Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1PK0F0H
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 57 arm-level events and 10 molecular subtypes across 494 patients, 166 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 57 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, 166 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
5q gain 17 (3%) 477 1e-05
(0.00534)
7e-05
(0.0297)
0.849
(1.00)
0.079
(1.00)
0.00023
(0.0911)
0.00022
(0.088)
0.0004
(0.151)
1e-05
(0.00534)
7e-05
(0.0297)
3e-05
(0.0136)
7q gain 20 (4%) 474 1e-05
(0.00534)
2e-05
(0.00938)
0.573
(1.00)
0.0137
(1.00)
6e-05
(0.0257)
6e-05
(0.0257)
0.00013
(0.0533)
2e-05
(0.00938)
5e-05
(0.0218)
2e-05
(0.00938)
12p gain 14 (3%) 480 1e-05
(0.00534)
1e-05
(0.00534)
0.852
(1.00)
0.0797
(1.00)
3e-05
(0.0136)
1e-05
(0.00534)
5e-05
(0.0218)
2e-05
(0.00938)
3e-05
(0.0136)
3e-05
(0.0136)
12q gain 15 (3%) 479 1e-05
(0.00534)
1e-05
(0.00534)
0.85
(1.00)
0.0801
(1.00)
1e-05
(0.00534)
4e-05
(0.0176)
1e-05
(0.00534)
1e-05
(0.00534)
2e-05
(0.00938)
1e-05
(0.00534)
16p gain 15 (3%) 479 1e-05
(0.00534)
3e-05
(0.0136)
0.632
(1.00)
0.0785
(1.00)
0.00011
(0.0455)
0.00029
(0.113)
0.00013
(0.0533)
0.00037
(0.141)
4e-05
(0.0176)
3e-05
(0.0136)
17p gain 16 (3%) 478 1e-05
(0.00534)
1e-05
(0.00534)
0.538
(1.00)
0.0279
(1.00)
2e-05
(0.00938)
1e-05
(0.00534)
1e-05
(0.00534)
1e-05
(0.00534)
1e-05
(0.00534)
1e-05
(0.00534)
17q gain 18 (4%) 476 1e-05
(0.00534)
1e-05
(0.00534)
0.631
(1.00)
0.0157
(1.00)
3e-05
(0.0136)
1e-05
(0.00534)
3e-05
(0.0136)
1e-05
(0.00534)
1e-05
(0.00534)
1e-05
(0.00534)
19p gain 8 (2%) 486 1e-05
(0.00534)
0.00021
(0.0844)
0.00063
(0.232)
0.00014
(0.057)
0.0001
(0.0416)
1e-05
(0.00534)
0.0003
(0.116)
4e-05
(0.0176)
19q gain 10 (2%) 484 1e-05
(0.00534)
2e-05
(0.00938)
0.637
(1.00)
0.0637
(1.00)
0.00012
(0.0494)
3e-05
(0.0136)
1e-05
(0.00534)
1e-05
(0.00534)
5e-05
(0.0218)
1e-05
(0.00534)
2p loss 10 (2%) 484 1e-05
(0.00534)
3e-05
(0.0136)
0.771
(1.00)
0.0906
(1.00)
8e-05
(0.0337)
2e-05
(0.00938)
1e-05
(0.00534)
1e-05
(0.00534)
6e-05
(0.0257)
1e-05
(0.00534)
2q loss 10 (2%) 484 1e-05
(0.00534)
1e-05
(0.00534)
0.774
(1.00)
0.0901
(1.00)
8e-05
(0.0337)
1e-05
(0.00534)
2e-05
(0.00938)
1e-05
(0.00534)
5e-05
(0.0218)
1e-05
(0.00534)
15q loss 8 (2%) 486 0.0001
(0.0416)
0.00016
(0.065)
0.193
(1.00)
0.0887
(1.00)
0.00045
(0.169)
0.00016
(0.065)
9e-05
(0.0377)
1e-05
(0.00534)
0.00022
(0.088)
5e-05
(0.0218)
7p gain 18 (4%) 476 1e-05
(0.00534)
9e-05
(0.0377)
0.66
(1.00)
0.0512
(1.00)
0.00056
(0.208)
0.00061
(0.226)
0.00108
(0.388)
2e-05
(0.00938)
0.00026
(0.102)
0.00012
(0.0494)
14q gain 11 (2%) 483 1e-05
(0.00534)
0.00023
(0.0911)
1
(1.00)
0.158
(1.00)
0.00049
(0.183)
9e-05
(0.0377)
0.00045
(0.169)
7e-05
(0.0297)
0.00092
(0.334)
0.00013
(0.0533)
22q loss 86 (17%) 408 1e-05
(0.00534)
3e-05
(0.0136)
0.118
(1.00)
0.502
(1.00)
1e-05
(0.00534)
1e-05
(0.00534)
0.00088
(0.32)
0.00018
(0.0725)
1e-05
(0.00534)
2e-05
(0.00938)
16q gain 13 (3%) 481 1e-05
(0.00534)
0.00011
(0.0455)
0.795
(1.00)
0.277
(1.00)
0.00109
(0.39)
0.00213
(0.731)
0.00167
(0.584)
0.00021
(0.0844)
0.00022
