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 subtypes.

Summary

Testing the association between copy number variation 45 arm-level results and 10 molecular subtypes across 497 patients, 128 significant findings detected with Q value < 0.25.

  • 1q 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',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 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', and 'MRNASEQ_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',  'MRNASEQ_CHIERARCHICAL',  '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'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

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

  • 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q 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'.

  • 15q loss cnv correlated to 'CN_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_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 45 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 128 significant findings detected.

Molecular
subtypes 		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
7q gain 0 (0%) 478 1.76e-23
(7.13e-21) 		3.65e-05
(0.0124) 		0.689
(1.00) 		0.00298
(0.752) 		5.06e-05
(0.0168) 		6.18e-06
(0.00224) 		0.000289
(0.0879) 		2.87e-05
(0.00992) 		0.0002
(0.0622) 		3.59e-05
(0.0122)
12p gain 0 (0%) 486 1.03e-12
(4.09e-10) 		2.87e-06
(0.00107) 		0.901
(1.00) 		0.0299
(1.00) 		1.6e-05
(0.00577) 		2.12e-06
(0.000794) 		5.19e-05
(0.0172) 		1.7e-05
(0.00606) 		3.43e-05
(0.0118) 		2e-05
(0.00701)
12q gain 0 (0%) 485 1.27e-12
(5.04e-10) 		6.48e-07
(0.000248) 		0.901
(1.00) 		0.0299
(1.00) 		4.46e-06
(0.00165) 		6.49e-07
(0.000248) 		1.64e-05
(0.00588) 		4.85e-06
(0.00179) 		6.11e-06
(0.00222) 		5.76e-06
(0.00211)
16p gain 0 (0%) 485 5.51e-14
(2.21e-11) 		3.21e-05
(0.011) 		1
(1.00) 		0.0445
(1.00) 		0.000132
(0.0422) 		2.69e-05
(0.00935) 		0.000214
(0.0657) 		5.88e-05
(0.0194) 		8.28e-05
(0.0271) 		8.35e-05
(0.0272)
17p gain 0 (0%) 485 2e-09
(7.81e-07) 		6.48e-07
(0.000248) 		0.772
(1.00) 		0.0179
(1.00) 		4.46e-06
(0.00165) 		6.49e-07
(0.000248) 		5.19e-05
(0.0172) 		1.7e-05
(0.00606) 		3.43e-05
(0.0118) 		2e-05
(0.00701)
17q gain 0 (0%) 484 3.83e-09
(1.49e-06) 		3.73e-07
(0.000143) 		0.795
(1.00) 		0.0206
(1.00) 		1.51e-06
(0.000569) 		1.6e-07
(6.15e-05) 		1.64e-05
(0.00588) 		4.85e-06
(0.00179) 		6.11e-06
(0.00222) 		5.76e-06
(0.00211)
2p loss 0 (0%) 489 5.02e-09
(1.95e-06) 		8.76e-05
(0.0285) 		1
(1.00) 		0.0817
(1.00) 		0.000325
(0.0975) 		0.000148
(0.0472) 		5.53e-05
(0.0182) 		2.27e-05
(0.0079) 		4.85e-05
(0.0162) 		2.81e-05
(0.00973)
22q loss 0 (0%) 431 6.79e-58
(2.76e-55) 		4.45e-05
(0.015) 		0.114
(1.00) 		0.0835
(1.00) 		2.26e-11
(8.89e-09) 		2.59e-11
(1.01e-08) 		4.33e-05
(0.0146) 		9.51e-06
(0.00343) 		3.93e-05
(0.0133) 		4.85e-06
(0.00179)
2q loss 0 (0%) 490 3.78e-09
(1.47e-06) 		0.000364
(0.108) 		0.837
(1.00) 		0.0549
(1.00) 		0.00153
(0.409) 		0.000534
(0.155) 		0.000192
(0.06) 		8.85e-05
(0.0286) 		0.000171
(0.0538) 		0.000107
(0.0342)
5q gain 0 (0%) 483 2.6e-18
(1.05e-15) 		4.02e-05
