.0108)
22q loss | 12 (12%) | 88 | 0.384 (0.604) | 0.0469 (0.153) | 0.0169 (0.0779)
xp loss | 19 (19%) | 81 | 0.651 (0.817) | 0.00046 (0.0126) | 0.00249 (0.0299)
xq loss | 19 (19%) | 81 | 0.648 (0.817) | 0.0003 (0.0108) | 0.00286 (0.0318)
3p gain | 10 (10%) | 90 | 0.226 (0.428) | 0.0186 (0.0822) | 0.0943 (0.26)
6p gain | 10 (10%) | 90 | 0.182 (0.367) | 0.0121 (0.0709) | 0.105 (0.273)
12p gain | 10 (10%) | 90 | 0.0353 (0.124) | 0.492 (0.677) | 0.992 (0.992)
12q gain | 10 (10%) | 90 | 0.0346 (0.124) | 0.492 (0.677) | 0.992 (0.992)
16p gain | 6 (6%) | 94 | 0.163 (0.346) | 0.04 (0.135) | 0.326 (0.542)
18q gain | 7 (7%) | 93 | 0.566 (0.755) | 0.148 (0.325) | 0.0386 (0.132)
21q gain | 6 (6%) | 94 | 0.434 (0.634) | 0.00327 (0.0336) | 0.21 (0.408)
22q gain | 8 (8%) | 92 | 0.766 (0.866) | 0.00232 (0.0299) | 0.165 (0.346)
3p loss | 6 (6%) | 94 | 0.434 (0.634) | 0.149 (0.325) | 0.0327 (0.124)
5p loss | 9 (9%) | 91 | 0.316 (0.529) | 0.0215 (0.0928) | 0.0951 (0.26)
5q loss | 11 (11%) | 89 | 0.185 (0.37) | 0.00609 (0.047) | 0.101 (0.27)
8q loss | 4 (4%) | 96 | 0.663 (0.819) | 0.00069 (0.0126) | 0.191 (0.379)
10q loss | 4 (4%) | 96 | 0.662 (0.819) | 0.0843 (0.243) | 0.0357 (0.124)
11p loss | 8 (8%) | 92 | 0.766 (0.866) | 0.0128 (0.0726) | 0.111 (0.276)
11q loss | 7 (7%) | 93 | 0.426 (0.634) | 0.0131 (0.0726) | 0.113 (0.276)
17q loss | 8 (8%) | 92 | 0.403 (0.61) | 0.00238 (0.0299) | 0.16 (0.343)
18p loss | 4 (4%) | 96 | 0.94 (0.953) | 0.0223 (0.0944) | 0.369 (0.6)
19p loss | 6 (6%) | 94 | 0.696 (0.835) | 0.00294 (0.0318) | 0.315 (0.529)
19q loss | 6 (6%) | 94 | 0.278 (0.494) | 0.0231 (0.0961) | 0.56 (0.752)
1p gain | 9 (9%) | 91 | 0.455 (0.643) | 0.0662 (0.199) | 0.239 (0.437)
2p gain | 15 (15%) | 85 | 0.848 (0.921) | 0.0669 (0.199) | 0.282 (0.494)
2q gain | 14 (14%) | 86 | 0.804 (0.885) | 0.0673 (0.199) | 0.282 (0.494)
5p gain | 5 (5%) | 95 | 0.241 (0.437) | 0.811 (0.885) | 0.445 (0.634)
6q gain | 8 (8%) | 92 | 0.383 (0.604) | 0.211 (0.408) | 0.721 (0.85)
7p gain | 13 (13%) | 87 | 0.293 (0.502) | 0.586 (0.767) | 0.861 (0.927)
7q gain | 14 (14%) | 86 | 0.143 (0.324) | 0.507 (0.693) | 0.79 (0.884)
8p gain | 19 (19%) | 81 | 0.0613 (0.189) | 0.789 (0.884) | 0.67 (0.822)
8q gain | 20 (20%) | 80 | 0.0547 (0.171) | 0.883 (0.937) | 0.6 (0.78)
10p gain | 25 (25%) | 75 | 0.933 (0.953) | 0.748 (0.859) | 0.172 (0.357)
10q gain | 24 (24%) | 76 | 0.739 (0.856) | 0.648 (0.817) | 0.105 (0.273)
11p gain | 3 (3%) | 97 | 0.684 (0.829) | 0.109 (0.276) | 0.404 (0.61)
11q gain | 4 (4%) | 96 | 0.381 (0.604) | 0.111 (0.276) | 0.404 (0.61)
16q gain | 5 (5%) | 95 | 0.359 (0.587) | 0.148 (0.325) | 0.417 (0.625)
17p gain | 7 (7%) | 93 | 0.0924 (0.26) | 0.136 (0.314) | 0.177 (0.365)
17q gain | 6 (6%) | 94 | 0.234 (0.433) | 0.204 (0.401) | 0.181 (0.367)
18p gain | 9 (9%) | 91 | 0.115 (0.277) | 0.0524 (0.166) | 0.0703 (0.205)
19p gain | 7 (7%) | 93 | 0.918 (0.949) | 0.695 (0.835) | 0.301 (0.512)
19q gain | 8 (8%) | 92 | 0.795 (0.885) | 0.335 (0.553) | 0.292 (0.502)
xp gain | 8 (8%) | 92 | 0.611 (0.79) | 0.872 (0.932) | 0.477 (0.665)
xq gain | 8 (8%) | 92 | 0.392 (0.61) | 0.439 (0.634) | 0.528 (0.718)
yp gain | 14 (14%) | 86 | 0.736 (0.856) | 0.386 (0.604) | 0.916 (0.949)
yq gain | 14 (14%) | 86 | 0.741 (0.856) | 0.384 (0.604) | 0.915 (0.949)
7p loss | 5 (5%) | 95 | 0.724 (0.85) | 0.811 (0.885) | 0.444 (0.634)
7q loss | 5 (5%) | 95 | 0.722 (0.85) | 0.811 (0.885) | 0.446 (0.634)
10p loss | 5 (5%) | 95 | 0.892 (0.937) | 0.144 (0.324) | 0.0932 (0.26)
13q loss | 10 (10%) | 90 | 0.214 (0.409) | 0.948 (0.957) | 0.664 (0.819)
18q loss | 5 (5%) | 95 | 0.72 (0.85) | 0.114 (0.277) | 0.678 (0.827)
21q loss | 5 (5%) | 95 | 0.891 (0.937) | 0.112 (0.276) | 0.4 (0.61)
yp loss | 47 (47%) | 53 | 0.645 (0.817) | 0.232 (0.433) | 0.575 (0.758)
yq loss | 47 (47%) | 53 | 0.646 (0.817) | 0.233 (0.433) | 0.575 (0.758)

