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 79 arm-level events and 10 molecular subtypes across 351 patients, 173 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF'.

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

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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'.

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 17q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

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

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

  • 20p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 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, 173 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
6p gain 65 (19%) 286 1.68e-12
(1.3e-09) 		5.12e-09
(3.84e-06) 		0.0791
(1.00) 		0.273
(1.00) 		7.36e-05
(0.0479) 		3.2e-05
(0.0214) 		5.5e-06
(0.00386) 		9.35e-05
(0.0604) 		6.83e-05
(0.0446) 		1.38e-06
(0.000993)
16p loss 74 (21%) 277 3.13e-17
(2.46e-14) 		0.000101
(0.0648) 		0.812
(1.00) 		0.807
(1.00) 		4.08e-10
(3.11e-07) 		5.3e-07
(0.000387) 		1.71e-06
(0.00123) 		0.000183
(0.116) 		3.1e-06
(0.00221) 		4.86e-06
(0.00342)
19p loss 89 (25%) 262 2.38e-23
(1.88e-20) 		2.03e-12
(1.57e-09) 		0.0081
(1.00) 		0.568
(1.00) 		3.2e-12
(2.48e-09) 		8.83e-12
(6.81e-09) 		1.22e-06
(0.000885) 		1.13e-12
(8.77e-10) 		0.000368
(0.228) 		2.23e-10
(1.71e-07)
5p gain 79 (23%) 272 1.51e-14
(1.18e-11) 		1.01e-05
(0.00694) 		0.26
(1.00) 		0.724
(1.00) 		1.59e-06
(0.00114) 		2.65e-05
(0.0178) 		0.00011
(0.0703) 		6.98e-06
(0.00488) 		0.00271
(1.00) 		1.31e-06
(0.000949)
6q gain 54 (15%) 297 1e-10
(7.69e-08) 		1.36e-05
(0.00934) 		0.0868
(1.00) 		0.441
(1.00) 		1.77e-05
(0.0121) 		0.00022
(0.138) 		2.45e-05
(0.0165) 		0.0119
(1.00) 		0.000189
(0.12) 		2.91e-05
(0.0195)
20q gain 223 (64%) 128 1.86e-18
(1.47e-15) 		3.11e-09
(2.34e-06) 		0.0527
(1.00) 		0.967
(1.00) 		1.84e-06
(0.00132) 		9.31e-05
(0.0603) 		3.3e-06
(0.00234) 		1.27e-09
(9.66e-07) 		0.0313
(1.00) 		2.97e-09
(2.24e-06)
9p loss 113 (32%) 238 5.95e-21
(4.69e-18) 		1.76e-05
(0.012) 		0.00104
(0.611) 		0.0388
(1.00) 		1.72e-08
(1.28e-05) 		5.88e-05
(0.0386) 		0.000317
(0.197) 		8.3e-06
(0.00576) 		0.229
(1.00) 		4.06e-06
(0.00287)
16q loss 83 (24%) 268 2.89e-16
(2.25e-13) 		1.02e-06
(0.000738) 		0.0464
(1.00) 		0.564
(1.00) 		4.99e-08
(3.7e-05) 		8.21e-06
(0.00571) 		1.96e-05
(0.0133) 		5.64e-05
(0.0371) 		0.00443
(1.00) 		8.99e-06
(0.00622)
17p loss 123 (35%) 228 1.7e-21
(1.34e-18) 		1.33e-11
(1.02e-08) 		0.463
(1.00) 		0.809
(1.00) 		4.44e-06
(0.00314) 		1.74e-06
(0.00125) 		0.000134
(0.0856) 		1.38e-05
(0.00946) 		0.00278
(1.00) 		4.59e-08
(3.41e-05)
19q loss 69 (20%) 282 1.31e-16
(1.03e-13) 		8.33e-10
(6.33e-07) 		0.0174
(1.00) 		0.1
(1.00) 		1.55e-07
(0.000114) 		2.43e-06
(0.00174) 		3.42e-05
(0.0227) 		1.7e-09
(1.28e-06) 		0.000656
(0.396) 		5.02e-08
(3.72e-05)
5q loss 76 (22%) 275 1.37e-11
(1.05e-08) 		1.11e-07
(8.18e-05) 		0.615
(1.00) 		0.929
(1.00) 		2.34e-07
(0.000172) 		6.63e-06
(0.00465) 		0.000555
(0.337) 		9.55e-07
(0.000694) 		0.00103
(0.606) 		9.77e-08
(7.22e-05)
15q loss 72 (21%) 279 2.02e-08
(1.51e-05) 		0.00143
(0.827) 		0.00512
(1.00) 		0.0693
(1.00) 		7.74e-05
(0.0503) 		7.52e-05
(0.0489) 		0.000209
(0.132) 		1.25e-05
(0.00857) 		0.00245
(1.00) 		9.84e-05
(0.0635)
4p loss 130 (37%) 221 1.53e-16
(1.19e-13) 		3.29e-05
(0.0219) 		0.212
(1.00) 		0.34
(1.00) 		0.000527
(0.321) 		0.00075
(0.45) 		4.69e-05
(0.031) 		6.01e-07
(0.000437) 		0.00384
(1.00) 		8.87e-06
(0.00614)
4q loss 128 (36%) 223 5.37e-18
(4.22e-15) 		4.35e-06
(0.00307) 		0.0506
(1.00) 		0.249
(1.00) 		0.00597
(1.00) 		0.00156
(0.892) 		0.000273
(0.17) 		2.93e-06
(0.00209) 		0.0225
(1.00) 		2.23e-05
(0.015)
12p loss 47 (13%) 304 5.29e-14
(4.12e-11) 		3.24e-10
(2.48e-07) 		0.249
(1.00) 		0.51
(1.00) 		1.92e-05
(0.013) 		0.000519
(0.317) 		0.00316
(1.00) 		3.78e-05
(0.0251) 		0.0551
(1.00) 		1.7e-07
(0.000125)
22q loss 111 (32%) 240 3.02e-17
(2.37e-14) 		7.47e-06
(0.00521) 		0.0151
(1.00) 		0.484
(1.00) 		0.000971
(0.574) 		0.00173
(0.987) 		5.75e-06
(0.00403) 		3.89e-08
(2.9e-05) 		0.0342
(1.00) 		1.34e-06
(0.000966)
20p gain 194 (55%) 157 1.14e-12
(8.86e-10) 		6.57e-05
(0.043) 		0.0842
(1.00) 		0.704
(1.00) 		0.000777
(0.463) 		0.00863
(1.00) 		0.000438
(0.27) 		5.98e-05
(0.0392) 		0.0168
(1.00) 		0.000142
(0.0905)
21q gain 21 (6%) 330 2.54e-05
(0.0171) 		0.000206
(0.13) 		0.14
(1.00) 		0.666
(1.00) 		0.0101
(1.00) 		0.0656
(1.00) 		0.0175
(1.00) 		0.000153
(0.0975) 		0.119
(1.00) 		3.84e-05
(0.0255)
3q loss 45 (13%) 306 4.13e-07
(0.000301) 		0.00315
(1.00) 		0.198
(1.00) 		0.292
(1.00) 		7.5e-06
(0.00522) 		4.31e-05
(0.0285) 		4.7e-05
(0.031) 		0.00126
(0.73) 		0.00584
(1.00) 		0.00447
(1.00)
14q loss 84 (24%) 267 3.55e-09
(2.67e-06) 		2.93e-05
(0.0196) 		0.559
(1.00) 		0.471
(1.00) 		0.000608
(0.367) 		0.00025
(0.156) 		0.000465
(0.286) 		0.00238
(1.00) 		0.0331
(1.00) 		2.08e-05
(0.0141)
18p gain 66 (19%) 285 2.57e-06
(0.00183) 		4.66e-06
(0.00328) 		0.0566
(1.00) 		0.502
(1.00) 		0.0158
(1.00) 		0.076
(1.00) 		0.00272
(1.00) 		0.000126
(0.0808) 		0.0595
(1.00) 		0.00106
(0.624)
9q loss 78 (22%) 273 2.37e-10
(1.81e-07) 		0.00178
(1.00) 		0.183
(1.00) 		0.287