(0.0136) 		0.901
(1.00) 		0.0299
(1.00) 		0.000164
(0.0518) 		4.71e-05
(0.0158) 		0.00146
(0.392) 		0.000106
(0.0341) 		0.000991
(0.275) 		0.000119
(0.0379)
7p gain 0 (0%) 480 1.59e-22
(6.42e-20) 		0.000169
(0.0531) 		1
(1.00) 		0.0129
(1.00) 		0.00041
(0.121) 		6.05e-05
(0.0199) 		0.00232
(0.601) 		0.000272
(0.0829) 		0.00135
(0.367) 		0.000418
(0.122)
16q gain 0 (0%) 487 5.67e-13
(2.26e-10) 		0.000224
(0.0686) 		0.856
(1.00) 		0.129
(1.00) 		0.00131
(0.361) 		0.00039
(0.115) 		0.00169
(0.448) 		0.000547
(0.157) 		0.000713
(0.201) 		0.000758
(0.212)
15q loss 0 (0%) 490 0.000464
(0.135) 		0.00226
(0.594) 		0.458
(1.00) 		0.256
(1.00) 		0.00153
(0.409) 		0.000534
(0.155) 		0.000664
(0.189) 		0.000342
(0.102) 		0.000602
(0.172) 		0.000402
(0.118)
5p gain 0 (0%) 480 6.97e-20
(2.81e-17) 		0.000873
(0.244) 		1
(1.00) 		0.125
(1.00) 		0.00235
(0.607) 		0.000538
(0.156) 		0.00691
(1.00) 		0.000541
(0.156) 		0.00487
(1.00) 		0.00075
(0.211)
14q gain 0 (0%) 489 5.02e-09
(1.95e-06) 		8.76e-05
(0.0285) 		1
(1.00) 		0.256
(1.00) 		0.000325
(0.0975) 		0.000148
(0.0472) 		0.00467
(1.00) 		0.00229
(0.599) 		0.00291
(0.735) 		0.00256
(0.65)
20p gain 0 (0%) 488 1.11e-11
(4.37e-09) 		0.000706
(0.2) 		1
(1.00) 		0.0817
(1.00) 		0.00374
(0.939) 		0.00144
(0.391) 		0.0124
(1.00) 		0.00619
(1.00) 		0.00573
(1.00) 		0.00645
(1.00)
20q gain 0 (0%) 488 1.11e-11
(4.37e-09) 		0.000706
(0.2) 		1
(1.00) 		0.0817
(1.00) 		0.00374
(0.939) 		0.00144
(0.391) 		0.0124
(1.00) 		0.00619
(1.00) 		0.00573
(1.00) 		0.00645
(1.00)
1q gain 0 (0%) 476 3.29e-06
(0.00122) 		0.0744
(1.00) 		0.0153
(1.00) 		0.0826
(1.00) 		0.012
(1.00) 		0.00102
(0.283) 		0.224
(1.00) 		0.204
(1.00) 		0.177
(1.00) 		0.216
(1.00)
4p gain 0 (0%) 493 1.85e-05
(0.00655) 		0.0186
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.112
(1.00) 		0.0975
(1.00) 		0.0719
(1.00) 		0.101
(1.00)
4q gain 0 (0%) 493 1.85e-05
(0.00655) 		0.0186
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.112
(1.00) 		0.0975
(1.00) 		0.0719
(1.00) 		0.101
(1.00)
11q gain 0 (0%) 493 0.000204
(0.0633) 		0.0186
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.00778
(1.00) 		0.00503
(1.00) 		0.0073
(1.00) 		0.00558
(1.00)
13q gain 0 (0%) 494 0.000294
(0.0892) 		0.0489
(1.00) 		0.103
(1.00) 		0.0656
(1.00)
19p gain 0 (0%) 493 1.85e-05
(0.00655) 		0.0186
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.0264
(1.00) 		0.0191
(1.00) 		0.0252
(1.00) 		0.0206
(1.00)
19q gain 0 (0%) 492 1.12e-06
(0.000425) 		0.00421
(1.00) 		0.636
(1.00) 		0.0551
(1.00) 		0.0127
(1.00) 		0.00552
(1.00) 		0.00778
(1.00) 		0.00503
(1.00) 		0.0073
(1.00) 		0.00558
(1.00)
1p loss 0 (0%) 494 0.000294
(0.0892) 		0.554
(1.00) 		0.503
(1.00) 		0.184
(1.00) 		0.3
(1.00) 		0.276
(1.00) 		0.2
(1.00) 		0.282
(1.00)
3q loss 0 (0%) 494 0.000294
(0.0892) 		0.0489
(1.00) 		0.103
(1.00) 		0.0656
(1.00) 		0.0264
(1.00) 		0.0191
(1.00) 		0.0252
(1.00) 		0.0206
(1.00)
8p loss 0 (0%) 493 1.85e-05
(0.00655) 		0.0457
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.00778
(1.00) 		0.00503
(1.00) 		0.0073
(1.00) 		0.00558
(1.00)