(0.088)
0.00053
(0.197)
20p gain 12 (2%) 482 1e-05
(0.00534)
0.00025
(0.0985)
0.794
(1.00)
0.0925
(1.00)
0.00304
(1.00)
0.00042
(0.158)
0.00444
(1.00)
0.00044
(0.165)
0.00038
(0.145)
0.00177
(0.618)
20q gain 12 (2%) 482 1e-05
(0.00534)
0.00033
(0.127)
0.793
(1.00)
0.0912
(1.00)
0.00291
(0.972)
0.00039
(0.148)
0.00403
(1.00)
0.00039
(0.148)
0.00036
(0.138)
0.002
(0.692)
5p gain 21 (4%) 473 1e-05
(0.00534)
0.00199
(0.691)
0.53
(1.00)
0.234
(1.00)
0.00583
(1.00)
0.00071
(0.261)
0.00376
(1.00)
1e-05
(0.00534)
0.001
(0.36)
5e-05
(0.0218)
1q gain 24 (5%) 470 4e-05
(0.0176)
0.0286
(1.00)
0.00113
(0.401)
0.0547
(1.00)
0.0007
(0.258)
2e-05
(0.00938)
0.156
(1.00)
0.0792
(1.00)
0.0887
(1.00)
0.00099
(0.357)
11q loss 9 (2%) 485 1e-05
(0.00534)
0.0168
(1.00)
0.321
(1.00)
0.814
(1.00)
0.0173
(1.00)
0.015
(1.00)
0.00032
(0.124)
0.00248
(0.843)
0.00131
(0.462)
0.00682
(1.00)
3p gain 3 (1%) 491 0.00029
(0.113)
0.552
(1.00)
0.486
(1.00)
0.336
(1.00)
0.208
(1.00)
0.117
(1.00)
0.325
(1.00)
0.214
(1.00)
4p gain 5 (1%) 489 1e-05
(0.00534)
0.00414
(1.00)
0.0185
(1.00)
0.00857
(1.00)
0.0265
(1.00)
0.0114
(1.00)
0.0687
(1.00)
0.029
(1.00)
4q gain 5 (1%) 489 1e-05
(0.00534)
0.00444
(1.00)
0.0182
(1.00)
0.00841
(1.00)
0.0254
(1.00)
0.0115
(1.00)
0.0693
(1.00)
0.0291
(1.00)
8p gain 6 (1%) 488 0.00033
(0.127)
0.423
(1.00)
0.459
(1.00)
0.63
(1.00)
0.625
(1.00)
0.286
(1.00)
0.526
(1.00)
0.445
(1.00)
0.333
(1.00)
0.467
(1.00)
8q gain 7 (1%) 487 3e-05
(0.0136)
0.203
(1.00)
0.458
(1.00)
0.629
(1.00)
0.869
(1.00)
0.329
(1.00)
0.8
(1.00)
0.558
(1.00)
0.319
(1.00)
0.302
(1.00)
11p gain 6 (1%) 488 0.00022
(0.088)
0.0204
(1.00)
0.782
(1.00)
0.298
(1.00)
0.0532
(1.00)
0.0187
(1.00)
0.0141
(1.00)
0.00615
(1.00)
0.00239
(0.817)
0.0196
(1.00)
11q gain 5 (1%) 489 1e-05
(0.00534)
0.0592
(1.00)
0.782
(1.00)
0.302
(1.00)
0.116
(1.00)
0.0597
(1.00)
0.0423
(1.00)
0.0195
(1.00)
0.00722
(1.00)
0.0644
(1.00)
13q gain 5 (1%) 489 1e-05
(0.00534)
0.0191
(1.00)
0.383
(1.00)
0.215
(1.00)
0.0443
(1.00)
0.113
(1.00)
0.168
(1.00)
0.0629
(1.00)
0.211
(1.00)
0.0564
(1.00)
18p gain 6 (1%) 488 2e-05
(0.00938)
0.0916
(1.00)
0.108
(1.00)
0.191
(1.00)
0.256
(1.00)
0.0848
(1.00)
0.0262
(1.00)
0.163
(1.00)
18q gain 6 (1%) 488 2e-05
(0.00938)
0.0936
(1.00)
0.108
(1.00)
0.191
(1.00)
0.256
(1.00)
0.0812
(1.00)
0.026
(1.00)
0.162
(1.00)
21q gain 5 (1%) 489 3e-05
(0.0136)
0.172
(1.00)
0.218
(1.00)
0.374
(1.00)
0.45
(1.00)
0.223
(1.00)
0.07
(1.00)
0.366
(1.00)
xq gain 9 (2%) 485 2e-05
(0.00938)
0.0111
(1.00)
0.84
(1.00)
0.505
(1.00)
0.0959
(1.00)
0.347
(1.00)
0.337
(1.00)
0.176
(1.00)
0.484
(1.00)
0.296
(1.00)
1p loss 4 (1%) 490 2e-05
(0.00938)
0.187
(1.00)
0.236
(1.00)
0.28
(1.00)
0.0746
(1.00)
0.0377
(1.00)
0.128
(1.00)
0.0733
(1.00)
1q loss 3 (1%) 491 0.00036
(0.138)
0.0492
(1.00)
0.0972
(1.00)
0.111
(1.00)
0.0273
(1.00)
0.0158
(1.00)
0.0703
(1.00)
0.0292
(1.00)
3p loss 3 (1%) 491 0.00026
(0.102)
0.0491
(1.00)
0.0956
(1.00)
0.109
(1.00)
0.0278
(1.00)
0.0165
(1.00)
0.0711
(1.00)
0.0292
(1.00)
3q loss 4 (1%) 490 1e-05
(0.00534)
0.0185
(1.00)
0.495
(1.00)
0.42
(1.00)
0.0428
(1.00)
0.0369
(1.00)
0.0079
(1.00)
