Correlation between copy number variations of arm-level result and molecular subtypes
Colon/Rectal Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1R78C71
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/C1R78C71
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 12 molecular subtypes across 575 patients, 103 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q 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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 103 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 Chi-square test
20q gain 0 (0%) 172 4.38e-17
(3.89e-14) 		4.38e-16
(3.88e-13) 		2.22e-46
(2.01e-43) 		1.68e-12
(1.48e-09) 		0.000311
(0.25) 		0.000133
(0.109) 		9.03e-18
(8.04e-15) 		1.13e-13
(9.97e-11) 		0.463
(1.00) 		0.101
(1.00) 		2.65e-09
(2.3e-06) 		1.39e-21
(1.25e-18)
13q gain 0 (0%) 261 4.38e-07
(0.000373) 		0.000109
(0.089) 		1.62e-37
(1.46e-34) 		2.86e-08
(2.47e-05) 		0.0129
(1.00) 		0.0683
(1.00) 		8.54e-09
(7.4e-06) 		6.4e-07
(0.000542) 		0.01
(1.00) 		0.45
(1.00) 		2.85e-07
(0.000244) 		1.21e-10
(1.05e-07)
18p loss 0 (0%) 251 1.24e-13
(1.09e-10) 		3.4e-12
(2.99e-09) 		4.26e-47
(3.85e-44) 		1.35e-18
(1.2e-15) 		0.012
(1.00) 		0.015
(1.00) 		5.39e-16
(4.77e-13) 		2.73e-11
(2.39e-08) 		0.065
(1.00) 		0.787
(1.00) 		1.08e-10
(9.36e-08) 		7.83e-12
(6.85e-09)
18q loss 0 (0%) 223 1.36e-12
(1.19e-09) 		4.31e-12
(3.77e-09) 		6.8e-51
(6.15e-48) 		1.99e-19
(1.78e-16) 		0.0241
(1.00) 		0.0948
(1.00) 		3.96e-16
(3.51e-13) 		3.68e-09
(3.19e-06) 		0.00938
(1.00) 		0.378
(1.00) 		1.07e-09
(9.26e-07) 		5.16e-12
(4.51e-09)
20p gain 0 (0%) 287 0.000145
(0.118) 		1.65e-07
(0.000141) 		4.25e-22
(3.81e-19) 		0.000106
(0.0866) 		0.00725
(1.00) 		0.0222
(1.00) 		3.2e-07
(0.000273) 		3.2e-07
(0.000273) 		0.625
(1.00) 		0.472
(1.00) 		0.000742
(0.587) 		6.81e-08
(5.87e-05)
14q loss 0 (0%) 432 6.52e-05
(0.0537) 		2.84e-07
(0.000243) 		1.12e-31
(1.01e-28) 		1.63e-07
(0.00014) 		0.000364
(0.291) 		0.012
(1.00) 		1.73e-07
(0.000148) 		0.000705
(0.559) 		0.114
(1.00) 		0.709
(1.00) 		1.51e-06
(0.00127) 		0.000145
(0.118)
7p gain 0 (0%) 285 0.00152
(1.00) 		0.00193
(1.00) 		1.89e-21
(1.7e-18) 		8.55e-08
(7.35e-05) 		0.22
(1.00) 		0.0313
(1.00) 		3.72e-08
(3.21e-05) 		9.54e-05
(0.0783) 		0.0703
(1.00) 		0.0304
(1.00) 		0.00865
(1.00) 		4.41e-08
(3.8e-05)
7q gain 0 (0%) 320 0.0019
(1.00) 		0.00889
(1.00) 		6.95e-16
(6.15e-13) 		5.98e-06
(0.005) 		0.777
(1.00) 		0.18
(1.00) 		8.79e-07
(0.000744) 		1.24e-05
(0.0103) 		0.245
(1.00) 		0.155
(1.00) 		0.0465
(1.00) 		4.73e-05
(0.0391)
17p loss 0 (0%) 323 0.000277
(0.223) 		0.00176
(1.00) 		5.49e-22
(4.92e-19) 		1.43e-06
(0.00121) 		0.317
(1.00) 		0.486
(1.00) 		3.25e-06
(0.00272) 		0.000795
(0.628) 		0.027
(1.00) 		0.497
(1.00) 		6.54e-05
(0.0538) 		0.000313
(0.251)
2q gain 0 (0%) 516 0.0178
(1.00) 		8.52e-05
(0.07) 		0.00101
(0.792) 		1.71e-05
(0.0142) 		0.209
(1.00) 		0.806
(1.00) 		0.000234
(0.189) 		0.000824
(0.65) 		0.251
(1.00) 		0.0504
(1.00) 		0.919
(1.00) 		0.0116
(1.00)
11p gain 0 (0%) 536 0.0615
(1.00) 		0.275
(1.00) 		1.71e-05
(0.0142) 		0.000204
(0.165) 		0.826
(1.00) 		0.764
(1.00) 		0.0491
(1.00) 		0.000153
(0.125) 		0.246
(1.00) 		0.882
(1.00) 		0.142
(1.00) 		0.00713
(1.00)
15q loss 0 (0%) 419 0.005
(1.00) 		0.00311
(1.00) 		2.09e-24
(1.88e-21) 		0.0131
(1.00) 		0.303
