Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1639N24
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1639N24
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 80 arm-level results and 12 molecular subtypes across 489 patients, 154 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 2q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 15q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

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

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

  • 18p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

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

  • 20q gain cnv correlated to 'CN_CNMF'.

  • 21q gain cnv correlated to 'METHLYATION_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 15q loss cnv correlated to 'METHLYATION_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 154 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
18p gain 0 (0%) 406 0.000266
(0.212) 		4.79e-06
(0.00419) 		2.15e-09
(1.98e-06) 		4.48e-05
(0.0375) 		0.136
(1.00) 		0.148
(1.00) 		3.12e-05
(0.0263) 		9.08e-05
(0.0752) 		0.00155
(1.00) 		0.0108
(1.00) 		0.000189
(0.153) 		1.18e-05
(0.0102)
2p gain 0 (0%) 369 0.0238
(1.00) 		0.0274
(1.00) 		1.15e-15
(1.08e-12) 		1.47e-08
(1.34e-05) 		0.0657
(1.00) 		0.216
(1.00) 		1.28e-09
(1.18e-06) 		3.64e-06
(0.0032) 		7.68e-05
(0.064) 		0.0028
(1.00) 		2.64e-05
(0.0224) 		3.75e-06
(0.0033)
4p loss 0 (0%) 289 0.105
(1.00) 		0.0329
(1.00) 		3.03e-14
(2.85e-11) 		1.58e-12
(1.47e-09) 		0.0533
(1.00) 		0.327
(1.00) 		0.000267
(0.212) 		8.57e-05
(0.071) 		1.27e-08
(1.16e-05) 		0.28
(1.00) 		6.27e-06
(0.00547) 		4.89e-07
(0.000439)
4q loss 0 (0%) 315 0.0245
(1.00) 		0.0103
(1.00) 		6.59e-14
(6.19e-11) 		7.76e-10
(7.18e-07) 		0.00934
(1.00) 		0.0815
(1.00) 		8.88e-06
(0.00772) 		6.54e-07
(0.000584) 		1.06e-07
(9.62e-05) 		0.00508
(1.00) 		0.000163
(0.133) 		3.7e-06
(0.00326)
10p loss 0 (0%) 379 0.0261
(1.00) 		0.128
(1.00) 		3.8e-10
(3.53e-07) 		5.42e-09
(4.97e-06) 		1
(1.00) 		0.16
(1.00) 		1.9e-05
(0.0163) 		9.29e-07
(0.000829) 		5.64e-08
(5.11e-05) 		0.000279
(0.222) 		0.000911
(0.686) 		0.000304
(0.241)
10q loss 0 (0%) 374 0.0013
(0.965) 		0.000417
(0.325) 		2.04e-12
(1.9e-09) 		1.37e-08
(1.26e-05) 		0.266
(1.00) 		0.0118
(1.00) 		5.69e-07
(0.00051) 		2.58e-08
(2.35e-05) 		7.44e-08
(6.74e-05) 		0.00322
(1.00) 		0.000138
(0.113) 		1.11e-05
(0.00964)
7q gain 0 (0%) 368 0.124
(1.00) 		0.0752
(1.00) 		2.17e-13
(2.03e-10) 		1.21e-06
(0.00108) 		0.679
(1.00) 		0.768
(1.00) 		1.31e-05
(0.0113) 		1.18e-05
(0.0102) 		0.000512
(0.395) 		0.0776
(1.00) 		7.77e-05
(0.0647) 		0.000141
(0.116)
1p loss 0 (0%) 412 0.00149
(1.00) 		0.000357
(0.281) 		2.95e-19
(2.78e-16) 		4.37e-10
(4.05e-07) 		0.265
(1.00) 		0.0131
(1.00) 		3.76e-13
(3.52e-10) 		1.23e-12
(1.15e-09) 		1.74e-05
(0.0149) 		0.0369
(1.00) 		0.0106
(1.00) 		1.21e-07
(0.000109)
1q gain 0 (0%) 385 0.5
(1.00) 		0.459
(1.00) 		4.69e-07
(0.000421) 		1.18e-05
(0.0102) 		0.597
(1.00) 		0.59
(1.00) 		1.2e-05
(0.0104) 		2.71e-06
(0.00239) 		0.000539
(0.415) 		0.000184
(0.149) 		0.00901
(1.00) 		0.00264
(1.00)
17q gain 0 (0%) 424 0.00631
(1.00) 		0.000935
(0.702) 		5.92e-14
(5.56e-11) 		4.7e-08
(4.27e-05) 		0.324
(1.00) 		0.394
(1.00) 		6.93e-08
(6.27e-05) 		1.09e-06
(0.000966) 		0.000411
(0.321) 		0.00143
(1.00) 		0.0005
(0.387) 		0.000194
(0.157)
18q gain 0 (0%) 442 9.24e-05
(0.0763) 		0.000373
(0.293) 		3.78e-06
(0.00331) 		0.00072
(0.548) 		0.113
(1.00) 		0.0463
(1.00) 		2.04e-05
(0.0174) 		1.22e-05
(0.0105) 		0.0115
(1.00) 		0.0041
(1.00) 		0.00661
(1.00) 		0.000308
(0.244)
9q loss 0 (0%) 359 0.0028
(1.00) 		0.00237
(1.00) 		5.03e-18
(4.74e-15) 		1.85e-07
(0.000166) 		1
(1.00) 		0.4
(1.00) 		1.03e-09
(9.54e-07) 		9.22e-09
(8.44e-06) 		3.8e-05
(0.032) 		0.000377
(0.296) 		0.446
(1.00) 		0.38
(1.00)
9q gain 0 (0%) 448 0.286
(1.00) 		0.264
(1.00) 		0.000105
(0.0862) 		0.000108
(0.0891) 		0.0746
(1.00) 		0.00212
(1.00) 		2.78e-05
(0.0235) 		1.43e-05
(0.0123) 		0.000875
(0.661) 		0.0464
(1.00) 		0.198
(1.00) 		0.0806
(1.00)
17p gain 0 (0%) 470 0.262
(1.00) 		0.241
(1.00) 		1.52e-06
(0.00135) 		0.000204
(0.164) 		0.277
(1.00) 		0.754
(1.00) 		4.14e-05
(0.0348) 		2.69e-06
(0.00238) 		0.0696
(1.00) 		0.000491
(0.381) 		0.012
(1.00) 		0.116
(1.00)
19p gain 0 (0%) 438 0.591
(1.00) 		0.84
(1.00) 		6.67e-09
(6.12e-06) 		0.000473
(0.368) 		0.000672
(0.514) 		0.00299
(1.00) 		0.000552
(0.423) 		4.28e-05
(0.0359) 		0.000173
(0.141) 		0.00417
(1.00) 		6.77e-06