0.00397
(1.00)
0.0222
(1.00)
0.00986
(1.00)
6q loss 7 (1%) 487 6e-05
(0.0257)
0.00209
(0.719)
0.0133
(1.00)
0.573
(1.00)
0.0317
(1.00)
0.0134
(1.00)
0.00287
(0.961)
0.00094
(0.34)
0.00948
(1.00)
0.00183
(0.637)
8p loss 4 (1%) 490 5e-05
(0.0218)
0.0179
(1.00)
0.0433
(1.00)
0.0383
(1.00)
0.00817
(1.00)
0.00411
(1.00)
0.0229
(1.00)
0.0099
(1.00)
8q loss 4 (1%) 490 1e-05
(0.00534)
0.0181
(1.00)
0.0429
(1.00)
0.0375
(1.00)
0.00828
(1.00)
0.00419
(1.00)
0.0229
(1.00)
0.00974
(1.00)
9p loss 19 (4%) 475 1e-05
(0.00534)
0.0364
(1.00)
0.243
(1.00)
0.646
(1.00)
0.0283
(1.00)
0.0428
(1.00)
0.00534
(1.00)
0.00309
(1.00)
0.00945
(1.00)
0.00111
(0.395)
9q loss 24 (5%) 470 1e-05
(0.00534)
0.0568
(1.00)
0.172
(1.00)
0.114
(1.00)
0.105
(1.00)
0.0403
(1.00)
0.0093
(1.00)
0.00444
(1.00)
0.0125
(1.00)
0.00273
(0.917)
10p loss 7 (1%) 487 1e-05
(0.00534)
0.011
(1.00)
0.494
(1.00)
0.42
(1.00)
0.0218
(1.00)
0.0103
(1.00)
0.00323
(1.00)
0.0011
(0.393)
0.00996
(1.00)
0.00291
(0.972)
10q loss 6 (1%) 488 1e-05
(0.00534)
0.0192
(1.00)
0.0529
(1.00)
0.0357
(1.00)
0.00914
(1.00)
0.00345
(1.00)
0.027
(1.00)
0.00829
(1.00)
11p loss 7 (1%) 487 1e-05
(0.00534)
0.0114
(1.00)
0.493
(1.00)
0.959
(1.00)
0.00681
(1.00)
0.0138
(1.00)
0.00311
(1.00)
0.00125
(0.442)
0.0106
(1.00)
0.00313
(1.00)
18p loss 4 (1%) 490 0.00029
(0.113)
0.187
(1.00)
1
(1.00)
0.387
(1.00)
0.238
(1.00)
0.161
(1.00)
0.113
(1.00)
0.0639
(1.00)
0.0226
(1.00)
0.209
(1.00)
18q loss 4 (1%) 490 0.00017
(0.0687)
0.185
(1.00)
1
(1.00)
0.387
(1.00)
0.236
(1.00)
0.161
(1.00)
0.115
(1.00)
0.0629
(1.00)
0.0224
(1.00)
0.209
(1.00)
21q loss 8 (2%) 486 6e-05
(0.0257)
0.141
(1.00)
0.383
(1.00)
0.213
(1.00)
0.652
(1.00)
0.575
(1.00)
0.0752
(1.00)
0.141
(1.00)
0.0983
(1.00)
0.00805
(1.00)
1p gain 3 (1%) 491 0.255
(1.00)
0.394
(1.00)
0.559
(1.00)
0.586
(1.00)
0.413
(1.00)
0.348
(1.00)
0.214
(1.00)
0.264
(1.00)
9p gain 3 (1%) 491 0.00245
(0.835)
0.548
(1.00)
0.486
(1.00)
0.34
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
9q gain 4 (1%) 490 0.00973
(1.00)
0.794
(1.00)
0.896
(1.00)
0.124
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
6p loss 4 (1%) 490 0.00267
(0.9)
0.0452
(1.00)
0.452
(1.00)
0.338
(1.00)
0.0764
(1.00)
0.0367
(1.00)
0.128
(1.00)
0.0605
(1.00)
13q loss 14 (3%) 480 0.00864
(1.00)
0.0147
(1.00)
0.0616
(1.00)
0.137
(1.00)
0.00494
(1.00)
0.00438
(1.00)
0.00145
(0.51)
0.00083
(0.304)
0.00201
(0.693)
0.00778
(1.00)
17p loss 8 (2%) 486 0.00165
(0.579)
0.419
(1.00)
1
(1.00)
0.389
(1.00)
0.653
(1.00)
0.645
(1.00)
0.329
(1.00)
0.141
(1.00)
0.671
(1.00)
0.192
(1.00)
17q loss 4 (1%) 490 0.0541
(1.00)
0.792
(1.00)
0.897
(1.00)
0.636
(1.00)
0.398
(1.00)
0.572
(1.00)
0.847
(1.00)
0.762
(1.00)
19p loss 5 (1%) 489 0.0254
(1.00)
0.00424
(1.00)
0.321
(1.00)
0.237
(1.00)
0.0178
(1.00)
0.00826
(1.00)
0.00262
(0.888)
0.00087
(0.318)
0.00752
(1.00)
0.00264
(0.892)
xq loss 3 (1%) 491 0.0219
(1.00)
0.0498
(1.00)
0.278
(1.00)
0.198
(1.00)
0.0965
(1.00)
0.111
(1.00)
0.0279
(1.00)
0.0157
(1.00)
0.0686
(1.00)
0.0287
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
1Q GAIN MUTATED 9 14 1
1Q GAIN WILD-TYPE 25 369 76