(1.00) 		3.51e-05
(0.0233) 		0.00357
(1.00) 		0.00793
(1.00) 		0.00285
(1.00) 		0.0744
(1.00) 		0.000375
(0.232)
17q loss 56 (16%) 295 3.92e-08
(2.91e-05) 		7.46e-06
(0.00521) 		0.283
(1.00) 		1
(1.00) 		0.00193
(1.00) 		0.000413
(0.255) 		0.00105
(0.615) 		0.000767
(0.458) 		0.0771
(1.00) 		0.000158
(0.1)
1q gain 83 (24%) 268 2.13e-09
(1.61e-06) 		0.00228
(1.00) 		0.0414
(1.00) 		0.145
(1.00) 		9.09e-06
(0.00628) 		0.00764
(1.00) 		0.000595
(0.36) 		0.0012
(0.699) 		0.00512
(1.00) 		0.00264
(1.00)
2p gain 60 (17%) 291 1.13e-06
(0.000822) 		0.00808
(1.00) 		0.0211
(1.00) 		0.967
(1.00) 		0.117
(1.00) 		0.255
(1.00) 		0.000483
(0.296) 		0.00799
(1.00) 		0.00546
(1.00) 		0.000151
(0.0961)
10p gain 84 (24%) 267 4.67e-12
(3.61e-09) 		1.67e-05
(0.0114) 		0.104
(1.00) 		0.429
(1.00) 		0.00075
(0.45) 		0.0199
(1.00) 		0.00798
(1.00) 		0.000548
(0.333) 		0.0849
(1.00) 		0.00209
(1.00)
13q gain 121 (34%) 230 8.41e-12
(6.49e-09) 		0.00122
(0.706) 		0.567
(1.00) 		0.348
(1.00) 		0.0222
(1.00) 		0.796
(1.00) 		0.00133
(0.768) 		0.00251
(1.00) 		0.0117
(1.00) 		0.000223
(0.14)
xq gain 43 (12%) 308 1.35e-05
(0.00925) 		0.000149
(0.0948) 		0.608
(1.00) 		0.141
(1.00) 		0.0267
(1.00) 		0.344
(1.00) 		0.0112
(1.00) 		0.451
(1.00) 		0.0623
(1.00) 		0.0362
(1.00)
1p loss 45 (13%) 306 2.41e-06
(0.00172) 		6.22e-05
(0.0407) 		0.0562
(1.00) 		0.586
(1.00) 		0.0353
(1.00) 		0.0592
(1.00) 		0.00657
(1.00) 		0.00341
(1.00) 		0.214
(1.00) 		0.0158
(1.00)
1q loss 20 (6%) 331 0.000245
(0.153) 		0.000211
(0.133) 		0.0328
(1.00) 		0.0735
(1.00) 		0.487
(1.00) 		0.0424
(1.00) 		0.354
(1.00) 		0.221
(1.00) 		0.451
(1.00) 		0.155
(1.00)
2q loss 22 (6%) 329 0.000202
(0.128) 		8.32e-05
(0.0539) 		0.852
(1.00) 		0.653
(1.00) 		0.0502
(1.00) 		0.511
(1.00) 		0.0504
(1.00) 		0.0198
(1.00) 		0.227
(1.00) 		0.171
(1.00)
12q loss 37 (11%) 314 4.03e-10
(3.07e-07) 		2.19e-06
(0.00157) 		0.497
(1.00) 		1
(1.00) 		0.00256
(1.00) 		0.101
(1.00) 		0.2
(1.00) 		0.00117
(0.685) 		0.498
(1.00) 		0.00255
(1.00)
21q loss 132 (38%) 219 1.56e-11
(1.2e-08) 		0.00622
(1.00) 		0.127
(1.00) 		0.254
(1.00) 		0.0243
(1.00) 		4.47e-05
(0.0296) 		0.00358
(1.00) 		0.00515
(1.00) 		0.0161
(1.00) 		0.01
(1.00)
1p gain 38 (11%) 313 6.76e-06
(0.00473) 		0.0422
(1.00) 		0.00445
(1.00) 		0.0652
(1.00) 		0.00758
(1.00) 		0.383
(1.00) 		0.0804
(1.00) 		0.183
(1.00) 		0.000498
(0.305) 		0.131
(1.00)
2q gain 51 (15%) 300 1.78e-05
(0.0121) 		0.114
(1.00) 		0.223
(1.00) 		0.736
(1.00) 		0.0285
(1.00) 		0.0715
(1.00) 		0.025
(1.00) 		0.0624
(1.00) 		0.0334
(1.00) 		0.0138
(1.00)
7p gain 155 (44%) 196 2.78e-11
(2.13e-08) 		0.000757
(0.453) 		0.639
(1.00) 		0.925
(1.00) 		0.39
(1.00) 		0.101
(1.00) 		0.395
(1.00) 		0.223
(1.00) 		0.134
(1.00) 		0.00902
(1.00)
7q gain 134 (38%) 217 4.83e-09
(3.63e-06) 		0.0213
(1.00) 		0.848
(1.00) 		0.649
(1.00) 		0.511
(1.00) 		0.318
(1.00) 		0.929
(1.00) 		0.87
(1.00) 		0.624
(1.00) 		0.227
(1.00)
8p gain 148 (42%) 203 1.92e-05
(0.013) 		0.0132
(1.00) 		0.642
(1.00) 		0.548
(1.00) 		0.257
(1.00) 		0.0977
(1.00) 		0.644
(1.00) 		0.727
(1.00) 		0.0638
(1.00) 		0.502
(1.00)
10q gain 59 (17%) 292 4.12e-10
(3.13e-07) 		0.0101
(1.00) 		0.0906
(1.00) 		0.474
(1.00) 		0.0045
(1.00) 		0.0427
(1.00) 		0.021
(1.00) 		0.0453
(1.00) 		0.354
(1.00) 		0.00536
(1.00)
11q gain 51 (15%) 300 0.00153
(0.876) 		0.0132
(1.00) 		0.799
(1.00) 		0.703
(1.00) 		0.263
(1.00) 		0.00273
(1.00) 		0.000398
(0.246) 		0.0092
(1.00) 		0.00897
(1.00) 		0.0084
(1.00)
15q gain 31 (9%) 320 2.93e-05
(0.0196) 		0.00159
(0.908) 		0.233
(1.00) 		0.783
(1.00) 		0.0266
(1.00) 		0.066
(1.00) 		0.625
(1.00) 		0.209
(1.00) 		0.569
(1.00) 		0.0275
(1.00)
3p loss 72 (21%) 279 5.94e-08
(4.4e-05) 		0.0521
(1.00) 		0.331
(1.00) 		0.455
(1.00) 		0.00177
(1.00) 		0.000871
(0.516) 		0.00139
(0.806) 		0.0569
(1.00) 		0.0607
(1.00) 		0.0148
(1.00)
5p loss 46 (13%) 305 3.22e-06
(0.00229) 		0.000503
(0.307) 		0.227
(1.00) 		0.512
(1.00) 		0.00345
(1.00) 		0.0106
(1.00) 		0.022
(1.00) 		0.0328
(1.00) 		0.00772
(1.00) 		0.00441
(1.00)
6p loss 41 (12%) 310 1.76e-07
(0.000129) 		0.0206
(1.00) 		0.146
(1.00) 		0.256
(1.00) 		0.0248
(1.00) 		0.0408
(1.00) 		0.212
(1.00) 		0.00433
(1.00) 		0.168
(1.00) 		0.00114
(0.669)
6q loss 53 (15%) 298 1.6e-07
(0.000118) 		0.0171
(1.00) 		0.749
(1.00) 		0.752
(1.00) 		0.0308
(1.00) 		0.154
(1.00) 		0.558
(1.00) 		0.032
(1.00) 		0.706
(1.00) 		0.0296
(1.00)
7q loss 23 (7%) 328 2.43e-05
(0.0164) 		0.000841
(0.5) 		0.431
(1.00) 		0.528
(1.00) 		0.00573
(1.00) 		0.0486
(1.00) 		0.0381
(1.00) 		0.0417
(1.00) 		0.00147
(0.847) 		0.057
(1.00)
8p loss 62 (18%) 289 1.74e-08
(1.3e-05) 		0.0298
(1.00) 		0.388
(1.00) 		0.341
(1.00) 		0.00517
(1.00) 		0.0029
(1.00) 		0.00166
(0.946) 		0.0011
(0.645) 		0.00596
(1.00) 		0.0394
(1.00)
10p loss 44 (13%) 307 9.96e-06
(0.00687) 		0.0241
(1.00) 		0.534
(1.00) 		0.268
(1.00) 		0.021
(1.00) 		0.0137
(1.00) 		0.0147
(1.00) 		0.0516
(1.00) 		0.144
(1.00) 		0.056
(1.00)
10q loss 49 (14%) 302 1.59e-08
(1.19e-05) 		0.0059
(1.00) 		0.632
(1.00) 		0.64
(1.00) 		0.00265
(1.00) 		0.00817
(1.00) 		0.028
(1.00) 		0.0437
(1.00) 		0.407
(1.00) 		0.109
(1.00)
11p loss 50 (14%) 301 2.45e-07
(0.00018) 		0.0122
(1.00) 		0.00905
(1.00) 		0.503
(1.00) 		0.0747
