Correlation between copy number variations of arm-level result and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C14T6GRH
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/C14T6GRH
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 78 arm-level results and 10 molecular subtypes across 305 patients, 112 significant findings detected with Q value < 0.25.

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

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

  • 2q gain cnv correlated to 'CN_CNMF'.

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

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 8q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

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

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

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_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'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 7q loss cnv correlated to 'CN_CNMF'.

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

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

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 20p loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 112 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20p gain 0 (0%) 177 7.59e-18
(5.85e-15) 		5.66e-09
(4.25e-06) 		0.0126
(1.00) 		0.115
(1.00) 		7.19e-07
(0.000531) 		2.41e-06
(0.00176) 		2.16e-05
(0.0153) 		5.86e-07
(0.000434) 		0.00112
(0.711) 		3.99e-06
(0.00289)
20q gain 0 (0%) 148 3.08e-26
(2.38e-23) 		7.34e-14
(5.61e-11) 		0.00347
(1.00) 		0.252
(1.00) 		1.83e-10
(1.38e-07) 		7.23e-10
(5.45e-07) 		3.03e-07
(0.000225) 		5.79e-12
(4.4e-09) 		0.00282
(1.00) 		1.51e-10
(1.14e-07)
5q loss 0 (0%) 270 2.21e-13
(1.68e-10) 		2.47e-06
(0.0018) 		0.671
(1.00) 		0.818
(1.00) 		4.12e-06
(0.00299) 		5.94e-06
(0.00429) 		0.00607
(1.00) 		0.000273
(0.183) 		0.0117
(1.00) 		8.44e-05
(0.0575)
16p loss 0 (0%) 276 5.37e-13
(4.08e-10) 		1.89e-05
(0.0135) 		0.336
(1.00) 		0.181
(1.00) 		2.39e-06
(0.00175) 		5.43e-06
(0.00392) 		1.31e-05
(0.00937) 		0.00949
(1.00) 		5.43e-05
(0.0376) 		0.0148
(1.00)
19p loss 0 (0%) 272 2.51e-13
(1.91e-10) 		4.4e-06
(0.00318) 		0.0262
(1.00) 		0.305
(1.00) 		3.15e-09
(2.37e-06) 		1.24e-05
(0.00891) 		0.0202
(1.00) 		1.62e-06
(0.00119) 		0.0116
(1.00) 		7.33e-05
(0.0502)
8q gain 0 (0%) 183 0.231
(1.00) 		2.44e-07
(0.000181) 		0.0175
(1.00) 		0.0506
(1.00) 		0.000343
(0.227) 		0.0733
(1.00) 		0.000171
(0.115) 		0.00361
(1.00) 		4.46e-05
(0.031) 		1.89e-05
(0.0134)
4q loss 0 (0%) 254 2.28e-14
(1.74e-11) 		4.26e-05
(0.0297) 		0.0365
(1.00) 		0.197
(1.00) 		0.000242
(0.162) 		0.000226
(0.152) 		0.00142
(0.895) 		6.4e-05
(0.044) 		0.00496
(1.00) 		0.0029
(1.00)
4p loss 0 (0%) 250 2.31e-11
(1.75e-08) 		0.000389
(0.257) 		0.249
(1.00) 		0.199
(1.00) 		8.51e-05
(0.0579) 		6.56e-05
(0.045) 		0.00462
(1.00) 		9.16e-05
(0.0622) 		0.00597
(1.00) 		0.000922
(0.591)
16q loss 0 (0%) 273 4.29e-10
(3.24e-07) 		3.51e-06
(0.00255) 		0.119
(1.00) 		0.00647
(1.00) 		5.92e-05
(0.0409) 		6.15e-05
(0.0424) 		0.000978
(0.624) 		0.0863
(1.00) 		0.00352
(1.00) 		0.177
(1.00)
19q loss 0 (0%) 282 1.33e-08
(9.97e-06) 		1.26e-05
(0.00899) 		0.0555
(1.00) 		0.436
(1.00) 		4.22e-07
(0.000313) 		0.00467
(1.00) 		0.0649
(1.00) 		1.25e-05
(0.00892) 		0.0923
(1.00) 		0.000574
(0.373)
22q loss 0 (0%) 265 6.63e-16
(5.1e-13) 		1.9e-06
(0.00139) 		2.34e-05
(0.0165) 		0.16
(1.00) 		5.87e-05
(0.0406) 		0.00625
(1.00) 		0.00163
(1.00) 		0.00105
(0.667) 		0.011
(1.00) 		0.00532
(1.00)
5p gain 0 (0%) 262 3.19e-06
(0.00232) 		0.00218
(1.00) 		0.338
(1.00) 		0.155
(1.00) 		6.25e-05
(0.043) 		0.000367
(0.242) 		0.00134
(0.845) 		0.0124
(1.00) 		0.00213
(1.00) 		0.00255
(1.00)
8p loss 0 (0%) 275 2.68e-06
(0.00195) 		0.0321
(1.00) 		0.758
(1.00) 		0.0644
(1.00) 		0.0122
(1.00) 		0.0209
(1.00) 		0.000323