'1q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.097

Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
1Q GAIN MUTATED | 6 | 2 | 1 | 8 | 10
1Q GAIN WILD-TYPE | 22 | 18 | 10 | 12 | 11

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

'1q gain' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
1Q GAIN MUTATED | 3 | 5 | 7 | 10
1Q GAIN WILD-TYPE | 32 | 28 | 9 | 2

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

'1q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.013

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
1Q GAIN MUTATED | 7 | 4 | 2 | 3 | 6 | 3 | 0
1Q GAIN WILD-TYPE | 27 | 7 | 7 | 4 | 0 | 17 | 9

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

'3p gain' versus 'METHYLATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.082

Table S4. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
3P GAIN MUTATED | 1 | 2 | 5 | 1
3P GAIN WILD-TYPE | 34 | 31 | 11 | 11

Figure S4. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'3q gain' versus 'METHYLATION_CNMF'

P value = 0.00526 (Fisher's exact test), Q value = 0.044

Table S5. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
3Q GAIN MUTATED | 2 | 3 | 7 | 1
3Q GAIN WILD-TYPE | 33 | 30 | 9 | 11

Figure S5. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'3q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00739 (Fisher's exact test), Q value = 0.05

Table S6. Gene #6: '3q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
3Q GAIN MUTATED | 4 | 5 | 0 | 3 | 0 | 1 | 0
3Q GAIN WILD-TYPE | 30 | 6 | 9 | 4 | 6 | 19 | 9

Figure S6. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'6p gain' versus 'METHYLATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.071

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
6P GAIN MUTATED | 2 | 1 | 5 | 0
6P GAIN WILD-TYPE | 33 | 32 | 11 | 12

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

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.12

Table S8. Gene #18: '12p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
12P GAIN MUTATED | 1 | 1 | 0 | 6 | 2
12P GAIN WILD-TYPE | 27 | 19 | 11 | 14 | 19

Figure S8. Get High-res Image Gene #18: '12p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.12

Table S9. Gene #19: '12q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
12Q GAIN MUTATED | 1 | 1 | 0 | 6 | 2
12Q GAIN WILD-TYPE | 27 | 19 | 11 | 14 | 19

