Correlation between copy number variations of arm-level result and molecular subtypes
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 501 patients, 134 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

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

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

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q 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', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 13q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

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

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 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'.

  • 13q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  '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, 134 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
22q loss 89 (18%) 412 1e-05
(0.00534) 		1e-05
(0.00534) 		0.116
(1.00) 		0.503
(1.00) 		1e-05
(0.00534) 		1e-05
(0.00534) 		0.00035
(0.144) 		5e-05
(0.023) 		0.00017
(0.0731) 		0.00023
(0.0966)
7q gain 20 (4%) 481 1e-05
(0.00534) 		1e-05
(0.00534) 		0.572
(1.00) 		0.0141
(1.00) 		0.0001
(0.0445) 		4e-05
(0.0187) 		7e-05
(0.0316) 		1e-05
(0.00534) 		0.612
(1.00) 		0.00062
(0.249)
17p gain 16 (3%) 485 1e-05
(0.00534) 		1e-05
(0.00534) 		0.538
(1.00) 		0.0278
(1.00) 		1e-05
(0.00534) 		1e-05
(0.00534) 		2e-05
(0.00962) 		1e-05
(0.00534) 		0.358
(1.00) 		0.00024
(0.1)
17q gain 18 (4%) 483 1e-05
(0.00534) 		1e-05
(0.00534) 		0.635
(1.00) 		0.0153
(1.00) 		1e-05
(0.00534) 		1e-05
(0.00534) 		2e-05
(0.00962) 		1e-05
(0.00534) 		0.513
(1.00) 		0.00027
(0.112)
2p loss 10 (2%) 491 1e-05
(0.00534) 		3e-05
(0.0141) 		0.775
(1.00) 		0.092
(1.00) 		8e-05
(0.0358) 		2e-05
(0.00962) 		1e-05
(0.00534) 		2e-05
(0.00962) 		0.235
(1.00) 		0.00036
(0.148)
2q loss 10 (2%) 491 1e-05
(0.00534) 		2e-05
(0.00962) 		0.773
(1.00) 		0.0893
(1.00) 		0.00013
(0.0573) 		5e-05
(0.023) 		1e-05
(0.00534) 		1e-05
(0.00534) 		0.234
(1.00) 		0.00056
(0.226)
5q gain 17 (3%) 484 1e-05
(0.00534) 		5e-05
(0.023) 		0.849
(1.00) 		0.0795
(1.00) 		0.00013
(0.0573) 		3e-05
(0.0141) 		0.0002
(0.0848) 		1e-05
(0.00534) 		0.84
(1.00) 		0.00425
(1.00)
12p gain 14 (3%) 487 1e-05
(0.00534) 		1e-05
(0.00534) 		0.85
(1.00) 		0.0811
(1.00) 		2e-05
(0.00962) 		1e-05
(0.00534) 		6e-05
(0.0271) 		1e-05
(0.00534) 		0.552
(1.00) 		0.00242
(0.888)
12q gain 15 (3%) 486 1e-05
(0.00534) 		1e-05
(0.00534) 		0.851
(1.00) 		0.0789
(1.00) 		1e-05
(0.00534) 		1e-05
(0.00534) 		3e-05
(0.0141) 		1e-05
(0.00534) 		0.383
(1.00) 		0.00086
(0.337)
14q gain 11 (2%) 490 1e-05
(0.00534) 		0.00022
(0.0931) 		1
(1.00) 		0.158