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
1Q GAIN MUTATED 2 0 2 16 4
1Q GAIN WILD-TYPE 124 100 71 99 74

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
3P GAIN MUTATED 3 0 0
3P GAIN WILD-TYPE 31 383 77

Figure S3.  Get High-res Image Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S4.  Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
4P GAIN MUTATED 5 0 0
4P GAIN WILD-TYPE 29 383 77

Figure S4.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S5.  Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
4Q GAIN MUTATED 5 0 0
4Q GAIN WILD-TYPE 29 383 77

Figure S5.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S6.  Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
5P GAIN MUTATED 19 2 0
5P GAIN WILD-TYPE 15 381 77

Figure S6.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
5P GAIN MUTATED 13 1 7
5P GAIN WILD-TYPE 112 204 156

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

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S8.  Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
5P GAIN MUTATED 13 1 2 5
5P GAIN WILD-TYPE 110 186 103 73

Figure S8.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S9.  Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
5Q GAIN MUTATED 17 0 0
5Q GAIN WILD-TYPE 17 383 77

Figure S9.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S10.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
5Q GAIN MUTATED 2 14 1
5Q GAIN WILD-TYPE 271 137 69

Figure S10.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.091

Table S11.  Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
5Q GAIN MUTATED 14 0 1 2
5Q GAIN WILD-TYPE 140 55 115 165

Figure S11.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.088

Table S12.  Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
5Q GAIN MUTATED 13 1 1 2 0
5Q GAIN WILD-TYPE 113 99 72 113 78

Figure S12.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.15

Table S13.  Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
5Q GAIN MUTATED 13 2 2
5Q GAIN WILD-TYPE 137 171 168

Figure S13.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S14.  Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
5Q GAIN MUTATED 13 1 3
5Q GAIN WILD-TYPE 112 204 160

Figure S14.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S15.  Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
5Q GAIN MUTATED 14 1 2
5Q GAIN WILD-TYPE 149 168 159

Figure S15.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S16.  Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
5Q GAIN MUTATED 13 1 1 2
5Q GAIN WILD-TYPE 110 186 104 76

Figure S16.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S17.  Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
7P GAIN MUTATED 18 0 0
7P GAIN WILD-TYPE 16 383 77

Figure S17.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.038

Table S18.  Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
7P GAIN MUTATED 2 14 2
7P GAIN WILD-TYPE 271 137 68

Figure S18.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
7P GAIN MUTATED 14 1 1 2
7P GAIN WILD-TYPE 140 54 115 165

Figure S19.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
7P GAIN MUTATED 13 2 1 2 0
7P GAIN WILD-TYPE 113 98 72 113 78

Figure S20.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S21.  Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
7P GAIN MUTATED 13 1 4
7P GAIN WILD-TYPE 112 204 159