(1.00) 		0.832
(1.00) 		1.19e-05
(0.00992) 		0.000572
(0.455) 		0.368
(1.00) 		0.246
(1.00) 		0.00873
(1.00) 		0.000158
(0.129)
2p gain 0 (0%) 515 0.0608
(1.00) 		0.000322
(0.258) 		0.00816
(1.00) 		0.000508
(0.405) 		0.0735
(1.00) 		0.357
(1.00) 		0.000224
(0.181) 		0.000137
(0.112) 		0.216
(1.00) 		0.0209
(1.00) 		0.445
(1.00) 		0.00282
(1.00)
17q gain 0 (0%) 508 0.0504
(1.00) 		0.035
(1.00) 		0.000269
(0.216) 		0.00271
(1.00) 		0.649
(1.00) 		0.0748
(1.00) 		1.47e-05
(0.0122) 		0.00195
(1.00) 		0.0785
(1.00) 		0.354
(1.00) 		0.474
(1.00) 		0.257
(1.00)
1p loss 0 (0%) 507 0.245
(1.00) 		0.00443
(1.00) 		7.55e-06
(0.0063) 		0.000189
(0.153) 		0.984
(1.00) 		0.821
(1.00) 		0.0764
(1.00) 		0.00823
(1.00) 		0.193
(1.00) 		0.62
(1.00) 		0.973
(1.00) 		0.0367
(1.00)
8p loss 0 (0%) 430 0.00406
(1.00) 		0.00186
(1.00) 		1.14e-18
(1.02e-15) 		0.000109
(0.089) 		0.28
(1.00) 		0.0393
(1.00) 		0.11
(1.00) 		0.152
(1.00) 		0.515
(1.00) 		0.73
(1.00) 		0.00232
(1.00) 		0.00767
(1.00)
3p gain 0 (0%) 539 0.133
(1.00) 		0.593
(1.00) 		0.000181
(0.147) 		0.148
(1.00) 		0.374
(1.00) 		0.77
(1.00) 		0.26
(1.00) 		0.885
(1.00) 		0.208
(1.00) 		0.366
(1.00) 		0.571
(1.00) 		0.0609
(1.00)
3q gain 0 (0%) 522 0.235
(1.00) 		0.0891
(1.00) 		2.49e-06
(0.00209) 		0.0159
(1.00) 		0.215
(1.00) 		0.655
(1.00) 		0.075
(1.00) 		0.588
(1.00) 		0.111
(1.00) 		0.544
(1.00) 		0.312
(1.00) 		0.133
(1.00)
6p gain 0 (0%) 498 0.185
(1.00) 		0.00295
(1.00) 		1.55e-06
(0.0013) 		0.278
(1.00) 		0.704
(1.00) 		0.12
(1.00) 		0.0227
(1.00) 		0.227
(1.00) 		0.848
(1.00) 		0.392
(1.00) 		0.952
(1.00) 		0.216
(1.00)
6q gain 0 (0%) 504 0.309
(1.00) 		0.0401
(1.00) 		7.47e-07
(0.000633) 		0.112
(1.00) 		0.317
(1.00) 		0.0418
(1.00) 		0.0607
(1.00) 		0.575
(1.00) 		0.749
(1.00) 		0.251
(1.00) 		0.372
(1.00) 		0.0608
(1.00)
8p gain 0 (0%) 467 0.963
(1.00) 		0.717
(1.00) 		1e-08
(8.68e-06) 		0.454
(1.00) 		0.28
(1.00) 		0.215
(1.00) 		0.181
(1.00) 		0.44
(1.00) 		0.49
(1.00) 		0.891
(1.00) 		0.187
(1.00) 		0.898
(1.00)
8q gain 0 (0%) 340 0.145
(1.00) 		0.0172
(1.00) 		1.06e-33
(9.52e-31) 		0.0135
(1.00) 		0.15
(1.00) 		0.33
(1.00) 		0.0011
(0.862) 		0.0265
(1.00) 		0.459
(1.00) 		0.633
(1.00) 		0.0345
(1.00) 		0.147
(1.00)
11q gain 0 (0%) 536 0.0956
(1.00) 		0.0299
(1.00) 		1.33e-06
(0.00112) 		0.000725
(0.575) 		0.497
(1.00) 		0.651
(1.00) 		0.0356
(1.00) 		0.00526
(1.00) 		0.559
(1.00) 		0.406
(1.00) 		0.00378
(1.00) 		0.0582
(1.00)
16p gain 0 (0%) 479 0.0882
(1.00) 		0.165
(1.00) 		1.26e-16
(1.12e-13) 		0.00119
(0.932) 		0.941
(1.00) 		0.0295
(1.00) 		0.0228
(1.00) 		0.136
(1.00) 		0.577
(1.00) 		0.347
(1.00) 		0.631
(1.00) 		0.00678
(1.00)
16q gain 0 (0%) 479 0.0988
(1.00) 		0.174
(1.00) 		3.02e-18
(2.69e-15) 		0.000413
(0.33) 		0.991
(1.00) 		0.0182
(1.00) 		0.0198
(1.00) 		0.0602
(1.00) 		0.465
(1.00) 		0.277
(1.00) 		0.214
(1.00) 		0.00166
(1.00)
19p gain 0 (0%) 523 0.194
(1.00) 		0.146
(1.00) 		5.84e-05
(0.0482) 		0.0188
(1.00) 		0.598
(1.00) 		0.0285
(1.00) 		0.423
(1.00) 		0.474
(1.00) 		0.718
(1.00) 		0.745
(1.00) 		0.965
(1.00) 		0.0747
(1.00)
4p loss 0 (0%) 453 0.227
(1.00) 		0.208
(1.00) 		5.5e-11
(4.79e-08) 		0.00276
(1.00) 		0.693
(1.00) 		0.889
(1.00) 		0.0062
(1.00) 		0.0572
(1.00) 		0.045
(1.00) 		0.769
(1.00) 		0.0802
(1.00) 		0.0273
(1.00)
4q loss 0 (0%) 462 0.213
(1.00) 		0.134