(1.00) 		0.00049
(0.2) 		9e-05
(0.0401) 		0.0006
(0.242) 		5e-05
(0.023) 		0.852
(1.00) 		0.00201
(0.748)
16p gain 15 (3%) 486 1e-05
(0.00534) 		4e-05
(0.0187) 		0.633
(1.00) 		0.0796
(1.00) 		0.00018
(0.077) 		5e-05
(0.023) 		0.00015
(0.0657) 		1e-05
(0.00534) 		0.435
(1.00) 		0.00076
(0.3)
19q gain 10 (2%) 491 1e-05
(0.00534) 		2e-05
(0.00962) 		0.635
(1.00) 		0.0642
(1.00) 		0.0001
(0.0445) 		4e-05
(0.0187) 		2e-05
(0.00962) 		1e-05
(0.00534) 		0.637
(1.00) 		0.0016
(0.603)
15q loss 8 (2%) 493 0.00023
(0.0966) 		0.00022
(0.0931) 		0.193
(1.00) 		0.0879
(1.00) 		0.00048
(0.196) 		0.00026
(0.108) 		7e-05
(0.0316) 		5e-05
(0.023) 		0.407
(1.00) 		0.00154
(0.585)
7p gain 18 (4%) 483 1e-05
(0.00534) 		5e-05
(0.023) 		0.659
(1.00) 		0.0524
(1.00) 		0.00065
(0.259) 		0.00013
(0.0573) 		0.00034
(0.14) 		4e-05
(0.0187) 		0.578
(1.00) 		0.00538
(1.00)
19p gain 8 (2%) 493 1e-05
(0.00534) 		0.00019
(0.0809) 		0.00063
(0.252) 		0.00022
(0.0931) 		7e-05
(0.0316) 		2e-05
(0.00962) 		0.449
(1.00) 		0.0226
(1.00)
16q gain 13 (3%) 488 1e-05
(0.00534) 		0.00016
(0.0696) 		0.797
(1.00) 		0.276
(1.00) 		0.00094
(0.367) 		0.00031
(0.129) 		0.00181
(0.679) 		0.00017
(0.0731) 		0.617
(1.00) 		0.00789
(1.00)
5p gain 21 (4%) 480 1e-05
(0.00534) 		0.00198
(0.739) 		0.529
(1.00) 		0.233
(1.00) 		0.00517
(1.00) 		0.00011
(0.0486) 		0.001
(0.389) 		0.0001
(0.0445) 		0.598
(1.00) 		0.00366
(1.00)
20p gain 12 (2%) 489 1e-05
(0.00534) 		0.00032
(0.132) 		0.796
(1.00) 		0.0929
(1.00) 		0.00257
(0.935) 		0.0009
(0.352) 		0.00453
(1.00) 		0.00049
(0.2) 		0.913
(1.00) 		0.095
(1.00)
1q gain 26 (5%) 475 1e-05
(0.00534) 		0.0166
(1.00) 		0.00281
(1.00) 		0.0645
(1.00) 		0.00112
(0.431) 		7e-05
(0.0316) 		0.0859
(1.00) 		0.0506
(1.00) 		0.0133
(1.00) 		0.0156
(1.00)
20q gain 12 (2%) 489 1e-05
(0.00534) 		0.00044
(0.18) 		0.795
(1.00) 		0.0927
(1.00) 		0.00251
(0.916) 		0.00067
(0.267) 		0.00426
(1.00) 		0.00077
(0.303) 		0.915
(1.00) 		0.0931
(1.00)
6q loss 7 (1%) 494 4e-05
(0.0187) 		0.00219
(0.808) 		0.0131
(1.00) 		0.574
(1.00) 		0.0272
(1.00) 		0.0181
(1.00) 		0.00489
(1.00) 		0.0006
(0.242) 		1
(1.00) 		0.00995
(1.00)
11q loss 9 (2%) 492 1e-05
(0.00534) 		0.0158
(1.00) 		0.319
(1.00) 		0.812
(1.00) 		0.0152
(1.00) 		0.0184
(1.00) 		0.00051
(0.207) 		0.00248
(0.908) 		0.908
(1.00) 		0.00201
(0.748)
4p gain 5 (1%) 496 1e-05
(0.00534) 		0.00645
(1.00) 		0.0164
(1.00) 		0.0126
(1.00) 		0.0416
(1.00) 		0.0147
(1.00) 		1
(1.00) 		0.0767
(1.00)
4q gain 5 (1%) 496 5e-05
(0.023) 		0.00676
(1.00) 		0.0171
(1.00) 		0.0123
(1.00) 		0.0404
(1.00) 		0.0142
(1.00) 		1
(1.00) 		0.0772
(1.00)
8p gain 6 (1%) 495 0.00015
(0.0657) 		0.416
(1.00) 		0.455
(1.00) 		0.629