8q loss 0 (0%) 493 1.85e-05
(0.00655) 		0.0457
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.00778
(1.00) 		0.00503
(1.00) 		0.0073
(1.00) 		0.00558
(1.00)
9p loss 0 (0%) 485 1.08e-11
(4.26e-09) 		0.267
(1.00) 		0.559
(1.00) 		0.206
(1.00) 		0.0911
(1.00) 		0.0944
(1.00) 		0.185
(1.00) 		0.159
(1.00) 		0.15
(1.00) 		0.176
(1.00)
9q loss 0 (0%) 480 1.58e-13
(6.32e-11) 		0.177
(1.00) 		0.21
(1.00) 		0.00441
(1.00) 		0.19
(1.00) 		0.139
(1.00) 		0.235
(1.00) 		0.228
(1.00) 		0.168
(1.00) 		0.241
(1.00)
10p loss 0 (0%) 491 6.62e-08
(2.56e-05) 		0.0944
(1.00) 		0.0479
(1.00) 		0.0142
(1.00) 		0.0399
(1.00) 		0.0333
(1.00) 		0.0251
(1.00) 		0.0348
(1.00)
10q loss 0 (0%) 492 1.12e-06
(0.000425) 		0.171
(1.00) 		0.104
(1.00) 		0.0415
(1.00) 		0.112
(1.00) 		0.0975
(1.00) 		0.0719
(1.00) 		0.101
(1.00)
11p loss 0 (0%) 490 7.74e-08
(2.98e-05) 		0.0116
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.00603
(1.00) 		0.0143
(1.00) 		0.0399
(1.00) 		0.0333
(1.00) 		0.0251
(1.00) 		0.0348
(1.00)
11q loss 0 (0%) 488 3.24e-06
(0.00121) 		0.0142
(1.00) 		0.388
(1.00) 		0.798
(1.00) 		0.0143
(1.00) 		0.0148
(1.00) 		0.0138
(1.00) 		0.0075
(1.00) 		0.00862
(1.00) 		0.0117
(1.00)
18p loss 0 (0%) 493 0.000204
(0.0633) 		0.186
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.224
(1.00) 		0.0814
(1.00) 		0.0743
(1.00) 		0.0671
(1.00) 		0.109
(1.00) 		0.0681
(1.00)
18q loss 0 (0%) 493 0.000204
(0.0633) 		0.186
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.224
(1.00) 		0.0814
(1.00) 		0.0743
(1.00) 		0.0671
(1.00) 		0.109
(1.00) 		0.0681
(1.00)
21q loss 0 (0%) 491 0.000192
(0.06) 		0.0944
(1.00) 		0.384
(1.00) 		0.0551
(1.00) 		0.209
(1.00) 		0.222
(1.00) 		0.0399
(1.00) 		0.0333
(1.00) 		0.0251
(1.00) 		0.0348
(1.00)
11p gain 0 (0%) 492 0.00134
(0.366) 		0.00421
(1.00) 		0.0127
(1.00) 		0.00552
(1.00) 		0.00228
(0.597) 		0.00132
(0.361) 		0.0021
(0.555) 		0.0015
(0.403)
18p gain 0 (0%) 494 0.00245
(0.629) 		0.0489
(1.00) 		0.103
(1.00) 		0.0656
(1.00)
18q gain 0 (0%) 494 0.00245
(0.629) 		0.0489
(1.00) 		0.103
(1.00) 		0.0656
(1.00)
21q gain 0 (0%) 494 0.00245
(0.629) 		0.0489
(1.00) 		0.103
(1.00) 		0.0656
(1.00) 		0.0264
(1.00) 		0.0191
(1.00) 		0.0252
(1.00) 		0.0206
(1.00)
6q loss 0 (0%) 494 0.0218
(1.00) 		0.0489
(1.00) 		0.103
(1.00) 		0.0656
(1.00) 		0.0264
(1.00) 		0.0191
(1.00) 		0.0252
(1.00) 		0.0206
(1.00)
13q loss 0 (0%) 486 0.0123
(1.00) 		0.0227
(1.00) 		0.0779
(1.00) 		1
(1.00) 		0.0208
(1.00) 		0.0129
(1.00) 		0.00774
(1.00) 		0.0164
(1.00) 		0.0086
(1.00) 		0.0023
(0.599)
17p loss 0 (0%) 490 0.00118
(0.326) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.79
(1.00) 		0.755
(1.00) 		0.518
(1.00) 		0.499
(1.00) 		0.799
(1.00) 		0.5
(1.00)
19p loss 0 (0%) 493 0.132
(1.00) 		0.0186
(1.00) 		0.281
(1.00) 		0.369
(1.00) 		0.0378
(1.00) 		0.0215
(1.00) 		0.00778
(1.00) 		0.00503
(1.00) 		0.0073
(1.00) 		0.00558
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 3.29e-06 (Fisher's exact test), Q value = 0.0012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
1Q GAIN CNV 9 11 1
1Q GAIN WILD-TYPE 25 374 77