(1.00) 		3.18e-12
(2.79e-09) 		0.00888
(1.00) 		0.606
(1.00) 		0.81
(1.00) 		0.00213
(1.00) 		0.0535
(1.00) 		0.0122
(1.00) 		0.564
(1.00) 		0.0346
(1.00) 		0.048
(1.00)
5q loss 0 (0%) 515 0.0144
(1.00) 		0.0106
(1.00) 		5.53e-07
(0.00047) 		0.17
(1.00) 		0.186
(1.00) 		0.812
(1.00) 		0.0211
(1.00) 		0.0985
(1.00) 		0.963
(1.00) 		0.579
(1.00) 		0.518
(1.00) 		0.0399
(1.00)
9p loss 0 (0%) 536 0.911
(1.00) 		0.286
(1.00) 		2.9e-05
(0.024) 		0.00499
(1.00) 		0.247
(1.00) 		0.147
(1.00) 		0.102
(1.00) 		0.0221
(1.00) 		0.127
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.0515
(1.00)
9q loss 0 (0%) 538 0.241
(1.00) 		0.0097
(1.00) 		1.95e-06
(0.00164) 		0.000468
(0.373) 		0.692
(1.00) 		0.209
(1.00) 		0.0214
(1.00) 		0.0167
(1.00) 		0.0491
(1.00) 		0.82
(1.00) 		0.122
(1.00) 		0.0228
(1.00)
10q loss 0 (0%) 529 0.335
(1.00) 		0.419
(1.00) 		1.44e-06
(0.00121) 		0.148
(1.00) 		0.0204
(1.00) 		0.772
(1.00) 		0.102
(1.00) 		0.231
(1.00) 		0.714
(1.00) 		0.811
(1.00) 		0.398
(1.00) 		0.916
(1.00)
12p loss 0 (0%) 542 0.0938
(1.00) 		0.228
(1.00) 		5.42e-07
(0.000461) 		0.271
(1.00) 		0.694
(1.00) 		0.373
(1.00) 		0.201
(1.00) 		0.46
(1.00) 		0.541
(1.00) 		0.222
(1.00) 		0.0764
(1.00) 		0.633
(1.00)
12q loss 0 (0%) 547 0.352
(1.00) 		0.0834
(1.00) 		1.11e-06
(0.000936) 		0.521
(1.00) 		0.885
(1.00) 		0.619
(1.00) 		0.143
(1.00) 		0.189
(1.00) 		0.616
(1.00) 		0.681
(1.00) 		0.132
(1.00) 		0.736
(1.00)
19p loss 0 (0%) 555 0.74
(1.00) 		0.431
(1.00) 		1.46e-05
(0.0122) 		0.0476
(1.00) 		0.579
(1.00) 		0.705
(1.00) 		0.00155
(1.00) 		0.00289
(1.00) 		0.235
(1.00) 		0.371
(1.00) 		0.0514
(1.00) 		0.558
(1.00)
19q loss 0 (0%) 557 0.74
(1.00) 		0.431
(1.00) 		0.000235
(0.19) 		0.128
(1.00) 		0.625
(1.00) 		0.912
(1.00) 		0.00155
(1.00) 		0.00289
(1.00) 		0.424
(1.00) 		0.0976
(1.00) 		0.0542
(1.00) 		0.408
(1.00)
20p loss 0 (0%) 528 0.0412
(1.00) 		0.184
(1.00) 		4.56e-07
(0.000388) 		0.117
(1.00) 		0.77
(1.00) 		0.365
(1.00) 		0.577
(1.00) 		0.391
(1.00) 		0.554
(1.00) 		0.486
(1.00) 		0.805
(1.00) 		0.686
(1.00)
21q loss 0 (0%) 461 0.305
(1.00) 		0.487
(1.00) 		3.64e-05
(0.0301) 		0.0782
(1.00) 		0.328
(1.00) 		0.31
(1.00) 		0.235
(1.00) 		0.392
(1.00) 		0.118
(1.00) 		0.342
(1.00) 		0.383
(1.00) 		0.166
(1.00)
22q loss 0 (0%) 453 0.0148
(1.00) 		0.00606
(1.00) 		7.8e-14
(6.89e-11) 		0.278
(1.00) 		0.419
(1.00) 		0.264
(1.00) 		0.0676
(1.00) 		0.0646
(1.00) 		0.0662
(1.00) 		0.1
(1.00) 		0.00226
(1.00) 		0.0954
(1.00)
1p gain 0 (0%) 560 0.408
(1.00) 		0.375
(1.00) 		0.932
(1.00) 		0.567
(1.00) 		0.497
(1.00) 		0.128
(1.00) 		0.178
(1.00) 		0.33
(1.00) 		0.111
(1.00) 		0.911
(1.00) 		0.485
(1.00) 		0.0368
(1.00)
1q gain 0 (0%) 495 0.497
(1.00) 		0.96
(1.00) 		0.0158
(1.00) 		0.825
(1.00) 		0.255
(1.00) 		0.15
(1.00) 		0.128
(1.00) 		0.0758
(1.00) 		0.0729
(1.00) 		0.978
(1.00) 		0.159
(1.00) 		0.0036
(1.00)
4p gain 0 (0%) 569 0.0622
(1.00) 		0.226
(1.00) 		0.184
(1.00) 		0.339
(1.00) 		0.137
(1.00) 		0.0525
(1.00) 		0.385
(1.00) 		0.226
(1.00)
4q gain 0 (0%) 568 0.707
(1.00) 		0.719
(1.00) 		0.25
(1.00) 		0.787
(1.00) 		0.732
(1.00) 		0.645
(1.00) 		0.383
(1.00) 		0.809
(1.00)
5p gain 0 (0%) 515 0.138
(1.00) 		0.661
(1.00) 		0.0015
(1.00) 		0.174
(1.00) 		0.795
(1.00) 		0.863
(1.00) 		0.401
(1.00) 		0.4
(1.00) 		0.784
(1.00) 		0.354
(1.00) 		0.853
(1.00) 		0.863