Figure S9. Get High-res Image Gene #19: '12q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'METHYLATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.013

Table S10. Gene #20: '13q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
13Q GAIN MUTATED | 0 | 1 | 5 | 0
13Q GAIN WILD-TYPE | 35 | 32 | 11 | 12

Figure S10. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'13q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00777 (Fisher's exact test), Q value = 0.051

Table S11. Gene #20: '13q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
13Q GAIN MUTATED | 0 | 3 | 0 | 2 | 0 | 1 | 0
13Q GAIN WILD-TYPE | 34 | 8 | 9 | 5 | 6 | 19 | 9

Figure S11. Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'14q gain' versus 'METHYLATION_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.037

Table S12. Gene #21: '14q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
14Q GAIN MUTATED | 1 | 0 | 4 | 1
14Q GAIN WILD-TYPE | 34 | 33 | 12 | 11

Figure S12. Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'14q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.12

Table S13. Gene #21: '14q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
14Q GAIN MUTATED | 1 | 2 | 0 | 2 | 1 | 0 | 0
14Q GAIN WILD-TYPE | 33 | 9 | 9 | 5 | 5 | 20 | 9

Figure S13. Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'16p gain' versus 'METHYLATION_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.13

Table S14. Gene #22: '16p gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
16P GAIN MUTATED | 0 | 2 | 3 | 1
16P GAIN WILD-TYPE | 35 | 31 | 13 | 11

Figure S14. Get High-res Image Gene #22: '16p gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'18q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.13

Table S15. Gene #27: '18q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
18Q GAIN MUTATED | 0 | 0 | 1 | 2 | 0 | 1 | 1
18Q GAIN WILD-TYPE | 34 | 11 | 8 | 5 | 6 | 19 | 8

Figure S15. Get High-res Image Gene #27: '18q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.12

Table S16. Gene #30: '20p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
20P GAIN MUTATED | 6 | 2 | 0 | 9 | 5
20P GAIN WILD-TYPE | 22 | 18 | 11 | 11 | 16

Figure S16. Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'METHYLATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.013

Table S17. Gene #30: '20p gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
20P GAIN MUTATED | 4 | 5 | 10 | 1
20P GAIN WILD-TYPE | 31 | 28 | 6 | 11

Figure S17. Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'20p gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.16

Table S18. Gene #30: '20p gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
20P GAIN MUTATED | 6 | 6 | 1 | 3 | 0 | 2 | 2
20P GAIN WILD-TYPE | 28 | 5 | 8 | 4 | 6 | 18 | 7

Figure S18. Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'20q gain' versus 'METHYLATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0036

Table S19. Gene #31: '20q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
20Q GAIN MUTATED | 4 | 4 | 11 | 1
20Q GAIN WILD-TYPE | 31 | 29 | 5 | 11

Figure S19. Get High-res Image Gene #31: '20q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'20q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00592 (Fisher's exact test), Q value = 0.047

Table S20. Gene #31: '20q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
20Q GAIN MUTATED | 6 | 6 | 1 | 4 | 0 | 1 | 2
20Q GAIN WILD-TYPE | 28 | 5 | 8 | 3 | 6 | 19 | 7

Figure S20. Get High-res Image Gene #31: '20q gain' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'21q gain' versus 'METHYLATION_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.034

Table S21. Gene #32: '21q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
21Q GAIN MUTATED | 0 | 1 | 4 | 1
21Q GAIN WILD-TYPE | 35 | 32 | 12 | 11

Figure S21. Get High-res Image Gene #32: '21q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'22q gain' versus 'METHYLATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.03

Table S22. Gene #33: '22q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
22Q GAIN MUTATED | 0 | 2 | 5 | 1
22Q GAIN WILD-TYPE | 35 | 31 | 11 | 11

Figure S22. Get High-res Image Gene #33: '22q gain' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'1p loss' versus 'METHYLATION_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.035

Table S23. Gene #38: '1p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
1P LOSS MUTATED | 0 | 0 | 3 | 1
1P LOSS WILD-TYPE | 35 | 33 | 13 | 11

Figure S23. Get High-res Image Gene #38: '1p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'1p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.12

Table S24. Gene #38: '1p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
1P LOSS MUTATED | 0 | 2 | 1 | 1 | 0 | 0 | 0
1P LOSS WILD-TYPE | 34 | 9 | 8 | 6 | 6 | 20 | 9

Figure S24. Get High-res Image Gene #38: '1p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'1q loss' versus 'METHYLATION_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.044