(1.00) 		0.0168
(1.00) 		0.693
(1.00) 		0.0191
(1.00) 		0.432
(1.00) 		0.0228
(1.00)
11q loss 46 (13%) 305 0.000309
(0.192) 		0.187
(1.00) 		0.517
(1.00) 		0.955
(1.00) 		0.714
(1.00) 		0.528
(1.00) 		0.636
(1.00) 		0.221
(1.00) 		0.712
(1.00) 		0.236
(1.00)
13q loss 31 (9%) 320 7.08e-05
(0.0462) 		0.637
(1.00) 		0.676
(1.00) 		0.138
(1.00) 		0.279
(1.00) 		0.539
(1.00) 		0.728
(1.00) 		0.445
(1.00) 		0.315
(1.00) 		0.819
(1.00)
18p loss 100 (28%) 251 0.000102
(0.0654) 		0.569
(1.00) 		0.68
(1.00) 		0.0836
(1.00) 		0.451
(1.00) 		0.309
(1.00) 		0.1
(1.00) 		0.44
(1.00) 		0.0498
(1.00) 		0.319
(1.00)
18q loss 124 (35%) 227 1.89e-09
(1.43e-06) 		0.0389
(1.00) 		0.338
(1.00) 		0.366
(1.00) 		0.0125
(1.00) 		0.0242
(1.00) 		0.00255
(1.00) 		0.0138
(1.00) 		0.118
(1.00) 		0.0126
(1.00)
20p loss 18 (5%) 333 0.0164
(1.00) 		0.000691
(0.416) 		1
(1.00) 		0.525
(1.00) 		0.000249
(0.156) 		0.268
(1.00) 		0.0676
(1.00) 		0.756
(1.00) 		0.726
(1.00) 		0.356
(1.00)
xq loss 43 (12%) 308 3.48e-07
(0.000255) 		0.000701
(0.421) 		0.262
(1.00) 		0.806
(1.00) 		0.0563
(1.00) 		0.0144
(1.00) 		0.0326
(1.00) 		0.446
(1.00) 		0.0142
(1.00) 		0.855
(1.00)
3p gain 39 (11%) 312 0.00199
(1.00) 		0.0268
(1.00) 		0.789
(1.00) 		0.0761
(1.00) 		0.648
(1.00) 		0.437
(1.00) 		0.565
(1.00) 		0.125
(1.00) 		0.42
(1.00) 		0.0455
(1.00)
3q gain 66 (19%) 285 0.00926
(1.00) 		0.227
(1.00) 		0.852
(1.00) 		0.326
(1.00) 		0.193
(1.00) 		0.0628
(1.00) 		0.932
(1.00) 		0.77
(1.00) 		0.755
(1.00) 		0.379
(1.00)
4p gain 14 (4%) 337 0.345
(1.00) 		0.81
(1.00) 		0.913
(1.00) 		1
(1.00) 		0.311
(1.00) 		0.469
(1.00) 		0.729
(1.00) 		0.673
(1.00) 		0.785
(1.00) 		0.67
(1.00)
4q gain 9 (3%) 342 0.385
(1.00) 		1
(1.00) 		0.692
(1.00) 		0.488
(1.00) 		0.0418
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.517
(1.00) 		0.583
(1.00)
5q gain 34 (10%) 317 0.00047
(0.289) 		0.0665
(1.00) 		0.644
(1.00) 		0.733
(1.00) 		0.0933
(1.00) 		0.125
(1.00) 		0.054
(1.00) 		0.17
(1.00) 		0.158
(1.00) 		0.0783
(1.00)
8q gain 200 (57%) 151 0.00408
(1.00) 		0.0114
(1.00) 		0.865
(1.00) 		0.0715
(1.00) 		0.0155
(1.00) 		0.264
(1.00) 		0.022
(1.00) 		0.0426
(1.00) 		0.00111
(0.649) 		0.0387
(1.00)
9p gain 44 (13%) 307 0.0801
(1.00) 		0.821
(1.00) 		0.551
(1.00) 		0.59
(1.00) 		0.359
(1.00) 		0.415
(1.00) 		0.676
(1.00) 		0.71
(1.00) 		0.808
(1.00) 		0.333
(1.00)
9q gain 56 (16%) 295 0.102
(1.00) 		0.673
(1.00) 		0.32
(1.00) 		0.732
(1.00) 		0.61
(1.00) 		0.493
(1.00) 		0.837
(1.00) 		0.829
(1.00) 		0.875
(1.00) 		0.484
(1.00)
11p gain 42 (12%) 309 0.0209
(1.00) 		0.068
(1.00) 		0.897
(1.00) 		0.81
(1.00) 		0.248
(1.00) 		0.0072
(1.00) 		0.00148
(0.854) 		0.0331
(1.00) 		0.201
(1.00) 		0.0516
(1.00)
12p gain 74 (21%) 277 0.0571
(1.00) 		0.462
(1.00) 		0.24
(1.00) 		0.141
(1.00) 		0.154
(1.00) 		0.312
(1.00) 		0.071
(1.00) 		0.79
(1.00) 		0.0109
(1.00) 		0.217
(1.00)
12q gain 64 (18%) 287 0.351
(1.00) 		0.974
(1.00) 		0.407
(1.00) 		0.179
(1.00) 		0.958
(1.00) 		0.777
(1.00) 		0.688
(1.00) 		0.745
(1.00) 		0.14
(1.00) 		0.779
(1.00)
14q gain 23 (7%) 328 0.000903
(0.534) 		0.211
(1.00) 		0.799
(1.00) 		0.777
(1.00) 		0.589
(1.00) 		0.848
(1.00) 		0.0405
(1.00) 		0.897
(1.00) 		0.258
(1.00) 		0.764
(1.00)
16p gain 52 (15%) 299 0.072
(1.00) 		0.011
(1.00) 		0.38
(1.00) 		0.151
(1.00) 		0.0667
(1.00) 		0.343
(1.00) 		0.76
(1.00) 		0.0896
(1.00) 		0.943
(1.00) 		0.495
(1.00)
16q gain 41 (12%) 310 0.146
(1.00) 		0.329
(1.00) 		0.688
(1.00) 		0.146
(1.00) 		0.121
(1.00) 		0.514
(1.00) 		0.586
(1.00) 		0.214
(1.00) 		0.941
(1.00) 		0.883
(1.00)
17p gain 22 (6%) 329 0.0115
(1.00) 		0.663
(1.00) 		0.727
(1.00) 		0.2
(1.00) 		0.283
(1.00) 		0.734
(1.00) 		0.542
(1.00) 		0.0944
(1.00) 		0.601
(1.00) 		0.791
(1.00)
17q gain 46 (13%) 305 0.00384
(1.00) 		0.49
(1.00) 		0.937
(1.00) 		0.94
(1.00) 		0.477
(1.00) 		0.388
(1.00) 		0.664
(1.00) 		0.894
(1.00) 		0.758
(1.00) 		0.947
(1.00)
18q gain 45 (13%) 306 0.00347
(1.00) 		0.0218
(1.00) 		0.473
(1.00) 		0.481
(1.00) 		0.325
(1.00) 		0.649
(1.00) 		0.0395
(1.00) 		0.0229
(1.00) 		0.0825
(1.00) 		0.118
(1.00)
19p gain 44 (13%) 307 0.0287
(1.00) 		0.826
(1.00) 		0.473
(1.00) 		0.0374
(1.00) 		0.665
(1.00) 		0.866
(1.00) 		0.692
(1.00) 		0.558
(1.00) 		0.408
(1.00) 		0.582
(1.00)
19q gain 61 (17%) 290 0.00155
(0.887) 		0.401
(1.00) 		0.214
(1.00) 		0.0795
(1.00) 		0.0215
(1.00) 		0.0827
(1.00) 		0.112
(1.00) 		0.132
(1.00) 		0.226
(1.00) 		0.143
(1.00)
22q gain 27 (8%) 324 0.0105
(1.00) 		0.179
(1.00) 		0.834
(1.00) 		0.392
(1.00) 		0.236
(1.00) 		0.645
(1.00) 		0.456
(1.00) 		0.639
(1.00) 		0.373
(1.00) 		0.575
(1.00)
2p loss 18 (5%) 333 0.00287
(1.00) 		0.000821
(0.489) 		0.52
(1.00) 		0.769
(1.00) 		0.0663
(1.00) 		0.289
(1.00) 		0.128
(1.00) 		0.108
(1.00) 		0.333
(1.00) 		0.538
(1.00)
7p loss 12 (3%) 339 0.00346
(1.00) 		0.00187
(1.00) 		0.444
(1.00) 		0.577
(1.00) 		0.000584
(0.354) 		0.139
(1.00) 		0.198
(1.00) 		0.118
(1.00) 		0.0101
(1.00) 		0.0334
(1.00)
8q loss 17 (5%) 334 0.025
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.769
(1.00) 		0.851
(1.00) 		0.419
(1.00) 		0.466
(1.00) 		0.565
(1.00) 		0.814
(1.00) 		0.47
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 6.76e-06 (Chi-square test), Q value = 0.0047