(0.00589) 		0.000616
(0.472)
22q gain 0 (0%) 370 0.00739
(1.00) 		0.0045
(1.00) 		7.59e-10
(7.03e-07) 		9.77e-05
(0.0806) 		0.227
(1.00) 		0.0167
(1.00) 		0.00026
(0.207) 		0.00101
(0.758) 		3.03e-05
(0.0256) 		0.00658
(1.00) 		0.0045
(1.00) 		0.00188
(1.00)
13q loss 0 (0%) 307 0.129
(1.00) 		0.376
(1.00) 		2.89e-09
(2.66e-06) 		1.03e-06
(0.000917) 		0.149
(1.00) 		0.44
(1.00) 		0.674
(1.00) 		0.178
(1.00) 		5.03e-05
(0.042) 		0.0718
(1.00) 		0.00126
(0.938) 		8.17e-05
(0.0678)
19p loss 0 (0%) 413 0.014
(1.00) 		0.0133
(1.00) 		1.89e-05
(0.0161) 		0.377
(1.00) 		0.832
(1.00) 		0.881
(1.00) 		0.000176
(0.143) 		0.000222
(0.178) 		0.0411
(1.00) 		7.88e-05
(0.0655) 		0.963
(1.00) 		0.763
(1.00)
7p gain 0 (0%) 350 0.421
(1.00) 		0.323
(1.00) 		5.74e-07
(0.000514) 		2.49e-05
(0.0211) 		0.731
(1.00) 		0.988
(1.00) 		0.0043
(1.00) 		0.00117
(0.87) 		0.0127
(1.00) 		0.235
(1.00) 		4.24e-05
(0.0355) 		0.000887
(0.669)
8q gain 0 (0%) 346 0.012
(1.00) 		0.0386
(1.00) 		1.56e-05
(0.0134) 		0.000175
(0.142) 		0.904
(1.00) 		0.826
(1.00) 		0.000501
(0.387) 		0.000243
(0.194) 		0.138
(1.00) 		0.137
(1.00) 		0.091
(1.00) 		0.27
(1.00)
5q loss 0 (0%) 312 0.214
(1.00) 		0.545
(1.00) 		1.95e-08
(1.78e-05) 		9.17e-08
(8.29e-05) 		0.084
(1.00) 		0.125
(1.00) 		0.135
(1.00) 		0.0378
(1.00) 		2.04e-05
(0.0174) 		0.0808
(1.00) 		0.00103
(0.772) 		0.00171
(1.00)
6p loss 0 (0%) 443 0.0916
(1.00) 		0.0391
(1.00) 		7.81e-06
(0.0068) 		0.00103
(0.773) 		0.0753
(1.00) 		0.0297
(1.00) 		0.000213
(0.171) 		0.000254
(0.203) 		0.0118
(1.00) 		0.735
(1.00) 		0.0153
(1.00) 		0.00146
(1.00)
8p loss 0 (0%) 336 0.55
(1.00) 		0.993
(1.00) 		1.15e-07
(0.000104) 		6.22e-06
(0.00543) 		0.0774
(1.00) 		0.753
(1.00) 		0.0229
(1.00) 		0.148
(1.00) 		7.35e-05
(0.0613) 		0.564
(1.00) 		0.0551
(1.00) 		0.00243
(1.00)
9p loss 0 (0%) 296 0.142
(1.00) 		0.229
(1.00) 		7.42e-13
(6.94e-10) 		5.51e-08
(5e-05) 		0.966
(1.00) 		0.399
(1.00) 		0.0134
(1.00) 		0.156
(1.00) 		9.19e-05
(0.076) 		0.125
(1.00) 		0.24
(1.00) 		0.733
(1.00)
14q loss 0 (0%) 403 0.0023
(1.00) 		0.0258
(1.00) 		0.000478
(0.371) 		0.0587
(1.00) 		0.0458
(1.00) 		0.0422
(1.00) 		1.48e-09
(1.37e-06) 		4.98e-13
(4.66e-10) 		2.88e-05
(0.0243) 		0.0169
(1.00) 		0.115
(1.00) 		0.0808
(1.00)
21q loss 0 (0%) 338 0.019
(1.00) 		0.064
(1.00) 		1.58e-11
(1.47e-08) 		5.68e-06
(0.00496) 		0.227
(1.00) 		0.181
(1.00) 		0.0439
(1.00) 		0.0194
(1.00) 		0.000259
(0.207) 		0.0748
(1.00) 		0.108
(1.00) 		0.00669
(1.00)
2q gain 0 (0%) 441 0.305
(1.00) 		0.178
(1.00) 		2.39e-06
(0.00211) 		0.000791
(0.599) 		0.214
(1.00) 		0.33
(1.00) 		2.12e-05
(0.018) 		0.000458
(0.357) 		0.099
(1.00) 		0.0683
(1.00) 		0.000544
(0.418) 		0.00314
(1.00)
12p gain 0 (0%) 347 0.0348
(1.00) 		0.323
(1.00) 		5.12e-09
(4.7e-06) 		0.00466
(1.00) 		0.272
(1.00) 		0.723
(1.00) 		0.00031
(0.245) 		0.00595
(1.00) 		0.0768
(1.00) 		0.173
(1.00) 		0.154
(1.00) 		0.142
(1.00)
12q gain 0 (0%) 428 0.0212
(1.00) 		0.278
(1.00) 		1.47e-05
(0.0126) 		0.247
(1.00) 		0.151
(1.00) 		0.73
(1.00) 		0.164
(1.00) 		0.0197
(1.00) 		0.263
(1.00) 		0.0499
(1.00) 		4.31e-05
(0.0361) 		0.0122
(1.00)
15q gain 0 (0%) 444 0.399
(1.00) 		0.107
(1.00) 		0.000915
(0.688) 		0.02
(1.00) 		0.184
(1.00) 		0.0727
(1.00) 		2.06e-06
(0.00183) 		0.000151
(0.123) 		0.000347
(0.274) 		0.00445
(1.00) 		0.000703
(0.535) 		0.0109
(1.00)
20p gain 0 (0%) 348 0.15
(1.00) 		0.0698
(1.00) 		2.15e-11
(2e-08) 		0.000737
(0.56) 		0.684
(1.00) 		0.194
(1.00) 		0.00189
(1.00) 		0.000148
(0.121) 		0.00755
(1.00) 		0.0458
(1.00) 		0.0156
(1.00) 		0.0276
(1.00)
3p loss 0 (0%) 288 0.0209
(1.00) 		0.258
(1.00) 		1.49e-05
(0.0128) 		1.61e-06
(0.00142) 		0.367
(1.00) 		0.166
(1.00) 		0.06
(1.00) 		0.00645
(1.00) 		0.000964
(0.723) 		0.154
(1.00) 		0.0287
(1.00) 		0.000666
(0.509)
11q loss 0 (0%) 430 0.662
(1.00) 		1
(1.00) 		4.28e-08
(3.89e-05) 		0.000328
(0.259) 		0.0804
(1.00) 		0.189
(1.00) 		0.00553
(1.00) 		0.0477
(1.00) 		0.000244
(0.195) 		0.183
(1.00) 		0.0458
(1.00) 		0.00345
(1.00)
16q loss 0 (0%) 394 0.217
(1.00) 		0.449
(1.00) 		0.00068
(0.519) 		0.00888
(1.00) 		0.172
(1.00) 		0.132
(1.00) 		0.0247
(1.00) 		0.000821
(0.621) 		0.000127
(0.104) 		0.00364
(1.00) 		0.000397
(0.311) 		0.000173
(0.141)
3q gain 0 (0%) 272 0.0931
(1.00) 		0.722
(1.00) 		3.13e-06
(0.00276) 		0.0156
(1.00) 		0.285
(1.00) 		0.409
(1.00) 		0.0136
(1.00) 		0.00259
(1.00) 		0.00895
(1.00) 		0.602
(1.00) 		0.291
(1.00) 		1
(1.00)
5p gain 0 (0%) 264 0.948
(1.00) 		0.27
(1.00) 		1.47e-07
