Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
13 July 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 51 arm-level events and 10 molecular subtypes across 80 patients, 118 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_THRESHOLDED_CNMF'.

  • 6p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MIR_MATURE_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'LINCRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 21q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'LINCRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 22q gain cnv correlated to 'LINCRNA_CNMF'.

  • xp gain cnv correlated to 'MIR_MATURE_CNMF' and 'METHYLATION_CNMF'.

  • xq gain cnv correlated to 'MIR_MATURE_CNMF' and 'METHYLATION_CNMF'.

  • 1p loss cnv correlated to 'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF', and 'CN_THRESHOLDED_CNMF'.

  • 1q loss cnv correlated to 'MIR_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'LINCRNA_CHIERARCHICAL',  'MIR_MATURE_CNMF',  'CN_CNMF',  'CN_THRESHOLDED_CNMF', and 'METHYLATION_CNMF'.

  • 9p loss cnv correlated to 'MRNA_CNMF' and 'CN_THRESHOLDED_CNMF'.

  • 9q loss cnv correlated to 'MRNA_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF' and 'CN_THRESHOLDED_CNMF'.

  • 16q loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CNMF'.

  • 19p loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_THRESHOLDED_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • xp loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

  • xq loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'LINCRNA_CNMF',  'MIR_MATURE_CHIERARCHICAL',  'CN_CNMF',  'CN_THRESHOLDED_CNMF',  '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 51 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 118 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
LINCRNA
CNMF
LINCRNA
CHIERARCHICAL
MIR
MATURE
CNMF
MIR
MATURE
CHIERARCHICAL
CN
CNMF
CN
THRESHOLDED
CNMF
METHYLATION
CNMF
METHYLATION
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 Fisher's exact test Fisher's exact test
6p gain 40 (50%) 40 0.00864
(0.0572)
0.00015
(0.00174)
0.0009
(0.00883)
5e-05
(0.000671)
1e-05
(0.000165)
1e-05
(0.000165)
2e-05
(0.000309)
3e-05
(0.000437)
0.00094
(0.00905)
1e-05
(0.000165)
8q gain 54 (68%) 26 0.00541
(0.0411)
4e-05
(0.000567)
2e-05
(0.000309)
1e-05
(0.000165)
8e-05
(0.000995)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
3e-05
(0.000437)
1e-05
(0.000165)
3p loss 42 (52%) 38 1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
3q loss 44 (55%) 36 1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
1e-05
(0.000165)
6q gain 20 (25%) 60 0.136
(0.372)
0.00057
(0.00593)
0.00701
(0.049)
7e-05
(0.000892)
0.00022
(0.00244)
5e-05
(0.000671)
0.00019
(0.00215)
0.00026
(0.00282)
0.0032
(0.0268)
9e-05
(0.00109)
6q loss 14 (18%) 66 0.0659
(0.258)
0.00043
(0.00457)
0.0322
(0.156)
0.00226
(0.0199)
0.00065
(0.00663)
0.075
(0.275)
6e-05
(0.000785)
1e-05
(0.000165)
0.00013
(0.00154)
0.0122
(0.0767)
xq loss 12 (15%) 68 0.0212
(0.119)
0.00259
(0.0224)
0.00104
(0.00982)
0.0829
(0.292)
0.0975
(0.325)
0.0268
(0.135)
0.0356
(0.166)
0.0259
(0.134)
0.00202
(0.0184)
0.0183
(0.11)
8p gain 32 (40%) 48 0.0708
(0.264)
0.0028
(0.0238)
0.0987
(0.325)
0.0246
(0.134)
0.257
(0.531)
0.0412
(0.181)
0.00381
(0.0308)
0.0757
(0.276)
0.0268
(0.135)
0.0235
(0.13)
8p loss 7 (9%) 73 0.161
(0.413)
0.00594
(0.0433)
0.0583
(0.244)