(0.215) 		0.0215
(1.00) 		9.73e-05
(0.0658) 		0.329
(1.00)
9p loss 0 (0%) 254 1.64e-13
(1.25e-10) 		2.64e-05
(0.0186) 		0.015
(1.00) 		0.529
(1.00) 		0.000171
(0.115) 		0.0015
(0.938) 		0.0501
(1.00) 		0.0205
(1.00) 		0.515
(1.00) 		0.0373
(1.00)
12p loss 0 (0%) 284 2.3e-05
(0.0162) 		0.000447
(0.293) 		0.0324
(1.00) 		0.242
(1.00) 		0.000163
(0.109) 		0.000127
(0.0858) 		0.0233
(1.00) 		0.0161
(1.00) 		0.141
(1.00) 		0.00205
(1.00)
17p loss 0 (0%) 241 6.43e-15
(4.93e-12) 		8.72e-07
(0.000643) 		0.671
(1.00) 		0.897
(1.00) 		0.000141
(0.0954) 		0.00103
(0.656) 		0.00872
(1.00) 		0.000645
(0.417) 		0.00174
(1.00) 		0.00299
(1.00)
1q gain 0 (0%) 263 1.75e-06
(0.00128) 		0.000395
(0.26) 		0.00222
(1.00) 		0.00297
(1.00) 		8.31e-05
(0.0567) 		0.000934
(0.598) 		0.00112
(0.709) 		0.026
(1.00) 		0.0152
(1.00) 		0.00865
(1.00)
2p gain 0 (0%) 281 2.12e-05
(0.0151) 		0.00148
(0.932) 		0.012
(1.00) 		0.874
(1.00) 		0.167
(1.00) 		0.116
(1.00) 		0.000635
(0.411) 		0.0631
(1.00) 		0.000278
(0.185) 		0.0127
(1.00)
6p gain 0 (0%) 279 1.07e-06
(0.000788) 		6.02e-05
(0.0416) 		0.928
(1.00) 		0.743
(1.00) 		0.00286
(1.00) 		0.0235
(1.00) 		0.000417
(0.274) 		0.019
(1.00) 		0.000748
(0.482) 		0.0035
(1.00)
6q gain 0 (0%) 283 1.08e-05
(0.00775) 		0.000353
(0.233) 		0.88
(1.00) 		0.866
(1.00) 		0.00588
(1.00) 		0.00253
(1.00) 		0.00244
(1.00) 		0.101
(1.00) 		0.0052
(1.00) 		0.0148
(1.00)
7p gain 0 (0%) 210 3.91e-15
(3.01e-12) 		3.85e-05
(0.0269) 		0.382
(1.00) 		0.36
(1.00) 		0.00898
(1.00) 		0.0704
(1.00) 		0.188
(1.00) 		0.0653
(1.00) 		0.0066
(1.00) 		0.00339
(1.00)
13q gain 0 (0%) 240 1.3e-07
(9.69e-05) 		0.000325
(0.216) 		0.266
(1.00) 		0.377
(1.00) 		0.0108
(1.00) 		0.386
(1.00) 		0.00385
(1.00) 		0.0331
(1.00) 		0.0018
(1.00) 		0.0281
(1.00)
18p gain 0 (0%) 280 0.000284
(0.189) 		3.87e-05
(0.027) 		0.0855
(1.00) 		0.241
(1.00) 		0.135
(1.00) 		0.257
(1.00) 		0.548
(1.00) 		0.112
(1.00) 		0.668
(1.00) 		0.089
(1.00)
5p loss 0 (0%) 288 1.74e-06
(0.00128) 		0.00392
(1.00) 		0.534
(1.00) 		0.414
(1.00) 		0.00375
(1.00) 		0.000329
(0.218) 		0.164
(1.00) 		0.0421
(1.00) 		0.13
(1.00) 		0.0153
(1.00)
11p loss 0 (0%) 286 3.13e-05
(0.0219) 		5.39e-05
(0.0374) 		0.00671
(1.00) 		0.443
(1.00) 		0.208
(1.00) 		0.0226
(1.00) 		0.161
(1.00) 		0.149
(1.00) 		0.00714
(1.00) 		0.318
(1.00)
15q loss 0 (0%) 280 3.08e-08
(2.3e-05) 		2.34e-05
(0.0165) 		0.0102
(1.00) 		0.0317
(1.00) 		0.00641
(1.00) 		0.00117
(0.741) 		0.00183
(1.00) 		0.000712
(0.46) 		0.0496
(1.00) 		0.0036
(1.00)
18q loss 0 (0%) 253 2.54e-05
(0.0178) 		0.0206
(1.00) 		0.0365
(1.00) 		0.0939
(1.00) 		0.00255
(1.00) 		9.55e-05
(0.0648) 		0.0244
(1.00) 		0.0257
(1.00) 		0.0306
(1.00) 		0.0422
(1.00)
21q loss 0 (0%) 244 1.96e-08
(1.47e-05) 		6.83e-06
(0.00492) 		0.311
(1.00) 		0.74
(1.00) 		0.109
(1.00) 		0.000966
(0.618) 		0.0319
(1.00) 		0.681
(1.00) 		0.126
(1.00) 		0.404
(1.00)
2q gain 0 (0%) 282 3.73e-05
(0.0261) 		0.0108
(1.00) 		0.0379
(1.00) 		0.771
(1.00) 		0.0375
(1.00) 		0.0172
(1.00) 		0.00648
(1.00) 		0.127
(1.00) 		0.00672
(1.00) 		0.0264
(1.00)
7q gain 0 (0%) 228 9.67e-15
(7.41e-12) 		0.000562
(0.366) 		0.398
(1.00) 		0.771
(1.00) 		0.16
(1.00) 		0.337
(1.00) 		0.255
(1.00) 		0.429
(1.00) 		0.261
(1.00) 		0.0539
(1.00)
8p gain 0 (0%) 214 0.0394
(1.00) 		0.00044
(0.289) 		0.0527
(1.00) 		0.0487
(1.00) 		0.0501
(1.00) 		0.0386
(1.00) 		0.00762
(1.00) 		0.0496
(1.00) 		2e-05
(0.0142) 		0.00194
(1.00)
10p gain 0 (0%) 260 5.75e-11
(4.36e-08) 		0.00204
(1.00) 		0.822
(1.00) 		0.765
(1.00) 		0.0529
(1.00) 		0.0134
(1.00) 		0.585
(1.00) 		0.0173
(1.00) 		0.532
(1.00) 		0.00467
(1.00)
10q gain 0 (0%) 279 6.15e-07
(0.000455) 		0.0481
(1.00) 		0.718
(1.00) 		0.501
(1.00) 		0.471
(1.00) 		0.64
(1.00) 		0.661
(1.00) 		0.782
(1.00) 		0.574
(1.00) 		0.183
(1.00)
1p loss 0 (0%) 291 8.32e-06
(0.00598) 		0.0945
(1.00) 		0.151
(1.00) 		0.5