(1.00)
5q gain 0 (0%) 542 0.527
(1.00) 		0.826
(1.00) 		0.00356
(1.00) 		0.0956
(1.00) 		0.742
(1.00) 		0.557
(1.00) 		0.73
(1.00) 		0.446
(1.00) 		0.818
(1.00) 		0.483
(1.00) 		0.488
(1.00) 		0.849
(1.00)
9p gain 0 (0%) 496 0.503
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.791
(1.00) 		0.91
(1.00) 		0.204
(1.00) 		0.539
(1.00) 		0.855
(1.00) 		0.78
(1.00) 		0.781
(1.00) 		0.813
(1.00) 		0.379
(1.00)
9q gain 0 (0%) 511 0.385
(1.00) 		0.854
(1.00) 		0.214
(1.00) 		0.582
(1.00) 		0.612
(1.00) 		0.0336
(1.00) 		0.989
(1.00) 		0.691
(1.00) 		0.408
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.525
(1.00)
10p gain 0 (0%) 547 0.196
(1.00) 		0.628
(1.00) 		0.00981
(1.00) 		0.0135
(1.00) 		0.673
(1.00) 		0.857
(1.00) 		0.617
(1.00) 		0.0446
(1.00) 		0.616
(1.00) 		0.496
(1.00) 		0.00697
(1.00) 		0.46
(1.00)
10q gain 0 (0%) 562 0.887
(1.00) 		0.277
(1.00) 		0.193
(1.00) 		0.0574
(1.00) 		0.597
(1.00) 		0.288
(1.00) 		0.448
(1.00) 		0.0762
(1.00) 		0.694
(1.00) 		0.902
(1.00) 		0.174
(1.00) 		0.693
(1.00)
12p gain 0 (0%) 482 0.383
(1.00) 		0.631
(1.00) 		0.256
(1.00) 		0.0205
(1.00) 		0.629
(1.00) 		0.205
(1.00) 		0.0232
(1.00) 		0.0134
(1.00) 		0.22
(1.00) 		0.112
(1.00) 		0.00132
(1.00) 		0.0114
(1.00)
12q gain 0 (0%) 497 0.328
(1.00) 		0.763
(1.00) 		0.0986
(1.00) 		0.00237
(1.00) 		0.91
(1.00) 		0.339
(1.00) 		0.0353
(1.00) 		0.0154
(1.00) 		0.222
(1.00) 		0.166
(1.00) 		0.00136
(1.00) 		0.00673
(1.00)
14q gain 0 (0%) 556 0.519
(1.00) 		0.251
(1.00) 		0.0301
(1.00) 		0.709
(1.00) 		0.724
(1.00) 		0.397
(1.00) 		0.0605
(1.00) 		0.048
(1.00) 		1
(1.00) 		0.371
(1.00) 		0.11
(1.00) 		0.076
(1.00)
15q gain 0 (0%) 568 0.515
(1.00) 		0.882
(1.00) 		0.133
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.244
(1.00) 		0.87
(1.00) 		0.374
(1.00) 		0.105
(1.00) 		0.866
(1.00)
17p gain 0 (0%) 562 0.78
(1.00) 		0.00703
(1.00) 		1
(1.00) 		0.922
(1.00) 		0.552
(1.00) 		0.721
(1.00) 		0.0157
(1.00) 		0.009
(1.00) 		0.694
(1.00) 		0.902
(1.00) 		0.361
(1.00) 		0.645
(1.00)
18p gain 0 (0%) 554 0.207
(1.00) 		0.0592
(1.00) 		0.00061
(0.484) 		0.0103
(1.00) 		0.514
(1.00) 		0.897
(1.00) 		0.133
(1.00) 		0.391
(1.00) 		0.568
(1.00) 		0.397
(1.00) 		0.55
(1.00) 		0.346
(1.00)
18q gain 0 (0%) 563 0.172
(1.00) 		0.00739
(1.00) 		0.648
(1.00) 		0.468
(1.00) 		0.122
(1.00) 		0.858
(1.00) 		0.105
(1.00) 		0.134
(1.00) 		0.611
(1.00) 		0.349
(1.00)
19q gain 0 (0%) 514 0.0157
(1.00) 		0.0412
(1.00) 		0.0122
(1.00) 		0.0777
(1.00) 		0.233
(1.00) 		0.0383
(1.00) 		0.507
(1.00) 		0.512
(1.00) 		0.832
(1.00) 		0.495
(1.00) 		0.42
(1.00) 		0.163
(1.00)
21q gain 0 (0%) 556 0.456
(1.00) 		0.715
(1.00) 		0.00268
(1.00) 		0.709
(1.00) 		0.48
(1.00) 		0.0895
(1.00) 		0.619
(1.00) 		0.834
(1.00) 		0.686
(1.00) 		0.143
(1.00) 		0.926
(1.00) 		0.617
(1.00)
22q gain 0 (0%) 568 0.691
(1.00) 		0.00703
(1.00) 		0.234
(1.00) 		0.573
(1.00) 		0.685
(1.00) 		0.47
(1.00) 		0.689
(1.00) 		0.499
(1.00) 		0.459
(1.00) 		0.596
(1.00)
Xq gain 0 (0%) 558 0.178
(1.00) 		0.446
(1.00) 		0.0167
(1.00) 		0.34
(1.00) 		0.244
(1.00) 		0.313
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.705
(1.00) 		0.521
(1.00) 		0.881
(1.00)
1q loss 0 (0%) 550 0.559
(1.00) 		0.0258
(1.00) 		0.0823
(1.00) 		0.155
(1.00) 		0.825
(1.00) 		0.949
(1.00) 		0.158
(1.00) 		0.324
(1.00) 		0.425