0.0287
(0.142)
0.0173
(0.105)
0.112
(0.348)
0.0153
(0.0942)
0.00223
(0.0199)
0.0469
(0.203)
0.172
(0.431)
xp loss 11 (14%) 69 0.0347
(0.164)
0.008
(0.0537)
0.00434
(0.0335)
0.0922
(0.316)
0.205
(0.48)
0.0788
(0.283)
0.0788
(0.283)
0.058
(0.244)
0.00763
(0.0519)
0.0261
(0.134)
20q gain 9 (11%) 71 0.366
(0.617)
0.00401
(0.0315)
0.124
(0.366)
0.0201
(0.115)
0.976
(1.00)
0.489
(0.695)
0.0251
(0.134)
0.354
(0.608)
0.678
(0.822)
0.511
(0.715)
21q gain 14 (18%) 66 0.106
(0.337)
0.00548
(0.0411)
0.105
(0.337)
0.0039
(0.0311)
0.0986
(0.325)
0.656
(0.815)
0.0389
(0.176)
0.495
(0.699)
0.267
(0.531)
0.427
(0.662)
1p loss 18 (22%) 62 0.109
(0.343)
0.101
(0.329)
0.417
(0.652)
0.321
(0.583)
0.962
(1.00)
0.0143
(0.0892)
0.00074
(0.0074)
1e-05
(0.000165)
0.068
(0.262)
0.351
(0.608)
20p gain 8 (10%) 72 0.703
(0.839)
0.00579
(0.0428)
0.0874
(0.303)
0.041
(0.181)
1
(1.00)
0.351
(0.608)
0.0615
(0.252)
0.402
(0.632)
0.338
(0.595)
0.38
(0.63)
xp gain 10 (12%) 70 0.896
(0.95)
0.321
(0.583)
0.652
(0.815)
0.402
(0.632)
0.00923
(0.0603)
0.453
(0.677)
0.687
(0.828)
0.877
(0.95)
0.00611
(0.0439)
0.601
(0.786)
xq gain 9 (11%) 71 0.959
(1.00)
0.4
(0.632)
0.397
(0.632)
0.115
(0.352)
0.0019
(0.0176)
0.132
(0.368)
0.714
(0.848)
0.794
(0.9)
0.0251
(0.134)
0.458
(0.679)
9p loss 8 (10%) 72 0.026
(0.134)
0.34
(0.595)
0.212
(0.481)
0.0829
(0.292)
0.194
(0.461)
0.337
(0.595)
0.0709
(0.264)
0.0406
(0.181)
0.149
(0.392)
0.1
(0.328)
15q loss 5 (6%) 75 0.457
(0.679)
0.481
(0.687)
0.2
(0.472)
0.667
(0.815)
0.215
(0.482)
1
(1.00)
0.0322
(0.156)
0.00762
(0.0519)
0.656
(0.815)
0.482
(0.687)
16q loss 16 (20%) 64 0.128
(0.366)
0.0902
(0.311)
0.563
(0.757)
0.353
(0.608)
0.238
(0.513)
0.387
(0.632)
0.212
(0.481)
1e-05
(0.000165)
0.0383
(0.176)
0.3
(0.56)
19p loss 3 (4%) 77 0.897
(0.95)
0.13
(0.366)
0.818
(0.913)
0.784
(0.893)
0.81
(0.91)
0.129
(0.366)
0.327
(0.584)
0.0104
(0.0664)
0.0652
(0.258)
0.0335
(0.161)
19q loss 3 (4%) 77 0.897
(0.95)
0.128
(0.366)
0.819
(0.913)
0.784
(0.893)
0.809
(0.91)
0.127
(0.366)
0.324
(0.584)
0.0101
(0.0651)
0.0668
(0.26)
0.0342
(0.163)
4p gain 8 (10%) 72 0.113
(0.35)
0.125
(0.366)
0.421
(0.656)
0.375
(0.623)
0.19
(0.46)
0.308
(0.568)
0.0386
(0.176)
0.0866
(0.302)
0.129
(0.366)
0.428
(0.662)
4q gain 5 (6%) 75 0.0683
(0.262)
0.482
(0.687)
0.606
(0.786)
0.666
(0.815)
0.469
(0.683)
0.644
(0.814)
0.11
(0.343)
0.00667
(0.0472)
0.175
(0.437)
0.262
(0.531)
11q gain 9 (11%) 71 0.822
(0.913)
0.448
(0.672)
0.32
(0.583)
0.121
(0.365)
0.248
(0.523)
0.0419
(0.183)
0.564
(0.757)
0.691
(0.829)
0.678
(0.822)
0.457
(0.679)
12p gain 3 (4%) 77 0.271
(0.531)
0.0713
(0.264)
0.903
(0.95)
0.0194
(0.113)
0.398
(0.632)
0.54
(0.741)
0.21
(0.481)
0.439
(0.664)
0.267
(0.531)
0.292
(0.553)
12q gain 3 (4%) 77 0.271
(0.531)
0.0714
(0.264)
0.902
(0.95)
0.0204
(0.116)
0.399
(0.632)
0.538
(0.741)
0.209
(0.481)
0.435
(0.664)
0.267
(0.531)
0.293
(0.553)
13q gain 6 (8%) 74 0.736
(0.863)
0.0251
(0.134)
0.212
(0.481)
0.353
(0.608)
0.383
(0.63)
0.383
(0.63)
0.567
(0.757)
0.154
(0.406)
0.645
(0.814)
0.648
(0.814)
14q gain 3 (4%) 77 0.272
(0.531)
0.0698
(0.264)
0.902
(0.95)
0.0189
(0.112)
0.67
(0.817)
0.844
(0.928)
0.0515
(0.219)
0.0651
(0.258)
1
(1.00)
1
(1.00)
17p gain 9 (11%) 71 0.147
(0.39)
0.187
(0.458)
0.307
(0.567)
0.0195
(0.113)
0.805
(0.91)
0.446
(0.671)
0.208
(0.481)
0.237
(0.512)
0.291
(0.553)
0.716
(0.848)
22q gain 6 (8%) 74 0.227
(0.496)
0.365
(0.616)
0.0366
(0.17)
0.136
(0.372)