(1.00) 		0.597
(1.00) 		0.536
(1.00) 		0.454
(1.00) 		0.452
(1.00) 		1
(1.00) 		1
(1.00)
8q gain 7 (1%) 494 2e-05
(0.00962) 		0.202
(1.00) 		0.455
(1.00) 		0.633
(1.00) 		0.83
(1.00) 		0.52
(1.00) 		0.8
(1.00) 		0.63
(1.00) 		0.9
(1.00) 		0.897
(1.00)
11q gain 5 (1%) 496 0.00016
(0.0696) 		0.0604
(1.00) 		0.779
(1.00) 		0.3
(1.00) 		0.11
(1.00) 		0.124
(1.00) 		0.0264
(1.00) 		0.0225
(1.00) 		0.311
(1.00) 		0.273
(1.00)
13q gain 5 (1%) 496 4e-05
(0.0187) 		0.0189
(1.00) 		0.38
(1.00) 		0.213
(1.00) 		0.0492
(1.00) 		0.102
(1.00) 		0.239
(1.00) 		0.0703
(1.00) 		0.844
(1.00) 		0.197
(1.00)
18p gain 6 (1%) 495 5e-05
(0.023) 		0.0919
(1.00) 		0.122
(1.00) 		0.267
(1.00) 		0.256
(1.00) 		0.111
(1.00) 		0.454
(1.00) 		0.399
(1.00)
18q gain 6 (1%) 495 3e-05
(0.0141) 		0.092
(1.00) 		0.12
(1.00) 		0.265
(1.00) 		0.254
(1.00) 		0.114
(1.00) 		0.454
(1.00) 		0.393
(1.00)
21q gain 5 (1%) 496 0.00015
(0.0657) 		0.169
(1.00) 		0.238
(1.00) 		0.488
(1.00) 		0.453
(1.00) 		0.312
(1.00) 		0.692
(1.00) 		0.681
(1.00)
xq gain 9 (2%) 492 1e-05
(0.00534) 		0.011
(1.00) 		0.838
(1.00) 		0.501
(1.00) 		0.0974
(1.00) 		0.141
(1.00) 		0.277
(1.00) 		0.133
(1.00) 		0.908
(1.00) 		0.398
(1.00)
1p loss 4 (1%) 497 0.00019
(0.0809) 		0.186
(1.00) 		0.243
(1.00) 		0.316
(1.00) 		0.115
(1.00) 		0.0663
(1.00) 		0.845
(1.00) 		0.195
(1.00)
3q loss 4 (1%) 497 0.00016
(0.0696) 		0.0181
(1.00) 		0.495
(1.00) 		0.42
(1.00) 		0.0372
(1.00) 		0.0478
(1.00) 		0.00878
(1.00) 		0.00408
(1.00) 		1
(1.00) 		0.0669
(1.00)
6p loss 4 (1%) 497 0.00016
(0.0696) 		0.0457
(1.00) 		0.46
(1.00) 		0.399
(1.00) 		0.115
(1.00) 		0.0675
(1.00) 		0.401
(1.00) 		0.195
(1.00)
8p loss 4 (1%) 497 0.00018
(0.077) 		0.0181
(1.00) 		0.0358
(1.00) 		0.0471
(1.00) 		0.00784
(1.00) 		0.00398
(1.00) 		0.11
(1.00) 		0.0186
(1.00)
8q loss 4 (1%) 497 0.00016
(0.0696) 		0.0182
(1.00) 		0.0355
(1.00) 		0.0464
(1.00) 		0.00841
(1.00) 		0.0039
(1.00) 		0.11
(1.00) 		0.0192
(1.00)
9p loss 19 (4%) 482 1e-05
(0.00534) 		0.0377
(1.00) 		0.243
(1.00) 		0.648
(1.00) 		0.0312
(1.00) 		0.0624
(1.00) 		0.00879
(1.00) 		0.00706
(1.00) 		0.303
(1.00) 		0.00387
(1.00)
9q loss 25 (5%) 476 1e-05
(0.00534) 		0.104
(1.00) 		0.172
(1.00) 		0.116
(1.00) 		0.171
(1.00) 		0.0628
(1.00) 		0.00979
(1.00) 		0.00637
(1.00) 		0.279
(1.00) 		0.00499
(1.00)
10p loss 7 (1%) 494 1e-05
(0.00534) 		0.0111
(1.00) 		0.493
(1.00) 		0.42
(1.00) 		0.0195
(1.00) 		0.0153
(1.00) 		0.00466
(1.00) 		0.00069
(0.274) 		1
(1.00) 		0.0103
(1.00)
10q loss 6 (1%) 495 1e-05
(0.00534) 		0.0291
(1.00) 		0.0516
(1.00) 		0.044
(1.00) 		0.0144
(1.00) 		0.00439
(1.00) 		1
(1.00) 		0.0287
(1.00)
11p loss 7 (1%) 494 1e-05
(0.00534) 		0.0113