Table S25. Gene #39: '1q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
1Q LOSS MUTATED | 0 | 0 | 3 | 0
1Q LOSS WILD-TYPE | 35 | 33 | 13 | 12

Figure S25. Get High-res Image Gene #39: '1q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'1q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.12

Table S26. Gene #39: '1q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
1Q LOSS MUTATED | 0 | 2 | 0 | 1 | 0 | 0 | 0
1Q LOSS WILD-TYPE | 34 | 9 | 9 | 6 | 6 | 20 | 9

Figure S26. Get High-res Image Gene #39: '1q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'3p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.12

Table S27. Gene #40: '3p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
3P LOSS MUTATED | 0 | 3 | 1 | 0 | 0 | 1 | 0
3P LOSS WILD-TYPE | 34 | 8 | 8 | 7 | 6 | 19 | 9

Figure S27. Get High-res Image Gene #40: '3p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.077

Table S28. Gene #41: '4p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
4P LOSS MUTATED | 5 | 0 | 0 | 6 | 1
4P LOSS WILD-TYPE | 23 | 20 | 11 | 14 | 20

Figure S28. Get High-res Image Gene #41: '4p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'METHYLATION_CNMF'

P value = 0.00913 (Fisher's exact test), Q value = 0.056

Table S29. Gene #41: '4p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
4P LOSS MUTATED | 3 | 1 | 6 | 1
4P LOSS WILD-TYPE | 32 | 32 | 10 | 11

Figure S29. Get High-res Image Gene #41: '4p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'4p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.079

Table S30. Gene #41: '4p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
4P LOSS MUTATED | 2 | 5 | 2 | 1 | 0 | 1 | 0
4P LOSS WILD-TYPE | 32 | 6 | 7 | 6 | 6 | 19 | 9

Figure S30. Get High-res Image Gene #41: '4p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.077

Table S31. Gene #42: '4q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
4Q LOSS MUTATED | 5 | 0 | 0 | 6 | 1
4Q LOSS WILD-TYPE | 23 | 20 | 11 | 14 | 20

Figure S31. Get High-res Image Gene #42: '4q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'METHYLATION_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.054

Table S32. Gene #42: '4q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
4Q LOSS MUTATED | 3 | 1 | 6 | 1
4Q LOSS WILD-TYPE | 32 | 32 | 10 | 11

Figure S32. Get High-res Image Gene #42: '4q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'4q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.077

Table S33. Gene #42: '4q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
4Q LOSS MUTATED | 2 | 5 | 2 | 1 | 0 | 1 | 0
4Q LOSS WILD-TYPE | 32 | 6 | 7 | 6 | 6 | 19 | 9

Figure S33. Get High-res Image Gene #42: '4q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'5p loss' versus 'METHYLATION_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.093

Table S34. Gene #43: '5p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
5P LOSS MUTATED | 3 | 0 | 4 | 1
5P LOSS WILD-TYPE | 32 | 33 | 12 | 11

Figure S34. Get High-res Image Gene #43: '5p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'5q loss' versus 'METHYLATION_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.047

Table S35. Gene #44: '5q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
5Q LOSS MUTATED | 3 | 0 | 5 | 1
5Q LOSS WILD-TYPE | 32 | 33 | 11 | 11

Figure S35. Get High-res Image Gene #44: '5q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'8p loss' versus 'METHYLATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0036

Table S36. Gene #47: '8p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
8P LOSS MUTATED | 0 | 1 | 6 | 0
8P LOSS WILD-TYPE | 35 | 32 | 10 | 12

Figure S36. Get High-res Image Gene #47: '8p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'8p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.12

Table S37. Gene #47: '8p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
8P LOSS MUTATED | 1 | 4 | 0 | 1 | 0 | 1 | 0
8P LOSS WILD-TYPE | 33 | 7 | 9 | 6 | 6 | 19 | 9

Figure S37. Get High-res Image Gene #47: '8p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'8q loss' versus 'METHYLATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.013

Table S38. Gene #48: '8q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
8Q LOSS MUTATED | 0 | 0 | 4 | 0
8Q LOSS WILD-TYPE | 35 | 33 | 12 | 12

Figure S38. Get High-res Image Gene #48: '8q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'9p loss' versus 'METHYLATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.076

Table S39. Gene #49: '9p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
9P LOSS MUTATED | 2 | 4 | 6 | 0
9P LOSS WILD-TYPE | 33 | 29 | 10 | 12