0.883
(0.95)
0.283
(0.547)
0.564
(0.757)
0.0617
(0.252)
0.245
(0.518)
0.469
(0.683)
1q loss 4 (5%) 76 0.0958
(0.325)
0.131
(0.366)
0.195
(0.461)
0.217
(0.482)
0.263
(0.531)
0.0282
(0.141)
0.26
(0.531)
0.159
(0.413)
0.384
(0.63)
0.181
(0.446)
9q loss 7 (9%) 73 0.00365
(0.03)
0.161
(0.413)
0.481
(0.687)
0.232
(0.505)
0.354
(0.608)
0.512
(0.716)
0.243
(0.518)
0.0633
(0.256)
0.0657
(0.258)
0.118
(0.357)
1q gain 10 (12%) 70 0.895
(0.95)
0.825
(0.914)
0.688
(0.828)
0.555
(0.753)
0.294
(0.553)
0.117
(0.357)
0.18
(0.446)
0.37
(0.62)
0.322
(0.583)
0.437
(0.664)
2p gain 10 (12%) 70 0.747
(0.866)
0.554
(0.753)
0.281
(0.546)
0.541
(0.741)
0.932
(0.976)
0.178
(0.442)
0.289
(0.553)
0.827
(0.915)
0.168
(0.427)
0.191
(0.461)
2q gain 8 (10%) 72 0.595
(0.785)
0.251
(0.527)
0.129
(0.366)
0.279
(0.544)
0.609
(0.786)
0.0804
(0.287)
0.503
(0.707)
0.648
(0.814)
0.11
(0.343)
0.134
(0.37)
5p gain 4 (5%) 76 0.604
(0.786)
0.757
(0.873)
0.533
(0.74)
0.468
(0.683)
0.217
(0.482)
0.812
(0.91)
0.473
(0.686)
0.721
(0.851)
0.26
(0.531)
0.396
(0.632)
5q gain 4 (5%) 76 0.605
(0.786)
0.759
(0.873)
0.534
(0.74)
0.468
(0.683)
0.219
(0.483)
0.811
(0.91)
0.473
(0.686)
0.724
(0.851)
0.26
(0.531)
0.399
(0.632)
7p gain 8 (10%) 72 0.215
(0.482)
0.193
(0.461)
0.16
(0.413)
0.445
(0.671)
0.743
(0.866)
0.912
(0.957)
0.869
(0.95)
0.357
(0.609)
0.561
(0.757)
0.543
(0.743)
7q gain 7 (9%) 73 0.428
(0.662)
0.0972
(0.325)
0.295
(0.553)
0.315
(0.578)
0.717
(0.848)
0.634
(0.804)
0.665
(0.815)
0.207
(0.481)
0.159
(0.413)
0.139
(0.379)
9p gain 4 (5%) 76 0.883
(0.95)
0.63
(0.801)
0.476
(0.687)
0.362
(0.613)
0.233
(0.505)
1
(1.00)
0.397
(0.632)
0.962
(1.00)
0.205
(0.48)
0.656
(0.815)
9q gain 3 (4%) 77 0.6
(0.786)
0.774
(0.887)
0.104
(0.335)
0.621
(0.797)
0.188
(0.46)
0.842
(0.928)
0.659
(0.815)
0.888
(0.95)
0.375
(0.623)
0.579
(0.768)
11p gain 9 (11%) 71 0.745
(0.866)
0.704
(0.839)
0.36
(0.612)
0.194
(0.461)
0.141
(0.383)
0.406
(0.637)
0.588
(0.777)
0.687
(0.828)
0.492
(0.698)
0.902
(0.95)
16p gain 3 (4%) 77 0.215
(0.482)
1
(1.00)
0.615
(0.793)
1
(1.00)
1
(1.00)
0.464
(0.683)
1
(1.00)
0.126
(0.366)
0.271
(0.531)
0.435
(0.664)
17q gain 10 (12%) 70 0.327
(0.584)
0.142
(0.383)
0.371
(0.621)
0.0609
(0.252)
0.624
(0.797)
0.244
(0.518)
0.259
(0.531)
0.223
(0.491)
0.169
(0.427)
0.439
(0.664)
4q loss 3 (4%) 77 0.897
(0.95)
0.388
(0.632)
1
(1.00)
0.702
(0.839)
0.671
(0.817)
0.498
(0.701)
1
(1.00)
0.125
(0.366)
0.877
(0.95)
1
(1.00)
5q loss 3 (4%) 77 0.894
(0.95)
1
(1.00)
0.567
(0.757)
0.785
(0.893)
0.609
(0.786)
0.467
(0.683)
0.325
(0.584)
0.889
(0.95)
0.147
(0.39)
0.762
(0.875)
11p loss 3 (4%) 77 0.302
(0.56)
0.33
(0.585)
0.744
(0.866)
0.265
(0.531)
0.164
(0.419)
0.724
(0.851)
0.0507
(0.217)
0.54
(0.741)
0.579
(0.768)
0.293
(0.553)
12p loss 3 (4%) 77 1
(1.00)
1
(1.00)
0.82
(0.913)
0.787
(0.894)
0.257
(0.531)
0.292
(0.553)
0.663
(0.815)
0.89
(0.95)
0.667
(0.815)
0.577
(0.768)
13q loss 3 (4%) 77 0.0971
(0.325)
1
(1.00)
0.743
(0.866)
0.482
(0.687)
0.355
(0.608)
0.623
(0.797)
1
(1.00)
0.126
(0.366)
0.269
(0.531)
0.435
(0.664)
16p loss 7 (9%) 73 0.391
(0.632)
0.24
(0.514)
0.625
(0.797)
0.33
(0.585)
0.752
(0.87)
0.857
(0.94)
0.843
(0.928)
0.26
(0.531)
0.608
(0.786)
0.87
(0.95)
17p loss 3 (4%) 77 0.302
(0.56)
0.389
(0.632)
0.515
(0.718)
1
(1.00)
0.55
(0.749)
0.146
(0.39)
1
(1.00)
0.661
(0.815)
0.874
(0.95)
0.435
(0.664)
'4p gain' versus 'CN_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.18