(1.00) 		0.494
(1.00) 		0.958
(1.00) 		0.00722
(1.00) 		0.0186
(1.00) 		0.00477
(1.00) 		0.00074
(0.293) 		0.798
(1.00) 		0.0109
(1.00)
13q loss 14 (3%) 487 0.00164
(0.617) 		0.015
(1.00) 		0.0611
(1.00) 		0.139
(1.00) 		0.00547
(1.00) 		0.00864
(1.00) 		0.00108
(0.418) 		0.00055
(0.223) 		0.104
(1.00) 		0.013
(1.00)
1p gain 5 (1%) 496 0.00105
(0.407) 		0.839
(1.00) 		0.922
(1.00) 		0.881
(1.00) 		0.108
(1.00) 		0.0516
(1.00) 		0.276
(1.00) 		0.142
(1.00)
3p gain 3 (1%) 498 0.00159
(0.601) 		0.548
(1.00) 		0.496
(1.00) 		0.592
(1.00) 		0.305
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.193
(1.00)
9p gain 3 (1%) 498 0.00143
(0.545) 		0.55
(1.00) 		0.495
(1.00) 		0.588
(1.00) 		1
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.632
(1.00)
9q gain 4 (1%) 497 0.011
(1.00) 		0.793
(1.00) 		0.9
(1.00) 		0.361
(1.00) 		0.839
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.568
(1.00)
11p gain 6 (1%) 495 0.00112
(0.431) 		0.0284
(1.00) 		0.779
(1.00) 		0.301
(1.00) 		0.0538
(1.00) 		0.0442
(1.00) 		0.00893
(1.00) 		0.00685
(1.00) 		0.468
(1.00) 		0.0977
(1.00)
1q loss 3 (1%) 498 0.00137
(0.523) 		0.0505
(1.00) 		0.0972
(1.00) 		0.154
(1.00) 		0.028
(1.00) 		0.0176
(1.00) 		1
(1.00) 		0.19
(1.00)
3p loss 3 (1%) 498 0.00123
(0.471) 		0.0489
(1.00) 		0.0995
(1.00) 		0.152
(1.00) 		0.0266
(1.00) 		0.0162
(1.00) 		1
(1.00) 		0.192
(1.00)
17p loss 8 (2%) 493 0.0145
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.391
(1.00) 		0.638
(1.00) 		0.599
(1.00) 		0.0919
(1.00) 		0.162
(1.00) 		0.129
(1.00) 		0.205
(1.00)
17q loss 4 (1%) 497 0.113
(1.00) 		0.79
(1.00) 		0.901
(1.00) 		0.666
(1.00) 		0.466
(1.00) 		0.568
(1.00) 		0.331
(1.00) 		0.684
(1.00)
18p loss 4 (1%) 497 0.00191
(0.714) 		0.183
(1.00) 		1
(1.00) 		0.388
(1.00) 		0.245
(1.00) 		0.316
(1.00) 		0.0758
(1.00) 		0.0923
(1.00) 		0.531
(1.00) 		0.273
(1.00)
18q loss 4 (1%) 497 0.0021
(0.777) 		0.185
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.246
(1.00) 		0.318
(1.00) 		0.0723
(1.00) 		0.0906
(1.00) 		0.534
(1.00) 		0.277
(1.00)
19p loss 5 (1%) 496 0.00915
(1.00) 		0.00743
(1.00) 		0.321
(1.00) 		0.237
(1.00) 		0.017
(1.00) 		0.0125
(1.00) 		0.00239
(0.88) 		0.00108
(0.418) 		0.0876
(1.00) 		0.00155
(0.587)
21q loss 8 (2%) 493 0.0008
(0.314) 		0.163
(1.00) 		0.384
(1.00) 		0.215
(1.00) 		0.711
(1.00) 		0.42
(1.00) 		0.0932
(1.00) 		0.0291
(1.00) 		0.46
(1.00) 		0.0545
(1.00)
xq loss 3 (1%) 498 0.0507
(1.00) 		0.049
(1.00) 		0.28
(1.00) 		0.199
(1.00) 		0.0989
(1.00) 		0.151
(1.00) 		0.0276
(1.00) 		0.0165
(1.00) 		0.111
(1.00) 		0.019
(1.00)
'1q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
1Q GAIN MUTATED 18 7 1
1Q GAIN WILD-TYPE 38 349 88