(1.00) 		0.408
(1.00) 		0.158
(1.00) 		0.835
(1.00) 		0.652
(1.00) 		0.225
(1.00) 		0.794
(1.00)
3p loss 0 (0%) 281 1.31e-06
(0.000966) 		0.00152
(0.95) 		0.182
(1.00) 		0.508
(1.00) 		0.000568
(0.369) 		0.0234
(1.00) 		0.00155
(0.969) 		0.112
(1.00) 		0.0346
(1.00) 		0.0211
(1.00)
3q loss 0 (0%) 291 7.61e-05
(0.0521) 		0.0197
(1.00) 		0.613
(1.00) 		0.927
(1.00) 		0.000459
(0.3) 		0.0965
(1.00) 		0.000747
(0.482) 		0.284
(1.00) 		0.00978
(1.00) 		0.265
(1.00)
7q loss 0 (0%) 292 2.12e-05
(0.0151) 		0.0414
(1.00) 		0.307
(1.00) 		0.479
(1.00) 		0.0156
(1.00) 		0.265
(1.00) 		0.0177
(1.00) 		0.103
(1.00) 		0.0178
(1.00) 		0.21
(1.00)
9q loss 0 (0%) 280 8.9e-08
(6.64e-05) 		0.00415
(1.00) 		0.265
(1.00) 		0.0634
(1.00) 		0.0695
(1.00) 		0.042
(1.00) 		0.247
(1.00) 		0.621
(1.00) 		0.712
(1.00) 		0.122
(1.00)
10q loss 0 (0%) 289 1.63e-05
(0.0116) 		0.00307
(1.00) 		0.547
(1.00) 		0.553
(1.00) 		0.012
(1.00) 		0.0536
(1.00) 		0.00374
(1.00) 		0.0639
(1.00) 		0.26
(1.00) 		0.0129
(1.00)
11q loss 0 (0%) 289 3.36e-05
(0.0235) 		0.00892
(1.00) 		0.399
(1.00) 		0.811
(1.00) 		0.422
(1.00) 		0.225
(1.00) 		0.358
(1.00) 		0.579
(1.00) 		0.0127
(1.00) 		0.527
(1.00)
14q loss 0 (0%) 277 7.85e-08
(5.86e-05) 		0.000905
(0.581) 		0.526
(1.00) 		0.672
(1.00) 		0.00125
(0.786) 		0.00364
(1.00) 		0.0342
(1.00) 		0.0483
(1.00) 		0.567
(1.00) 		0.0209
(1.00)
17q loss 0 (0%) 286 8.04e-05
(0.0549) 		0.0245
(1.00) 		0.772
(1.00) 		0.53
(1.00) 		0.0175
(1.00) 		0.0122
(1.00) 		0.0455
(1.00) 		0.00451
(1.00) 		0.111
(1.00) 		0.156
(1.00)
20p loss 0 (0%) 296 0.000145
(0.0976) 		0.017
(1.00) 		0.69
(1.00) 		0.074
(1.00) 		0.000993
(0.632) 		0.173
(1.00) 		0.438
(1.00) 		0.512
(1.00) 		0.17
(1.00) 		0.415
(1.00)
1p gain 0 (0%) 291 0.0016
(0.995) 		0.507
(1.00) 		0.0327
(1.00) 		0.204
(1.00) 		0.13
(1.00) 		0.0928
(1.00) 		0.277
(1.00) 		0.0324
(1.00) 		0.149
(1.00) 		0.275
(1.00)
3p gain 0 (0%) 292 1
(1.00) 		0.202
(1.00) 		0.142
(1.00) 		0.0144
(1.00) 		0.336
(1.00) 		0.362
(1.00) 		0.166
(1.00) 		0.823
(1.00) 		0.109
(1.00) 		0.512
(1.00)
3q gain 0 (0%) 274 0.00815
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.0224
(1.00) 		0.0231
(1.00) 		0.4
(1.00) 		0.138
(1.00) 		0.0834
(1.00) 		0.117
(1.00)
4p gain 0 (0%) 300 0.0117
(1.00) 		0.286
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.111
(1.00) 		0.444
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.789
(1.00)
5q gain 0 (0%) 295 0.0436
(1.00) 		0.95
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.125
(1.00) 		0.545
(1.00) 		0.282
(1.00) 		0.921
(1.00) 		0.687
(1.00) 		0.127
(1.00)
9p gain 0 (0%) 283 0.122
(1.00) 		0.139
(1.00) 		0.309
(1.00) 		0.346
(1.00) 		0.439
(1.00) 		0.309
(1.00) 		0.729
(1.00) 		0.0345
(1.00) 		0.668
(1.00) 		0.0566
(1.00)
9q gain 0 (0%) 276 0.0384
(1.00) 		0.113
(1.00) 		0.117
(1.00) 		0.24
(1.00) 		0.583
(1.00) 		0.252
(1.00) 		0.97
(1.00) 		0.447
(1.00) 		0.823
(1.00) 		0.152
(1.00)
11p gain 0 (0%) 293 0.784
(1.00) 		0.115
(1.00) 		0.84
(1.00) 		0.911
(1.00) 		0.537
(1.00) 		0.183
(1.00) 		0.0863
(1.00) 		0.05
(1.00) 		0.521
(1.00) 		0.0258
(1.00)
11q gain 0 (0%) 285 0.186
(1.00) 		0.0338
(1.00) 		0.949
(1.00) 		0.523
(1.00) 		0.382
(1.00) 		0.0634
(1.00) 		0.0571
(1.00) 		0.0303
(1.00) 		0.0849
(1.00) 		0.00818
(1.00)
12p gain 0 (0%) 270 0.00281
(1.00) 		0.178
(1.00) 		0.124
(1.00) 		0.327
(1.00) 		0.0616
(1.00) 		0.152
(1.00) 		0.00352
(1.00) 		0.453
(1.00) 		0.00192
(1.00) 		0.022
(1.00)
12q gain 0 (0%) 277 0.11
(1.00) 		0.168
(1.00) 		0.336
(1.00) 		0.243
(1.00) 		0.819
(1.00) 		0.635
(1.00) 		0.334
(1.00) 		0.26
(1.00) 		0.0164
(1.00) 		0.0453
(1.00)
14q gain 0 (0%) 300 0.0536
(1.00) 		0.283
(1.00) 		0.0359
(1.00) 		0.532
(1.00) 		0.28
(1.00) 		0.612
(1.00) 		0.43
(1.00) 		0.34
(1.00)
15q gain 0 (0%) 295 0.00736
(1.00) 		0.543
(1.00) 		0.0364
(1.00) 		0.824
(1.00) 		0.0723
(1.00) 		0.00699
(1.00) 		0.724