Table S1.  Gene #4: '4p gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
4P GAIN MUTATED 0 6 2 0 0
4P GAIN WILD-TYPE 18 15 35 2 2

Figure S1.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #7: 'CN_CNMF'

'4q gain' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.047

Table S2.  Gene #5: '4q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
4Q GAIN MUTATED 0 3 0 1 0 0 1 0
4Q GAIN WILD-TYPE 16 4 22 11 2 14 4 2

Figure S2.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.057

Table S3.  Gene #8: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
6P GAIN MUTATED 4 3 22 9 2
6P GAIN WILD-TYPE 7 8 7 12 6

Figure S3.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0017

Table S4.  Gene #8: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
6P GAIN MUTATED 5 8 22 5
6P GAIN WILD-TYPE 10 7 5 18

Figure S4.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'LINCRNA_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0088

Table S5.  Gene #8: '6p gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
6P GAIN MUTATED 5 3 13 4 15
6P GAIN WILD-TYPE 13 4 15 7 1

Figure S5.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'6p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S6.  Gene #8: '6p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
6P GAIN MUTATED 4 17 6 13
6P GAIN WILD-TYPE 17 7 14 2

Figure S6.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'6p gain' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S7.  Gene #8: '6p gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
6P GAIN MUTATED 1 8 7 22 2
6P GAIN WILD-TYPE 12 13 11 2 2

Figure S7.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'6p gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
6P GAIN MUTATED 2 7 4 16 11
6P GAIN WILD-TYPE 19 13 4 1 3

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

'6p gain' versus 'CN_CNMF'

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

Table S9.  Gene #8: '6p gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
6P GAIN MUTATED 4 7 29 0 0
6P GAIN WILD-TYPE 14 14 8 2 2

Figure S9.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'CN_CNMF'

'6p gain' versus 'CN_THRESHOLDED_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
6P GAIN MUTATED 3 2 16 10 2 2 3 2
6P GAIN WILD-TYPE 13 5 6 2 0 12 2 0

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

'6p gain' versus 'METHYLATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.009

Table S11.  Gene #8: '6p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
6P GAIN MUTATED 8 7 6 19
6P GAIN WILD-TYPE 20 6 10 4

Figure S11.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'6p gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S12.  Gene #8: '6p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
6P GAIN MUTATED 9 10 21
6P GAIN WILD-TYPE 31 5 4

Figure S12.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0059

Table S13.  Gene #9: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
6Q GAIN MUTATED 1 5 13 1
6Q GAIN WILD-TYPE 14 10 14 22

Figure S13.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'LINCRNA_CNMF'

P value = 0.00701 (Fisher's exact test), Q value = 0.049

Table S14.  Gene #9: '6q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
6Q GAIN MUTATED 2 2 7 0 9
6Q GAIN WILD-TYPE 16 5 21 11 7

Figure S14.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'6q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00089

Table S15.  Gene #9: '6q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
6Q GAIN MUTATED 0 13 2 5
6Q GAIN WILD-TYPE 21 11 18 10

Figure S15.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'6q gain' versus 'MIR_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0024

Table S16.  Gene #9: '6q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
6Q GAIN MUTATED 0 1 5 13 1
6Q GAIN WILD-TYPE 13 20 13 11 3

Figure S16.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'6q gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
6Q GAIN MUTATED 0 2 2 8 8
6Q GAIN WILD-TYPE 21 18 6 9 6

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

'6q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0022

Table S18.  Gene #9: '6q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
6Q GAIN MUTATED 1 1 18 0 0
6Q GAIN WILD-TYPE 17 20 19 2 2

Figure S18.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #7: 'CN_CNMF'

'6q gain' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0028

Table S19.  Gene #9: '6q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
6Q GAIN MUTATED 1 0 8 7 1 0 1 2
6Q GAIN WILD-TYPE 15 7 14 5 1 14 4 0

Figure S19.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6q gain' versus 'METHYLATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
6Q GAIN MUTATED 1 4 5 10
6Q GAIN WILD-TYPE 27 9 11 13

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

'6q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S21.  Gene #9: '6q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
6Q GAIN MUTATED 2 6 12
6Q GAIN WILD-TYPE 38 9 13

Figure S21.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.024

Table S22.  Gene #12: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
8P GAIN MUTATED 6 7 4 15
8P GAIN WILD-TYPE 9 8 23 8

Figure S22.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #12: '8p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
8P GAIN MUTATED 11 5 12 4
8P GAIN WILD-TYPE 10 19 8 11