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
1Q GAIN MUTATED 16 2 1 3 4
1Q GAIN WILD-TYPE 89 132 85 93 74

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

'4p gain' versus 'CN_CNMF'

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

Table S3.  Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
4P GAIN MUTATED 5 0 0
4P GAIN WILD-TYPE 51 356 89

Figure S3.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S4.  Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
4Q GAIN MUTATED 5 0 0
4Q GAIN WILD-TYPE 51 356 89

Figure S4.  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 S5.  Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
5P GAIN MUTATED 21 0 0
5P GAIN WILD-TYPE 35 356 89

Figure S5.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.049

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
5P GAIN MUTATED 6 14 0 1 0
5P GAIN WILD-TYPE 99 120 86 95 78

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
5P GAIN MUTATED 7 13 1
5P GAIN WILD-TYPE 172 115 192

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

'5q gain' versus 'CN_CNMF'

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

Table S8.  Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
5Q GAIN MUTATED 17 0 0
5Q GAIN WILD-TYPE 39 356 89

Figure S8.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S9.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
5Q GAIN MUTATED 2 14 1
5Q GAIN WILD-TYPE 275 140 69

Figure S9.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
5Q GAIN MUTATED 2 14 0 1
5Q GAIN WILD-TYPE 166 141 59 116

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S11.  Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
5Q GAIN MUTATED 2 14 0 1 0
5Q GAIN WILD-TYPE 103 120 86 95 78

Figure S11.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 179 138 166

Figure S12.  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 S13.  Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 176 115 192

Figure S13.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

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

Table S14.  Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
7P GAIN MUTATED 18 0 0
7P GAIN WILD-TYPE 38 356 89

Figure S14.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S15.  Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
7P GAIN MUTATED 2 14 2
7P GAIN WILD-TYPE 275 140 68

Figure S15.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

Table S16.  Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
7P GAIN MUTATED 2 14 1 1 0
7P GAIN WILD-TYPE 103 120 85 95 78

Figure S16.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 178 138 166

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 175 115 192

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

'7q gain' versus 'CN_CNMF'

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

Table S19.  Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
7Q GAIN MUTATED 19 0 1
7Q GAIN WILD-TYPE 37 356 88

Figure S19.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

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

Table S20.  Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
7Q GAIN MUTATED 2 16 2
7Q GAIN WILD-TYPE 275 138 68

Figure S20.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S21.  Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
7Q GAIN MUTATED 2 16 1 1
7Q GAIN WILD-TYPE 166 139 58 116

Figure S21.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S22.  Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
7Q GAIN MUTATED 2 16 1 1 0
7Q GAIN WILD-TYPE 103 118 85 95 78

Figure S22.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S23.  Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 178 136 166

Figure S23.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S24.  Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 175 113 192

Figure S24.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.25

Table S25.  Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
7Q GAIN MUTATED 5 11 1
7Q GAIN WILD-TYPE 160 115 178

Figure S25.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S26.  Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8P GAIN MUTATED 5 1 0
8P GAIN WILD-TYPE 51 355 89

Figure S26.  Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S27.  Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8Q GAIN MUTATED 6 1 0
8Q GAIN WILD-TYPE 50 355 89

Figure S27.  Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S28.  Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11Q GAIN MUTATED 4 0 1
11Q GAIN WILD-TYPE 52 356 88

Figure S28.  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 S29.  Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
12P GAIN MUTATED 13 0 1
12P GAIN WILD-TYPE 43 356 88