(1.00) 		0.153
(1.00) 		0.336
(1.00) 		0.0613
(1.00)
16p gain 0 (0%) 292 0.0453
(1.00) 		0.116
(1.00) 		0.782
(1.00) 		0.916
(1.00) 		0.0407
(1.00) 		0.814
(1.00) 		0.726
(1.00) 		0.0964
(1.00) 		0.113
(1.00) 		0.674
(1.00)
16q gain 0 (0%) 293 0.0187
(1.00) 		0.826
(1.00) 		0.569
(1.00) 		0.278
(1.00) 		0.17
(1.00) 		0.581
(1.00) 		0.757
(1.00) 		0.121
(1.00) 		0.572
(1.00) 		1
(1.00)
17p gain 0 (0%) 298 0.011
(1.00) 		0.457
(1.00) 		0.626
(1.00) 		0.135
(1.00) 		0.539
(1.00) 		1
(1.00) 		0.636
(1.00) 		0.89
(1.00) 		0.0726
(1.00) 		0.56
(1.00)
17q gain 0 (0%) 290 0.00908
(1.00) 		0.664
(1.00) 		0.598
(1.00) 		0.333
(1.00) 		0.172
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.439
(1.00) 		0.135
(1.00) 		0.253
(1.00)
18q gain 0 (0%) 291 0.0496
(1.00) 		0.0615
(1.00) 		0.221
(1.00) 		0.0943
(1.00) 		0.316
(1.00) 		0.189
(1.00) 		0.112
(1.00) 		0.116
(1.00) 		0.0397
(1.00) 		0.478
(1.00)
19p gain 0 (0%) 292 0.636
(1.00) 		0.0219
(1.00) 		0.685
(1.00) 		0.217
(1.00) 		0.857
(1.00) 		0.399
(1.00) 		0.493
(1.00) 		0.935
(1.00) 		0.495
(1.00) 		0.552
(1.00)
19q gain 0 (0%) 273 0.0875
(1.00) 		0.382
(1.00) 		0.487
(1.00) 		0.268
(1.00) 		0.245
(1.00) 		0.0624
(1.00) 		0.139
(1.00) 		0.218
(1.00) 		0.249
(1.00) 		0.431
(1.00)
21q gain 0 (0%) 302 0.105
(1.00) 		0.86
(1.00) 		0.529
(1.00) 		0.411
(1.00) 		0.112
(1.00) 		0.343
(1.00) 		0.311
(1.00) 		0.195
(1.00)
22q gain 0 (0%) 299 0.0208
(1.00) 		0.181
(1.00) 		0.866
(1.00) 		0.135
(1.00) 		0.741
(1.00) 		0.35
(1.00) 		0.253
(1.00) 		0.244
(1.00) 		0.185
(1.00) 		0.308
(1.00)
Xq gain 0 (0%) 300 0.361
(1.00) 		0.223
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.135
(1.00) 		0.265
(1.00) 		0.134
(1.00) 		0.00969
(1.00) 		0.816
(1.00) 		0.0193
(1.00)
1q loss 0 (0%) 302 0.74
(1.00) 		0.86
(1.00) 		0.724
(1.00) 		0.196
(1.00) 		0.516
(1.00) 		0.26
(1.00) 		0.194
(1.00) 		0.436
(1.00)
2p loss 0 (0%) 299 0.00486
(1.00) 		0.4
(1.00) 		0.067
(1.00) 		0.422
(1.00) 		0.108
(1.00) 		0.0273
(1.00) 		0.385
(1.00) 		0.0471
(1.00) 		0.508
(1.00) 		0.712
(1.00)
2q loss 0 (0%) 300 0.0117
(1.00) 		0.68
(1.00) 		0.745
(1.00) 		0.728
(1.00) 		0.279
(1.00) 		0.0737
(1.00) 		0.631
(1.00) 		0.0791
(1.00) 		0.816
(1.00) 		0.34
(1.00)
6p loss 0 (0%) 291 0.00837
(1.00) 		0.29
(1.00) 		0.269
(1.00) 		0.126
(1.00) 		0.165
(1.00) 		0.454
(1.00) 		0.835
(1.00) 		0.345
(1.00) 		0.494
(1.00) 		0.527
(1.00)
6q loss 0 (0%) 287 0.00283
(1.00) 		0.107
(1.00) 		0.108
(1.00) 		0.0653
(1.00) 		0.0299
(1.00) 		0.203
(1.00) 		0.511
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.885
(1.00)
7p loss 0 (0%) 301 0.0273
(1.00) 		0.217
(1.00) 		0.106
(1.00) 		0.109
(1.00) 		0.444
(1.00) 		0.557
(1.00) 		0.287
(1.00)
8q loss 0 (0%) 297 0.00513
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.497
(1.00) 		0.61
(1.00) 		0.89
(1.00) 		0.144
(1.00) 		0.0583
(1.00) 		0.185
(1.00) 		0.75
(1.00)
10p loss 0 (0%) 289 0.000506
(0.33) 		0.00808
(1.00) 		0.123
(1.00) 		0.254
(1.00) 		0.0317
(1.00) 		0.0237
(1.00) 		0.02
(1.00) 		0.0169
(1.00) 		0.183
(1.00) 		0.011
(1.00)
12q loss 0 (0%) 293 0.0015
(0.938) 		0.00679
(1.00) 		0.0734
(1.00) 		0.839
(1.00) 		0.0432
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.154
(1.00) 		0.91
(1.00) 		0.0147
(1.00)
13q loss 0 (0%) 294 0.000478
(0.312) 		0.106
(1.00) 		0.619
(1.00) 		0.638
(1.00) 		0.519
(1.00) 		0.225
(1.00) 		0.213
(1.00) 		0.794
(1.00) 		0.46
(1.00) 		0.897
(1.00)
18p loss 0 (0%) 265 0.000837
(0.538) 		0.013
(1.00) 		0.244
(1.00) 		0.85
(1.00) 		0.026
(1.00) 		0.00499
(1.00) 		0.0528
(1.00) 		0.113
(1.00) 		0.00277
(1.00) 		0.144
(1.00)
Xq loss 0 (0%) 290 0.00391
(1.00) 		0.0701
(1.00) 		0.616
(1.00) 		0.389
(1.00) 		0.274
(1.00) 		0.116
(1.00) 		0.00731
(1.00) 		0.269
(1.00) 		0.00672
(1.00) 		0.331
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
1Q GAIN CNV 6 10 26
1Q GAIN WILD-TYPE 144 36 83