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

'4p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S2.  Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
4P GAIN CNV 4 0 0
4P GAIN WILD-TYPE 30 385 78

Figure S2.  Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S3.  Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
4Q GAIN CNV 4 0 0
4Q GAIN WILD-TYPE 30 385 78

Figure S3.  Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 6.97e-20 (Fisher's exact test), Q value = 2.8e-17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
5P GAIN CNV 16 1 0
5P GAIN WILD-TYPE 18 384 78

Figure S4.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000873 (Fisher's exact test), Q value = 0.24

Table S5.  Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
5P GAIN CNV 12 2 3
5P GAIN WILD-TYPE 138 70 272

Figure S5.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000538 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
5P GAIN CNV 0 5 12 0
5P GAIN WILD-TYPE 89 194 118 65

Figure S6.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000541 (Fisher's exact test), Q value = 0.16

Table S7.  Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
5P GAIN CNV 10 6 0
5P GAIN WILD-TYPE 104 162 142

Figure S7.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.21

Table S8.  Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
5P GAIN CNV 6 10 0
5P GAIN WILD-TYPE 161 107 140

Figure S8.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2.6e-18 (Fisher's exact test), Q value = 1e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
5Q GAIN CNV 14 0 0
5Q GAIN WILD-TYPE 20 385 78

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

'5q gain' versus 'METHLYATION_CNMF'

P value = 4.02e-05 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
5Q GAIN CNV 12 1 1
5Q GAIN WILD-TYPE 138 71 274

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

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
5Q GAIN CNV 12 0 0 2
5Q GAIN WILD-TYPE 136 59 115 159

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.71e-05 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
5Q GAIN CNV 0 2 12 0
5Q GAIN WILD-TYPE 89 197 118 65

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

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.034

Table S13.  Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
5Q GAIN CNV 10 3 0
5Q GAIN WILD-TYPE 104 165 142

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

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.038

Table S14.  Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
5Q GAIN CNV 3 10 0
5Q GAIN WILD-TYPE 164 107 140

Figure S14.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.59e-22 (Fisher's exact test), Q value = 6.4e-20

Table S15.  Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
7P GAIN CNV 17 0 0
7P GAIN WILD-TYPE 17 385 78

Figure S15.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.053

Table S16.  Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
7P GAIN CNV 12 3 2
7P GAIN WILD-TYPE 138 69 273

Figure S16.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.12

Table S17.  Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
7P GAIN CNV 13 0 1 2
7P GAIN WILD-TYPE 135 59 114 159

Figure S17.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.02

Table S18.  Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
7P GAIN CNV 1 2 13 0
7P GAIN WILD-TYPE 88 197 117 65

Figure S18.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000272 (Fisher's exact test), Q value = 0.083

Table S19.  Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
7P GAIN CNV 12 4 1
7P GAIN WILD-TYPE 102 164 141

Figure S19.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
7P GAIN CNV 4 12 1
7P GAIN WILD-TYPE 163 105 139

Figure S20.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.76e-23 (Fisher's exact test), Q value = 7.1e-21