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.202
(1.00)
2p loss 0 (0%) 565 1
(1.00) 		0.739
(1.00) 		0.0735
(1.00) 		0.0168
(1.00) 		0.658
(1.00) 		0.0151
(1.00) 		0.0133
(1.00)
2q loss 0 (0%) 567 0.74
(1.00) 		0.614
(1.00) 		0.548
(1.00) 		0.157
(1.00) 		0.299
(1.00) 		0.0584
(1.00) 		0.0455
(1.00)
3p loss 0 (0%) 540 1
(1.00) 		0.292
(1.00) 		0.831
(1.00) 		0.834
(1.00) 		0.703
(1.00) 		0.536
(1.00) 		0.441
(1.00) 		0.157
(1.00) 		0.105
(1.00) 		0.729
(1.00) 		0.588
(1.00) 		0.302
(1.00)
3q loss 0 (0%) 558 0.45
(1.00) 		0.0138
(1.00) 		0.757
(1.00) 		0.0198
(1.00) 		0.0903
(1.00) 		0.398
(1.00) 		0.385
(1.00) 		0.184
(1.00) 		0.74
(1.00) 		0.772
(1.00) 		0.903
(1.00) 		0.411
(1.00)
5p loss 0 (0%) 541 0.269
(1.00) 		0.45
(1.00) 		0.000544
(0.433) 		0.0928
(1.00) 		0.556
(1.00) 		0.449
(1.00) 		0.234
(1.00) 		0.0352
(1.00) 		0.969
(1.00) 		0.829
(1.00) 		0.727
(1.00) 		0.0884
(1.00)
6p loss 0 (0%) 557 0.132
(1.00) 		0.186
(1.00) 		0.026
(1.00) 		0.278
(1.00) 		0.611
(1.00) 		0.641
(1.00) 		0.89
(1.00) 		0.601
(1.00) 		0.602
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.646
(1.00)
6q loss 0 (0%) 542 0.784
(1.00) 		0.621
(1.00) 		0.0983
(1.00) 		0.939
(1.00) 		0.132
(1.00) 		0.145
(1.00) 		0.737
(1.00) 		0.677
(1.00) 		0.262
(1.00) 		0.298
(1.00) 		0.679
(1.00) 		0.799
(1.00)
7q loss 0 (0%) 572 0.212
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.764
(1.00) 		1
(1.00)
8q loss 0 (0%) 563 0.669
(1.00) 		0.667
(1.00) 		0.0828
(1.00) 		0.58
(1.00) 		0.0237
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.159
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.692
(1.00)
10p loss 0 (0%) 535 0.72
(1.00) 		0.49
(1.00) 		0.000862
(0.679) 		0.434
(1.00) 		0.053
(1.00) 		0.682
(1.00) 		0.409
(1.00) 		0.532
(1.00) 		0.132
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.973
(1.00)
11p loss 0 (0%) 535 0.73
(1.00) 		0.336
(1.00) 		0.00977
(1.00) 		0.705
(1.00) 		0.322
(1.00) 		0.201
(1.00) 		0.0716
(1.00) 		0.0838
(1.00) 		0.113
(1.00) 		0.359
(1.00) 		0.0803
(1.00) 		0.0629
(1.00)
11q loss 0 (0%) 524 0.827
(1.00) 		0.464
(1.00) 		0.00166
(1.00) 		0.322
(1.00) 		0.731
(1.00) 		0.292
(1.00) 		0.0997
(1.00) 		0.509
(1.00) 		0.129
(1.00) 		0.835
(1.00) 		0.0742
(1.00) 		0.00583
(1.00)
13q loss 0 (0%) 563 0.297
(1.00) 		0.282
(1.00) 		0.0495
(1.00) 		0.181
(1.00) 		0.0716
(1.00) 		0.108
(1.00) 		0.236
(1.00) 		0.668
(1.00) 		0.726
(1.00) 		0.403
(1.00) 		0.438
(1.00) 		0.445
(1.00)
16p loss 0 (0%) 560 0.266
(1.00) 		0.184
(1.00) 		0.0995
(1.00) 		0.181
(1.00) 		0.561
(1.00) 		0.646
(1.00) 		0.589
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.911
(1.00) 		0.602
(1.00) 		0.605
(1.00)
16q loss 0 (0%) 558 0.0284
(1.00) 		0.243
(1.00) 		0.00221
(1.00) 		0.493
(1.00) 		0.459
(1.00) 		0.748
(1.00) 		0.0911
(1.00) 		0.121
(1.00) 		0.134
(1.00) 		0.257
(1.00) 		0.386
(1.00) 		0.34
(1.00)
17q loss 0 (0%) 530 0.844
(1.00) 		0.487
(1.00) 		0.0023
(1.00) 		0.926
(1.00) 		0.576
(1.00) 		0.587
(1.00) 		0.101
(1.00) 		0.105
(1.00) 		0.116
(1.00) 		0.635
(1.00) 		0.198
(1.00) 		0.304
(1.00)
Xq loss 0 (0%) 564 0.765
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.507
(1.00) 		0.108
(1.00) 		0.495
(1.00) 		0.0157
(1.00) 		0.0674
(1.00) 		0.515
(1.00) 		0.652
(1.00) 		0.247
(1.00) 		0.176
(1.00)
'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.18

