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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