Figure S23.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'8p gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #12: '8p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
8P GAIN MUTATED 13 10 1 4 4
8P GAIN WILD-TYPE 8 10 7 13 10

Figure S24.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.031

Table S25.  Gene #12: '8p gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
8P GAIN MUTATED 12 11 8 0 1
8P GAIN WILD-TYPE 6 10 29 2 1

Figure S25.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'CN_CNMF'

'8p gain' versus 'METHYLATION_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.14

Table S26.  Gene #12: '8p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
8P GAIN MUTATED 16 2 8 6
8P GAIN WILD-TYPE 12 11 8 17

Figure S26.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'8p gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #12: '8p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
8P GAIN MUTATED 22 4 6
8P GAIN WILD-TYPE 18 11 19

Figure S27.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.041

Table S28.  Gene #13: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
8Q GAIN MUTATED 10 9 13 14 8
8Q GAIN WILD-TYPE 1 2 16 7 0

Figure S28.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00057

Table S29.  Gene #13: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
8Q GAIN MUTATED 15 9 10 20
8Q GAIN WILD-TYPE 0 6 17 3

Figure S29.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'LINCRNA_CNMF'

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

Table S30.  Gene #13: '8q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
8Q GAIN MUTATED 18 0 20 6 10
8Q GAIN WILD-TYPE 0 7 8 5 6

Figure S30.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'8q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S31.  Gene #13: '8q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
8Q GAIN MUTATED 20 9 18 7
8Q GAIN WILD-TYPE 1 15 2 8

Figure S31.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'8q gain' versus 'MIR_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.001

Table S32.  Gene #13: '8q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
8Q GAIN MUTATED 11 20 5 16 2
8Q GAIN WILD-TYPE 2 1 13 8 2

Figure S32.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'8q gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S33.  Gene #13: '8q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
8Q GAIN MUTATED 20 18 1 8 7
8Q GAIN WILD-TYPE 1 2 7 9 7

Figure S33.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S34.  Gene #13: '8q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
8Q GAIN MUTATED 16 20 14 2 2
8Q GAIN WILD-TYPE 2 1 23 0 0

Figure S34.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'CN_CNMF'

'8q gain' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
8Q GAIN MUTATED 15 7 4 8 2 12 5 1
8Q GAIN WILD-TYPE 1 0 18 4 0 2 0 1

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

'8q gain' versus 'METHYLATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S36.  Gene #13: '8q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
8Q GAIN MUTATED 27 3 12 12
8Q GAIN WILD-TYPE 1 10 4 11

Figure S36.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'8q gain' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S37.  Gene #13: '8q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
8Q GAIN MUTATED 37 5 12
8Q GAIN WILD-TYPE 3 10 13

Figure S37.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'11q gain' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.18

Table S38.  Gene #17: '11q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
11Q GAIN MUTATED 0 2 0 5 2
11Q GAIN WILD-TYPE 21 18 8 12 12

Figure S38.  Get High-res Image Gene #17: '11q gain' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'12p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.11

Table S39.  Gene #18: '12p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
12P GAIN MUTATED 0 0 3 0
12P GAIN WILD-TYPE 21 24 17 15

Figure S39.  Get High-res Image Gene #18: '12p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'12q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.12

Table S40.  Gene #19: '12q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
12Q GAIN MUTATED 0 0 3 0
12Q GAIN WILD-TYPE 21 24 17 15

Figure S40.  Get High-res Image Gene #19: '12q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'13q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S41.  Gene #20: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
13Q GAIN MUTATED 0 3 0 3
13Q GAIN WILD-TYPE 15 12 27 20

Figure S41.  Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.11

Table S42.  Gene #21: '14q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
14Q GAIN MUTATED 0 0 3 0
14Q GAIN WILD-TYPE 21 24 17 15

Figure S42.  Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'17p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.11

Table S43.  Gene #23: '17p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
17P GAIN MUTATED 0 4 5 0
17P GAIN WILD-TYPE 21 20 15 15

Figure S43.  Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00579 (Fisher's exact test), Q value = 0.043

Table S44.  Gene #25: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
20P GAIN MUTATED 0 4 0 4
20P GAIN WILD-TYPE 15 11 27 19

Figure S44.  Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.18

Table S45.  Gene #25: '20p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
20P GAIN MUTATED 0 4 4 0
20P GAIN WILD-TYPE 21 20 16 15

Figure S45.  Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00401 (Fisher's exact test), Q value = 0.031

Table S46.  Gene #26: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
20Q GAIN MUTATED 0 4 0 5
20Q GAIN WILD-TYPE 15 11 27 18

Figure S46.  Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.12

Table S47.  Gene #26: '20q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
20Q GAIN MUTATED 0 4 5 0
20Q GAIN WILD-TYPE 21 20 15 15

Figure S47.  Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S48.  Gene #26: '20q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
20Q GAIN MUTATED 6 0 3 0 0
20Q GAIN WILD-TYPE 12 21 34 2 2

Figure S48.  Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #7: 'CN_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00548 (Fisher's exact test), Q value = 0.041