(0.000133) 		0.122
(1.00) 		0.449
(1.00) 		0.461
(1.00) 		0.0699
(1.00) 		0.365
(1.00) 		0.434
(1.00) 		0.239
(1.00) 		0.0208
(1.00) 		0.825
(1.00)
6p gain 0 (0%) 448 0.00617
(1.00) 		0.325
(1.00) 		2.66e-05
(0.0225) 		0.219
(1.00) 		0.813
(1.00) 		0.281
(1.00) 		0.00865
(1.00) 		0.276
(1.00) 		0.834
(1.00) 		0.764
(1.00) 		0.533
(1.00) 		1
(1.00)
6q gain 0 (0%) 459 0.0462
(1.00) 		0.339
(1.00) 		4.51e-06
(0.00395) 		0.0247
(1.00) 		0.606
(1.00) 		0.733
(1.00) 		0.0249
(1.00) 		0.0906
(1.00) 		0.644
(1.00) 		0.84
(1.00) 		0.0592
(1.00) 		0.12
(1.00)
9p gain 0 (0%) 463 0.534
(1.00) 		0.624
(1.00) 		0.0802
(1.00) 		0.33
(1.00) 		0.172
(1.00) 		0.000216
(0.174) 		0.14
(1.00) 		0.00823
(1.00) 		0.0294
(1.00) 		0.159
(1.00) 		0.0666
(1.00) 		0.297
(1.00)
16p gain 0 (0%) 465 0.458
(1.00) 		0.853
(1.00) 		0.000216
(0.174) 		0.254
(1.00) 		0.723
(1.00) 		0.341
(1.00) 		0.108
(1.00) 		0.272
(1.00) 		0.103
(1.00) 		0.541
(1.00) 		0.1
(1.00) 		0.297
(1.00)
16q gain 0 (0%) 463 0.162
(1.00) 		0.234
(1.00) 		9.44e-07
(0.000841) 		0.254
(1.00) 		0.455
(1.00) 		0.154
(1.00) 		0.371
(1.00) 		0.143
(1.00) 		0.0479
(1.00) 		0.592
(1.00) 		0.712
(1.00) 		0.603
(1.00)
19q gain 0 (0%) 417 0.548
(1.00) 		1
(1.00) 		2.2e-05
(0.0187) 		0.0264
(1.00) 		0.0668
(1.00) 		0.0193
(1.00) 		0.00274
(1.00) 		0.00306
(1.00) 		0.244
(1.00) 		0.28
(1.00) 		0.00133
(0.982) 		0.066
(1.00)
20q gain 0 (0%) 359 0.408
(1.00) 		0.413
(1.00) 		3.42e-11
(3.18e-08) 		0.00643
(1.00) 		0.648
(1.00) 		0.357
(1.00) 		0.0952
(1.00) 		0.00546
(1.00) 		0.0232
(1.00) 		0.00586
(1.00) 		0.0307
(1.00) 		0.134
(1.00)
21q gain 0 (0%) 467 0.969
(1.00) 		0.306
(1.00) 		0.317
(1.00) 		0.000154
(0.126) 		0.524
(1.00) 		0.937
(1.00) 		0.678
(1.00) 		0.581
(1.00) 		0.374
(1.00) 		0.149
(1.00) 		0.862
(1.00) 		0.357
(1.00)
3q loss 0 (0%) 455 0.302
(1.00) 		0.6
(1.00) 		0.0002
(0.161) 		0.134
(1.00) 		0.654
(1.00) 		0.912
(1.00) 		0.457
(1.00) 		0.485
(1.00) 		0.501
(1.00) 		0.909
(1.00) 		0.00189
(1.00) 		0.00199
(1.00)
11p loss 0 (0%) 409 0.0644
(1.00) 		0.0719
(1.00) 		8.58e-07
(0.000766) 		0.000514
(0.396) 		0.0333
(1.00) 		0.0076
(1.00) 		0.00402
(1.00) 		0.0395
(1.00) 		0.00195
(1.00) 		0.336
(1.00) 		0.0202
(1.00) 		0.00776
(1.00)
15q loss 0 (0%) 428 0.805
(1.00) 		0.00984
(1.00) 		0.00114
(0.852) 		2.98e-05
(0.0251) 		0.00801
(1.00) 		0.00172
(1.00) 		0.272
(1.00) 		0.0103
(1.00) 		0.154
(1.00) 		0.447
(1.00) 		0.446
(1.00) 		0.73
(1.00)
16p loss 0 (0%) 416 0.794
(1.00) 		0.153
(1.00) 		0.000115
(0.0946) 		0.0179
(1.00) 		0.412
(1.00) 		0.326
(1.00) 		0.375
(1.00) 		0.0302
(1.00) 		0.0274
(1.00) 		0.0449
(1.00) 		0.462
(1.00) 		0.287
(1.00)
17p loss 0 (0%) 310 0.113
(1.00) 		0.433
(1.00) 		1.53e-05
(0.0131) 		0.00145
(1.00) 		0.0107
(1.00) 		0.0694
(1.00) 		0.327
(1.00) 		0.348
(1.00) 		0.0438
(1.00) 		0.305
(1.00) 		0.648
(1.00) 		0.138
(1.00)
1p gain 0 (0%) 464 0.576
(1.00) 		0.581
(1.00) 		0.0264
(1.00) 		0.138
(1.00) 		0.595
(1.00) 		0.112
(1.00) 		0.177
(1.00) 		0.00779
(1.00) 		0.438
(1.00) 		0.877
(1.00) 		0.253
(1.00) 		0.179
(1.00)
3p gain 0 (0%) 435 0.353
(1.00) 		0.55
(1.00) 		0.00128
(0.955) 		0.00874
(1.00) 		0.65
(1.00) 		0.249
(1.00) 		0.064
(1.00) 		0.0294
(1.00) 		0.939
(1.00) 		0.958
(1.00) 		0.418
(1.00) 		0.591
(1.00)
4p gain 0 (0%) 473 0.101
(1.00) 		0.339
(1.00) 		0.0124
(1.00) 		0.0663
(1.00) 		0.132
(1.00) 		0.464
(1.00) 		0.00409
(1.00) 		0.0222
(1.00) 		0.896
(1.00) 		0.611
(1.00) 		0.742
(1.00) 		0.0744
(1.00)
4q gain 0 (0%) 482 1
(1.00) 		0.683
(1.00) 		0.386
(1.00) 		0.589
(1.00) 		0.00949
(1.00) 		0.411
(1.00) 		0.544
(1.00) 		0.21
(1.00)
5q gain 0 (0%) 438 0.114
(1.00) 		0.239
(1.00) 		0.00196
(1.00) 		0.204
(1.00) 		0.82
(1.00) 		0.853
(1.00) 		0.0902
(1.00) 		0.51
(1.00) 		0.827
(1.00) 		0.484
(1.00) 		0.574
(1.00) 		0.858
(1.00)
8p gain 0 (0%) 427 0.0424
(1.00) 		0.0715
(1.00) 		0.00709
(1.00) 		0.164
(1.00) 		0.551
(1.00) 		0.363
(1.00) 		0.041
(1.00) 		0.000835
(0.631) 		0.336
(1.00) 		0.268
(1.00) 		0.871
(1.00) 		0.404
(1.00)
10p gain 0 (0%) 462 0.636
(1.00) 		1
(1.00) 		0.0149
(1.00) 		0.382
(1.00) 		0.53
(1.00) 		0.389
(1.00) 		0.836
(1.00) 		0.75
(1.00) 		0.246
(1.00) 		0.14
(1.00) 		0.79
(1.00) 		0.825
(1.00)
10q gain 0 (0%) 481 0.227
(1.00) 		0.497
(1.00) 		0.162
(1.00) 		0.684
(1.00) 		0.891
(1.00) 		0.9
(1.00) 		0.256
(1.00) 		0.791
(1.00) 		0.249
(1.00) 		1
(1.00)
11p gain 0 (0%) 463 0.929
(1.00) 		0.79
(1.00) 		0.175
(1.00) 		0.0725
(1.00) 		0.23
(1.00) 		0.149
(1.00) 		0.0563