Table S1.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
2P GAIN CNV 1 20 4 3
2P GAIN WILD-TYPE 37 61 52 63

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
2P GAIN CNV 9 1 18
2P GAIN WILD-TYPE 86 66 61

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.52e-05 (Fisher's exact test), Q value = 0.07

Table S3.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
2Q GAIN CNV 7 1 0 10
2Q GAIN WILD-TYPE 35 49 63 50

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.014

Table S4.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
2Q GAIN CNV 27 9 1
2Q GAIN WILD-TYPE 115 105 90

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.19

Table S5.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
2Q GAIN CNV 2 19 3 2
2Q GAIN WILD-TYPE 36 62 53 64

Figure S5.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
3P GAIN CNV 25 7 4 0
3P GAIN WILD-TYPE 175 227 96 41

Figure S6.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.0021

Table S7.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
3Q GAIN CNV 35 7 9 2
3Q GAIN WILD-TYPE 165 227 91 39

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0013

Table S8.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
6P GAIN CNV 46 15 8 8
6P GAIN WILD-TYPE 154 219 92 33

Figure S8.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00063

Table S9.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
6Q GAIN CNV 43 12 8 8
6Q GAIN WILD-TYPE 157 222 92 33

Figure S9.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.89e-21 (Fisher's exact test), Q value = 1.7e-18

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
7P GAIN CNV 144 62 59 25
7P GAIN WILD-TYPE 56 172 41 16

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 8.55e-08 (Fisher's exact test), Q value = 7.4e-05

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
7P GAIN CNV 103 52 35
7P GAIN WILD-TYPE 39 62 56

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.72e-08 (Fisher's exact test), Q value = 3.2e-05

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
7P GAIN CNV 22 61 31 17
7P GAIN WILD-TYPE 16 20 25 49

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.54e-05 (Fisher's exact test), Q value = 0.078

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
7P GAIN CNV 53 23 55
7P GAIN WILD-TYPE 42 44 24

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.41e-08 (Chi-square test), Q value = 3.8e-05

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
7P GAIN CNV 13 13 41 42 33 15
7P GAIN WILD-TYPE 17 10 21 23 13 54

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.95e-16 (Fisher's exact test), Q value = 6.1e-13

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
7Q GAIN CNV 126 56 52 21
7Q GAIN WILD-TYPE 74 178 48 20

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 5.98e-06 (Fisher's exact test), Q value = 0.005

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
7Q GAIN CNV 88 47 28
7Q GAIN WILD-TYPE 54 67 63

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 8.79e-07 (Fisher's exact test), Q value = 0.00074

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
7Q GAIN CNV 17 56 24 16
7Q GAIN WILD-TYPE 21 25 32 50

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.01

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
7Q GAIN CNV 43 18 52
7Q GAIN WILD-TYPE 52 49 27

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.73e-05 (Chi-square test), Q value = 0.039

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
7Q GAIN CNV 13 10 36 36 27 14
7Q GAIN WILD-TYPE 17 13 26 29 19 55

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-08 (Fisher's exact test), Q value = 8.7e-06

Table S20.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8P GAIN CNV 26 29 39 14
8P GAIN WILD-TYPE 174 205 61 27

Figure S20.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.06e-33 (Fisher's exact test), Q value = 9.5e-31

Table S21.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8Q GAIN CNV 78 44 88 25
8Q GAIN WILD-TYPE 122 190 12 16

Figure S21.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.014

Table S22.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
11P GAIN CNV 26 4 5 4
11P GAIN WILD-TYPE 174 230 95 37

Figure S22.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.17

Table S23.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
11P GAIN CNV 20 2 3
11P GAIN WILD-TYPE 122 112 88

Figure S23.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.12

Table S24.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
11P GAIN CNV 3 0 12
11P GAIN WILD-TYPE 92 67 67

Figure S24.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.0011

Table S25.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
11Q GAIN CNV 24 3 5 7
11Q GAIN WILD-TYPE 176 231 95 34

Figure S25.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 4.38e-07 (Fisher's exact test), Q value = 0.00037

Table S26.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
13Q GAIN CNV 12 45 48 15
13Q GAIN WILD-TYPE 31 17 21 26

Figure S26.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.089

Table S27.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
13Q GAIN CNV 27 33 20 40
13Q GAIN WILD-TYPE 15 17 43 20

Figure S27.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1.62e-37 (Fisher's exact test), Q value = 1.5e-34

Table S28.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
13Q GAIN CNV 175 64 56 19
13Q GAIN WILD-TYPE 25 170 44 22

Figure S28.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 2.86e-08 (Fisher's exact test), Q value = 2.5e-05

Table S29.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
13Q GAIN CNV 105 47 40
13Q GAIN WILD-TYPE 37 67 51

Figure S29.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 8.54e-09 (Fisher's exact test), Q value = 7.4e-06

Table S30.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
13Q GAIN CNV 25 57 28 14
13Q GAIN WILD-TYPE 13 24 28 52

Figure S30.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-07 (Fisher's exact test), Q value = 0.00054

Table S31.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
13Q GAIN CNV 53 17 54
13Q GAIN WILD-TYPE 42 50 25

Figure S31.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.85e-07 (Fisher's exact test), Q value = 0.00024

Table S32.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 105 85
13Q GAIN CNV 39 78 50
13Q GAIN WILD-TYPE 66 27 35

Figure S32.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-10 (Chi-square test), Q value = 1.1e-07

Table S33.  Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
13Q GAIN CNV 15 13 43 48 34 14
13Q GAIN WILD-TYPE 15 10 19 17 12 55

Figure S33.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 1.1e-13

Table S34.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
16P GAIN CNV 66 7 16 7
16P GAIN WILD-TYPE 134 227 84 34

Figure S34.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 3.02e-18 (Fisher's exact test), Q value = 2.7e-15

Table S35.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
16Q GAIN CNV 68 6 16 6
16Q GAIN WILD-TYPE 132 228 84 35

Figure S35.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.22

Table S36.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
17Q GAIN CNV 36 13 15 3
17Q GAIN WILD-TYPE 164 221 85 38

Figure S36.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.012

Table S37.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
17Q GAIN CNV 5 22 2 2
17Q GAIN WILD-TYPE 33 59 54 64

Figure S37.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.048

Table S38.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19P GAIN CNV 29 7 10 6
19P GAIN WILD-TYPE 171 227 90 35

Figure S38.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20P GAIN CNV 13 38 47 16
20P GAIN WILD-TYPE 30 24 22 25

Figure S39.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.65e-07 (Fisher's exact test), Q value = 0.00014

Table S40.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20P GAIN CNV 32 30 15 37
20P GAIN WILD-TYPE 10 20 48 23

Figure S40.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 4.25e-22 (Fisher's exact test), Q value = 3.8e-19