Table S49.  Gene #27: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
21Q GAIN MUTATED 1 3 1 9
21Q GAIN WILD-TYPE 14 12 26 14

Figure S49.  Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.031

Table S50.  Gene #27: '21q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
21Q GAIN MUTATED 1 3 9 1
21Q GAIN WILD-TYPE 20 21 11 14

Figure S50.  Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.18

Table S51.  Gene #27: '21q gain' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
21Q GAIN MUTATED 7 3 3 1 0
21Q GAIN WILD-TYPE 11 18 34 1 2

Figure S51.  Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #7: 'CN_CNMF'

'22q gain' versus 'LINCRNA_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.17

Table S52.  Gene #28: '22q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
22Q GAIN MUTATED 0 0 6 0 0
22Q GAIN WILD-TYPE 18 7 22 11 16

Figure S52.  Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'xp gain' versus 'MIR_MATURE_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.06

Table S53.  Gene #29: 'xp gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
XP GAIN MUTATED 1 0 1 8 0
XP GAIN WILD-TYPE 12 21 17 16 4

Figure S53.  Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'xp gain' versus 'METHYLATION_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.044

Table S54.  Gene #29: 'xp gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
XP GAIN MUTATED 1 0 6 3
XP GAIN WILD-TYPE 27 13 10 20

Figure S54.  Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'xq gain' versus 'MIR_MATURE_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.018

Table S55.  Gene #30: 'xq gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
XQ GAIN MUTATED 1 0 0 8 0
XQ GAIN WILD-TYPE 12 21 18 16 4

Figure S55.  Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'xq gain' versus 'METHYLATION_CNMF'

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

Table S56.  Gene #30: 'xq gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
XQ GAIN MUTATED 1 0 5 3
XQ GAIN WILD-TYPE 27 13 11 20

Figure S56.  Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'1p loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.089

Table S57.  Gene #31: '1p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
1P LOSS MUTATED 9 2 0 6 1
1P LOSS WILD-TYPE 12 18 8 11 13

Figure S57.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0074

Table S58.  Gene #31: '1p loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
1P LOSS MUTATED 11 2 5 0 0
1P LOSS WILD-TYPE 7 19 32 2 2

Figure S58.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #7: 'CN_CNMF'

'1p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S59.  Gene #31: '1p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
1P LOSS MUTATED 11 1 2 1 0 0 1 2
1P LOSS WILD-TYPE 5 6 20 11 2 14 4 0

Figure S59.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'1q loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.14

Table S60.  Gene #32: '1q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
1Q LOSS MUTATED 4 0 0 0 0
1Q LOSS WILD-TYPE 17 20 8 17 14

Figure S60.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S61.  Gene #33: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
3P LOSS MUTATED 11 7 1 15 8
3P LOSS WILD-TYPE 0 4 28 6 0

Figure S61.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S62.  Gene #33: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
3P LOSS MUTATED 15 3 1 23
3P LOSS WILD-TYPE 0 12 26 0

Figure S62.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S63.  Gene #33: '3p loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
3P LOSS MUTATED 18 0 17 6 1
3P LOSS WILD-TYPE 0 7 11 5 15

Figure S63.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'3p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S64.  Gene #33: '3p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
3P LOSS MUTATED 20 1 20 1
3P LOSS WILD-TYPE 1 23 0 14

Figure S64.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'3p loss' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S65.  Gene #33: '3p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
3P LOSS MUTATED 11 20 6 3 2
3P LOSS WILD-TYPE 2 1 12 21 2

Figure S65.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'3p loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S66.  Gene #33: '3p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
3P LOSS MUTATED 21 17 0 2 2
3P LOSS WILD-TYPE 0 3 8 15 12

Figure S66.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S67.  Gene #33: '3p loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
3P LOSS MUTATED 17 21 1 2 1
3P LOSS WILD-TYPE 1 0 36 0 1

Figure S67.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #7: 'CN_CNMF'

'3p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S68.  Gene #33: '3p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
3P LOSS MUTATED 15 7 0 0 1 14 5 0
3P LOSS WILD-TYPE 1 0 22 12 1 0 0 2

Figure S68.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'3p loss' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S69.  Gene #33: '3p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
3P LOSS MUTATED 28 1 11 2
3P LOSS WILD-TYPE 0 12 5 21

Figure S69.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'3p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S70.  Gene #33: '3p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
3P LOSS MUTATED 40 0 2
3P LOSS WILD-TYPE 0 15 23

Figure S70.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S71.  Gene #34: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
3Q LOSS MUTATED 11 7 3 15 8
3Q LOSS WILD-TYPE 0 4 26 6 0

Figure S71.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S72.  Gene #34: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
3Q LOSS MUTATED 15 4 2 23
3Q LOSS WILD-TYPE 0 11 25 0

Figure S72.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
3Q LOSS MUTATED 18 0 17 7 2
3Q LOSS WILD-TYPE 0 7 11 4 14

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

'3q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S74.  Gene #34: '3q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
3Q LOSS MUTATED 21 1 20 2
3Q LOSS WILD-TYPE 0 23 0 13

Figure S74.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'3q loss' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S75.  Gene #34: '3q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
3Q LOSS MUTATED 11 21 7 3 2
3Q LOSS WILD-TYPE 2 0 11 21 2