Table S21.  Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
7Q GAIN CNV 18 0 1
7Q GAIN WILD-TYPE 16 385 77

Figure S21.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.012

Table S22.  Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
7Q GAIN CNV 14 3 2
7Q GAIN WILD-TYPE 136 69 273

Figure S22.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 5.06e-05 (Fisher's exact test), Q value = 0.017

Table S23.  Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
7Q GAIN CNV 15 0 1 2
7Q GAIN WILD-TYPE 133 59 114 159

Figure S23.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.18e-06 (Fisher's exact test), Q value = 0.0022

Table S24.  Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
7Q GAIN CNV 1 2 15 0
7Q GAIN WILD-TYPE 88 197 115 65

Figure S24.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.088

Table S25.  Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
7Q GAIN CNV 14 2 3
7Q GAIN WILD-TYPE 113 146 146

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.0099

Table S26.  Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
7Q GAIN CNV 14 4 1
7Q GAIN WILD-TYPE 100 164 141

Figure S26.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
7Q GAIN CNV 14 2 3
7Q GAIN WILD-TYPE 111 155 139

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

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.59e-05 (Fisher's exact test), Q value = 0.012

Table S28.  Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
7Q GAIN CNV 4 14 1
7Q GAIN WILD-TYPE 163 103 139

Figure S28.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.063

Table S29.  Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
11Q GAIN CNV 3 0 1
11Q GAIN WILD-TYPE 31 385 77

Figure S29.  Get High-res Image Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 4.1e-10

Table S30.  Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 24 385 77

Figure S30.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0011

Table S31.  Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
12P GAIN CNV 11 0 0
12P GAIN WILD-TYPE 139 72 275

Figure S31.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0058

Table S32.  Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
12P GAIN CNV 11 0 0 0
12P GAIN WILD-TYPE 137 59 115 161

Figure S32.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.00079

Table S33.  Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
12P GAIN CNV 0 0 11 0
12P GAIN WILD-TYPE 89 199 119 65

Figure S33.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.017

Table S34.  Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 117 148 148

Figure S34.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0061

Table S35.  Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
12P GAIN CNV 10 1 0
12P GAIN WILD-TYPE 104 167 142

Figure S35.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.012

Table S36.  Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 115 157 141

Figure S36.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.007

Table S37.  Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
12P GAIN CNV 1 10 0
12P GAIN WILD-TYPE 166 107 140

Figure S37.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.27e-12 (Fisher's exact test), Q value = 5e-10

Table S38.  Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
12Q GAIN CNV 10 0 2
12Q GAIN WILD-TYPE 24 385 76

Figure S38.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 6.48e-07 (Fisher's exact test), Q value = 0.00025

Table S39.  Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
12Q GAIN CNV 12 0 0
12Q GAIN WILD-TYPE 138 72 275

Figure S39.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0017

Table S40.  Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
12Q GAIN CNV 12 0 0 0
12Q GAIN WILD-TYPE 136 59 115 161

Figure S40.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.49e-07 (Fisher's exact test), Q value = 0.00025

Table S41.  Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
12Q GAIN CNV 0 0 12 0
12Q GAIN WILD-TYPE 89 199 118 65

Figure S41.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0059

Table S42.  Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
12Q GAIN CNV 11 0 1
12Q GAIN WILD-TYPE 116 148 148

Figure S42.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0018

Table S43.  Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
12Q GAIN CNV 11 1 0
12Q GAIN WILD-TYPE 103 167 142

Figure S43.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.11e-06 (Fisher's exact test), Q value = 0.0022

Table S44.  Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
12Q GAIN CNV 11 0 1
12Q GAIN WILD-TYPE 114 157 141

Figure S44.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.76e-06 (Fisher's exact test), Q value = 0.0021

Table S45.  Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
12Q GAIN CNV 1 11 0
12Q GAIN WILD-TYPE 166 106 140

Figure S45.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.089

Table S46.  Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
13Q GAIN CNV 3 0 0
13Q GAIN WILD-TYPE 31 385 78

Figure S46.  Get High-res Image Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.9e-06

Table S47.  Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
14Q GAIN CNV 7 0 1
14Q GAIN WILD-TYPE 27 385 77

Figure S47.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 8.76e-05 (Fisher's exact test), Q value = 0.028

Table S48.  Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
14Q GAIN CNV 8 0 0
14Q GAIN WILD-TYPE 142 72 275