Figure S21.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
7P GAIN MUTATED 14 1 3
7P GAIN WILD-TYPE 149 168 158

Figure S22.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.049

Table S23.  Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
7P GAIN MUTATED 13 1 2 2
7P GAIN WILD-TYPE 110 186 103 76

Figure S23.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S24.  Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
7Q GAIN MUTATED 19 0 1
7Q GAIN WILD-TYPE 15 383 76

Figure S24.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S25.  Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
7Q GAIN MUTATED 2 16 2
7Q GAIN WILD-TYPE 271 135 68

Figure S25.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S26.  Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
7Q GAIN MUTATED 16 1 1 2
7Q GAIN WILD-TYPE 138 54 115 165

Figure S26.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S27.  Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
7Q GAIN MUTATED 15 2 1 2 0
7Q GAIN WILD-TYPE 111 98 72 113 78

Figure S27.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.053

Table S28.  Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
7Q GAIN MUTATED 15 2 3
7Q GAIN WILD-TYPE 135 171 167

Figure S28.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S29.  Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
7Q GAIN MUTATED 14 2 4
7Q GAIN WILD-TYPE 111 203 159

Figure S29.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S30.  Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
7Q GAIN MUTATED 16 1 3
7Q GAIN WILD-TYPE 147 168 158

Figure S30.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S31.  Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
7Q GAIN MUTATED 15 1 2 2
7Q GAIN WILD-TYPE 108 186 103 76

Figure S31.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S32.  Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
8P GAIN MUTATED 4 2 0
8P GAIN WILD-TYPE 30 381 77

Figure S32.  Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S33.  Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
8Q GAIN MUTATED 5 2 0
8Q GAIN WILD-TYPE 29 381 77

Figure S33.  Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.088

Table S34.  Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11P GAIN MUTATED 4 1 1
11P GAIN WILD-TYPE 30 382 76

Figure S34.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S35.  Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11Q GAIN MUTATED 4 0 1
11Q GAIN WILD-TYPE 30 383 76

Figure S35.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S36.  Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
12P GAIN MUTATED 13 0 1
12P GAIN WILD-TYPE 21 383 76

Figure S36.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S37.  Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
12P GAIN MUTATED 1 13 0
12P GAIN WILD-TYPE 272 138 70

Figure S37.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S38.  Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
12P GAIN MUTATED 13 0 1 0
12P GAIN WILD-TYPE 141 55 115 167

Figure S38.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S39.  Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
12P GAIN MUTATED 12 1 1 0 0
12P GAIN WILD-TYPE 114 99 72 115 78

Figure S39.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S40.  Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
12P GAIN MUTATED 12 1 1
12P GAIN WILD-TYPE 138 172 169

Figure S40.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S41.  Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
12P GAIN MUTATED 12 1 1
12P GAIN WILD-TYPE 113 204 162

Figure S41.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S42.  Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
12P GAIN MUTATED 13 0 1
12P GAIN WILD-TYPE 150 169 160

Figure S42.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S43.  Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
12P GAIN MUTATED 12 1 1 0
12P GAIN WILD-TYPE 111 186 104 78

Figure S43.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S44.  Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
12Q GAIN MUTATED 13 0 2
12Q GAIN WILD-TYPE 21 383 75

Figure S44.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S45.  Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
12Q GAIN MUTATED 1 14 0
12Q GAIN WILD-TYPE 272 137 70

Figure S45.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S46.  Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
12Q GAIN MUTATED 14 0 1 0
12Q GAIN WILD-TYPE 140 55 115 167

Figure S46.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S47.  Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
12Q GAIN MUTATED 13 1 1 0 0
12Q GAIN WILD-TYPE 113 99 72 115 78

Figure S47.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S48.  Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
12Q GAIN MUTATED 13 1 1
12Q GAIN WILD-TYPE 137 172 169

Figure S48.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S49.  Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
12Q GAIN MUTATED 13 1 1
12Q GAIN WILD-TYPE 112 204 162

Figure S49.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S50.  Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
12Q GAIN MUTATED 14 0 1
12Q GAIN WILD-TYPE 149 169 160

Figure S50.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S51.  Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
12Q GAIN MUTATED 13 1 1 0
12Q GAIN WILD-TYPE 110 186 104 78

Figure S51.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S52.  Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
13Q GAIN MUTATED 5 0 0
13Q GAIN WILD-TYPE 29 383 77

Figure S52.  Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S53.  Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
14Q GAIN MUTATED 9 1 1
14Q GAIN WILD-TYPE 25 382 76

Figure S53.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.091

Table S54.  Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
14Q GAIN MUTATED 1 10 0
14Q GAIN WILD-TYPE 272 141 70

Figure S54.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.18

Table S55.  Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
14Q GAIN MUTATED 10 0 0 1
14Q GAIN WILD-TYPE 144 55 116 166

Figure S55.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.038

Table S56.  Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
14Q GAIN MUTATED 10 0 0 0 1
14Q GAIN WILD-TYPE 116 100 73 115 77