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
1P GAIN MUTATED 3 4 10 1 20
1P GAIN WILD-TYPE 156 29 52 11 65

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

'1q gain' versus 'CN_CNMF'

P value = 2.13e-09 (Chi-square test), Q value = 1.6e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
1Q GAIN MUTATED 12 11 18 5 37
1Q GAIN WILD-TYPE 147 22 44 7 48

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 9.09e-06 (Chi-square test), Q value = 0.0063

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
1Q GAIN MUTATED 11 7 8 9 30
1Q GAIN WILD-TYPE 54 55 38 28 32

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1.13e-06 (Chi-square test), Q value = 0.00082

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
2P GAIN MUTATED 8 12 17 2 21
2P GAIN WILD-TYPE 151 21 45 10 64

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.096

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
2P GAIN MUTATED 21 22 5
2P GAIN WILD-TYPE 43 107 76

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1.78e-05 (Chi-square test), Q value = 0.012

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
2Q GAIN MUTATED 8 11 15 1 16
2Q GAIN WILD-TYPE 151 22 47 11 69

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.51e-14 (Chi-square test), Q value = 1.2e-11

Table S7.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
5P GAIN MUTATED 12 6 14 1 46
5P GAIN WILD-TYPE 147 27 48 11 39

Figure S7.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0069

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
5P GAIN MUTATED 15 34 16
5P GAIN WILD-TYPE 98 50 90

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1.59e-06 (Chi-square test), Q value = 0.0011

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5P GAIN MUTATED 10 5 7 8 29
5P GAIN WILD-TYPE 55 57 39 29 33

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.018

Table S10.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
5P GAIN MUTATED 27 24 8
5P GAIN WILD-TYPE 42 89 82

Figure S10.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.07

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
5P GAIN MUTATED 20 12 41
5P GAIN WILD-TYPE 85 89 74

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0049

Table S12.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
5P GAIN MUTATED 15 35 23
5P GAIN WILD-TYPE 87 46 115

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00095

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
5P GAIN MUTATED 29 22 8
5P GAIN WILD-TYPE 35 107 73

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.68e-12 (Chi-square test), Q value = 1.3e-09

Table S14.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
6P GAIN MUTATED 5 8 13 2 37
6P GAIN WILD-TYPE 154 25 49 10 48

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 5.12e-09 (Fisher's exact test), Q value = 3.8e-06

Table S15.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
6P GAIN MUTATED 13 33 6
6P GAIN WILD-TYPE 100 51 100

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 7.36e-05 (Chi-square test), Q value = 0.048

Table S16.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6P GAIN MUTATED 9 5 6 5 24
6P GAIN WILD-TYPE 56 57 40 32 38

Figure S16.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.021

Table S17.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
6P GAIN MUTATED 24 19 6
6P GAIN WILD-TYPE 45 94 84

Figure S17.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 5.5e-06 (Fisher's exact test), Q value = 0.0039

Table S18.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
6P GAIN MUTATED 17 6 36
6P GAIN WILD-TYPE 88 95 79