Figure S48.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.098

Table S49.  Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
14Q GAIN CNV 8 0 0 0
14Q GAIN WILD-TYPE 140 59 115 161

Figure S49.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.047

Table S50.  Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
14Q GAIN CNV 0 0 8 0
14Q GAIN WILD-TYPE 89 199 122 65

Figure S50.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 5.51e-14 (Fisher's exact test), Q value = 2.2e-11

Table S51.  Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
16P GAIN CNV 11 0 1
16P GAIN WILD-TYPE 23 385 77

Figure S51.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.011

Table S52.  Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
16P GAIN CNV 10 2 0
16P GAIN WILD-TYPE 140 70 275

Figure S52.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.042

Table S53.  Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
16P GAIN CNV 11 0 0 1
16P GAIN WILD-TYPE 137 59 115 160

Figure S53.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.0093

Table S54.  Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
16P GAIN CNV 0 1 11 0
16P GAIN WILD-TYPE 89 198 119 65

Figure S54.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.066

Table S55.  Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
16P GAIN CNV 10 0 2
16P GAIN WILD-TYPE 117 148 147

Figure S55.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.019

Table S56.  Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
16P GAIN CNV 10 2 0
16P GAIN WILD-TYPE 104 166 142

Figure S56.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.28e-05 (Fisher's exact test), Q value = 0.027

Table S57.  Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
16P GAIN CNV 10 0 2
16P GAIN WILD-TYPE 115 157 140

Figure S57.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.35e-05 (Fisher's exact test), Q value = 0.027

Table S58.  Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
16P GAIN CNV 2 10 0
16P GAIN WILD-TYPE 165 107 140

Figure S58.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5.67e-13 (Fisher's exact test), Q value = 2.3e-10

Table S59.  Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
16Q GAIN CNV 10 0 0
16Q GAIN WILD-TYPE 24 385 78

Figure S59.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.069

Table S60.  Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
16Q GAIN CNV 8 2 0
16Q GAIN WILD-TYPE 142 70 275

Figure S60.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.12

Table S61.  Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
16Q GAIN CNV 0 1 9 0
16Q GAIN WILD-TYPE 89 198 121 65

Figure S61.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000547 (Fisher's exact test), Q value = 0.16

Table S62.  Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
16Q GAIN CNV 8 2 0
16Q GAIN WILD-TYPE 106 166 142

Figure S62.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000713 (Fisher's exact test), Q value = 0.2

Table S63.  Gene #15: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
16Q GAIN CNV 8 0 2
16Q GAIN WILD-TYPE 117 157 140

Figure S63.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000758 (Fisher's exact test), Q value = 0.21

Table S64.  Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
16Q GAIN CNV 2 8 0
16Q GAIN WILD-TYPE 165 109 140

Figure S64.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2e-09 (Fisher's exact test), Q value = 7.8e-07

Table S65.  Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
17P GAIN CNV 9 2 1
17P GAIN WILD-TYPE 25 383 77

Figure S65.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 6.48e-07 (Fisher's exact test), Q value = 0.00025

Table S66.  Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
17P GAIN CNV 12 0 0
17P GAIN WILD-TYPE 138 72 275

Figure S66.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0017

Table S67.  Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
17P GAIN CNV 12 0 0 0
17P GAIN WILD-TYPE 136 59 115 161

Figure S67.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.49e-07 (Fisher's exact test), Q value = 0.00025

Table S68.  Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
17P GAIN CNV 0 0 12 0
17P GAIN WILD-TYPE 89 199 118 65

Figure S68.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.017

Table S69.  Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
17P GAIN CNV 10 0 1
17P GAIN WILD-TYPE 117 148 148

Figure S69.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0061

Table S70.  Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
17P GAIN CNV 10 1 0
17P GAIN WILD-TYPE 104 167 142

Figure S70.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.012

Table S71.  Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
17P GAIN CNV 10 0 1
17P GAIN WILD-TYPE 115 157 141

Figure S71.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.007

Table S72.  Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
17P GAIN CNV 1 10 0
17P GAIN WILD-TYPE 166 107 140

Figure S72.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 3.83e-09 (Fisher's exact test), Q value = 1.5e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
17Q GAIN CNV 9 2 2
17Q GAIN WILD-TYPE 25 383 76

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

'17q gain' versus 'METHLYATION_CNMF'