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 8.31e-05 (Chi-square test), Q value = 0.057

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
1Q GAIN CNV 7 1 4 6 19
1Q GAIN WILD-TYPE 54 62 39 36 43

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.015

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
2P GAIN CNV 2 8 14
2P GAIN WILD-TYPE 148 38 95

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000278 (Fisher's exact test), Q value = 0.19

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 78 127
2P GAIN CNV 4 0 18
2P GAIN WILD-TYPE 50 78 109

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.026

Table S5.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
2Q GAIN CNV 2 8 13
2Q GAIN WILD-TYPE 148 38 96

Figure S5.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.0023

Table S6.  Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
5P GAIN CNV 7 8 28
5P GAIN WILD-TYPE 143 38 81

Figure S6.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 6.25e-05 (Chi-square test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
5P GAIN CNV 7 2 4 5 20
5P GAIN WILD-TYPE 54 61 39 37 42

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000367 (Fisher's exact test), Q value = 0.24

Table S8.  Gene #8: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
5P GAIN CNV 2 19 17
5P GAIN WILD-TYPE 64 122 47

Figure S8.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00079

Table S9.  Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
6P GAIN CNV 2 3 21
6P GAIN WILD-TYPE 148 43 88

Figure S9.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 6.02e-05 (Fisher's exact test), Q value = 0.042

Table S10.  Gene #10: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6P GAIN CNV 0 7 0 14
6P GAIN WILD-TYPE 37 73 65 62

Figure S10.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0077

Table S11.  Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
6Q GAIN CNV 2 2 18
6Q GAIN WILD-TYPE 148 44 91

Figure S11.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.000353 (Fisher's exact test), Q value = 0.23

Table S12.  Gene #11: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6Q GAIN CNV 0 6 0 12
6Q GAIN WILD-TYPE 37 74 65 64

Figure S12.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.91e-15 (Fisher's exact test), Q value = 3e-12

Table S13.  Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
7P GAIN CNV 19 34 42
7P GAIN WILD-TYPE 131 12 67

Figure S13.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.027

Table S14.  Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
7P GAIN CNV 11 30 6 32
7P GAIN WILD-TYPE 26 50 59 44

Figure S14.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 9.67e-15 (Fisher's exact test), Q value = 7.4e-12

Table S15.  Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
7Q GAIN CNV 18 34 25
7Q GAIN WILD-TYPE 132 12 84

Figure S15.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S16.  Gene #14: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 78 127
8P GAIN CNV 20 7 44
8P GAIN WILD-TYPE 34 71 83

Figure S16.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2.44e-07 (Fisher's exact test), Q value = 0.00018

Table S17.  Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
8Q GAIN CNV 13 39 7 39
8Q GAIN WILD-TYPE 24 41 58 37

Figure S17.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.000343 (Chi-square test), Q value = 0.23

Table S18.  Gene #15: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
8Q GAIN CNV 24 14 11 21 35
8Q GAIN WILD-TYPE 37 49 32 21 27

Figure S18.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 91 114
8Q GAIN CNV 43 21 58
8Q GAIN WILD-TYPE 57 70 56

Figure S19.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.031

Table S20.  Gene #15: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 78 127
8Q GAIN CNV 24 14 60
8Q GAIN WILD-TYPE 30 64 67

Figure S20.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 72 130
8Q GAIN CNV 30 12 56
8Q GAIN WILD-TYPE 27 60 74

Figure S21.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 5.75e-11 (Fisher's exact test), Q value = 4.4e-08

Table S22.  Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
10P GAIN CNV 3 9 33
10P GAIN WILD-TYPE 147 37 76

Figure S22.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 6.15e-07 (Fisher's exact test), Q value = 0.00045