Figure S56.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
14Q GAIN MUTATED 9 0 2
14Q GAIN WILD-TYPE 141 173 168

Figure S57.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S58.  Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
14Q GAIN MUTATED 9 0 2
14Q GAIN WILD-TYPE 116 205 161

Figure S58.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.053

Table S59.  Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
14Q GAIN MUTATED 9 0 1 1
14Q GAIN WILD-TYPE 114 187 104 77

Figure S59.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S60.  Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
16P GAIN MUTATED 14 0 1
16P GAIN WILD-TYPE 20 383 76

Figure S60.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S61.  Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
16P GAIN MUTATED 1 13 1
16P GAIN WILD-TYPE 272 138 69

Figure S61.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.046

Table S62.  Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
16P GAIN MUTATED 13 0 1 1
16P GAIN WILD-TYPE 141 55 115 166

Figure S62.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S63.  Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
16P GAIN MUTATED 12 1 1 1 0
16P GAIN WILD-TYPE 114 99 72 114 78

Figure S63.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.053

Table S64.  Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
16P GAIN MUTATED 12 1 2
16P GAIN WILD-TYPE 138 172 168

Figure S64.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.14

Table S65.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
16P GAIN MUTATED 11 2 2
16P GAIN WILD-TYPE 114 203 161

Figure S65.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S66.  Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
16P GAIN MUTATED 13 0 2
16P GAIN WILD-TYPE 150 169 159

Figure S66.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S67.  Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
16P GAIN MUTATED 12 1 1 1
16P GAIN WILD-TYPE 111 186 104 77

Figure S67.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S68.  Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
16Q GAIN MUTATED 13 0 0
16Q GAIN WILD-TYPE 21 383 77

Figure S68.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.046

Table S69.  Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
16Q GAIN MUTATED 1 11 1
16Q GAIN WILD-TYPE 272 140 69

Figure S69.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.084

Table S70.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
16Q GAIN MUTATED 10 1 2
16Q GAIN WILD-TYPE 115 204 161

Figure S70.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.088

Table S71.  Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
16Q GAIN MUTATED 11 0 2
16Q GAIN WILD-TYPE 152 169 159

Figure S71.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.2

Table S72.  Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
16Q GAIN MUTATED 10 1 1 1
16Q GAIN WILD-TYPE 113 186 104 77

Figure S72.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S73.  Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
17P GAIN MUTATED 12 2 2
17P GAIN WILD-TYPE 22 381 75

Figure S73.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S74.  Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
17P GAIN MUTATED 1 15 0
17P GAIN WILD-TYPE 272 136 70

Figure S74.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S75.  Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
17P GAIN MUTATED 15 0 1 0
17P GAIN WILD-TYPE 139 55 115 167

Figure S75.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S76.  Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
17P GAIN MUTATED 15 0 1 0 0
17P GAIN WILD-TYPE 111 100 72 115 78

Figure S76.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S77.  Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
17P GAIN MUTATED 14 1 1
17P GAIN WILD-TYPE 136 172 169

Figure S77.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S78.  Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
17P GAIN MUTATED 14 1 1
17P GAIN WILD-TYPE 111 204 162

Figure S78.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S79.  Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
17P GAIN MUTATED 15 0 1
17P GAIN WILD-TYPE 148 169 160

Figure S79.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S80.  Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
17P GAIN MUTATED 14 1 1 0
17P GAIN WILD-TYPE 109 186 104 78

Figure S80.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S81.  Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
17Q GAIN MUTATED 13 2 3
17Q GAIN WILD-TYPE 21 381 74

Figure S81.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S82.  Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
17Q GAIN MUTATED 2 16 0
17Q GAIN WILD-TYPE 271 135 70

Figure S82.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S83.  Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
17Q GAIN MUTATED 16 0 1 1
17Q GAIN WILD-TYPE 138 55 115 166

Figure S83.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S84.  Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
17Q GAIN MUTATED 16 0 1 1 0
17Q GAIN WILD-TYPE 110 100 72 114 78

Figure S84.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S85.  Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
17Q GAIN MUTATED 15 2 1
17Q GAIN WILD-TYPE 135 171 169

Figure S85.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S86.  Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
17Q GAIN MUTATED 15 1 2
17Q GAIN WILD-TYPE 110 204 161

Figure S86.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S87.  Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
17Q GAIN MUTATED 16 1 1
17Q GAIN WILD-TYPE 147 168 160

Figure S87.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S88.  Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
17Q GAIN MUTATED 15 1 1 1
17Q GAIN WILD-TYPE 108 186 104 77

Figure S88.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S89.  Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
18P GAIN MUTATED 5 0 1
18P GAIN WILD-TYPE 29 383 76

Figure S89.  Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S90.  Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
18Q GAIN MUTATED 5 0 1
18Q GAIN WILD-TYPE 29 383 76

Figure S90.  Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S91.  Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 26 383 77

Figure S91.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.084

Table S92.  Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 273 143 70

Figure S92.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.23

Table S93.  Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
19P GAIN MUTATED 8 0 0 0
19P GAIN WILD-TYPE 146 55 116 167

Figure S93.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.057

Table S94.  Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
19P GAIN MUTATED 8 0 0 0 0
19P GAIN WILD-TYPE 118 100 73 115 78

Figure S94.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.042

Table S95.  Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 142 173 170

Figure S95.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S96.  Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 117 205 163

Figure S96.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S97.  Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 155 169 161

Figure S97.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S98.  Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
19P GAIN MUTATED 8 0 0 0
19P GAIN WILD-TYPE 115 187 105 78

Figure S98.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S99.  Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
19Q GAIN MUTATED 9 0 1
19Q GAIN WILD-TYPE 25 383 76

Figure S99.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S100.  Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 273 141 70

Figure S100.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.049

Table S101.  Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
19Q GAIN MUTATED 10 0 0 0
19Q GAIN WILD-TYPE 144 55 116 167

Figure S101.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S102.  Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
19Q GAIN MUTATED 10 0 0 0 0
19Q GAIN WILD-TYPE 116 100 73 115 78

Figure S102.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S103.  Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
19Q GAIN MUTATED 10 0 0
19Q GAIN WILD-TYPE 140 173 170

Figure S103.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S104.  Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
19Q GAIN MUTATED 10 0 0
19Q GAIN WILD-TYPE 115 205 163

Figure S104.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S105.  Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
19Q GAIN MUTATED 10 0 0
19Q GAIN WILD-TYPE 153 169 161

Figure S105.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S106.  Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
19Q GAIN MUTATED 10 0 0 0
19Q GAIN WILD-TYPE 113 187 105 78

Figure S106.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S107.  Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
20P GAIN MUTATED 12 0 0
20P GAIN WILD-TYPE 22 383 77

Figure S107.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.098

Table S108.  Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
20P GAIN MUTATED 1 10 1
20P GAIN WILD-TYPE 272 141 69

Figure S108.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.16

Table S109.  Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
20P GAIN MUTATED 10 0 1 1 0
20P GAIN WILD-TYPE 116 100 72 114 78

Figure S109.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.17

Table S110.  Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
20P GAIN MUTATED 9 1 2
20P GAIN WILD-TYPE 116 204 161

Figure S110.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.14

Table S111.  Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
20P GAIN MUTATED 10 0 2
20P GAIN WILD-TYPE 153 169 159

Figure S111.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S112.  Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
20Q GAIN MUTATED 12 0 0
20Q GAIN WILD-TYPE 22 383 77

Figure S112.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S113.  Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
20Q GAIN MUTATED 1 10 1
20Q GAIN WILD-TYPE 272 141 69

Figure S113.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S114.  Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
20Q GAIN MUTATED 10 0 1 1 0
20Q GAIN WILD-TYPE 116 100 72 114 78

Figure S114.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S115.  Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
20Q GAIN MUTATED 9 1 2
20Q GAIN WILD-TYPE 116 204 161

Figure S115.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.14

Table S116.  Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
20Q GAIN MUTATED 10 0 2
20Q GAIN WILD-TYPE 153 169 159

Figure S116.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S117.  Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
21Q GAIN MUTATED 4 0 1
21Q GAIN WILD-TYPE 30 383 76

Figure S117.  Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S118.  Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
XQ GAIN MUTATED 7 2 0
XQ GAIN WILD-TYPE 27 381 77

Figure S118.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S119.  Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
1P LOSS MUTATED 4 0 0
1P LOSS WILD-TYPE 30 383 77

Figure S119.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.14

Table S120.  Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
1Q LOSS MUTATED 3 0 0
1Q LOSS WILD-TYPE 31 383 77

Figure S120.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S121.  Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
2P LOSS MUTATED 9 0 1
2P LOSS WILD-TYPE 25 383 76

Figure S121.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S122.  Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 273 141 70

Figure S122.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.034

Table S123.  Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
2P LOSS MUTATED 10 0 0 0
2P LOSS WILD-TYPE 144 55 116 167

Figure S123.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S124.  Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
2P LOSS MUTATED 10 0 0 0 0
2P LOSS WILD-TYPE 116 100 73 115 78

Figure S124.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S125.  Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
2P LOSS MUTATED 10 0 0
2P LOSS WILD-TYPE 140 173 170

Figure S125.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S126.  Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
2P LOSS MUTATED 10 0 0
2P LOSS WILD-TYPE 115 205 163

Figure S126.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S127.  Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
2P LOSS MUTATED 10 0 0
2P LOSS WILD-TYPE 153 169 161

Figure S127.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S128.  Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
2P LOSS MUTATED 10 0 0 0
2P LOSS WILD-TYPE 113 187 105 78

Figure S128.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S129.  Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 24 383 77

Figure S129.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S130.  Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 273 141 70

Figure S130.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.034

Table S131.  Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
2Q LOSS MUTATED 10 0 0 0
2Q LOSS WILD-TYPE 144 55 116 167

Figure S131.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S132.  Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
2Q LOSS MUTATED 10 0 0 0 0
2Q LOSS WILD-TYPE 116 100 73 115 78

Figure S132.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S133.  Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 140 173 170

Figure S133.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S134.  Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 115 205 163

Figure S134.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S135.  Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 153 169 161

Figure S135.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S136.  Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
2Q LOSS MUTATED 10 0 0 0
2Q LOSS WILD-TYPE 113 187 105 78

Figure S136.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S137.  Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
3P LOSS MUTATED 3 0 0
3P LOSS WILD-TYPE 31 383 77

Figure S137.  Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S138.  Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
3Q LOSS MUTATED 4 0 0
3Q LOSS WILD-TYPE 30 383 77

Figure S138.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S139.  Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
6Q LOSS MUTATED 5 2 0
6Q LOSS WILD-TYPE 29 381 77

Figure S139.  Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S140.  Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 30 383 77

Figure S140.  Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S141.  Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 30 383 77

Figure S141.  Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S142.  Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
9P LOSS MUTATED 13 5 1
9P LOSS WILD-TYPE 21 378 76

Figure S142.  Get High-res Image Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S143.  Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
9Q LOSS MUTATED 16 7 1
9Q LOSS WILD-TYPE 18 376 76

Figure S143.  Get High-res Image Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S144.  Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
10P LOSS MUTATED 7 0 0
10P LOSS WILD-TYPE 27 383 77

Figure S144.  Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S145.  Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
10Q LOSS MUTATED 6 0 0
10Q LOSS WILD-TYPE 28 383 77

Figure S145.  Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S146.  Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11P LOSS MUTATED 6 0 1
11P LOSS WILD-TYPE 28 383 76

Figure S146.  Get High-res Image Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S147.  Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11Q LOSS MUTATED 6 2 1
11Q LOSS WILD-TYPE 28 381 76

Figure S147.  Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.12

Table S148.  Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
11Q LOSS MUTATED 8 0 1
11Q LOSS WILD-TYPE 142 173 169

Figure S148.  Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.042

Table S149.  Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
15Q LOSS MUTATED 5 2 1
15Q LOSS WILD-TYPE 29 381 76

Figure S149.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.065

Table S150.  Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 273 143 70

Figure S150.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S151.  Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
15Q LOSS MUTATED 8 0 0 0
15Q LOSS WILD-TYPE 146 55 116 167

Figure S151.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.065

Table S152.  Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
15Q LOSS MUTATED 8 0 0 0 0
15Q LOSS WILD-TYPE 118 100 73 115 78

Figure S152.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.038

Table S153.  Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
15Q LOSS MUTATED 8 0 0
15Q LOSS WILD-TYPE 142 173 170

Figure S153.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S154.  Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
15Q LOSS MUTATED 8 0 0
15Q LOSS WILD-TYPE 117 205 163

Figure S154.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.088

Table S155.  Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
15Q LOSS MUTATED 8 0 0
15Q LOSS WILD-TYPE 155 169 161

Figure S155.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S156.  Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
15Q LOSS MUTATED 8 0 0 0
15Q LOSS WILD-TYPE 115 187 105 78

Figure S156.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S157.  Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
18P LOSS MUTATED 3 0 1
18P LOSS WILD-TYPE 31 383 76

Figure S157.  Get High-res Image Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.069

Table S158.  Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
18Q LOSS MUTATED 3 0 1
18Q LOSS WILD-TYPE 31 383 76

Figure S158.  Get High-res Image Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S159.  Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
21Q LOSS MUTATED 5 2 1
21Q LOSS WILD-TYPE 29 381 76

Figure S159.  Get High-res Image Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S160.  Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
22Q LOSS MUTATED 9 0 77
22Q LOSS WILD-TYPE 25 383 0

Figure S160.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S161.  Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 151 70
22Q LOSS MUTATED 35 45 6
22Q LOSS WILD-TYPE 238 106 64

Figure S161.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S162.  Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 55 116 167
22Q LOSS MUTATED 45 8 26 7
22Q LOSS WILD-TYPE 109 47 90 160

Figure S162.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S163.  Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 126 100 73 115 78
22Q LOSS MUTATED 40 13 22 9 2
22Q LOSS WILD-TYPE 86 87 51 106 76

Figure S163.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.073

Table S164.  Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 205 163
22Q LOSS MUTATED 38 28 20
22Q LOSS WILD-TYPE 87 177 143

Figure S164.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S165.  Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
22Q LOSS MUTATED 49 18 19
22Q LOSS WILD-TYPE 114 151 142

Figure S165.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S166.  Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 187 105 78
22Q LOSS MUTATED 38 26 18 4
22Q LOSS WILD-TYPE 85 161 87 74

Figure S166.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = THCA-TP.transferedmergedcluster.txt

  • Number of patients = 494

  • Number of significantly arm-level cnvs = 57

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)