Figure S75.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'3q loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S76.  Gene #34: '3q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
3Q LOSS MUTATED 21 18 1 2 2
3Q LOSS WILD-TYPE 0 2 7 15 12

Figure S76.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S77.  Gene #34: '3q loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
3Q LOSS MUTATED 17 21 2 2 2
3Q LOSS WILD-TYPE 1 0 35 0 0

Figure S77.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #7: 'CN_CNMF'

'3q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S78.  Gene #34: '3q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
3Q LOSS MUTATED 16 7 0 0 2 14 5 0
3Q LOSS WILD-TYPE 0 0 22 12 0 0 0 2

Figure S78.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'3q loss' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S79.  Gene #34: '3q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
3Q LOSS MUTATED 28 3 11 2
3Q LOSS WILD-TYPE 0 10 5 21

Figure S79.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'3q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S80.  Gene #34: '3q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
3Q LOSS MUTATED 40 2 2
3Q LOSS WILD-TYPE 0 13 23

Figure S80.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0046

Table S81.  Gene #37: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
6Q LOSS MUTATED 6 1 0 7
6Q LOSS WILD-TYPE 9 14 27 16

Figure S81.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'LINCRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.16

Table S82.  Gene #37: '6q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
6Q LOSS MUTATED 7 0 6 0 1
6Q LOSS WILD-TYPE 11 7 22 11 15

Figure S82.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'6q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
6Q LOSS MUTATED 6 0 7 1
6Q LOSS WILD-TYPE 15 24 13 14

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

'6q loss' versus 'MIR_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0066

Table S84.  Gene #37: '6q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
6Q LOSS MUTATED 4 9 0 1 0
6Q LOSS WILD-TYPE 9 12 18 23 4

Figure S84.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00078

Table S85.  Gene #37: '6q loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
6Q LOSS MUTATED 2 11 1 0 0
6Q LOSS WILD-TYPE 16 10 36 2 2

Figure S85.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'CN_CNMF'

'6q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S86.  Gene #37: '6q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
6Q LOSS MUTATED 1 7 0 1 1 0 4 0
6Q LOSS WILD-TYPE 15 0 22 11 1 14 1 2

Figure S86.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'6q loss' versus 'METHYLATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0015

Table S87.  Gene #37: '6q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
6Q LOSS MUTATED 12 0 0 2
6Q LOSS WILD-TYPE 16 13 16 21

Figure S87.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'6q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.077

Table S88.  Gene #37: '6q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
6Q LOSS MUTATED 12 0 2
6Q LOSS WILD-TYPE 28 15 23

Figure S88.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00594 (Fisher's exact test), Q value = 0.043

Table S89.  Gene #38: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
8P LOSS MUTATED 5 0 1 1
8P LOSS WILD-TYPE 10 15 26 22

Figure S89.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.14

Table S90.  Gene #38: '8p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 24 20 15
8P LOSS MUTATED 5 0 1 1
8P LOSS WILD-TYPE 16 24 19 14

Figure S90.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'8p loss' versus 'MIR_MATURE_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.1

Table S91.  Gene #38: '8p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 21 18 24 4
8P LOSS MUTATED 2 5 0 0 0
8P LOSS WILD-TYPE 11 16 18 24 4

Figure S91.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.094

Table S92.  Gene #38: '8p loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
8P LOSS MUTATED 0 6 1 0 0
8P LOSS WILD-TYPE 18 15 36 2 2

Figure S92.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #7: 'CN_CNMF'

'8p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.02

Table S93.  Gene #38: '8p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
8P LOSS MUTATED 0 4 0 1 0 1 1 0
8P LOSS WILD-TYPE 16 3 22 11 2 13 4 2

Figure S93.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'8p loss' versus 'METHYLATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.2

Table S94.  Gene #38: '8p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
8P LOSS MUTATED 6 0 0 1
8P LOSS WILD-TYPE 22 13 16 22

Figure S94.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.13

Table S95.  Gene #39: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
9P LOSS MUTATED 4 0 1 3 0
9P LOSS WILD-TYPE 7 11 28 18 8

Figure S95.  Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.18

Table S96.  Gene #39: '9p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
9P LOSS MUTATED 4 1 0 0 0 1 1 1
9P LOSS WILD-TYPE 12 6 22 12 2 13 4 1

Figure S96.  Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.03

Table S97.  Gene #40: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
9Q LOSS MUTATED 4 0 0 3 0
9Q LOSS WILD-TYPE 7 11 29 18 8

Figure S97.  Get High-res Image Gene #40: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.16

Table S98.  Gene #44: '15q loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
15Q LOSS MUTATED 3 0 1 0 1
15Q LOSS WILD-TYPE 15 21 36 2 1

Figure S98.  Get High-res Image Gene #44: '15q loss' versus Molecular Subtype #7: 'CN_CNMF'

'15q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.052

Table S99.  Gene #44: '15q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
15Q LOSS MUTATED 3 0 0 0 1 0 0 1
15Q LOSS WILD-TYPE 13 7 22 12 1 14 5 1