Table S23.  Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
10Q GAIN CNV 3 1 22
10Q GAIN WILD-TYPE 147 45 87

Figure S23.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1.3e-07 (Fisher's exact test), Q value = 9.7e-05

Table S24.  Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
13Q GAIN CNV 14 21 30
13Q GAIN WILD-TYPE 136 25 79

Figure S24.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.22

Table S25.  Gene #24: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
13Q GAIN CNV 7 15 5 28
13Q GAIN WILD-TYPE 30 65 60 48

Figure S25.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.19

Table S26.  Gene #31: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
18P GAIN CNV 4 3 18
18P GAIN WILD-TYPE 146 43 91

Figure S26.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 3.87e-05 (Fisher's exact test), Q value = 0.027

Table S27.  Gene #31: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
18P GAIN CNV 0 5 0 14
18P GAIN WILD-TYPE 37 75 65 62

Figure S27.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 7.59e-18 (Fisher's exact test), Q value = 5.8e-15

Table S28.  Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
20P GAIN CNV 31 41 56
20P GAIN WILD-TYPE 119 5 53

Figure S28.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 5.66e-09 (Fisher's exact test), Q value = 4.3e-06

Table S29.  Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20P GAIN CNV 21 30 8 46
20P GAIN WILD-TYPE 16 50 57 30

Figure S29.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 7.19e-07 (Chi-square test), Q value = 0.00053

Table S30.  Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
20P GAIN CNV 19 13 14 23 41
20P GAIN WILD-TYPE 42 50 29 19 21

Figure S30.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.41e-06 (Fisher's exact test), Q value = 0.0018

Table S31.  Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
20P GAIN CNV 12 59 39
20P GAIN WILD-TYPE 54 82 25

Figure S31.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.015

Table S32.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 91 114
20P GAIN CNV 40 23 65
20P GAIN WILD-TYPE 60 68 49

Figure S32.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.86e-07 (Fisher's exact test), Q value = 0.00043

Table S33.  Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
20P GAIN CNV 52 51 25
20P GAIN WILD-TYPE 81 26 70

Figure S33.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.99e-06 (Fisher's exact test), Q value = 0.0029

Table S34.  Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 72 130
20P GAIN CNV 38 17 50
20P GAIN WILD-TYPE 19 55 80

Figure S34.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.08e-26 (Fisher's exact test), Q value = 2.4e-23

Table S35.  Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
20Q GAIN CNV 33 43 81
20Q GAIN WILD-TYPE 117 3 28

Figure S35.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 7.34e-14 (Fisher's exact test), Q value = 5.6e-11

Table S36.  Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20Q GAIN CNV 21 37 12 63
20Q GAIN WILD-TYPE 16 43 53 13

Figure S36.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.83e-10 (Chi-square test), Q value = 1.4e-07

Table S37.  Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
20Q GAIN CNV 22 17 19 25 53
20Q GAIN WILD-TYPE 39 46 24 17 9

Figure S37.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.23e-10 (Fisher's exact test), Q value = 5.4e-07

Table S38.  Gene #36: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
20Q GAIN CNV 16 69 51
20Q GAIN WILD-TYPE 50 72 13

Figure S38.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 3.03e-07 (Fisher's exact test), Q value = 0.00022

Table S39.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 91 114
20Q GAIN CNV 44 32 81
20Q GAIN WILD-TYPE 56 59 33

Figure S39.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.79e-12 (Fisher's exact test), Q value = 4.4e-09

Table S40.  Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
20Q GAIN CNV 61 65 31
20Q GAIN WILD-TYPE 72 12 64

Figure S40.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.51e-10 (Fisher's exact test), Q value = 1.1e-07

Table S41.  Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 72 130
20Q GAIN CNV 48 19 66
20Q GAIN WILD-TYPE 9 53 64

Figure S41.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 8.32e-06 (Fisher's exact test), Q value = 0.006

Table S42.  Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
1P LOSS CNV 0 1 13
1P LOSS WILD-TYPE 150 45 96

Figure S42.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00097

Table S43.  Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
3P LOSS CNV 1 5 18
3P LOSS WILD-TYPE 149 41 91

Figure S43.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.052

Table S44.  Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
3Q LOSS CNV 0 3 11
3Q LOSS WILD-TYPE 150 43 98

Figure S44.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 2.31e-11 (Fisher's exact test), Q value = 1.7e-08

Table S45.  Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
4P LOSS CNV 6 9 40
4P LOSS WILD-TYPE 144 37 69

Figure S45.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 8.51e-05 (Chi-square test), Q value = 0.058

Table S46.  Gene #46: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
4P LOSS CNV 7 5 5 6 23
4P LOSS WILD-TYPE 54 58 38 36 39

Figure S46.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.56e-05 (Fisher's exact test), Q value = 0.045

Table S47.  Gene #46: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
4P LOSS CNV 6 17 23
4P LOSS WILD-TYPE 60 124 41

Figure S47.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.16e-05 (Fisher's exact test), Q value = 0.062

Table S48.  Gene #46: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
4P LOSS CNV 15 27 13
4P LOSS WILD-TYPE 118 50 82

Figure S48.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 2.28e-14 (Fisher's exact test), Q value = 1.7e-11

Table S49.  Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
4Q LOSS CNV 3 7 41
4Q LOSS WILD-TYPE 147 39 68

Figure S49.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 4.26e-05 (Fisher's exact test), Q value = 0.03

Table S50.  Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4Q LOSS CNV 1 18 4 23
4Q LOSS WILD-TYPE 36 62 61 53

Figure S50.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Chi-square test), Q value = 0.16

Table S51.  Gene #47: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
4Q LOSS CNV 6 4 5 7 21
4Q LOSS WILD-TYPE 55 59 38 35 41

Figure S51.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000226 (Fisher's exact test), Q value = 0.15