P value = 3.73e-07 (Fisher's exact test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
17Q GAIN CNV 13 0 0
17Q GAIN WILD-TYPE 137 72 275

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

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
17Q GAIN CNV 13 0 0 0
17Q GAIN WILD-TYPE 135 59 115 161

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

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.6e-07 (Fisher's exact test), Q value = 6.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
17Q GAIN CNV 0 0 13 0
17Q GAIN WILD-TYPE 89 199 117 65

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

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0059

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
17Q GAIN CNV 11 0 1
17Q GAIN WILD-TYPE 116 148 148

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

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
17Q GAIN CNV 11 1 0
17Q GAIN WILD-TYPE 103 167 142

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

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.11e-06 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
17Q GAIN CNV 11 0 1
17Q GAIN WILD-TYPE 114 157 141

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

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.76e-06 (Fisher's exact test), Q value = 0.0021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
17Q GAIN CNV 1 11 0
17Q GAIN WILD-TYPE 166 106 140

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

'19p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S81.  Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
19P GAIN CNV 4 0 0
19P GAIN WILD-TYPE 30 385 78

Figure S81.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00042

Table S82.  Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
19Q GAIN CNV 5 0 0
19Q GAIN WILD-TYPE 29 385 78

Figure S82.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 4.4e-09

Table S83.  Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
20P GAIN CNV 9 0 0
20P GAIN WILD-TYPE 25 385 78

Figure S83.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000706 (Fisher's exact test), Q value = 0.2

Table S84.  Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
20P GAIN CNV 7 2 0
20P GAIN WILD-TYPE 143 70 275

Figure S84.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 4.4e-09

Table S85.  Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
20Q GAIN CNV 9 0 0
20Q GAIN WILD-TYPE 25 385 78

Figure S85.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000706 (Fisher's exact test), Q value = 0.2

Table S86.  Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
20Q GAIN CNV 7 2 0
20Q GAIN WILD-TYPE 143 70 275

Figure S86.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.089

Table S87.  Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
1P LOSS CNV 3 0 0
1P LOSS WILD-TYPE 31 385 78

Figure S87.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.9e-06

Table S88.  Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
2P LOSS CNV 7 0 1
2P LOSS WILD-TYPE 27 385 77

Figure S88.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8.76e-05 (Fisher's exact test), Q value = 0.028

Table S89.  Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 142 72 275

Figure S89.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.098

Table S90.  Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
2P LOSS CNV 8 0 0 0
2P LOSS WILD-TYPE 140 59 115 161

Figure S90.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.047

Table S91.  Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
2P LOSS CNV 0 0 8 0
2P LOSS WILD-TYPE 89 199 122 65

Figure S91.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.018

Table S92.  Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 119 148 149

Figure S92.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0079

Table S93.  Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 106 168 142

Figure S93.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.85e-05 (Fisher's exact test), Q value = 0.016

Table S94.  Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 117 157 142

Figure S94.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.0097

Table S95.  Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
2P LOSS CNV 0 8 0
2P LOSS WILD-TYPE 167 109 140

Figure S95.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3.78e-09 (Fisher's exact test), Q value = 1.5e-06

Table S96.  Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 27 385 78

Figure S96.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.000364 (Fisher's exact test), Q value = 0.11

Table S97.  Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 143 72 275

Figure S97.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000534 (Fisher's exact test), Q value = 0.16

Table S98.  Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
2Q LOSS CNV 0 0 7 0
2Q LOSS WILD-TYPE 89 199 123 65

Figure S98.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.06

Table S99.  Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 120 148 149

Figure S99.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.85e-05 (Fisher's exact test), Q value = 0.029

Table S100.  Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 107 168 142

Figure S100.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.054

Table S101.  Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 118 157 142

Figure S101.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.034

Table S102.  Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
2Q LOSS CNV 0 7 0
2Q LOSS WILD-TYPE 167 110 140

Figure S102.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.089

Table S103.  Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
3Q LOSS CNV 3 0 0
3Q LOSS WILD-TYPE 31 385 78

Figure S103.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S104.  Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
8P LOSS CNV 4 0 0
8P LOSS WILD-TYPE 30 385 78

Figure S104.  Get High-res Image Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S105.  Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
8Q LOSS CNV 4 0 0
8Q LOSS WILD-TYPE 30 385 78

Figure S105.  Get High-res Image Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 4.3e-09

Table S106.  Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
9P LOSS CNV 10 1 1
9P LOSS WILD-TYPE 24 384 77

Figure S106.  Get High-res Image Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.58e-13 (Fisher's exact test), Q value = 6.3e-11

Table S107.  Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
9Q LOSS CNV 13 3 1
9Q LOSS WILD-TYPE 21 382 77

Figure S107.  Get High-res Image Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 6.62e-08 (Fisher's exact test), Q value = 2.6e-05

Table S108.  Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
10P LOSS CNV 6 0 0
10P LOSS WILD-TYPE 28 385 78

Figure S108.  Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00042

Table S109.  Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
10Q LOSS CNV 5 0 0
10Q LOSS WILD-TYPE 29 385 78

Figure S109.  Get High-res Image Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.74e-08 (Fisher's exact test), Q value = 3e-05

Table S110.  Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
11P LOSS CNV 6 0 1
11P LOSS WILD-TYPE 28 385 77

Figure S110.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.0012

Table S111.  Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
11Q LOSS CNV 6 2 1
11Q LOSS WILD-TYPE 28 383 77

Figure S111.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000464 (Fisher's exact test), Q value = 0.14

Table S112.  Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
15Q LOSS CNV 4 2 1
15Q LOSS WILD-TYPE 30 383 77

Figure S112.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000534 (Fisher's exact test), Q value = 0.16

Table S113.  Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
15Q LOSS CNV 0 0 7 0
15Q LOSS WILD-TYPE 89 199 123 65

Figure S113.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000664 (Fisher's exact test), Q value = 0.19

Table S114.  Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
15Q LOSS CNV 6 0 0
15Q LOSS WILD-TYPE 121 148 149

Figure S114.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.1

Table S115.  Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
15Q LOSS CNV 6 0 0
15Q LOSS WILD-TYPE 108 168 142

Figure S115.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000602 (Fisher's exact test), Q value = 0.17

Table S116.  Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
15Q LOSS CNV 6 0 0
15Q LOSS WILD-TYPE 119 157 142

Figure S116.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000402 (Fisher's exact test), Q value = 0.12

Table S117.  Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
15Q LOSS CNV 0 6 0
15Q LOSS WILD-TYPE 167 111 140

Figure S117.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.063

Table S118.  Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
18P LOSS CNV 3 0 1
18P LOSS WILD-TYPE 31 385 77

Figure S118.  Get High-res Image Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.063

Table S119.  Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
18Q LOSS CNV 3 0 1
18Q LOSS WILD-TYPE 31 385 77

Figure S119.  Get High-res Image Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.06

Table S120.  Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
21Q LOSS CNV 4 1 1
21Q LOSS WILD-TYPE 30 384 77

Figure S120.  Get High-res Image Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.79e-58 (Fisher's exact test), Q value = 2.8e-55

Table S121.  Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
22Q LOSS CNV 8 0 58
22Q LOSS WILD-TYPE 26 385 20

Figure S121.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.015

Table S122.  Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 72 275
22Q LOSS CNV 36 7 23
22Q LOSS WILD-TYPE 114 65 252

Figure S122.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.26e-11 (Fisher's exact test), Q value = 8.9e-09

Table S123.  Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 59 115 161
22Q LOSS CNV 36 5 20 1
22Q LOSS WILD-TYPE 112 54 95 160

Figure S123.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.59e-11 (Fisher's exact test), Q value = 1e-08

Table S124.  Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 199 130 65
22Q LOSS CNV 17 6 36 3
22Q LOSS WILD-TYPE 72 193 94 62

Figure S124.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.015

Table S125.  Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
22Q LOSS CNV 31 14 10
22Q LOSS WILD-TYPE 96 134 139

Figure S125.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.51e-06 (Fisher's exact test), Q value = 0.0034

Table S126.  Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
22Q LOSS CNV 30 11 14
22Q LOSS WILD-TYPE 84 157 128

Figure S126.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.93e-05 (Fisher's exact test), Q value = 0.013

Table S127.  Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 157 142
22Q LOSS CNV 31 14 10
22Q LOSS WILD-TYPE 94 143 132

Figure S127.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0018

Table S128.  Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 117 140
22Q LOSS CNV 9 30 16
22Q LOSS WILD-TYPE 158 87 124

Figure S128.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 497

  • Number of significantly arm-level cnvs = 45

  • 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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