Table S41.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20P GAIN CNV 130 67 52 39
20P GAIN WILD-TYPE 70 167 48 2

Figure S41.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.087

Table S42.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
20P GAIN CNV 88 42 38
20P GAIN WILD-TYPE 54 72 53

Figure S42.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00027

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
20P GAIN CNV 19 48 26 10
20P GAIN WILD-TYPE 19 33 30 56

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
20P GAIN CNV 46 11 46
20P GAIN WILD-TYPE 49 56 33

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

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.81e-08 (Chi-square test), Q value = 5.9e-05

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
20P GAIN CNV 16 13 42 40 20 12
20P GAIN WILD-TYPE 14 10 20 25 26 57

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 4.38e-17 (Fisher's exact test), Q value = 3.9e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20Q GAIN CNV 14 60 62 20
20Q GAIN WILD-TYPE 29 2 7 21

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

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.38e-16 (Fisher's exact test), Q value = 3.9e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20Q GAIN CNV 38 42 20 56
20Q GAIN WILD-TYPE 4 8 43 4

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

'20q gain' versus 'CN_CNMF'

P value = 2.22e-46 (Fisher's exact test), Q value = 2e-43

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20Q GAIN CNV 193 91 79 40
20Q GAIN WILD-TYPE 7 143 21 1

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1.68e-12 (Fisher's exact test), Q value = 1.5e-09

Table S49.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
20Q GAIN CNV 127 58 53
20Q GAIN WILD-TYPE 15 56 38

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.25

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 115 184 33 119
20Q GAIN CNV 85 141 23 64
20Q GAIN WILD-TYPE 30 43 10 55

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 248 92 35
20Q GAIN CNV 62 182 50 19
20Q GAIN WILD-TYPE 14 66 42 16

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 9.03e-18 (Fisher's exact test), Q value = 8e-15

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
20Q GAIN CNV 27 74 41 15
20Q GAIN WILD-TYPE 11 7 15 51

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-13 (Fisher's exact test), Q value = 1e-10

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
20Q GAIN CNV 69 19 69
20Q GAIN WILD-TYPE 26 48 10

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.65e-09 (Fisher's exact test), Q value = 2.3e-06

Table S54.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 105 85
20Q GAIN CNV 49 90 64
20Q GAIN WILD-TYPE 56 15 21

Figure S54.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.39e-21 (Chi-square test), Q value = 1.2e-18

Table S55.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
20Q GAIN CNV 27 18 53 57 35 13
20Q GAIN WILD-TYPE 3 5 9 8 11 56

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0063

Table S56.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
1P LOSS CNV 39 14 6 9
1P LOSS WILD-TYPE 161 220 94 32

Figure S56.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
1P LOSS CNV 28 5 6
1P LOSS WILD-TYPE 114 109 85

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 5.5e-11 (Fisher's exact test), Q value = 4.8e-08

Table S58.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
4P LOSS CNV 70 21 17 14
4P LOSS WILD-TYPE 130 213 83 27

Figure S58.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 3.18e-12 (Fisher's exact test), Q value = 2.8e-09

Table S59.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
4Q LOSS CNV 68 16 17 12
4Q LOSS WILD-TYPE 132 218 83 29

Figure S59.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 5.53e-07 (Fisher's exact test), Q value = 0.00047

Table S60.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
5Q LOSS CNV 31 6 17 6
5Q LOSS WILD-TYPE 169 228 83 35

Figure S60.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.14e-18 (Fisher's exact test), Q value = 1e-15

Table S61.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8P LOSS CNV 88 17 31 9
8P LOSS WILD-TYPE 112 217 69 32

Figure S61.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.089

Table S62.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
8P LOSS CNV 50 17 14
8P LOSS WILD-TYPE 92 97 77

Figure S62.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.024

Table S63.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
9P LOSS CNV 26 4 7 2
9P LOSS WILD-TYPE 174 230 93 39

Figure S63.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0016

Table S64.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
9Q LOSS CNV 28 4 3 2
9Q LOSS WILD-TYPE 172 230 97 39

Figure S64.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.0012

Table S65.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
10Q LOSS CNV 16 6 13 11
10Q LOSS WILD-TYPE 184 228 87 30

Figure S65.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 5.42e-07 (Fisher's exact test), Q value = 0.00046

Table S66.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
12P LOSS CNV 21 2 3 7
12P LOSS WILD-TYPE 179 232 97 34

Figure S66.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00094

Table S67.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
12Q LOSS CNV 19 2 1 6
12Q LOSS WILD-TYPE 181 232 99 35

Figure S67.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 6.52e-05 (Fisher's exact test), Q value = 0.054

Table S68.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
14Q LOSS CNV 6 27 26 4
14Q LOSS WILD-TYPE 37 35 43 37

Figure S68.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.84e-07 (Fisher's exact test), Q value = 0.00024

Table S69.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
14Q LOSS CNV 20 17 3 23
14Q LOSS WILD-TYPE 22 33 60 37

Figure S69.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.12e-31 (Fisher's exact test), Q value = 1e-28

Table S70.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
14Q LOSS CNV 109 20 6 8
14Q LOSS WILD-TYPE 91 214 94 33

Figure S70.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00014

Table S71.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
14Q LOSS CNV 53 13 11
14Q LOSS WILD-TYPE 89 101 80

Figure S71.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.73e-07 (Fisher's exact test), Q value = 0.00015

Table S72.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
14Q LOSS CNV 9 33 10 2
14Q LOSS WILD-TYPE 29 48 46 64

Figure S72.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.0013

Table S73.  Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 105 85
14Q LOSS CNV 10 41 16
14Q LOSS WILD-TYPE 95 64 69

Figure S73.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000145 (Chi-square test), Q value = 0.12

Table S74.  Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
14Q LOSS CNV 11 5 18 19 13 1
14Q LOSS WILD-TYPE 19 18 44 46 33 68