Figure S29.  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 S30.  Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
12P GAIN MUTATED 1 13 0
12P GAIN WILD-TYPE 276 141 70

Figure S30.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S31.  Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
12P GAIN MUTATED 0 13 0 1
12P GAIN WILD-TYPE 168 142 59 116

Figure S31.  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 S32.  Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
12P GAIN MUTATED 0 13 0 1 0
12P GAIN WILD-TYPE 105 121 86 95 78

Figure S32.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S33.  Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
12P GAIN MUTATED 1 12 1
12P GAIN WILD-TYPE 181 139 166

Figure S33.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S34.  Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
12P GAIN MUTATED 1 12 1
12P GAIN WILD-TYPE 178 116 192

Figure S34.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

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

Table S35.  Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
12Q GAIN MUTATED 14 0 1
12Q GAIN WILD-TYPE 42 356 88

Figure S35.  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 S36.  Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
12Q GAIN MUTATED 1 14 0
12Q GAIN WILD-TYPE 276 140 70

Figure S36.  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 S37.  Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
12Q GAIN MUTATED 0 14 0 1
12Q GAIN WILD-TYPE 168 141 59 116

Figure S37.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S38.  Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
12Q GAIN MUTATED 0 14 0 1 0
12Q GAIN WILD-TYPE 105 120 86 95 78

Figure S38.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

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

Table S39.  Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 181 138 166

Figure S39.  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 S40.  Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 178 115 192

Figure S40.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S41.  Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
13Q GAIN MUTATED 5 0 0
13Q GAIN WILD-TYPE 51 356 89

Figure S41.  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 S42.  Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
14Q GAIN MUTATED 10 0 1
14Q GAIN WILD-TYPE 46 356 88

Figure S42.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093

Table S43.  Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
14Q GAIN MUTATED 1 10 0
14Q GAIN WILD-TYPE 276 144 70

Figure S43.  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 = 0.2

Table S44.  Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
14Q GAIN MUTATED 1 10 0 0
14Q GAIN WILD-TYPE 167 145 59 117

Figure S44.  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 = 0.04

Table S45.  Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
14Q GAIN MUTATED 0 10 0 0 1
14Q GAIN WILD-TYPE 105 124 86 96 77

Figure S45.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.24

Table S46.  Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 180 142 167

Figure S46.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S47.  Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 177 119 193

Figure S47.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

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

Table S48.  Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
16P GAIN MUTATED 14 0 1
16P GAIN WILD-TYPE 42 356 88

Figure S48.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S49.  Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
16P GAIN MUTATED 1 13 1
16P GAIN WILD-TYPE 276 141 69

Figure S49.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.077

Table S50.  Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
16P GAIN MUTATED 1 13 0 1
16P GAIN WILD-TYPE 167 142 59 116

Figure S50.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S51.  Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
16P GAIN MUTATED 1 13 0 1 0
16P GAIN WILD-TYPE 104 121 86 95 78

Figure S51.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S52.  Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 180 139 166

Figure S52.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S53.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 177 116 192

Figure S53.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

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

Table S54.  Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
16Q GAIN MUTATED 13 0 0
16Q GAIN WILD-TYPE 43 356 89

Figure S54.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S55.  Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
16Q GAIN MUTATED 1 11 1
16Q GAIN WILD-TYPE 276 143 69

Figure S55.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S56.  Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
16Q GAIN MUTATED 1 11 0 1 0
16Q GAIN WILD-TYPE 104 123 86 95 78

Figure S56.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.073

Table S57.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
16Q GAIN MUTATED 2 10 1
16Q GAIN WILD-TYPE 177 118 192

Figure S57.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

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

Table S58.  Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
17P GAIN MUTATED 12 2 2
17P GAIN WILD-TYPE 44 354 87

Figure S58.  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 S59.  Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
17P GAIN MUTATED 1 15 0
17P GAIN WILD-TYPE 276 139 70

Figure S59.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

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

Table S60.  Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
17P GAIN MUTATED 0 15 0 1
17P GAIN WILD-TYPE 168 140 59 116

Figure S60.  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 S61.  Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
17P GAIN MUTATED 0 15 0 1 0
17P GAIN WILD-TYPE 105 119 86 95 78

Figure S61.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S62.  Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 181 137 166

Figure S62.  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 S63.  Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 178 114 192