Figure S99.  Get High-res Image Gene #44: '15q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'16q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S100.  Gene #46: '16q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
16Q LOSS MUTATED 3 7 1 2 0 1 0 2
16Q LOSS WILD-TYPE 13 0 21 10 2 13 5 0

Figure S100.  Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'16q loss' versus 'METHYLATION_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.18

Table S101.  Gene #46: '16q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
16Q LOSS MUTATED 10 0 3 3
16Q LOSS WILD-TYPE 18 13 13 20

Figure S101.  Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'19p loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.066

Table S102.  Gene #48: '19p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
19P LOSS MUTATED 0 0 1 0 1 0 0 1
19P LOSS WILD-TYPE 16 7 21 12 1 14 5 1

Figure S102.  Get High-res Image Gene #48: '19p loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'19p loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.16

Table S103.  Gene #48: '19p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
19P LOSS MUTATED 0 0 3
19P LOSS WILD-TYPE 40 15 22

Figure S103.  Get High-res Image Gene #48: '19p loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'19q loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.065

Table S104.  Gene #49: '19q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
19Q LOSS MUTATED 0 0 1 0 1 0 0 1
19Q LOSS WILD-TYPE 16 7 21 12 1 14 5 1

Figure S104.  Get High-res Image Gene #49: '19q loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'19q loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.16

Table S105.  Gene #49: '19q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
19Q LOSS MUTATED 0 0 3
19Q LOSS WILD-TYPE 40 15 22

Figure S105.  Get High-res Image Gene #49: '19q loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.16

Table S106.  Gene #50: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
XP LOSS MUTATED 2 0 2 7 0
XP LOSS WILD-TYPE 9 11 27 14 8

Figure S106.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.008 (Fisher's exact test), Q value = 0.054

Table S107.  Gene #50: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
XP LOSS MUTATED 0 1 2 8
XP LOSS WILD-TYPE 15 14 25 15

Figure S107.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'LINCRNA_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.034

Table S108.  Gene #50: 'xp loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
XP LOSS MUTATED 0 0 7 4 0
XP LOSS WILD-TYPE 18 7 21 7 16

Figure S108.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'xp loss' versus 'METHYLATION_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.052

Table S109.  Gene #50: 'xp loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
XP LOSS MUTATED 4 1 6 0
XP LOSS WILD-TYPE 24 12 10 23

Figure S109.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'xp loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.13

Table S110.  Gene #50: 'xp loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
XP LOSS MUTATED 8 3 0
XP LOSS WILD-TYPE 32 12 25

Figure S110.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.12

Table S111.  Gene #51: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 11 29 21 8
XQ LOSS MUTATED 3 0 2 7 0
XQ LOSS WILD-TYPE 8 11 27 14 8

Figure S111.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.022

Table S112.  Gene #51: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 15 27 23
XQ LOSS MUTATED 0 1 2 9
XQ LOSS WILD-TYPE 15 14 25 14

Figure S112.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'LINCRNA_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0098

Table S113.  Gene #51: 'xq loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 7 28 11 16
XQ LOSS MUTATED 0 0 7 5 0
XQ LOSS WILD-TYPE 18 7 21 6 16

Figure S113.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'xq loss' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.14

Table S114.  Gene #51: 'xq loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 21 20 8 17 14
XQ LOSS MUTATED 8 1 0 2 1
XQ LOSS WILD-TYPE 13 19 8 15 13

Figure S114.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.17

Table S115.  Gene #51: 'xq loss' versus Molecular Subtype #7: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 21 37 2 2
XQ LOSS MUTATED 6 3 2 0 1
XQ LOSS WILD-TYPE 12 18 35 2 1

Figure S115.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #7: 'CN_CNMF'

'xq loss' versus 'CN_THRESHOLDED_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.13

Table S116.  Gene #51: 'xq loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 16 7 22 12 2 14 5 2
XQ LOSS MUTATED 6 2 1 0 0 1 1 1
XQ LOSS WILD-TYPE 10 5 21 12 2 13 4 1

Figure S116.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'xq loss' versus 'METHYLATION_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.018

Table S117.  Gene #51: 'xq loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 13 16 23
XQ LOSS MUTATED 4 1 7 0
XQ LOSS WILD-TYPE 24 12 9 23

Figure S117.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'xq loss' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #51: 'xq loss' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 15 25
XQ LOSS MUTATED 9 3 0
XQ LOSS WILD-TYPE 31 12 25

Figure S118.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #10: '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-f5144117-2d5a-42c2-8998-5b38e52db5d9/18c76f9c-e604-4517-bc19-4bda4cb583f6/correlate_genomic_events_all/597ba7df-da6d-44b2-a96c-e44efd0c26c0/call-preprocess_genomic_event/transformed.cor.cli.txt

  • Molecular subtypes file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/9d897bdb-7a9a-423a-ad17-06f28ae98803/aggregate_clusters_workflow/1d8bac82-5a1d-4cd2-aeb1-8ddd0e1e7a20/call-aggregate_clusters/TCGA-UVM-TP.transposedmergedcluster.txt

  • Number of patients = 80

  • Number of significantly arm-level cnvs = 51

  • Number of molecular subtypes = 10

  • 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)