Figure S74.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2.09e-24 (Fisher's exact test), Q value = 1.9e-21

Table S75.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
15Q LOSS CNV 88 16 26 26
15Q LOSS WILD-TYPE 112 218 74 15

Figure S75.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0099

Table S76.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
15Q LOSS CNV 11 30 13 3
15Q LOSS WILD-TYPE 27 51 43 63

Figure S76.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000158 (Chi-square test), Q value = 0.13

Table S77.  Gene #66: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
15Q LOSS CNV 8 1 20 22 14 4
15Q LOSS WILD-TYPE 22 22 42 43 32 65

Figure S77.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.000277 (Fisher's exact test), Q value = 0.22

Table S78.  Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17P LOSS CNV 12 36 41 12
17P LOSS WILD-TYPE 31 26 28 29

Figure S78.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 5.49e-22 (Fisher's exact test), Q value = 4.9e-19

Table S79.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
17P LOSS CNV 128 46 57 21
17P LOSS WILD-TYPE 72 188 43 20

Figure S79.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0012

Table S80.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
17P LOSS CNV 84 37 27
17P LOSS WILD-TYPE 58 77 64

Figure S80.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 3.25e-06 (Fisher's exact test), Q value = 0.0027

Table S81.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
17P LOSS CNV 21 45 21 11
17P LOSS WILD-TYPE 17 36 35 55

Figure S81.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.54e-05 (Fisher's exact test), Q value = 0.054

Table S82.  Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 105 85
17P LOSS CNV 29 60 33
17P LOSS WILD-TYPE 76 45 52

Figure S82.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 1.24e-13 (Fisher's exact test), Q value = 1.1e-10

Table S83.  Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18P LOSS CNV 10 52 52 12
18P LOSS WILD-TYPE 33 10 17 29

Figure S83.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.4e-12 (Fisher's exact test), Q value = 3e-09

Table S84.  Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18P LOSS CNV 35 30 14 47
18P LOSS WILD-TYPE 7 20 49 13

Figure S84.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 4.26e-47 (Fisher's exact test), Q value = 3.9e-44

Table S85.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
18P LOSS CNV 176 53 62 33
18P LOSS WILD-TYPE 24 181 38 8

Figure S85.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1.35e-18 (Fisher's exact test), Q value = 1.2e-15

Table S86.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
18P LOSS CNV 119 40 34
18P LOSS WILD-TYPE 23 74 57

Figure S86.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 5.39e-16 (Fisher's exact test), Q value = 4.8e-13

Table S87.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
18P LOSS CNV 20 66 33 9
18P LOSS WILD-TYPE 18 15 23 57

Figure S87.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-11 (Fisher's exact test), Q value = 2.4e-08

Table S88.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
18P LOSS CNV 56 13 59
18P LOSS WILD-TYPE 39 54 20

Figure S88.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.08e-10 (Fisher's exact test), Q value = 9.4e-08

Table S89.  Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 105 85
18P LOSS CNV 33 81 47
18P LOSS WILD-TYPE 72 24 38

Figure S89.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.83e-12 (Chi-square test), Q value = 6.8e-09

Table S90.  Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
18P LOSS CNV 22 12 42 44 31 10
18P LOSS WILD-TYPE 8 11 20 21 15 59

Figure S90.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1.36e-12 (Fisher's exact test), Q value = 1.2e-09

Table S91.  Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q LOSS CNV 13 54 54 14
18Q LOSS WILD-TYPE 30 8 15 27

Figure S91.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.31e-12 (Fisher's exact test), Q value = 3.8e-09

Table S92.  Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18Q LOSS CNV 36 32 17 50
18Q LOSS WILD-TYPE 6 18 46 10

Figure S92.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 6.8e-51 (Fisher's exact test), Q value = 6.2e-48

Table S93.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
18Q LOSS CNV 180 59 77 36
18Q LOSS WILD-TYPE 20 175 23 5

Figure S93.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.99e-19 (Fisher's exact test), Q value = 1.8e-16

Table S94.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 91
18Q LOSS CNV 126 47 38
18Q LOSS WILD-TYPE 16 67 53

Figure S94.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3.96e-16 (Fisher's exact test), Q value = 3.5e-13

Table S95.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
18Q LOSS CNV 26 68 34 11
18Q LOSS WILD-TYPE 12 13 22 55

Figure S95.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-09 (Fisher's exact test), Q value = 3.2e-06

Table S96.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
18Q LOSS CNV 58 19 62
18Q LOSS WILD-TYPE 37 48 17

Figure S96.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.07e-09 (Fisher's exact test), Q value = 9.3e-07

Table S97.  Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 105 85
18Q LOSS CNV 40 85 50
18Q LOSS WILD-TYPE 65 20 35

Figure S97.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.16e-12 (Chi-square test), Q value = 4.5e-09

Table S98.  Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 23 62 65 46 69
18Q LOSS CNV 20 16 46 46 34 13
18Q LOSS WILD-TYPE 10 7 16 19 12 56

Figure S98.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.012

Table S99.  Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19P LOSS CNV 7 1 5 7
19P LOSS WILD-TYPE 193 233 95 34

Figure S99.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.19

Table S100.  Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19Q LOSS CNV 6 1 6 5
19Q LOSS WILD-TYPE 194 233 94 36

Figure S100.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00039

Table S101.  Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20P LOSS CNV 27 5 15 0
20P LOSS WILD-TYPE 173 229 85 41

Figure S101.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.03

Table S102.  Gene #76: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
21Q LOSS CNV 58 28 16 12
21Q LOSS WILD-TYPE 142 206 84 29

Figure S102.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.8e-14 (Fisher's exact test), Q value = 6.9e-11

Table S103.  Gene #77: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
22Q LOSS CNV 76 20 13 13
22Q LOSS WILD-TYPE 124 214 87 28

Figure S103.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 575

  • Number of significantly arm-level cnvs = 78

  • 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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