Figure S18.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.35e-05 (Fisher's exact test), Q value = 0.06

Table S19.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
6P GAIN MUTATED 10 28 21
6P GAIN WILD-TYPE 92 53 117

Figure S19.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.83e-05 (Fisher's exact test), Q value = 0.045

Table S20.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
6P GAIN MUTATED 7 35 4
6P GAIN WILD-TYPE 57 96 75

Figure S20.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00099

Table S21.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
6P GAIN MUTATED 23 20 3
6P GAIN WILD-TYPE 41 109 78

Figure S21.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-10 (Chi-square test), Q value = 7.7e-08

Table S22.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
6Q GAIN MUTATED 6 4 9 2 33
6Q GAIN WILD-TYPE 153 29 53 10 52

Figure S22.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.0093

Table S23.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
6Q GAIN MUTATED 12 25 6
6Q GAIN WILD-TYPE 101 59 100

Figure S23.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1.77e-05 (Chi-square test), Q value = 0.012

Table S24.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6Q GAIN MUTATED 5 4 5 5 22
6Q GAIN WILD-TYPE 60 58 41 32 40

Figure S24.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S25.  Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
6Q GAIN MUTATED 21 14 6
6Q GAIN WILD-TYPE 48 99 84

Figure S25.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.017

Table S26.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
6Q GAIN MUTATED 13 5 31
6Q GAIN WILD-TYPE 92 96 84

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.12

Table S27.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
6Q GAIN MUTATED 4 30 4
6Q GAIN WILD-TYPE 60 101 75

Figure S27.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.91e-05 (Fisher's exact test), Q value = 0.02

Table S28.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
6Q GAIN MUTATED 18 18 2
6Q GAIN WILD-TYPE 46 111 79

Figure S28.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 2.78e-11 (Chi-square test), Q value = 2.1e-08

Table S29.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
7P GAIN MUTATED 40 29 33 7 46
7P GAIN WILD-TYPE 119 4 29 5 39

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 4.83e-09 (Chi-square test), Q value = 3.6e-06

Table S30.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
7Q GAIN MUTATED 39 28 27 6 34
7Q GAIN WILD-TYPE 120 5 35 6 51

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.013

Table S31.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
8P GAIN MUTATED 70 19 17 12 30
8P GAIN WILD-TYPE 89 14 45 0 55

Figure S31.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 4.67e-12 (Chi-square test), Q value = 3.6e-09

Table S32.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
10P GAIN MUTATED 11 9 31 1 32
10P GAIN WILD-TYPE 148 24 31 11 53

Figure S32.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.011

Table S33.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
10P GAIN MUTATED 20 36 16
10P GAIN WILD-TYPE 93 48 90

Figure S33.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 4.12e-10 (Chi-square test), Q value = 3.1e-07

Table S34.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
10Q GAIN MUTATED 9 3 27 1 19
10Q GAIN WILD-TYPE 150 30 35 11 66

Figure S34.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.000398 (Fisher's exact test), Q value = 0.25

Table S35.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
11Q GAIN MUTATED 13 4 25
11Q GAIN WILD-TYPE 92 97 90

Figure S35.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 8.41e-12 (Chi-square test), Q value = 6.5e-09

Table S36.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
13Q GAIN MUTATED 32 25 14 4 46
13Q GAIN WILD-TYPE 127 8 48 8 39

Figure S36.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.14

Table S37.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
13Q GAIN MUTATED 35 36 20
13Q GAIN WILD-TYPE 29 93 61

Figure S37.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.02

Table S38.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
15Q GAIN MUTATED 4 1 13 0 13
15Q GAIN WILD-TYPE 155 32 49 12 72

Figure S38.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 2.57e-06 (Chi-square test), Q value = 0.0018

Table S39.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
18P GAIN MUTATED 12 6 18 1 29
18P GAIN WILD-TYPE 147 27 44 11 56

Figure S39.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 4.66e-06 (Fisher's exact test), Q value = 0.0033

Table S40.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
18P GAIN MUTATED 14 32 12
18P GAIN WILD-TYPE 99 52 94

Figure S40.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.081

Table S41.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
18P GAIN MUTATED 12 28 18
18P GAIN WILD-TYPE 90 53 120

Figure S41.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.14e-12 (Chi-square test), Q value = 8.9e-10

Table S42.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
20P GAIN MUTATED 52 28 45 8 61
20P GAIN WILD-TYPE 107 5 17 4 24

Figure S42.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 6.57e-05 (Fisher's exact test), Q value = 0.043

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
20P GAIN MUTATED 55 63 49
20P GAIN WILD-TYPE 58 21 57

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.98e-05 (Fisher's exact test), Q value = 0.039

Table S44.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
20P GAIN MUTATED 43 60 72
20P GAIN WILD-TYPE 59 21 66

Figure S44.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.09

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
20P GAIN MUTATED 49 60 39
20P GAIN WILD-TYPE 15 69 42

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.86e-18 (Chi-square test), Q value = 1.5e-15

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
20Q GAIN MUTATED 59 31 52 9 72
20Q GAIN WILD-TYPE 100 2 10 3 13

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 3.11e-09 (Fisher's exact test), Q value = 2.3e-06

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
20Q GAIN MUTATED 61 76 58
20Q GAIN WILD-TYPE 52 8 48

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.84e-06 (Chi-square test), Q value = 0.0013

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20Q GAIN MUTATED 30 31 27 24 56
20Q GAIN WILD-TYPE 35 31 19 13 6

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.31e-05 (Fisher's exact test), Q value = 0.06

Table S49.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
20Q GAIN MUTATED 57 64 47
20Q GAIN WILD-TYPE 12 49 43

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 3.3e-06 (Fisher's exact test), Q value = 0.0023

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
20Q GAIN MUTATED 57 53 93
20Q GAIN WILD-TYPE 48 48 22

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.27e-09 (Fisher's exact test), Q value = 9.7e-07

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
20Q GAIN MUTATED 49 73 81
20Q GAIN WILD-TYPE 53 8 57

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.97e-09 (Fisher's exact test), Q value = 2.2e-06

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
20Q GAIN MUTATED 60 74 41
20Q GAIN WILD-TYPE 4 55 40

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 2.54e-05 (Chi-square test), Q value = 0.017

Table S53.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
21Q GAIN MUTATED 1 1 5 0 14
21Q GAIN WILD-TYPE 158 32 57 12 71

Figure S53.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.13

Table S54.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
21Q GAIN MUTATED 4 14 2
21Q GAIN WILD-TYPE 109 70 104

Figure S54.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.097

Table S55.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
21Q GAIN MUTATED 1 13 6
21Q GAIN WILD-TYPE 101 68 132

Figure S55.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.025

Table S56.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
21Q GAIN MUTATED 12 7 0
21Q GAIN WILD-TYPE 52 122 81

Figure S56.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1.35e-05 (Chi-square test), Q value = 0.0092

Table S57.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
XQ GAIN MUTATED 8 9 4 4 18
XQ GAIN WILD-TYPE 151 24 58 8 67

Figure S57.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.095

Table S58.  Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
XQ GAIN MUTATED 13 20 4
XQ GAIN WILD-TYPE 100 64 102

Figure S58.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 2.41e-06 (Chi-square test), Q value = 0.0017

Table S59.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
1P LOSS MUTATED 4 5 14 1 21
1P LOSS WILD-TYPE 155 28 48 11 64