(1.00) 		0.195
(1.00) 		0.00798
(1.00) 		0.282
(1.00) 		0.331
(1.00) 		0.179
(1.00)
11q gain 0 (0%) 461 0.0812
(1.00) 		0.691
(1.00) 		0.00154
(1.00) 		0.102
(1.00) 		0.551
(1.00) 		0.486
(1.00) 		0.333
(1.00) 		0.301
(1.00) 		0.213
(1.00) 		0.306
(1.00) 		0.152
(1.00) 		0.0885
(1.00)
13q gain 0 (0%) 476 0.701
(1.00) 		0.664
(1.00) 		0.49
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.349
(1.00) 		0.55
(1.00) 		0.531
(1.00) 		0.744
(1.00) 		0.616
(1.00) 		0.584
(1.00) 		0.187
(1.00)
14q gain 0 (0%) 431 0.186
(1.00) 		0.498
(1.00) 		0.19
(1.00) 		0.0834
(1.00) 		0.862
(1.00) 		0.656
(1.00) 		0.264
(1.00) 		0.0924
(1.00) 		0.287
(1.00) 		0.00929
(1.00) 		0.0588
(1.00) 		0.479
(1.00)
Xq gain 0 (0%) 472 0.701
(1.00) 		0.589
(1.00) 		0.141
(1.00) 		0.0197
(1.00) 		0.451
(1.00) 		0.582
(1.00) 		0.876
(1.00) 		0.523
(1.00) 		0.104
(1.00) 		0.0909
(1.00) 		0.489
(1.00) 		0.27
(1.00)
1q loss 0 (0%) 471 0.883
(1.00) 		0.62
(1.00) 		0.0026
(1.00) 		0.123
(1.00) 		0.735
(1.00) 		0.177
(1.00) 		0.131
(1.00) 		0.0664
(1.00) 		0.0372
(1.00) 		0.948
(1.00) 		0.221
(1.00) 		0.00765
(1.00)
2p loss 0 (0%) 483 0.0267
(1.00) 		0.0142
(1.00) 		0.605
(1.00) 		0.566
(1.00) 		0.144
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.0196
(1.00)
2q loss 0 (0%) 473 0.813
(1.00) 		0.192
(1.00) 		0.00481
(1.00) 		0.0511
(1.00) 		0.737
(1.00) 		0.582
(1.00) 		0.207
(1.00) 		0.0168
(1.00) 		0.0358
(1.00) 		0.454
(1.00) 		0.502
(1.00) 		0.12
(1.00)
5p loss 0 (0%) 453 0.168
(1.00) 		0.837
(1.00) 		0.0034
(1.00) 		0.00579
(1.00) 		0.391
(1.00) 		0.22
(1.00) 		0.471
(1.00) 		0.282
(1.00) 		0.615
(1.00) 		0.887
(1.00) 		0.0294
(1.00) 		0.0176
(1.00)
6q loss 0 (0%) 437 0.189
(1.00) 		0.0774
(1.00) 		0.000403
(0.315) 		0.00717
(1.00) 		0.0883
(1.00) 		0.159
(1.00) 		0.00864
(1.00) 		0.0191
(1.00) 		0.0272
(1.00) 		0.591
(1.00) 		0.0122
(1.00) 		0.0122
(1.00)
7p loss 0 (0%) 459 0.34
(1.00) 		0.289
(1.00) 		0.00281
(1.00) 		0.000394
(0.309) 		0.754
(1.00) 		0.0594
(1.00) 		0.944
(1.00) 		0.771
(1.00) 		0.541
(1.00) 		0.194
(1.00) 		0.958
(1.00) 		0.248
(1.00)
7q loss 0 (0%) 474 0.356
(1.00) 		0.302
(1.00) 		0.078
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.0617
(1.00) 		0.128
(1.00) 		0.0925
(1.00) 		0.216
(1.00) 		0.368
(1.00) 		1
(1.00)
8q loss 0 (0%) 469 0.136
(1.00) 		0.066
(1.00) 		0.0103
(1.00) 		0.0312
(1.00) 		0.157
(1.00) 		0.23
(1.00) 		0.546
(1.00) 		0.54
(1.00) 		0.161
(1.00) 		0.429
(1.00) 		0.444
(1.00) 		0.322
(1.00)
12p loss 0 (0%) 480 0.534
(1.00) 		0.0777
(1.00) 		1
(1.00) 		0.143
(1.00) 		0.133
(1.00) 		0.376
(1.00) 		0.44
(1.00) 		0.477
(1.00)
12q loss 0 (0%) 475 0.276
(1.00) 		0.0385
(1.00) 		0.292
(1.00) 		0.381
(1.00) 		0.658
(1.00) 		0.449
(1.00) 		0.0182
(1.00) 		0.0483
(1.00) 		0.939
(1.00) 		0.583
(1.00)
17q loss 0 (0%) 457 0.299
(1.00) 		0.135
(1.00) 		0.175
(1.00) 		0.00175
(1.00) 		0.304
(1.00) 		0.943
(1.00) 		0.0042
(1.00) 		0.0162
(1.00) 		0.736
(1.00) 		0.939
(1.00) 		0.737
(1.00) 		0.525
(1.00)
18p loss 0 (0%) 432 0.318
(1.00) 		0.971
(1.00) 		0.00206
(1.00) 		0.621
(1.00) 		0.138
(1.00) 		0.868
(1.00) 		0.659
(1.00) 		0.405
(1.00) 		0.216
(1.00) 		0.699
(1.00) 		0.56
(1.00) 		0.861
(1.00)
18q loss 0 (0%) 395 0.59
(1.00) 		0.753
(1.00) 		0.000516
(0.397) 		0.101
(1.00) 		0.205
(1.00) 		0.829
(1.00) 		0.646
(1.00) 		0.117
(1.00) 		0.313
(1.00) 		0.672
(1.00) 		0.539
(1.00) 		1
(1.00)
19q loss 0 (0%) 440 0.316
(1.00) 		0.528
(1.00) 		0.056
(1.00) 		0.125
(1.00) 		0.0346
(1.00) 		0.103
(1.00) 		0.979
(1.00) 		0.939
(1.00) 		0.179
(1.00) 		0.706
(1.00) 		0.186
(1.00) 		0.135
(1.00)
20p loss 0 (0%) 469 0.208
(1.00) 		0.11
(1.00) 		0.191
(1.00) 		0.0821
(1.00) 		0.0772
(1.00) 		0.644
(1.00) 		0.417
(1.00) 		0.682
(1.00) 		0.191
(1.00) 		0.577
(1.00) 		0.782
(1.00) 		0.196
(1.00)
20q loss 0 (0%) 465 0.00698
(1.00) 		0.0144
(1.00) 		0.00234
(1.00) 		0.284
(1.00) 		0.137
(1.00) 		0.486
(1.00) 		0.00045
(0.35) 		0.000361
(0.284) 		0.0324
(1.00) 		0.149
(1.00) 		0.331
(1.00) 		0.179
(1.00)
22q loss 0 (0%) 441 0.0729
(1.00) 		0.0687
(1.00) 		0.307
(1.00) 		0.39
(1.00) 		0.485
(1.00) 		0.202
(1.00) 		0.0373
(1.00) 		0.018
(1.00) 		0.227
(1.00) 		0.179
(1.00) 		0.223
(1.00) 		0.125
(1.00)
Xq loss 0 (0%) 463 0.523
(1.00) 		0.598
(1.00) 		0.0313
(1.00) 		0.0224
(1.00) 		0.577
(1.00) 		0.000766
(0.581) 		0.221
(1.00) 		0.0934
(1.00) 		0.0058
(1.00) 		0.36
(1.00) 		0.0125
(1.00) 		0.345
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 4.69e-07 (Fisher's exact test), Q value = 0.00042

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
1Q GAIN CNV 26 58 20
1Q GAIN WILD-TYPE 168 104 113

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.01

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
1Q GAIN CNV 16 41 20
1Q GAIN WILD-TYPE 126 73 79

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.01

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
1Q GAIN CNV 13 48 31 8
1Q GAIN WILD-TYPE 105 95 111 67

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-06 (Fisher's exact test), Q value = 0.0024

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
1Q GAIN CNV 23 47 30
1Q GAIN WILD-TYPE 70 93 215

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.15

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
1Q GAIN CNV 29 27 43
1Q GAIN WILD-TYPE 42 136 186

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1.15e-15 (Fisher's exact test), Q value = 1.1e-12

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
2P GAIN CNV 16 74 30
2P GAIN WILD-TYPE 178 88 103

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.47e-08 (Fisher's exact test), Q value = 1.3e-05

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
2P GAIN CNV 18 52 22
2P GAIN WILD-TYPE 124 62 77

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1.28e-09 (Fisher's exact test), Q value = 1.2e-06

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
2P GAIN CNV 14 59 36 6
2P GAIN WILD-TYPE 104 84 106 69

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.64e-06 (Fisher's exact test), Q value = 0.0032

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
2P GAIN CNV 20 55 40
2P GAIN WILD-TYPE 73 85 205

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 7.68e-05 (Fisher's exact test), Q value = 0.064

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
2P GAIN CNV 32 47 16 21
2P GAIN WILD-TYPE 113 83 108 43

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.022

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
2P GAIN CNV 49 15 20
2P GAIN WILD-TYPE 76 96 71

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.75e-06 (Fisher's exact test), Q value = 0.0033

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
2P GAIN CNV 27 57
2P GAIN WILD-TYPE 150 93

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 2.39e-06 (Fisher's exact test), Q value = 0.0021

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
2Q GAIN CNV 6 31 11
2Q GAIN WILD-TYPE 188 131 122

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.018

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
2Q GAIN CNV 4 26 13 1
2Q GAIN WILD-TYPE 114 117 129 74

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.0028

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
3Q GAIN CNV 60 81 76
3Q GAIN WILD-TYPE 134 81 57

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.47e-07 (Fisher's exact test), Q value = 0.00013

Table S16.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
5P GAIN CNV 69 68 88
5P GAIN WILD-TYPE 125 94 45

Figure S16.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.023

Table S17.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
6P GAIN CNV 7 10 24
6P GAIN WILD-TYPE 187 152 109

Figure S17.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 4.51e-06 (Fisher's exact test), Q value = 0.004

Table S18.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
6Q GAIN CNV 3 7 20
6Q GAIN WILD-TYPE 191 155 113

Figure S18.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00051

Table S19.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
7P GAIN CNV 34 70 35
7P GAIN WILD-TYPE 160 92 98

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2.49e-05 (Fisher's exact test), Q value = 0.021

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
7P GAIN CNV 24 49 28
7P GAIN WILD-TYPE 118 65 71

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.24e-05 (Fisher's exact test), Q value = 0.036

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
7P GAIN CNV 54 23 17
7P GAIN WILD-TYPE 71 88 74

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.17e-13 (Fisher's exact test), Q value = 2e-10

Table S22.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
7Q GAIN CNV 20 73 28
7Q GAIN WILD-TYPE 174 89 105

Figure S22.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.0011

Table S23.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
7Q GAIN CNV 14 41 27
7Q GAIN WILD-TYPE 128 73 72

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.011

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
7Q GAIN CNV 21 57 28 11
7Q GAIN WILD-TYPE 97 86 114 64

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.01

Table S25.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
7Q GAIN CNV 19 55 43
7Q GAIN WILD-TYPE 74 85 202

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.77e-05 (Fisher's exact test), Q value = 0.065

Table S26.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
7Q GAIN CNV 46 17 14
7Q GAIN WILD-TYPE 79 94 77

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000141 (Fisher's exact test), Q value = 0.12

Table S27.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
7Q GAIN CNV 27 50
7Q GAIN WILD-TYPE 150 100

Figure S27.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.013

Table S28.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
8Q GAIN CNV 49 34 60
8Q GAIN WILD-TYPE 145 128 73

Figure S28.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
8Q GAIN CNV 40 19 42
8Q GAIN WILD-TYPE 102 95 57

Figure S29.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000243 (Fisher's exact test), Q value = 0.19

Table S30.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
8Q GAIN CNV 39 25 75
8Q GAIN WILD-TYPE 54 115 170

Figure S30.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000216 (Fisher's exact test), Q value = 0.17

Table S31.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
9P GAIN CNV 9 0 0 1
9P GAIN WILD-TYPE 49 47 49 39

Figure S31.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.000105 (Fisher's exact test), Q value = 0.086

Table S32.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
9Q GAIN CNV 11 26 4
9Q GAIN WILD-TYPE 183 136 129

Figure S32.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.089

Table S33.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
9Q GAIN CNV 4 19 4
9Q GAIN WILD-TYPE 138 95 95

Figure S33.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.024

Table S34.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
9Q GAIN CNV 2 24 12 2
9Q GAIN WILD-TYPE 116 119 130 73

Figure S34.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.012

Table S35.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
9Q GAIN CNV 8 24 8
9Q GAIN WILD-TYPE 85 116 237

Figure S35.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 5.12e-09 (Fisher's exact test), Q value = 4.7e-06

Table S36.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
12P GAIN CNV 27 65 50
12P GAIN WILD-TYPE 167 97 83

Figure S36.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.25

Table S37.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
12P GAIN CNV 21 53 50 14
12P GAIN WILD-TYPE 97 90 92 61

Figure S37.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.013

Table S38.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
12Q GAIN CNV 10 35 16
12Q GAIN WILD-TYPE 184 127 117

Figure S38.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.036

Table S39.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
12Q GAIN CNV 26 4 6
12Q GAIN WILD-TYPE 99 107 85

Figure S39.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 2.06e-06 (Fisher's exact test), Q value = 0.0018

Table S40.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
15Q GAIN CNV 0 24 10 7
15Q GAIN WILD-TYPE 118 119 132 68

Figure S40.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
15Q GAIN CNV 6 24 11
15Q GAIN WILD-TYPE 87 116 234

Figure S41.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.17

Table S42.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
16P GAIN CNV 1 12 11
16P GAIN WILD-TYPE 193 150 122

Figure S42.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 9.44e-07 (Fisher's exact test), Q value = 0.00084

Table S43.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
16Q GAIN CNV 0 11 15
16Q GAIN WILD-TYPE 194 151 118

Figure S43.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1.52e-06 (Fisher's exact test), Q value = 0.0014

Table S44.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
17P GAIN CNV 0 16 3
17P GAIN WILD-TYPE 194 146 130

Figure S44.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.16

Table S45.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
17P GAIN CNV 1 12 2
17P GAIN WILD-TYPE 141 102 97

Figure S45.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.035

Table S46.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
17P GAIN CNV 0 15 3 1
17P GAIN WILD-TYPE 118 128 139 74

Figure S46.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.69e-06 (Fisher's exact test), Q value = 0.0024

Table S47.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
17P GAIN CNV 3 15 1
17P GAIN WILD-TYPE 90 125 244

Figure S47.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.92e-14 (Fisher's exact test), Q value = 5.6e-11

Table S48.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
17Q GAIN CNV 3 46 16
17Q GAIN WILD-TYPE 191 116 117

Figure S48.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 4.7e-08 (Fisher's exact test), Q value = 4.3e-05

Table S49.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
17Q GAIN CNV 5 32 11
17Q GAIN WILD-TYPE 137 82 88

Figure S49.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6.93e-08 (Fisher's exact test), Q value = 6.3e-05

Table S50.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
17Q GAIN CNV 6 38 17 2
17Q GAIN WILD-TYPE 112 105 125 73

Figure S50.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00097

Table S51.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
17Q GAIN CNV 11 36 16
17Q GAIN WILD-TYPE 82 104 229

Figure S51.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000194 (Fisher's exact test), Q value = 0.16

Table S52.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
17Q GAIN CNV 11 30
17Q GAIN WILD-TYPE 166 120

Figure S52.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.21

Table S53.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
18P GAIN CNV 3 20 4 2
18P GAIN WILD-TYPE 39 32 28 26

Figure S53.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0042

Table S54.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
18P GAIN CNV 1 23 1 4
18P GAIN WILD-TYPE 21 33 22 49

Figure S54.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 2.15e-09 (Fisher's exact test), Q value = 2e-06

Table S55.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
18P GAIN CNV 17 53 13
18P GAIN WILD-TYPE 177 109 120

Figure S55.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 4.48e-05 (Fisher's exact test), Q value = 0.037

Table S56.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
18P GAIN CNV 10 31 19
18P GAIN WILD-TYPE 132 83 80

Figure S56.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.026

Table S57.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
18P GAIN CNV 15 42 18 5
18P GAIN WILD-TYPE 103 101 124 70

Figure S57.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.075

Table S58.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
18P GAIN CNV 10 40 30
18P GAIN WILD-TYPE 83 100 215

Figure S58.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
18P GAIN CNV 33 9 9
18P GAIN WILD-TYPE 92 102 82

Figure S59.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.01

Table S60.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
18P GAIN CNV 13 38
18P GAIN WILD-TYPE 164 112

Figure S60.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.076

Table S61.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
18Q GAIN CNV 2 16 0 4
18Q GAIN WILD-TYPE 40 36 32 24

Figure S61.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 3.78e-06 (Fisher's exact test), Q value = 0.0033

Table S62.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
18Q GAIN CNV 7 31 9
18Q GAIN WILD-TYPE 187 131 124

Figure S62.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 2.04e-05 (Fisher's exact test), Q value = 0.017

Table S63.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
18Q GAIN CNV 7 26 12 0
18Q GAIN WILD-TYPE 111 117 130 75

Figure S63.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.011

Table S64.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
18Q GAIN CNV 11 25 9
18Q GAIN WILD-TYPE 82 115 236

Figure S64.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000308 (Fisher's exact test), Q value = 0.24

Table S65.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
18Q GAIN CNV 4 19
18Q GAIN WILD-TYPE 173 131

Figure S65.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 6.67e-09 (Fisher's exact test), Q value = 6.1e-06

Table S66.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
19P GAIN CNV 9 37 5
19P GAIN WILD-TYPE 185 125 128

Figure S66.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.036

Table S67.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
19P GAIN CNV 13 25 11
19P GAIN WILD-TYPE 80 115 234

Figure S67.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.14

Table S68.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
19P GAIN CNV 19 14 3 14
19P GAIN WILD-TYPE 126 116 121 50

Figure S68.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.77e-06 (Fisher's exact test), Q value = 0.0059

Table S69.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
19P GAIN CNV 25 5 2
19P GAIN WILD-TYPE 100 106 89

Figure S69.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 2.2e-05 (Fisher's exact test), Q value = 0.019

Table S70.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
19Q GAIN CNV 14 40 18
19Q GAIN WILD-TYPE 180 122 115

Figure S70.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 2.15e-11 (Fisher's exact test), Q value = 2e-08

Table S71.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
20P GAIN CNV 23 66 52
20P GAIN WILD-TYPE 171 96 81

Figure S71.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.12

Table S72.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
20P GAIN CNV 35 53 50
20P GAIN WILD-TYPE 58 87 195

Figure S72.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.42e-11 (Fisher's exact test), Q value = 3.2e-08

Table S73.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
20Q GAIN CNV 21 52 57
20Q GAIN WILD-TYPE 173 110 76

Figure S73.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.13

Table S74.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
21Q GAIN CNV 0 4 10
21Q GAIN WILD-TYPE 142 110 89

Figure S74.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 7.59e-10 (Fisher's exact test), Q value = 7e-07

Table S75.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
22Q GAIN CNV 20 63 36
22Q GAIN WILD-TYPE 174 99 97

Figure S75.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 9.77e-05 (Fisher's exact test), Q value = 0.081

Table S76.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
22Q GAIN CNV 18 38 30
22Q GAIN WILD-TYPE 124 76 69

Figure S76.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.21

Table S77.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
22Q GAIN CNV 25 53 28 10
22Q GAIN WILD-TYPE 93 90 114 65

Figure S77.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.026

Table S78.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
22Q GAIN CNV 31 49 16 20
22Q GAIN WILD-TYPE 114 81 108 44

Figure S78.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 2.95e-19 (Fisher's exact test), Q value = 2.8e-16

Table S79.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
1P LOSS CNV 5 60 12
1P LOSS WILD-TYPE 189 102 121

Figure S79.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.37e-10 (Fisher's exact test), Q value = 4e-07

Table S80.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
1P LOSS CNV 5 38 17
1P LOSS WILD-TYPE 137 76 82

Figure S80.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 3.76e-13 (Fisher's exact test), Q value = 3.5e-10

Table S81.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
1P LOSS CNV 9 53 11 4
1P LOSS WILD-TYPE 109 90 131 71

Figure S81.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-12 (Fisher's exact test), Q value = 1.1e-09

Table S82.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
1P LOSS CNV 7 51 19
1P LOSS WILD-TYPE 86 89 226

Figure S82.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.015

Table S83.  Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
1P LOSS CNV 21 29 6 18
1P LOSS WILD-TYPE 124 101 118 46

Figure S83.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-07 (Fisher's exact test), Q value = 0.00011

Table S84.  Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
1P LOSS CNV 11 42
1P LOSS WILD-TYPE 166 108

Figure S84.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.013

Table S85.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
3P LOSS CNV 55 82 64
3P LOSS WILD-TYPE 139 80 69

Figure S85.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.0014

Table S86.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
3P LOSS CNV 34 53 54
3P LOSS WILD-TYPE 108 61 45

Figure S86.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

Table S87.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
3Q LOSS CNV 4 21 9
3Q LOSS WILD-TYPE 190 141 124

Figure S87.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 3.03e-14 (Fisher's exact test), Q value = 2.9e-11

Table S88.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
4P LOSS CNV 44 103 53
4P LOSS WILD-TYPE 150 59 80

Figure S88.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.58e-12 (Fisher's exact test), Q value = 1.5e-09

Table S89.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
4P LOSS CNV 23 62 53
4P LOSS WILD-TYPE 119 52 46

Figure S89.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.21

Table S90.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
4P LOSS CNV 48 79 50 21
4P LOSS WILD-TYPE 70 64 92 54

Figure S90.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.57e-05 (Fisher's exact test), Q value = 0.071

Table S91.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
4P LOSS CNV 41 77 80
4P LOSS WILD-TYPE 52 63 165

Figure S91.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.27e-08 (Fisher's exact test), Q value = 1.2e-05

Table S92.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
4P LOSS CNV 68 69 23 31
4P LOSS WILD-TYPE 77 61 101 33

Figure S92.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.27e-06 (Fisher's exact test), Q value = 0.0055

Table S93.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
4P LOSS CNV 70 31 27
4P LOSS WILD-TYPE 55 80 64

Figure S93.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.89e-07 (Fisher's exact test), Q value = 0.00044

Table S94.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
4P LOSS CNV 47 81
4P LOSS WILD-TYPE 130 69

Figure S94.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 6.59e-14 (Fisher's exact test), Q value = 6.2e-11

Table S95.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
4Q LOSS CNV 35 93 46
4Q LOSS WILD-TYPE 159 69 87

Figure S95.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 7.76e-10 (Fisher's exact test), Q value = 7.2e-07

Table S96.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
4Q LOSS CNV 21 55 45
4Q LOSS WILD-TYPE 121 59 54

Figure S96.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 8.88e-06 (Fisher's exact test), Q value = 0.0077

Table S97.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
4Q LOSS CNV 35 73 50 14
4Q LOSS WILD-TYPE 83 70 92 61

Figure S97.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.54e-07 (Fisher's exact test), Q value = 0.00058

Table S98.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
4Q LOSS CNV 40 71 61
4Q LOSS WILD-TYPE 53 69 184

Figure S98.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 9.6e-05

Table S99.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
4Q LOSS CNV 57 62 19 27
4Q LOSS WILD-TYPE 88 68 105 37

Figure S99.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.13

Table S100.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
4Q LOSS CNV 59 26 24
4Q LOSS WILD-TYPE 66 85 67

Figure S100.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.7e-06 (Fisher's exact test), Q value = 0.0033

Table S101.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
4Q LOSS CNV 39 70
4Q LOSS WILD-TYPE 138 80

Figure S101.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1.95e-08 (Fisher's exact test), Q value = 1.8e-05

Table S102.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
5Q LOSS CNV 40 78 59
5Q LOSS WILD-TYPE 154 84 74

Figure S102.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 9.17e-08 (Fisher's exact test), Q value = 8.3e-05

Table S103.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
5Q LOSS CNV 25 50 48
5Q LOSS WILD-TYPE 117 64 51

Figure S103.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2.04e-05 (Fisher's exact test), Q value = 0.017

Table S104.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
5Q LOSS CNV 54 56 24 32
5Q LOSS WILD-TYPE 91 74 100 32

Figure S104.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 7.81e-06 (Fisher's exact test), Q value = 0.0068

Table S105.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
6P LOSS CNV 7 30 9
6P LOSS WILD-TYPE 187 132 124

Figure S105.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.000213 (Fisher's exact test), Q value = 0.17

Table S106.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
6P LOSS CNV 8 27 9 2
6P LOSS WILD-TYPE 110 116 133 73

Figure S106.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000254 (Fisher's exact test), Q value = 0.2

Table S107.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
6P LOSS CNV 5 26 15
6P LOSS WILD-TYPE 88 114 230

Figure S107.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 1e-04

Table S108.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
8P LOSS CNV 34 59 60
8P LOSS WILD-TYPE 160 103 73

Figure S108.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0054

Table S109.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
8P LOSS CNV 26 49 42
8P LOSS WILD-TYPE 116 65 57

Figure S109.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 7.35e-05 (Fisher's exact test), Q value = 0.061

Table S110.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
8P LOSS CNV 44 62 26 18
8P LOSS WILD-TYPE 101 68 98 46

Figure S110.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 7.42e-13 (Fisher's exact test), Q value = 6.9e-10

Table S111.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
9P LOSS CNV 48 58 87
9P LOSS WILD-TYPE 146 104 46

Figure S111.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 5.51e-08 (Fisher's exact test), Q value = 5e-05

Table S112.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
9P LOSS CNV 34 41 60
9P LOSS WILD-TYPE 108 73 39

Figure S112.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.076

Table S113.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
9P LOSS CNV 58 69 31 25
9P LOSS WILD-TYPE 87 61 93 39

Figure S113.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 5.03e-18 (Fisher's exact test), Q value = 4.7e-15

Table S114.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
9Q LOSS CNV 35 20 75
9Q LOSS WILD-TYPE 159 142 58

Figure S114.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.85e-07 (Fisher's exact test), Q value = 0.00017

Table S115.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
9Q LOSS CNV 29 16 46
9Q LOSS WILD-TYPE 113 98 53

Figure S115.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.03e-09 (Fisher's exact test), Q value = 9.5e-07

Table S116.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
9Q LOSS CNV 45 11 49 21
9Q LOSS WILD-TYPE 73 132 93 54

Figure S116.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.22e-09 (Fisher's exact test), Q value = 8.4e-06

Table S117.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
9Q LOSS CNV 32 12 82
9Q LOSS WILD-TYPE 61 128 163

Figure S117.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 3.8e-05 (Fisher's exact test), Q value = 0.032

Table S118.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
9Q LOSS CNV 36 53 27 7
9Q LOSS WILD-TYPE 109 77 97 57

Figure S118.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3.8e-10 (Fisher's exact test), Q value = 3.5e-07

Table S119.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
10P LOSS CNV 17 60 33
10P LOSS WILD-TYPE 177 102 100

Figure S119.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 5.42e-09 (Fisher's exact test), Q value = 5e-06

Table S120.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
10P LOSS CNV 12 46 20
10P LOSS WILD-TYPE 130 68 79

Figure S120.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1.9e-05 (Fisher's exact test), Q value = 0.016

Table S121.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
10P LOSS CNV 19 54 27 10
10P LOSS WILD-TYPE 99 89 115 65

Figure S121.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.29e-07 (Fisher's exact test), Q value = 0.00083

Table S122.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
10P LOSS CNV 20 54 36
10P LOSS WILD-TYPE 73 86 209

Figure S122.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 5.64e-08 (Fisher's exact test), Q value = 5.1e-05

Table S123.  Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
10P LOSS CNV 28 38 10 28
10P LOSS WILD-TYPE 117 92 114 36

Figure S123.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000279 (Fisher's exact test), Q value = 0.22

Table S124.  Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
10P LOSS CNV 28 39 37
10P LOSS WILD-TYPE 43 124 192

Figure S124.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000304 (Fisher's exact test), Q value = 0.24

Table S125.  Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
10P LOSS CNV 26 48
10P LOSS WILD-TYPE 151 102

Figure S125.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 2.04e-12 (Fisher's exact test), Q value = 1.9e-09

Table S126.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
10Q LOSS CNV 15 63 37
10Q LOSS WILD-TYPE 179 99 96

Figure S126.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1.37e-08 (Fisher's exact test), Q value = 1.3e-05

Table S127.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
10Q LOSS CNV 13 46 27
10Q LOSS WILD-TYPE 129 68 72

Figure S127.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 5.69e-07 (Fisher's exact test), Q value = 0.00051

Table S128.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
10Q LOSS CNV 20 58 29 8
10Q LOSS WILD-TYPE 98 85 113 67

Figure S128.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.58e-08 (Fisher's exact test), Q value = 2.4e-05

Table S129.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
10Q LOSS CNV 22 58 35
10Q LOSS WILD-TYPE 71 82 210

Figure S129.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 7.44e-08 (Fisher's exact test), Q value = 6.7e-05

Table S130.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
10Q LOSS CNV 24 44 14 28
10Q LOSS WILD-TYPE 121 86 110 36

Figure S130.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.11

Table S131.  Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
10Q LOSS CNV 45 14 23
10Q LOSS WILD-TYPE 80 97 68

Figure S131.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0096

Table S132.  Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
10Q LOSS CNV 27 55
10Q LOSS WILD-TYPE 150 95

Figure S132.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 8.58e-07 (Fisher's exact test), Q value = 0.00077

Table S133.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
11P LOSS CNV 13 30 37
11P LOSS WILD-TYPE 181 132 96

Figure S133.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 4.28e-08 (Fisher's exact test), Q value = 3.9e-05

Table S134.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
11Q LOSS CNV 5 26 28
11Q LOSS WILD-TYPE 189 136 105

Figure S134.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.2

Table S135.  Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
11Q LOSS CNV 13 30 7 8
11Q LOSS WILD-TYPE 132 100 117 56

Figure S135.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 2.89e-09 (Fisher's exact test), Q value = 2.7e-06

Table S136.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
13Q LOSS CNV 43 65 74
13Q LOSS WILD-TYPE 151 97 59

Figure S136.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00092

Table S137.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
13Q LOSS CNV 31 43 54
13Q LOSS WILD-TYPE 111 71 45

Figure S137.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 5.03e-05 (Fisher's exact test), Q value = 0.042

Table S138.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
13Q LOSS CNV 55 64 27 28
13Q LOSS WILD-TYPE 90 66 97 36

Figure S138.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.17e-05 (Fisher's exact test), Q value = 0.068

Table S139.  Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
13Q LOSS CNV 47 72
13Q LOSS WILD-TYPE 130 78

Figure S139.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.48e-09 (Fisher's exact test), Q value = 1.4e-06

Table S140.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
14Q LOSS CNV 6 31 45 4
14Q LOSS WILD-TYPE 112 112 97 71

Figure S140.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.98e-13 (Fisher's exact test), Q value = 4.7e-10

Table S141.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
14Q LOSS CNV 38 32 16
14Q LOSS WILD-TYPE 55 108 229

Figure S141.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.024

Table S142.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
14Q LOSS CNV 25 22 10 24
14Q LOSS WILD-TYPE 120 108 114 40

Figure S142.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.025

Table S143.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
15Q LOSS CNV 7 10 24
15Q LOSS WILD-TYPE 135 104 75

Figure S143.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.095

Table S144.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
16P LOSS CNV 15 25 33
16P LOSS WILD-TYPE 179 137 100

Figure S144.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.1

Table S145.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
16Q LOSS CNV 26 36 10 18
16Q LOSS WILD-TYPE 119 94 114 46

Figure S145.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.14

Table S146.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 177 150
16Q LOSS CNV 22 44
16Q LOSS WILD-TYPE 155 106

Figure S146.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.013

Table S147.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
17P LOSS CNV 51 59 69
17P LOSS WILD-TYPE 143 103 64

Figure S147.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.016

Table S148.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
19P LOSS CNV 22 16 38
19P LOSS WILD-TYPE 172 146 95

Figure S148.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.14

Table S149.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
19P LOSS CNV 15 10 36 14
19P LOSS WILD-TYPE 103 133 106 61

Figure S149.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.18

Table S150.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
19P LOSS CNV 27 12 36
19P LOSS WILD-TYPE 66 128 209

Figure S150.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.88e-05 (Fisher's exact test), Q value = 0.066

Table S151.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
19P LOSS CNV 2 38 31
19P LOSS WILD-TYPE 69 125 198

Figure S151.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1.58e-11 (Fisher's exact test), Q value = 1.5e-08

Table S152.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
21Q LOSS CNV 26 71 54
21Q LOSS WILD-TYPE 168 91 79

Figure S152.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.005

Table S153.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
21Q LOSS CNV 21 41 40
21Q LOSS WILD-TYPE 121 73 59

Figure S153.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.21

Table S154.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
21Q LOSS CNV 56 49 21 19
21Q LOSS WILD-TYPE 89 81 103 45

Figure S154.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 489

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

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