Table S52.  Gene #47: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
4Q LOSS CNV 5 17 21
4Q LOSS WILD-TYPE 61 124 43

Figure S52.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.044

Table S53.  Gene #47: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
4Q LOSS CNV 15 26 10
4Q LOSS WILD-TYPE 118 51 85

Figure S53.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.0013

Table S54.  Gene #48: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
5P LOSS CNV 0 2 15
5P LOSS WILD-TYPE 150 44 94

Figure S54.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000329 (Fisher's exact test), Q value = 0.22

Table S55.  Gene #48: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
5P LOSS CNV 1 3 10
5P LOSS WILD-TYPE 65 138 54

Figure S55.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 2.21e-13 (Fisher's exact test), Q value = 1.7e-10

Table S56.  Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
5Q LOSS CNV 0 4 31
5Q LOSS WILD-TYPE 150 42 78

Figure S56.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 2.47e-06 (Fisher's exact test), Q value = 0.0018

Table S57.  Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
5Q LOSS CNV 0 11 1 20
5Q LOSS WILD-TYPE 37 69 64 56

Figure S57.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 4.12e-06 (Chi-square test), Q value = 0.003

Table S58.  Gene #49: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
5Q LOSS CNV 4 2 2 4 19
5Q LOSS WILD-TYPE 57 61 41 38 43

Figure S58.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.94e-06 (Fisher's exact test), Q value = 0.0043

Table S59.  Gene #49: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
5Q LOSS CNV 3 9 19
5Q LOSS WILD-TYPE 63 132 45

Figure S59.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000273 (Fisher's exact test), Q value = 0.18

Table S60.  Gene #49: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
5Q LOSS CNV 11 19 5
5Q LOSS WILD-TYPE 122 58 90

Figure S60.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.44e-05 (Fisher's exact test), Q value = 0.057

Table S61.  Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 72 130
5Q LOSS CNV 17 3 13
5Q LOSS WILD-TYPE 40 69 117

Figure S61.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.015

Table S62.  Gene #53: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
7Q LOSS CNV 0 1 12
7Q LOSS WILD-TYPE 150 45 97

Figure S62.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2.68e-06 (Fisher's exact test), Q value = 0.002

Table S63.  Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
8P LOSS CNV 3 5 22
8P LOSS WILD-TYPE 147 41 87

Figure S63.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.000323 (Fisher's exact test), Q value = 0.21

Table S64.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 91 114
8P LOSS CNV 10 1 19
8P LOSS WILD-TYPE 90 90 95

Figure S64.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.73e-05 (Fisher's exact test), Q value = 0.066

Table S65.  Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 78 127
8P LOSS CNV 2 1 22
8P LOSS WILD-TYPE 52 77 105

Figure S65.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.64e-13 (Fisher's exact test), Q value = 1.3e-10

Table S66.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
9P LOSS CNV 4 6 41
9P LOSS WILD-TYPE 146 40 68

Figure S66.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.019

Table S67.  Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
9P LOSS CNV 0 13 6 24
9P LOSS WILD-TYPE 37 67 59 52

Figure S67.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.000171 (Chi-square test), Q value = 0.12

Table S68.  Gene #56: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
9P LOSS CNV 5 5 9 6 22
9P LOSS WILD-TYPE 56 58 34 36 40

Figure S68.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 8.9e-08 (Fisher's exact test), Q value = 6.6e-05

Table S69.  Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
9Q LOSS CNV 2 1 22
9Q LOSS WILD-TYPE 148 45 87

Figure S69.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.012

Table S70.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
10Q LOSS CNV 0 6 10
10Q LOSS WILD-TYPE 150 40 99

Figure S70.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.022

Table S71.  Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
11P LOSS CNV 2 1 16
11P LOSS WILD-TYPE 148 45 93

Figure S71.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.037

Table S72.  Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
11P LOSS CNV 0 2 0 12
11P LOSS WILD-TYPE 37 78 65 64

Figure S72.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.36e-05 (Fisher's exact test), Q value = 0.024

Table S73.  Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
11Q LOSS CNV 1 1 14
11Q LOSS WILD-TYPE 149 45 95

Figure S73.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 2.3e-05 (Fisher's exact test), Q value = 0.016

Table S74.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
12P LOSS CNV 2 2 17
12P LOSS WILD-TYPE 148 44 92

Figure S74.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Chi-square test), Q value = 0.11

Table S75.  Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
12P LOSS CNV 1 1 3 1 12
12P LOSS WILD-TYPE 60 62 40 41 50

Figure S75.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.086

Table S76.  Gene #62: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
12P LOSS CNV 1 5 12
12P LOSS WILD-TYPE 65 136 52

Figure S76.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 7.85e-08 (Fisher's exact test), Q value = 5.9e-05

Table S77.  Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
14Q LOSS CNV 3 1 24
14Q LOSS WILD-TYPE 147 45 85

Figure S77.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 3.08e-08 (Fisher's exact test), Q value = 2.3e-05

Table S78.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
15Q LOSS CNV 0 7 18
15Q LOSS WILD-TYPE 150 39 91

Figure S78.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.017

Table S79.  Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
15Q LOSS CNV 0 7 0 15
15Q LOSS WILD-TYPE 37 73 65 61

Figure S79.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 5.37e-13 (Fisher's exact test), Q value = 4.1e-10

Table S80.  Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
16P LOSS CNV 0 1 28
16P LOSS WILD-TYPE 150 45 81

Figure S80.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.013

Table S81.  Gene #67: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16P LOSS CNV 0 10 0 15
16P LOSS WILD-TYPE 37 70 65 61

Figure S81.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 2.39e-06 (Chi-square test), Q value = 0.0017

Table S82.  Gene #67: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
16P LOSS CNV 3 1 1 4 17
16P LOSS WILD-TYPE 58 62 42 38 45

Figure S82.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.43e-06 (Fisher's exact test), Q value = 0.0039