Figure S59.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 6.22e-05 (Fisher's exact test), Q value = 0.041

Table S60.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
1P LOSS MUTATED 11 23 6
1P LOSS WILD-TYPE 102 61 100

Figure S60.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.000245 (Chi-square test), Q value = 0.15

Table S61.  Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
1Q LOSS MUTATED 1 0 8 1 10
1Q LOSS WILD-TYPE 158 33 54 11 75

Figure S61.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.13

Table S62.  Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
1Q LOSS MUTATED 5 13 1
1Q LOSS WILD-TYPE 108 71 105

Figure S62.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.000202 (Chi-square test), Q value = 0.13

Table S63.  Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
2Q LOSS MUTATED 1 3 5 0 13
2Q LOSS WILD-TYPE 158 30 57 12 72

Figure S63.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 8.32e-05 (Fisher's exact test), Q value = 0.054

Table S64.  Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
2Q LOSS MUTATED 3 14 2
2Q LOSS WILD-TYPE 110 70 104

Figure S64.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 5.94e-08 (Chi-square test), Q value = 4.4e-05

Table S65.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
3P LOSS MUTATED 11 14 19 1 27
3P LOSS WILD-TYPE 148 19 43 11 58

Figure S65.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 4.13e-07 (Chi-square test), Q value = 3e-04

Table S66.  Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
3Q LOSS MUTATED 4 10 9 1 21
3Q LOSS WILD-TYPE 155 23 53 11 64

Figure S66.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 7.5e-06 (Chi-square test), Q value = 0.0052

Table S67.  Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
3Q LOSS MUTATED 2 3 1 6 17
3Q LOSS WILD-TYPE 63 59 45 31 45

Figure S67.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.029

Table S68.  Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
3Q LOSS MUTATED 18 7 4
3Q LOSS WILD-TYPE 51 106 86

Figure S68.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 4.7e-05 (Fisher's exact test), Q value = 0.031

Table S69.  Gene #46: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
3Q LOSS MUTATED 3 10 25
3Q LOSS WILD-TYPE 102 91 90

Figure S69.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.53e-16 (Chi-square test), Q value = 1.2e-13

Table S70.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
4P LOSS MUTATED 21 15 41 3 50
4P LOSS WILD-TYPE 138 18 21 9 35

Figure S70.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 3.29e-05 (Fisher's exact test), Q value = 0.022

Table S71.  Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
4P LOSS MUTATED 31 48 32
4P LOSS WILD-TYPE 82 36 74

Figure S71.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.031

Table S72.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
4P LOSS MUTATED 24 33 59
4P LOSS WILD-TYPE 81 68 56

Figure S72.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00044

Table S73.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
4P LOSS MUTATED 33 49 34
4P LOSS WILD-TYPE 69 32 104

Figure S73.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.87e-06 (Fisher's exact test), Q value = 0.0061

Table S74.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
4P LOSS MUTATED 39 33 26
4P LOSS WILD-TYPE 25 96 55

Figure S74.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 5.37e-18 (Chi-square test), Q value = 4.2e-15

Table S75.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
4Q LOSS MUTATED 20 12 43 3 50
4Q LOSS WILD-TYPE 139 21 19 9 35

Figure S75.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 4.35e-06 (Fisher's exact test), Q value = 0.0031

Table S76.  Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
4Q LOSS MUTATED 33 50 29
4Q LOSS WILD-TYPE 80 34 77

Figure S76.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.17

Table S77.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
4Q LOSS MUTATED 25 33 57
4Q LOSS WILD-TYPE 80 68 58

Figure S77.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.93e-06 (Fisher's exact test), Q value = 0.0021

Table S78.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
4Q LOSS MUTATED 31 48 36
4Q LOSS WILD-TYPE 71 33 102

Figure S78.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.23e-05 (Fisher's exact test), Q value = 0.015

Table S79.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
4Q LOSS MUTATED 39 35 26
4Q LOSS WILD-TYPE 25 94 55

Figure S79.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 3.22e-06 (Chi-square test), Q value = 0.0023

Table S80.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
5P LOSS MUTATED 4 8 14 4 16
5P LOSS WILD-TYPE 155 25 48 8 69

Figure S80.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.37e-11 (Chi-square test), Q value = 1.1e-08

Table S81.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
5Q LOSS MUTATED 6 11 20 4 35
5Q LOSS WILD-TYPE 153 22 42 8 50

Figure S81.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.11e-07 (Fisher's exact test), Q value = 8.2e-05

Table S82.  Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
5Q LOSS MUTATED 19 38 12
5Q LOSS WILD-TYPE 94 46 94

Figure S82.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 2.34e-07 (Chi-square test), Q value = 0.00017

Table S83.  Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5Q LOSS MUTATED 11 3 5 7 28
5Q LOSS WILD-TYPE 54 59 41 30 34

Figure S83.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.63e-06 (Fisher's exact test), Q value = 0.0046

Table S84.  Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
5Q LOSS MUTATED 27 20 7
5Q LOSS WILD-TYPE 42 93 83

Figure S84.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.55e-07 (Fisher's exact test), Q value = 0.00069

Table S85.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
5Q LOSS MUTATED 10 34 25
5Q LOSS WILD-TYPE 92 47 113

Figure S85.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.77e-08 (Fisher's exact test), Q value = 7.2e-05

Table S86.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
5Q LOSS MUTATED 32 22 9
5Q LOSS WILD-TYPE 32 107 72

Figure S86.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1.76e-07 (Chi-square test), Q value = 0.00013

Table S87.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
6P LOSS MUTATED 4 3 18 0 16
6P LOSS WILD-TYPE 155 30 44 12 69

Figure S87.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1.6e-07 (Chi-square test), Q value = 0.00012

Table S88.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
6Q LOSS MUTATED 8 5 22 0 18
6Q LOSS WILD-TYPE 151 28 40 12 67

Figure S88.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 2.43e-05 (Chi-square test), Q value = 0.016

Table S89.  Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
7Q LOSS MUTATED 0 1 8 1 13
7Q LOSS WILD-TYPE 159 32 54 11 72

Figure S89.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.74e-08 (Chi-square test), Q value = 1.3e-05

Table S90.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
8P LOSS MUTATED 8 7 22 0 25
8P LOSS WILD-TYPE 151 26 40 12 60

Figure S90.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 5.95e-21 (Chi-square test), Q value = 4.7e-18

Table S91.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
9P LOSS MUTATED 13 11 46 3 40
9P LOSS WILD-TYPE 146 22 16 9 45

Figure S91.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.012

Table S92.  Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
9P LOSS MUTATED 26 45 29
9P LOSS WILD-TYPE 87 39 77

Figure S92.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.72e-08 (Chi-square test), Q value = 1.3e-05

Table S93.  Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9P LOSS MUTATED 6 13 19 9 36
9P LOSS WILD-TYPE 59 49 27 28 26

Figure S93.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.039

Table S94.  Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
9P LOSS MUTATED 36 25 22
9P LOSS WILD-TYPE 33 88 68

Figure S94.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.2

Table S95.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
9P LOSS MUTATED 21 27 51
9P LOSS WILD-TYPE 84 74 64

Figure S95.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0058

Table S96.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
9P LOSS MUTATED 29 42 28
9P LOSS WILD-TYPE 73 39 110

Figure S96.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.06e-06 (Fisher's exact test), Q value = 0.0029