Figure S39. Get High-res Image Gene #49: '9p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'9p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.03

Table S40. Gene #49: '9p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
9P LOSS MUTATED | 2 | 6 | 0 | 2 | 0 | 2 | 0
9P LOSS WILD-TYPE | 32 | 5 | 9 | 5 | 6 | 18 | 9

Figure S40. Get High-res Image Gene #49: '9p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'9q loss' versus 'METHYLATION_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.05

Table S41. Gene #50: '9q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
9Q LOSS MUTATED | 3 | 4 | 7 | 0
9Q LOSS WILD-TYPE | 32 | 29 | 9 | 12

Figure S41. Get High-res Image Gene #50: '9q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'9q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.066

Table S42. Gene #50: '9q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
9Q LOSS MUTATED | 3 | 6 | 1 | 2 | 0 | 2 | 0
9Q LOSS WILD-TYPE | 31 | 5 | 8 | 5 | 6 | 18 | 9

Figure S42. Get High-res Image Gene #50: '9q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'10q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.12

Table S43. Gene #52: '10q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
10Q LOSS MUTATED | 0 | 2 | 0 | 1 | 0 | 0 | 0
10Q LOSS WILD-TYPE | 34 | 9 | 9 | 6 | 6 | 20 | 9

Figure S43. Get High-res Image Gene #52: '10q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'11p loss' versus 'METHYLATION_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.073

Table S44. Gene #53: '11p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
11P LOSS MUTATED | 2 | 0 | 4 | 1
11P LOSS WILD-TYPE | 33 | 33 | 12 | 11

Figure S44. Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'11q loss' versus 'METHYLATION_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.073

Table S45. Gene #54: '11q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
11Q LOSS MUTATED | 2 | 0 | 4 | 1
11Q LOSS WILD-TYPE | 33 | 33 | 12 | 11

Figure S45. Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'12p loss' versus 'METHYLATION_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.077

Table S46. Gene #55: '12p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
12P LOSS MUTATED | 0 | 1 | 3 | 0
12P LOSS WILD-TYPE | 35 | 32 | 13 | 12

Figure S46. Get High-res Image Gene #55: '12p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'12p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00651 (Fisher's exact test), Q value = 0.048

Table S47. Gene #55: '12p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
12P LOSS MUTATED | 0 | 2 | 0 | 2 | 0 | 0 | 0
12P LOSS WILD-TYPE | 34 | 9 | 9 | 5 | 6 | 20 | 9

Figure S47. Get High-res Image Gene #55: '12p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'12q loss' versus 'METHYLATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.077

Table S48. Gene #56: '12q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
12Q LOSS MUTATED | 0 | 1 | 3 | 0
12Q LOSS WILD-TYPE | 35 | 32 | 13 | 12

Figure S48. Get High-res Image Gene #56: '12q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'12q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00677 (Fisher's exact test), Q value = 0.049

Table S49. Gene #56: '12q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
12Q LOSS MUTATED | 0 | 2 | 0 | 2 | 0 | 0 | 0
12Q LOSS WILD-TYPE | 34 | 9 | 9 | 5 | 6 | 20 | 9

Figure S49. Get High-res Image Gene #56: '12q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'15q loss' versus 'METHYLATION_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.02

Table S50. Gene #58: '15q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
15Q LOSS MUTATED | 2 | 2 | 7 | 0
15Q LOSS WILD-TYPE | 33 | 31 | 9 | 12

Figure S50. Get High-res Image Gene #58: '15q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'15q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0054

Table S51. Gene #58: '15q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
15Q LOSS MUTATED | 2 | 7 | 1 | 1 | 0 | 0 | 0
15Q LOSS WILD-TYPE | 32 | 4 | 8 | 6 | 6 | 20 | 9

Figure S51. Get High-res Image Gene #58: '15q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'16p loss' versus 'METHYLATION_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.038

Table S52. Gene #59: '16p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
16P LOSS MUTATED | 1 | 0 | 4 | 0
16P LOSS WILD-TYPE | 34 | 33 | 12 | 12

Figure S52. Get High-res Image Gene #59: '16p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'16p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.15

Table S53. Gene #59: '16p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
16P LOSS MUTATED | 1 | 3 | 0 | 1 | 0 | 0 | 0
16P LOSS WILD-TYPE | 33 | 8 | 9 | 6 | 6 | 20 | 9

Figure S53. Get High-res Image Gene #59: '16p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'16q loss' versus 'METHYLATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.013

Table S54. Gene #60: '16q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
16Q LOSS MUTATED | 1 | 0 | 5 | 0
16Q LOSS WILD-TYPE | 34 | 33 | 11 | 12

Figure S54. Get High-res Image Gene #60: '16q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'16q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.076

Table S55. Gene #60: '16q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
16Q LOSS MUTATED | 1 | 3 | 0 | 2 | 0 | 0 | 0
16Q LOSS WILD-TYPE | 33 | 8 | 9 | 5 | 6 | 20 | 9

Figure S55. Get High-res Image Gene #60: '16q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'17p loss' versus 'METHYLATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.03

Table S56. Gene #61: '17p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
17P LOSS MUTATED | 3 | 2 | 7 | 0
17P LOSS WILD-TYPE | 32 | 31 | 9 | 12

Figure S56. Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'17p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.011

Table S57. Gene #61: '17p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
17P LOSS MUTATED | 3 | 7 | 1 | 1 | 0 | 0 | 0
17P LOSS WILD-TYPE | 31 | 4 | 8 | 6 | 6 | 20 | 9

Figure S57. Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'17q loss' versus 'METHYLATION_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.03

Table S58. Gene #62: '17q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
17Q LOSS MUTATED | 3 | 0 | 5 | 0
17Q LOSS WILD-TYPE | 32 | 33 | 11 | 12

Figure S58. Get High-res Image Gene #62: '17q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'18p loss' versus 'METHYLATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.094

Table S59. Gene #63: '18p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
18P LOSS MUTATED | 1 | 0 | 3 | 0
18P LOSS WILD-TYPE | 34 | 33 | 13 | 12

Figure S59. Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'19p loss' versus 'METHYLATION_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.032

Table S60. Gene #65: '19p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
19P LOSS MUTATED | 0 | 1 | 4 | 0
19P LOSS WILD-TYPE | 35 | 32 | 12 | 12

Figure S60. Get High-res Image Gene #65: '19p loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'19q loss' versus 'METHYLATION_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.096

Table S61. Gene #66: '19q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
19Q LOSS MUTATED | 1 | 1 | 4 | 0
19Q LOSS WILD-TYPE | 34 | 32 | 12 | 12

Figure S61. Get High-res Image Gene #66: '19q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'22q loss' versus 'METHYLATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.15

Table S62. Gene #68: '22q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
22Q LOSS MUTATED | 4 | 2 | 5 | 0
22Q LOSS WILD-TYPE | 31 | 31 | 11 | 12

Figure S62. Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'22q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.078

Table S63. Gene #68: '22q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
22Q LOSS MUTATED | 4 | 5 | 1 | 1 | 0 | 0 | 0
22Q LOSS WILD-TYPE | 30 | 6 | 8 | 6 | 6 | 20 | 9

Figure S63. Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'xp loss' versus 'METHYLATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.013

Table S64. Gene #69: 'xp loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
XP LOSS MUTATED | 3 | 5 | 9 | 0
XP LOSS WILD-TYPE | 32 | 28 | 7 | 12

Figure S64. Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'xp loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.03

Table S65. Gene #69: 'xp loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
XP LOSS MUTATED | 3 | 6 | 1 | 3 | 0 | 1 | 3
XP LOSS WILD-TYPE | 31 | 5 | 8 | 4 | 6 | 19 | 6

Figure S65. Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'xq loss' versus 'METHYLATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.011

Table S66. Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
XQ LOSS MUTATED | 3 | 5 | 9 | 0
XQ LOSS WILD-TYPE | 32 | 28 | 7 | 12

Figure S66. Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'xq loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.032

Table S67. Gene #70: 'xq loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
XQ LOSS MUTATED | 3 | 6 | 1 | 3 | 0 | 1 | 3
XQ LOSS WILD-TYPE | 31 | 5 | 8 | 4 | 6 | 19 | 6

Figure S67. Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

Methods & Data
Input

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

- Processed Copy number data file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/7d40bb96-d50a-43da-8092-a511a1314618/correlate_genomic_events_all/f2d23ad8-12fc-428e-bd64-52ab7a789763/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtypes file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/10d02b45-07ea-40cc-ac82-013e5f89ebb2/aggregate_clusters_workflow/b0f8dcb2-0993-4424-ad42-552c0bd1a2d5/call-aggregate_clusters/CPTAC3-UCEC-TP.transposedmergedcluster.txt

- Number of patients = 100

- Number of significantly arm-level cnvs = 72

- Number of molecular subtypes = 3

- 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.

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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