Figure S63.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.1

Table S64.  Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
17P GAIN MUTATED 2 10 1
17P GAIN WILD-TYPE 163 116 178

Figure S64.  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 S65.  Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
17Q GAIN MUTATED 13 2 3
17Q GAIN WILD-TYPE 43 354 86

Figure S65.  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 S66.  Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
17Q GAIN MUTATED 2 16 0
17Q GAIN WILD-TYPE 275 138 70

Figure S66.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
17Q GAIN MUTATED 1 16 0 1
17Q GAIN WILD-TYPE 167 139 59 116

Figure S67.  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 S68.  Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
17Q GAIN MUTATED 1 16 0 1 0
17Q GAIN WILD-TYPE 104 118 86 95 78

Figure S68.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S69.  Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 180 136 166

Figure S69.  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 S70.  Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 177 113 192

Figure S70.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.11

Table S71.  Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
17Q GAIN MUTATED 3 11 1
17Q GAIN WILD-TYPE 162 115 178

Figure S71.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S72.  Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
18P GAIN MUTATED 5 0 1
18P GAIN WILD-TYPE 51 356 88

Figure S72.  Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

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

Table S73.  Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
18Q GAIN MUTATED 5 0 1
18Q GAIN WILD-TYPE 51 356 88

Figure S73.  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 S74.  Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 48 356 89

Figure S74.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.081

Table S75.  Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 277 146 70

Figure S75.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.093

Table S76.  Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
19P GAIN MUTATED 0 8 0 0 0
19P GAIN WILD-TYPE 105 126 86 96 78

Figure S76.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S77.  Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 182 143 167

Figure S77.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S78.  Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 179 120 193

Figure S78.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

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

Table S79.  Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
19Q GAIN MUTATED 10 0 0
19Q GAIN WILD-TYPE 46 356 89

Figure S79.  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 = 0.0096

Table S80.  Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 277 144 70

Figure S80.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S81.  Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
19Q GAIN MUTATED 0 10 0 0
19Q GAIN WILD-TYPE 168 145 59 117

Figure S81.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S82.  Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
19Q GAIN MUTATED 0 10 0 0 0
19Q GAIN WILD-TYPE 105 124 86 96 78

Figure S82.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S83.  Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 182 141 167

Figure S83.  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 S84.  Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 179 118 193

Figure S84.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

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

Table S85.  Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
20P GAIN MUTATED 12 0 0
20P GAIN WILD-TYPE 44 356 89

Figure S85.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.13

Table S86.  Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
20P GAIN MUTATED 1 10 1
20P GAIN WILD-TYPE 276 144 69

Figure S86.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.2

Table S87.  Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
20P GAIN MUTATED 2 9 1
20P GAIN WILD-TYPE 177 119 192

Figure S87.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S88.  Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
20Q GAIN MUTATED 12 0 0
20Q GAIN WILD-TYPE 44 356 89

Figure S88.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.18

Table S89.  Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
20Q GAIN MUTATED 1 10 1
20Q GAIN WILD-TYPE 276 144 69

Figure S89.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S90.  Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
21Q GAIN MUTATED 4 0 1
21Q GAIN WILD-TYPE 52 356 88

Figure S90.  Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

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

Table S91.  Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
XQ GAIN MUTATED 8 1 0
XQ GAIN WILD-TYPE 48 355 89

Figure S91.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.081

Table S92.  Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
1P LOSS MUTATED 4 0 0
1P LOSS WILD-TYPE 52 356 89

Figure S92.  Get High-res Image Gene #32: '1p 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 S93.  Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
2P LOSS MUTATED 9 0 1
2P LOSS WILD-TYPE 47 356 88

Figure S93.  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 S94.  Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 277 144 70

Figure S94.  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 = 0.036

Table S95.  Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
2P LOSS MUTATED 0 10 0 0
2P LOSS WILD-TYPE 168 145 59 117

Figure S95.  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 = 0.0096

Table S96.  Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
2P LOSS MUTATED 0 10 0 0 0
2P LOSS WILD-TYPE 105 124 86 96 78

Figure S96.  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 S97.  Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 182 141 167

Figure S97.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S98.  Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 179 118 193

Figure S98.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.15

Table S99.  Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
2P LOSS MUTATED 1 7 0
2P LOSS WILD-TYPE 164 119 179

Figure S99.  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 S100.  Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 46 356 89

Figure S100.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S101.  Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 277 144 70

Figure S101.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

Table S102.  Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
2Q LOSS MUTATED 0 10 0 0
2Q LOSS WILD-TYPE 168 145 59 117

Figure S102.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S103.  Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
2Q LOSS MUTATED 0 10 0 0 0
2Q LOSS WILD-TYPE 105 124 86 96 78

Figure S103.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

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

Table S104.  Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 182 141 167

Figure S104.  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 S105.  Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 179 118 193

Figure S105.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.23

Table S106.  Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
2Q LOSS MUTATED 1 7 0
2Q LOSS WILD-TYPE 164 119 179

Figure S106.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S107.  Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
3Q LOSS MUTATED 4 0 0
3Q LOSS WILD-TYPE 52 356 89

Figure S107.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S108.  Gene #38: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
6P LOSS MUTATED 4 0 0
6P LOSS WILD-TYPE 52 356 89

Figure S108.  Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S109.  Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
6Q LOSS MUTATED 6 1 0
6Q LOSS WILD-TYPE 50 355 89

Figure S109.  Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.24

Table S110.  Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 178 122 193

Figure S110.  Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.077

Table S111.  Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 52 356 89

Figure S111.  Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S112.  Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 52 356 89

Figure S112.  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 S113.  Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
9P LOSS MUTATED 15 2 2
9P LOSS WILD-TYPE 41 354 87

Figure S113.  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 S114.  Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
9Q LOSS MUTATED 20 2 3
9Q LOSS WILD-TYPE 36 354 86

Figure S114.  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 S115.  Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
10P LOSS MUTATED 7 0 0
10P LOSS WILD-TYPE 49 356 89

Figure S115.  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 S116.  Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
10Q LOSS MUTATED 6 0 0
10Q LOSS WILD-TYPE 50 356 89

Figure S116.  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 S117.  Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11P LOSS MUTATED 6 0 1
11P LOSS WILD-TYPE 50 356 88

Figure S117.  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 S118.  Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11Q LOSS MUTATED 7 1 1
11Q LOSS WILD-TYPE 49 355 88

Figure S118.  Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.21

Table S119.  Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
11Q LOSS MUTATED 1 8 0
11Q LOSS WILD-TYPE 181 143 167

Figure S119.  Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.22

Table S120.  Gene #48: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 179 119 188

Figure S120.  Get High-res Image Gene #48: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.097

Table S121.  Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
15Q LOSS MUTATED 5 1 2
15Q LOSS WILD-TYPE 51 355 87

Figure S121.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093

Table S122.  Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 277 146 70

Figure S122.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.2

Table S123.  Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
15Q LOSS MUTATED 0 8 0 0
15Q LOSS WILD-TYPE 168 147 59 117

Figure S123.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S124.  Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
15Q LOSS MUTATED 0 8 0 0 0
15Q LOSS WILD-TYPE 105 126 86 96 78

Figure S124.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S125.  Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 182 143 167

Figure S125.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S126.  Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 179 120 193

Figure S126.  Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

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

Table S127.  Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
22Q LOSS MUTATED 13 0 76
22Q LOSS WILD-TYPE 43 356 13

Figure S127.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

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

Table S128.  Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
22Q LOSS MUTATED 36 47 6
22Q LOSS WILD-TYPE 241 107 64

Figure S128.  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 S129.  Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
22Q LOSS MUTATED 8 47 8 26
22Q LOSS WILD-TYPE 160 108 51 91

Figure S129.  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 S130.  Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
22Q LOSS MUTATED 9 42 13 23 2
22Q LOSS WILD-TYPE 96 92 73 73 76

Figure S130.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.14

Table S131.  Gene #56: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
22Q LOSS MUTATED 23 43 23
22Q LOSS WILD-TYPE 159 108 144

Figure S131.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S132.  Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
22Q LOSS MUTATED 21 40 28
22Q LOSS WILD-TYPE 158 88 165

Figure S132.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.073

Table S133.  Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
22Q LOSS MUTATED 17 23 41
22Q LOSS WILD-TYPE 143 141 105

Figure S133.  Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.097

Table S134.  Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
22Q LOSS MUTATED 22 37 22
22Q LOSS WILD-TYPE 143 89 157

Figure S134.  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 = 501

  • 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.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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