Table S97.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
9P LOSS MUTATED 37 32 18
9P LOSS WILD-TYPE 27 97 63

Figure S97.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 2.37e-10 (Chi-square test), Q value = 1.8e-07

Table S98.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
9Q LOSS MUTATED 11 8 30 2 27
9Q LOSS WILD-TYPE 148 25 32 10 58

Figure S98.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 3.51e-05 (Chi-square test), Q value = 0.023

Table S99.  Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9Q LOSS MUTATED 6 10 13 4 26
9Q LOSS WILD-TYPE 59 52 33 33 36

Figure S99.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.23

Table S100.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
9Q LOSS MUTATED 26 22 12
9Q LOSS WILD-TYPE 38 107 69

Figure S100.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 9.96e-06 (Chi-square test), Q value = 0.0069

Table S101.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
10P LOSS MUTATED 5 6 10 1 22
10P LOSS WILD-TYPE 154 27 52 11 63

Figure S101.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.59e-08 (Chi-square test), Q value = 1.2e-05

Table S102.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
10Q LOSS MUTATED 4 9 9 1 26
10Q LOSS WILD-TYPE 155 24 53 11 59

Figure S102.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 2.45e-07 (Chi-square test), Q value = 0.00018

Table S103.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
11P LOSS MUTATED 7 3 15 0 25
11P LOSS WILD-TYPE 152 30 47 12 60

Figure S103.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.000309 (Chi-square test), Q value = 0.19

Table S104.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
11Q LOSS MUTATED 9 4 13 0 20
11Q LOSS WILD-TYPE 150 29 49 12 65

Figure S104.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 5.29e-14 (Chi-square test), Q value = 4.1e-11

Table S105.  Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
12P LOSS MUTATED 1 2 11 1 32
12P LOSS WILD-TYPE 158 31 51 11 53

Figure S105.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 3.24e-10 (Fisher's exact test), Q value = 2.5e-07

Table S106.  Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
12P LOSS MUTATED 3 28 6
12P LOSS WILD-TYPE 110 56 100

Figure S106.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.013

Table S107.  Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
12P LOSS MUTATED 3 4 6 3 20
12P LOSS WILD-TYPE 62 58 40 34 42

Figure S107.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-05 (Fisher's exact test), Q value = 0.025

Table S108.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
12P LOSS MUTATED 8 24 12
12P LOSS WILD-TYPE 94 57 126

Figure S108.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.7e-07 (Fisher's exact test), Q value = 0.00013

Table S109.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
12P LOSS MUTATED 22 7 5
12P LOSS WILD-TYPE 42 122 76

Figure S109.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 4.03e-10 (Chi-square test), Q value = 3.1e-07

Table S110.  Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
12Q LOSS MUTATED 0 2 10 1 24
12Q LOSS WILD-TYPE 159 31 52 11 61

Figure S110.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.0016

Table S111.  Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
12Q LOSS MUTATED 4 21 5
12Q LOSS WILD-TYPE 109 63 101

Figure S111.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 7.08e-05 (Chi-square test), Q value = 0.046

Table S112.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
13Q LOSS MUTATED 8 0 15 1 7
13Q LOSS WILD-TYPE 151 33 47 11 78

Figure S112.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 3.55e-09 (Chi-square test), Q value = 2.7e-06

Table S113.  Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
14Q LOSS MUTATED 15 7 30 2 30
14Q LOSS WILD-TYPE 144 26 32 10 55

Figure S113.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.02

Table S114.  Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
14Q LOSS MUTATED 18 36 19
14Q LOSS WILD-TYPE 95 48 87

Figure S114.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S115.  Gene #66: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
14Q LOSS MUTATED 29 18 17
14Q LOSS WILD-TYPE 40 95 73

Figure S115.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.014

Table S116.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
14Q LOSS MUTATED 30 22 14
14Q LOSS WILD-TYPE 34 107 67

Figure S116.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2.02e-08 (Chi-square test), Q value = 1.5e-05

Table S117.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
15Q LOSS MUTATED 9 12 20 2 29
15Q LOSS WILD-TYPE 150 21 42 10 56

Figure S117.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7.74e-05 (Chi-square test), Q value = 0.05

Table S118.  Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
15Q LOSS MUTATED 8 4 9 4 23
15Q LOSS WILD-TYPE 57 58 37 33 39

Figure S118.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.049

Table S119.  Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
15Q LOSS MUTATED 23 19 6
15Q LOSS WILD-TYPE 46 94 84

Figure S119.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.13

Table S120.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
15Q LOSS MUTATED 14 12 37
15Q LOSS WILD-TYPE 91 89 78

Figure S120.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0086

Table S121.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
15Q LOSS MUTATED 11 31 21
15Q LOSS WILD-TYPE 91 50 117

Figure S121.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.84e-05 (Fisher's exact test), Q value = 0.063

Table S122.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
15Q LOSS MUTATED 25 23 8
15Q LOSS WILD-TYPE 39 106 73

Figure S122.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 3.13e-17 (Chi-square test), Q value = 2.5e-14

Table S123.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
16P LOSS MUTATED 7 2 24 0 41
16P LOSS WILD-TYPE 152 31 38 12 44

Figure S123.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.065

Table S124.  Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
16P LOSS MUTATED 17 32 15
16P LOSS WILD-TYPE 96 52 91

Figure S124.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 4.08e-10 (Chi-square test), Q value = 3.1e-07

Table S125.  Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16P LOSS MUTATED 7 5 5 4 31
16P LOSS WILD-TYPE 58 57 41 33 31

Figure S125.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.3e-07 (Fisher's exact test), Q value = 0.00039

Table S126.  Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
16P LOSS MUTATED 29 15 8
16P LOSS WILD-TYPE 40 98 82

Figure S126.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0012

Table S127.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
16P LOSS MUTATED 12 12 42
16P LOSS WILD-TYPE 93 89 73

Figure S127.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.12

Table S128.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
16P LOSS MUTATED 13 30 23
16P LOSS WILD-TYPE 89 51 115

Figure S128.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.1e-06 (Fisher's exact test), Q value = 0.0022

Table S129.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
16P LOSS MUTATED 3 43 11
16P LOSS WILD-TYPE 61 88 68

Figure S129.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.86e-06 (Fisher's exact test), Q value = 0.0034

Table S130.  Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
16P LOSS MUTATED 28 20 9
16P LOSS WILD-TYPE 36 109 72

Figure S130.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 2.89e-16 (Chi-square test), Q value = 2.3e-13

Table S131.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
16Q LOSS MUTATED 12 2 25 0 44
16Q LOSS WILD-TYPE 147 31 37 12 41

Figure S131.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 0.00074

Table S132.  Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
16Q LOSS MUTATED 12 36 23
16Q LOSS WILD-TYPE 101 48 83

Figure S132.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 4.99e-08 (Chi-square test), Q value = 3.7e-05

Table S133.  Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16Q LOSS MUTATED 6 10 9 5 32
16Q LOSS WILD-TYPE 59 52 37 32 30

Figure S133.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.21e-06 (Fisher's exact test), Q value = 0.0057

Table S134.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
16Q LOSS MUTATED 31 17 14
16Q LOSS WILD-TYPE 38 96 76

Figure S134.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.013

Table S135.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
16Q LOSS MUTATED 14 17 44
16Q LOSS WILD-TYPE 91 84 71

Figure S135.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.64e-05 (Fisher's exact test), Q value = 0.037

Table S136.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
16Q LOSS MUTATED 16 34 25
16Q LOSS WILD-TYPE 86 47 113

Figure S136.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.99e-06 (Fisher's exact test), Q value = 0.0062

Table S137.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
16Q LOSS MUTATED 30 21 13
16Q LOSS WILD-TYPE 34 108 68

Figure S137.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1.7e-21 (Chi-square test), Q value = 1.3e-18

Table S138.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
17P LOSS MUTATED 12 22 35 3 51
17P LOSS WILD-TYPE 147 11 27 9 34

Figure S138.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.33e-11 (Fisher's exact test), Q value = 1e-08

Table S139.  Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
17P LOSS MUTATED 34 55 18
17P LOSS WILD-TYPE 79 29 88

Figure S139.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 4.44e-06 (Chi-square test), Q value = 0.0031

Table S140.  Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
17P LOSS MUTATED 14 10 18 12 36
17P LOSS WILD-TYPE 51 52 28 25 26

Figure S140.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.0012

Table S141.  Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
17P LOSS MUTATED 40 32 18
17P LOSS WILD-TYPE 29 81 72

Figure S141.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.086

Table S142.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
17P LOSS MUTATED 33 22 56
17P LOSS WILD-TYPE 72 79 59

Figure S142.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0095

Table S143.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
17P LOSS MUTATED 23 45 43
17P LOSS WILD-TYPE 79 36 95

Figure S143.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.59e-08 (Fisher's exact test), Q value = 3.4e-05

Table S144.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
17P LOSS MUTATED 42 36 18
17P LOSS WILD-TYPE 22 93 63

Figure S144.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 3.92e-08 (Chi-square test), Q value = 2.9e-05

Table S145.  Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
17Q LOSS MUTATED 4 9 17 2 24
17Q LOSS WILD-TYPE 155 24 45 10 61

Figure S145.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 7.46e-06 (Fisher's exact test), Q value = 0.0052

Table S146.  Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
17Q LOSS MUTATED 13 26 6
17Q LOSS WILD-TYPE 100 58 100

Figure S146.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.1

Table S147.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
17Q LOSS MUTATED 21 14 7
17Q LOSS WILD-TYPE 43 115 74

Figure S147.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000102 (Chi-square test), Q value = 0.065

Table S148.  Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
18P LOSS MUTATED 27 13 28 2 30
18P LOSS WILD-TYPE 132 20 34 10 55

Figure S148.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1.89e-09 (Chi-square test), Q value = 1.4e-06

Table S149.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
18Q LOSS MUTATED 28 16 34 2 44
18Q LOSS WILD-TYPE 131 17 28 10 41

Figure S149.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 2.38e-23 (Chi-square test), Q value = 1.9e-20

Table S150.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
19P LOSS MUTATED 2 8 24 3 52
19P LOSS WILD-TYPE 157 25 38 9 33

Figure S150.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 2.03e-12 (Fisher's exact test), Q value = 1.6e-09

Table S151.  Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
19P LOSS MUTATED 20 47 11
19P LOSS WILD-TYPE 93 37 95

Figure S151.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 3.2e-12 (Chi-square test), Q value = 2.5e-09

Table S152.  Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19P LOSS MUTATED 8 3 8 5 35
19P LOSS WILD-TYPE 57 59 38 32 27

Figure S152.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-12 (Fisher's exact test), Q value = 6.8e-09

Table S153.  Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
19P LOSS MUTATED 36 18 5
19P LOSS WILD-TYPE 33 95 85

Figure S153.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00089

Table S154.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
19P LOSS MUTATED 17 13 47
19P LOSS WILD-TYPE 88 88 68

Figure S154.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-12 (Fisher's exact test), Q value = 8.8e-10

Table S155.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
19P LOSS MUTATED 8 44 25
19P LOSS WILD-TYPE 94 37 113

Figure S155.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000368 (Fisher's exact test), Q value = 0.23

Table S156.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
19P LOSS MUTATED 14 44 8
19P LOSS WILD-TYPE 50 87 71

Figure S156.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.23e-10 (Fisher's exact test), Q value = 1.7e-07

Table S157.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
19P LOSS MUTATED 35 25 6
19P LOSS WILD-TYPE 29 104 75

Figure S157.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.31e-16 (Chi-square test), Q value = 1e-13

Table S158.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
19Q LOSS MUTATED 1 7 18 3 40
19Q LOSS WILD-TYPE 158 26 44 9 45

Figure S158.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 8.33e-10 (Fisher's exact test), Q value = 6.3e-07

Table S159.  Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
19Q LOSS MUTATED 14 37 8
19Q LOSS WILD-TYPE 99 47 98

Figure S159.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1.55e-07 (Chi-square test), Q value = 0.00011

Table S160.  Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19Q LOSS MUTATED 5 2 8 5 25
19Q LOSS WILD-TYPE 60 60 38 32 37

Figure S160.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0017

Table S161.  Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
19Q LOSS MUTATED 24 17 4
19Q LOSS WILD-TYPE 45 96 86

Figure S161.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.023

Table S162.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
19Q LOSS MUTATED 13 10 37
19Q LOSS WILD-TYPE 92 91 78

Figure S162.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-09 (Fisher's exact test), Q value = 1.3e-06

Table S163.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
19Q LOSS MUTATED 7 35 18
19Q LOSS WILD-TYPE 95 46 120

Figure S163.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.02e-08 (Fisher's exact test), Q value = 3.7e-05

Table S164.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
19Q LOSS MUTATED 28 18 5
19Q LOSS WILD-TYPE 36 111 76

Figure S164.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.000249 (Chi-square test), Q value = 0.16

Table S165.  Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20P LOSS MUTATED 0 2 8 0 3
20P LOSS WILD-TYPE 65 60 38 37 59

Figure S165.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1.56e-11 (Chi-square test), Q value = 1.2e-08

Table S166.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
21Q LOSS MUTATED 27 16 40 6 43
21Q LOSS WILD-TYPE 132 17 22 6 42

Figure S166.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.47e-05 (Fisher's exact test), Q value = 0.03

Table S167.  Gene #77: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
21Q LOSS MUTATED 39 28 26
21Q LOSS WILD-TYPE 30 85 64

Figure S167.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 3.02e-17 (Chi-square test), Q value = 2.4e-14

Table S168.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
22Q LOSS MUTATED 13 11 38 4 45
22Q LOSS WILD-TYPE 146 22 24 8 40

Figure S168.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 7.47e-06 (Fisher's exact test), Q value = 0.0052

Table S169.  Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 84 106
22Q LOSS MUTATED 30 45 23
22Q LOSS WILD-TYPE 83 39 83

Figure S169.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 5.75e-06 (Fisher's exact test), Q value = 0.004

Table S170.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
22Q LOSS MUTATED 17 27 53
22Q LOSS WILD-TYPE 88 74 62

Figure S170.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.89e-08 (Fisher's exact test), Q value = 2.9e-05

Table S171.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
22Q LOSS MUTATED 21 46 30
22Q LOSS WILD-TYPE 81 35 108

Figure S171.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.00097

Table S172.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
22Q LOSS MUTATED 37 29 18
22Q LOSS WILD-TYPE 27 100 63

Figure S172.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 3.48e-07 (Chi-square test), Q value = 0.00025

Table S173.  Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 159 33 62 12 85
XQ LOSS MUTATED 4 5 18 0 16
XQ LOSS WILD-TYPE 155 28 44 12 69

Figure S173.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 351

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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