Table S83.  Gene #67: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
16P LOSS CNV 2 7 17
16P LOSS WILD-TYPE 64 134 47

Figure S83.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0094

Table S84.  Gene #67: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 91 114
16P LOSS CNV 6 1 22
16P LOSS WILD-TYPE 94 90 92

Figure S84.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.038

Table S85.  Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 78 127
16P LOSS CNV 2 1 23
16P LOSS WILD-TYPE 52 77 104

Figure S85.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 4.29e-10 (Fisher's exact test), Q value = 3.2e-07

Table S86.  Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
16Q LOSS CNV 2 2 28
16Q LOSS WILD-TYPE 148 44 81

Figure S86.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 3.51e-06 (Fisher's exact test), Q value = 0.0026

Table S87.  Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16Q LOSS CNV 0 9 0 17
16Q LOSS WILD-TYPE 37 71 65 59

Figure S87.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 5.92e-05 (Chi-square test), Q value = 0.041

Table S88.  Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
16Q LOSS CNV 3 2 4 3 17
16Q LOSS WILD-TYPE 58 61 39 39 45

Figure S88.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.042

Table S89.  Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
16Q LOSS CNV 3 9 17
16Q LOSS WILD-TYPE 63 132 47

Figure S89.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 6.43e-15 (Fisher's exact test), Q value = 4.9e-12

Table S90.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
17P LOSS CNV 5 14 45
17P LOSS WILD-TYPE 145 32 64

Figure S90.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 8.72e-07 (Fisher's exact test), Q value = 0.00064

Table S91.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
17P LOSS CNV 2 18 4 30
17P LOSS WILD-TYPE 35 62 61 46

Figure S91.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.000141 (Chi-square test), Q value = 0.095

Table S92.  Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
17P LOSS CNV 6 5 12 8 23
17P LOSS WILD-TYPE 55 58 31 34 39

Figure S92.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 8.04e-05 (Fisher's exact test), Q value = 0.055

Table S93.  Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
17Q LOSS CNV 1 5 13
17Q LOSS WILD-TYPE 149 41 96

Figure S93.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2.54e-05 (Fisher's exact test), Q value = 0.018

Table S94.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
18Q LOSS CNV 11 12 29
18Q LOSS WILD-TYPE 139 34 80

Figure S94.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.55e-05 (Fisher's exact test), Q value = 0.065

Table S95.  Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
18Q LOSS CNV 2 23 19
18Q LOSS WILD-TYPE 64 118 45

Figure S95.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2.51e-13 (Fisher's exact test), Q value = 1.9e-10

Table S96.  Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
19P LOSS CNV 0 3 30
19P LOSS WILD-TYPE 150 43 79

Figure S96.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0032

Table S97.  Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19P LOSS CNV 0 7 1 19
19P LOSS WILD-TYPE 37 73 64 57

Figure S97.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 3.15e-09 (Chi-square test), Q value = 2.4e-06

Table S98.  Gene #73: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
19P LOSS CNV 2 1 1 3 20
19P LOSS WILD-TYPE 59 62 42 39 42

Figure S98.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0089

Table S99.  Gene #73: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 141 64
19P LOSS CNV 2 8 17
19P LOSS WILD-TYPE 64 133 47

Figure S99.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.0012

Table S100.  Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
19P LOSS CNV 9 21 3
19P LOSS WILD-TYPE 124 56 92

Figure S100.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.33e-05 (Fisher's exact test), Q value = 0.05

Table S101.  Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 72 130
19P LOSS CNV 15 2 10
19P LOSS WILD-TYPE 42 70 120

Figure S101.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.33e-08 (Fisher's exact test), Q value = 1e-05

Table S102.  Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
19Q LOSS CNV 0 3 20
19Q LOSS WILD-TYPE 150 43 89

Figure S102.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.009

Table S103.  Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19Q LOSS CNV 0 2 1 15
19Q LOSS WILD-TYPE 37 78 64 61

Figure S103.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 4.22e-07 (Chi-square test), Q value = 0.00031

Table S104.  Gene #74: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
19Q LOSS CNV 0 1 1 3 15
19Q LOSS WILD-TYPE 61 62 42 39 47

Figure S104.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0089

Table S105.  Gene #74: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 77 95
19Q LOSS CNV 4 16 3
19Q LOSS WILD-TYPE 129 61 92

Figure S105.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.098

Table S106.  Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
20P LOSS CNV 0 0 9
20P LOSS WILD-TYPE 150 46 100

Figure S106.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1.96e-08 (Fisher's exact test), Q value = 1.5e-05

Table S107.  Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
21Q LOSS CNV 11 10 40
21Q LOSS WILD-TYPE 139 36 69

Figure S107.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 6.83e-06 (Fisher's exact test), Q value = 0.0049

Table S108.  Gene #76: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
21Q LOSS CNV 1 28 5 18
21Q LOSS WILD-TYPE 36 52 60 58

Figure S108.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.63e-16 (Fisher's exact test), Q value = 5.1e-13

Table S109.  Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 46 109
22Q LOSS CNV 0 4 36
22Q LOSS WILD-TYPE 150 42 73

Figure S109.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.9e-06 (Fisher's exact test), Q value = 0.0014

Table S110.  Gene #77: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
22Q LOSS CNV 0 9 2 22
22Q LOSS WILD-TYPE 37 71 63 54

Figure S110.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.017

Table S111.  Gene #77: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 90 91
22Q LOSS CNV 4 7 25
22Q LOSS WILD-TYPE 77 83 66

Figure S111.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 5.87e-05 (Chi-square test), Q value = 0.041

Table S112.  Gene #77: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 63 43 42 62
22Q LOSS CNV 4 2 5 3 18
22Q LOSS WILD-TYPE 57 61 38 39 44

Figure S112.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 305

  • Number of significantly arm-level cnvs = 78

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle