Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1TM791J
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TM791J
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 528 patients, 215 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

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

  • 4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • 4q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

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

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 21q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 2p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 17q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 215 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
14q loss 216 (41%) 312 3e-05
(0.0217) 		3e-05
(0.0217) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.0499
(1.00) 		0.88
(1.00)
20p gain 112 (21%) 416 0.117
(1.00) 		0.115
(1.00) 		1e-05
(0.00875) 		3e-05
(0.0217) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		3e-05
(0.0217) 		0.0517
(1.00)
20q gain 115 (22%) 413 0.0416
(1.00) 		0.0743
(1.00) 		1e-05
(0.00875) 		2e-05
(0.0148) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.0316
(1.00)
18p loss 93 (18%) 435 0.059
(1.00) 		0.46
(1.00) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00031
(0.208) 		0.00422
(1.00)
12p gain 121 (23%) 407 0.013
(1.00) 		0.0327
(1.00) 		1e-05
(0.00875) 		4e-05
(0.0286) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00153
(0.958) 		0.102
(1.00)
12q gain 122 (23%) 406 0.0131
(1.00) 		0.033
(1.00) 		1e-05
(0.00875) 		5e-05
(0.0354) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00319
(1.00) 		0.127
(1.00)
2p loss 14 (3%) 514 3e-05
(0.0217) 		0.00077
(0.497) 		1e-05
(0.00875) 		0.663
(1.00) 		0.00021
(0.143) 		2e-05
(0.0148) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		6e-05
(0.0423) 		0.132
(1.00) 		0.0963
(1.00)
6p loss 100 (19%) 428 0.011
(1.00) 		0.0141
(1.00) 		1e-05
(0.00875) 		6e-05
(0.0423) 		0.00013
(0.0898) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.0813
(1.00) 		0.0238
(1.00)
9p loss 149 (28%) 379 0.00351
(1.00) 		0.0369
(1.00) 		1e-05
(0.00875) 		1e-05
(0.00875) 		2e-05
(0.0148) 		5e-05
(0.0354) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.0164
(1.00) 		0.0988
(1.00)
9q loss 150 (28%) 378 0.01
(1.00) 		0.0588
(1.00) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00019
(0.13) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00373
(1.00) 		0.0371
(1.00)
13q loss 71 (13%) 457 0.00321
(1.00) 		0.047
(1.00) 		1e-05
(0.00875) 		0.00031
(0.208) 		2e-05
(0.0148) 		3e-05
(0.0217) 		2e-05
(0.0148) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.108
(1.00) 		0.105
(1.00)
18q loss 95 (18%) 433 0.0467
(1.00) 		0.222
(1.00) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		8e-05
(0.0558) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00307
(1.00) 		0.0316
(1.00)
8q gain 62 (12%) 466 0.229
(1.00) 		0.106
(1.00) 		1e-05
(0.00875) 		1e-05
(0.00875) 		4e-05
(0.0286) 		0.00044
(0.29) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		8e-05
(0.0558) 		0.0004
(0.264) 		0.407
(1.00)
2q loss 14 (3%) 514 0.00035
(0.232) 		0.00069
(0.448) 		3e-05
(0.0217) 		1
(1.00) 		0.00053
(0.347) 		2e-05
(0.0148) 		1e-05
(0.00875) 		4e-05
(0.0286) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.131
(1.00) 		0.0974
(1.00)
6q loss 128 (24%) 400 0.0503
(1.00) 		0.052
(1.00) 		1e-05
(0.00875) 		0.00628
(1.00) 		5e-05
(0.0354) 		7e-05
(0.049) 		0.00027
(0.182) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.17
(1.00) 		0.0252
(1.00)
17p loss 46 (9%) 482 0.00014
(0.0965) 		0.00019
(0.13) 		1e-05
(0.00875) 		0.0877
(1.00) 		0.00936
(1.00) 		0.00053
(0.347) 		1e-05
(0.00875) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00022
(0.15) 		0.206
(1.00) 		0.0869
(1.00)
3q gain 61 (12%) 467 0.0118
(1.00) 		0.0308
(1.00) 		1e-05
(0.00875) 		0.00363
(1.00) 		0.00077
(0.497) 		1e-05
(0.00875) 		2e-05
(0.0148) 		1e-05
(0.00875) 		1e-05
(0.00875) 		0.00039
(0.257) 		0.00187
(1.00) 		0.0812
(1.00)
8p gain 31 (6%) 497 1e-05
(0.00875) 		0.00036
(0.239) 		0.00971
(1.00) 		0.0649
(1.00) 		1e-05
(0.00875) 		7e-05
(0.049) 		1e-05
(0.00875) 		0.00529
(1.00) 		0.011
(1.00) 		0.107
(1.00)
19q gain 57 (11%) 471 0.102
(1.00) 		0.225
(1.00) 		1e-05
(0.00875) 		2e-05
(0.0148) 		0.00023
(0.156) 		0.0138
(1.00) 		0.00063
(0.409) 		4e-05
(0.0286) 		1e-05
(0.00875) 		0.17
(1.00) 		0.578
(1.00) 		0.287
(1.00)
17q loss 28 (5%) 500 0.00073
(0.473) 		0.00034
(0.226) 		1e-05
(0.00875) 		0.582
(1.00) 		0.277
(1.00) 		0.00782
(1.00) 		7e-05
(0.049) 		4e-05
(0.0286) 		1e-05
(0.00875) 		0.00497
(1.00) 		0.458
(1.00) 		0.15
(1.00)
19p gain 51 (10%) 477 0.227
(1.00) 		0.483
(1.00) 		1e-05
(0.00875) 		8e-05
(0.0558) 		0.00419
(1.00) 		0.13
(1.00) 		0.0014
(0.881) 		0.00034
(0.226) 		1e-05
(0.00875) 		0.355
(1.00) 		0.92
(1.00) 		0.625
(1.00)
4q loss 65 (12%) 463 0.389
(1.00) 		0.783
(1.00) 		1e-05
(0.00875) 		4e-05
(0.0286) 		0.182
(1.00) 		0.092
(1.00) 		0.00036
(0.239) 		1e-05
(0.00875) 		0.198
(1.00) 		0.0643
(1.00) 		0.433
(1.00) 		0.0569
(1.00)
22q loss 39 (7%) 489 0.00965
(1.00) 		0.00129
(0.813) 		1e-05
(0.00875) 		0.00345
(1.00) 		0.00122
(0.778) 		0.0686
(1.00) 		2e-05
(0.0148) 		3e-05
(0.0217) 		1e-05
(0.00875) 		0.00352
(1.00) 		0.0261
(1.00) 		0.26
(1.00)
1q gain 51 (10%) 477 0.41
(1.00) 		0.9
(1.00) 		1e-05
(0.00875) 		0.0144
(1.00) 		0.0271
(1.00) 		0.0159
(1.00) 		2e-05
(0.0148) 		0.00647
(1.00) 		1e-05
(0.00875) 		0.00526
(1.00) 		0.419
(1.00) 		0.755
(1.00)
7p gain 171 (32%) 357 0.449
(1.00) 		0.859
(1.00) 		1e-05
(0.00875) 		0.00166
(1.00) 		0.00025
(0.169) 		0.00511
(1.00) 		0.00011
(0.0761) 		0.00311
(1.00) 		0.00411
(1.00) 		0.0301
(1.00) 		0.103
(1.00) 		0.766
(1.00)
7q gain 172 (33%) 356 0.454
(1.00) 		0.86
(1.00) 		1e-05
(0.00875) 		0.00377
(1.00) 		0.00024
(0.163) 		0.00256
(1.00) 		6e-05
(0.0423) 		0.00296
(1.00) 		0.00528
(1.00) 		0.018
(1.00) 		0.173
(1.00) 		0.589
(1.00)
21q gain 50 (9%) 478 0.27
(1.00) 		0.209
(1.00) 		1e-05
(0.00875) 		0.00127
(0.803) 		0.00186
(1.00) 		0.517
(1.00) 		0.00031
(0.208) 		0.00028
(0.189) 		0.00281
(1.00) 		0.0323
(1.00) 		0.35
(1.00) 		0.476
(1.00)
3p loss 380 (72%) 148 0.00326
(1.00) 		0.0104
(1.00) 		1e-05
(0.00875) 		0.00054
(0.352) 		0.0338
(1.00) 		0.0455
(1.00) 		1e-05
(0.00875) 		2e-05
(0.0148) 		0.0214
(1.00) 		0.0082
(1.00) 		0.0913
(1.00) 		0.732
(1.00)
4p loss 72 (14%) 456 0.531
(1.00) 		0.817
(1.00) 		1e-05
(0.00875) 		0.0001
(0.0693) 		0.204
(1.00) 		0.288
(1.00) 		0.00052
(0.341) 		1e-05
(0.00875) 		0.573
(1.00) 		0.073
(1.00) 		0.0791
(1.00) 		0.00721
(1.00)
15q loss 36 (7%) 492 0.119
(1.00) 		0.333
(1.00) 		1e-05
(0.00875) 		0.00073
(0.473) 		0.0295
(1.00) 		0.108
(1.00) 		2e-05
(0.0148) 		1e-05
(0.00875) 		0.00081
(0.52) 		0.0165
(1.00) 		0.0702
(1.00) 		0.133
(1.00)
19p loss 11 (2%) 517 3e-05
(0.0217) 		0.0318
(1.00) 		0.00515
(1.00) 		0.00036
(0.239) 		0.162
(1.00) 		6e-05
(0.0423) 		0.243
(1.00) 		0.0094
(1.00) 		0.0341
(1.00) 		0.038
(1.00)
1p gain 24 (5%) 504 0.819
(1.00) 		0.926
(1.00) 		1e-05
(0.00875) 		0.00058
(0.378) 		0.00126
(0.799) 		0.0264
(1.00) 		0.00126
(0.799) 		0.0003
(0.202) 		0.00212
(1.00) 		0.0066
(1.00) 		0.751
(1.00) 		0.0391
(1.00)
3p gain 19 (4%) 509 0.0537
(1.00) 		0.43
(1.00) 		0.00028
(0.189) 		0.583
(1.00) 		0.0237
(1.00) 		0.00242
(1.00) 		0.00892
(1.00) 		0.00265
(1.00) 		0.00016
(0.11) 		0.125
(1.00) 		0.391
(1.00) 		0.736
(1.00)
4p gain 13 (2%) 515 0.0722
(1.00) 		0.374
(1.00) 		0.0704
(1.00) 		0.0102
(1.00) 		0.00021
(0.143) 		0.00102
(0.653) 		0.00025
(0.169) 		0.044
(1.00)
4q gain 13 (2%) 515 0.211
(1.00) 		0.456
(1.00) 		0.0702
(1.00) 		0.0497
(1.00) 		0.00026
(0.176) 		0.0121
(1.00) 		0.0003
(0.202) 		0.0444
(1.00)
11q loss 23 (4%) 505 0.188
(1.00) 		0.375
(1.00) 		1e-05
(0.00875) 		0.00588
(1.00) 		0.18
(1.00) 		0.0696
(1.00) 		0.012
(1.00) 		9e-05
(0.0625) 		0.0236
(1.00) 		0.0363
(1.00) 		0.297
(1.00) 		0.307
(1.00)
2p gain 77 (15%) 451 0.704
(1.00) 		0.461
(1.00) 		1e-05
(0.00875) 		0.0832
(1.00) 		0.0528
(1.00) 		0.941
(1.00) 		0.305
(1.00) 		0.00907
(1.00) 		0.62
(1.00) 		0.145
(1.00) 		0.229
(1.00) 		0.472
(1.00)
2q gain 79 (15%) 449 0.558
(1.00) 		0.266
(1.00) 		1e-05
(0.00875) 		0.164
(1.00) 		0.0435
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.0247
(1.00) 		0.706
(1.00) 		0.0261
(1.00) 		0.32
(1.00) 		0.655
(1.00)
5p gain 193 (37%) 335 0.88
(1.00) 		0.923
(1.00) 		0.00031
(0.208) 		0.261
(1.00) 		0.305
(1.00) 		0.337
(1.00) 		0.0221
(1.00) 		0.0343
(1.00) 		0.0693
(1.00) 		0.153
(1.00) 		0.0836
(1.00) 		0.907
(1.00)
10p gain 17 (3%) 511 0.00013
(0.0898) 		0.256
(1.00) 		0.0988
(1.00) 		0.176
(1.00) 		0.00093
(0.596) 		0.00044
(0.29) 		0.0195
(1.00) 		0.0689
(1.00)
10q gain 12 (2%) 516 0.00015
(0.103) 		0.116
(1.00) 		0.0571
(1.00) 		0.218
(1.00) 		0.0122
(1.00) 		0.00123
(0.782) 		0.0153
(1.00) 		0.214
(1.00)
11p gain 31 (6%) 497 0.232
(1.00) 		0.671
(1.00) 		2e-05
(0.0148) 		0.271
(1.00) 		0.0866
(1.00) 		0.0952
(1.00) 		0.143
(1.00) 		0.0857
(1.00) 		0.146
(1.00) 		0.28
(1.00) 		0.393
(1.00) 		0.855
(1.00)
11q gain 29 (5%) 499 0.341
(1.00) 		0.907
(1.00) 		0.00016
(0.11) 		0.527
(1.00) 		0.336
(1.00) 		0.517
(1.00) 		0.346
(1.00) 		0.43
(1.00) 		0.36
(1.00) 		0.186
(1.00) 		0.749
(1.00) 		0.682
(1.00)
16p gain 107 (20%) 421 0.273
(1.00) 		0.382
(1.00) 		6e-05
(0.0423) 		0.166
(1.00) 		0.0377
(1.00) 		0.413
(1.00) 		0.0118
(1.00) 		0.00273
(1.00) 		0.0602
(1.00) 		0.0265
(1.00) 		0.129
(1.00) 		0.396
(1.00)
16q gain 99 (19%) 429 0.233
(1.00) 		0.349
(1.00) 		5e-05
(0.0354) 		0.0871
(1.00) 		0.052
(1.00) 		0.302
(1.00) 		0.00967
(1.00) 		0.00124
(0.787) 		0.0163
(1.00) 		0.147
(1.00) 		0.181
(1.00) 		0.268
(1.00)
17p gain 26 (5%) 502 0.0191
(1.00) 		0.00579
(1.00) 		1e-05
(0.00875) 		0.819
(1.00) 		0.0955
(1.00) 		0.144
(1.00) 		0.116
(1.00) 		0.0532
(1.00) 		0.146
(1.00) 		0.268
(1.00) 		0.0363
(1.00) 		0.737
(1.00)
17q gain 33 (6%) 495 0.0682
(1.00) 		0.0255
(1.00) 		3e-05
(0.0217) 		0.236
(1.00) 		0.0841
(1.00) 		0.127
(1.00) 		0.0636
(1.00) 		0.0108
(1.00) 		0.0774
(1.00) 		0.223
(1.00) 		0.00198
(1.00) 		0.293
(1.00)
22q gain 40 (8%) 488 0.327
(1.00) 		0.217
(1.00) 		2e-05
(0.0148) 		0.21
(1.00) 		0.42
(1.00) 		0.974
(1.00) 		0.0434
(1.00) 		0.0355
(1.00) 		0.0617
(1.00) 		0.412
(1.00) 		0.909
(1.00) 		0.307
(1.00)
1p loss 57 (11%) 471 0.00075
(0.484) 		0.00289
(1.00) 		1e-05
(0.00875) 		0.679
(1.00) 		0.00146
(0.915) 		0.156
(1.00) 		0.0718
(1.00) 		0.0394
(1.00) 		0.00813
(1.00) 		0.023
(1.00) 		0.0359
(1.00) 		0.823
(1.00)
1q loss 36 (7%) 492 0.0108
(1.00) 		0.0114
(1.00) 		1e-05
(0.00875) 		0.369
(1.00) 		0.0281
(1.00) 		0.105
(1.00) 		0.00245
(1.00) 		0.00801
(1.00) 		0.00577
(1.00) 		0.0428
(1.00) 		0.224
(1.00) 		0.708
(1.00)
8p loss 137 (26%) 391 0.379
(1.00) 		0.167
(1.00) 		1e-05
(0.00875) 		0.277
(1.00) 		0.122
(1.00) 		0.0885
(1.00) 		0.0989
(1.00) 		0.0016
(0.998) 		0.043
(1.00) 		0.0224
(1.00) 		0.276
(1.00) 		0.242
(1.00)
10p loss 67 (13%) 461 0.173
(1.00) 		0.409
(1.00) 		1e-05
(0.00875) 		0.0817
(1.00) 		0.807
(1.00) 		0.0681
(1.00) 		0.125
(1.00) 		0.0625
(1.00) 		0.0173
(1.00) 		0.109
(1.00) 		0.776
(1.00) 		0.294
(1.00)
10q loss 89 (17%) 439 0.328
(1.00) 		0.402
(1.00) 		1e-05
(0.00875) 		0.00454
(1.00) 		0.985
(1.00) 		0.02
(1.00) 		0.115
(1.00) 		0.0356
(1.00) 		0.0386
(1.00) 		0.00051
(0.335) 		0.802
(1.00) 		0.437
(1.00)
11p loss 18 (3%) 510 1e-05
(0.00875) 		0.0227
(1.00) 		0.298
(1.00) 		0.259
(1.00) 		0.175
(1.00) 		0.00914
(1.00) 		0.169
(1.00) 		0.15
(1.00) 		0.299
(1.00) 		0.306
(1.00)
21q loss 55 (10%) 473 0.0263
(1.00) 		0.0906
(1.00) 		1e-05
(0.00875) 		0.0138
(1.00) 		0.0741
(1.00) 		0.00106
(0.677) 		0.00366
(1.00) 		0.015
(1.00) 		0.00642
(1.00) 		0.00883
(1.00) 		0.884
(1.00) 		1
(1.00)
xq loss 47 (9%) 481 0.0236
(1.00) 		0.0637
(1.00) 		1e-05
(0.00875) 		0.0187
(1.00) 		0.228
(1.00) 		0.00122
(0.778) 		0.0688
(1.00) 		0.173
(1.00) 		0.0115
(1.00) 		0.0017
(1.00) 		0.23
(1.00) 		0.176
(1.00)
5q gain 207 (39%) 321 0.334
(1.00) 		0.625
(1.00) 		0.0216
(1.00) 		0.434
(1.00) 		0.668
(1.00) 		0.446
(1.00) 		0.124
(1.00) 		0.174
(1.00) 		0.447
(1.00) 		0.204
(1.00) 		0.127
(1.00) 		0.907
(1.00)
6p gain 11 (2%) 517 0.15
(1.00) 		0.445
(1.00) 		0.0747
(1.00) 		0.431
(1.00) 		0.68
(1.00) 		0.859
(1.00) 		0.859
(1.00) 		0.113
(1.00) 		0.604
(1.00) 		0.779
(1.00)
6q gain 9 (2%) 519 0.0806
(1.00) 		0.682
(1.00) 		0.0191
(1.00) 		0.631
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.186
(1.00) 		0.606
(1.00) 		0.78
(1.00)
9p gain 13 (2%) 515 0.015
(1.00) 		0.903
(1.00) 		0.866
(1.00) 		1
(1.00) 		0.219
(1.00) 		0.828
(1.00) 		1
(1.00) 		0.862
(1.00) 		1
(1.00) 		1
(1.00)
9q gain 12 (2%) 516 0.00128
(0.808) 		0.907
(1.00) 		0.687
(1.00) 		0.231
(1.00) 		0.22
(1.00) 		0.606
(1.00) 		0.532
(1.00) 		0.671
(1.00) 		1
(1.00) 		1
(1.00)
13q gain 22 (4%) 506 0.485
(1.00) 		0.0342
(1.00) 		0.637
(1.00) 		0.799
(1.00) 		0.0615
(1.00) 		0.924
(1.00) 		0.348
(1.00) 		0.261
(1.00) 		0.288
(1.00) 		0.326
(1.00)
14q gain 16 (3%) 512 0.768
(1.00) 		0.575
(1.00) 		0.00141
(0.885) 		0.35
(1.00) 		0.00616
(1.00) 		0.0394
(1.00) 		0.00573
(1.00) 		0.0125
(1.00) 		0.00377
(1.00) 		0.112
(1.00)
15q gain 26 (5%) 502 1
(1.00) 		0.117
(1.00) 		0.00079
(0.508) 		0.724
(1.00) 		0.499
(1.00) 		0.464
(1.00) 		0.582
(1.00) 		0.867
(1.00) 		0.704
(1.00) 		0.408
(1.00) 		0.686
(1.00) 		0.826
(1.00)
18p gain 25 (5%) 503 0.311
(1.00) 		0.0767
(1.00) 		0.073
(1.00) 		0.448
(1.00) 		0.814
(1.00) 		0.0809
(1.00) 		0.368
(1.00) 		0.93
(1.00) 		0.835
(1.00) 		0.454
(1.00) 		0.201
(1.00) 		0.0446
(1.00)
18q gain 25 (5%) 503 0.313
(1.00) 		0.0771
(1.00) 		0.0669
(1.00) 		0.559
(1.00) 		0.427
(1.00) 		0.212
(1.00) 		0.367
(1.00) 		0.929
(1.00) 		0.966
(1.00) 		0.453
(1.00) 		0.201
(1.00) 		0.0445
(1.00)
xq gain 31 (6%) 497 0.39
(1.00) 		0.703
(1.00) 		0.223
(1.00) 		0.293
(1.00) 		0.0306
(1.00) 		0.00753
(1.00) 		0.133
(1.00) 		0.0263
(1.00) 		0.321
(1.00) 		0.604
(1.00) 		0.919
(1.00) 		0.813
(1.00)
3q loss 99 (19%) 429 0.922
(1.00) 		0.52
(1.00) 		0.00154
(0.962) 		0.405
(1.00) 		0.253
(1.00) 		0.213
(1.00) 		0.121
(1.00) 		0.744
(1.00) 		0.651
(1.00) 		0.0263
(1.00) 		0.799
(1.00) 		0.861
(1.00)
5p loss 7 (1%) 521 0.0161
(1.00) 		0.288
(1.00) 		0.466
(1.00) 		0.127
(1.00) 		0.0244
(1.00) 		0.00394
(1.00) 		0.0412
(1.00) 		0.066
(1.00)
5q loss 6 (1%) 522 0.0441
(1.00) 		0.543
(1.00) 		0.349
(1.00) 		0.395
(1.00) 		0.0335
(1.00) 		0.00239
(1.00) 		0.0731
(1.00) 		0.0926
(1.00)
7p loss 3 (1%) 525 0.165
(1.00) 		0.105
(1.00) 		0.0129
(1.00) 		0.0587
(1.00) 		0.356
(1.00)
7q loss 4 (1%) 524 0.119
(1.00) 		0.348
(1.00) 		0.0846
(1.00) 		0.177
(1.00) 		0.047
(1.00) 		0.00308
(1.00) 		0.0193
(1.00) 		0.772
(1.00)
8q loss 64 (12%) 464 0.648
(1.00) 		0.125
(1.00) 		0.122
(1.00) 		0.0445
(1.00) 		0.16
(1.00) 		0.934
(1.00) 		0.706
(1.00) 		0.941
(1.00) 		0.59
(1.00) 		0.407
(1.00) 		0.684
(1.00) 		0.0885
(1.00)
12p loss 4 (1%) 524 0.0852
(1.00) 		0.199
(1.00) 		0.693
(1.00) 		0.296
(1.00) 		0.143
(1.00)
12q loss 4 (1%) 524 0.482
(1.00) 		0.376
(1.00) 		0.261
(1.00) 		1
(1.00) 		1
(1.00) 		0.233
(1.00) 		0.611
(1.00)
16p loss 10 (2%) 518 0.201
(1.00) 		0.878
(1.00) 		0.129
(1.00) 		0.0269
(1.00) 		0.319
(1.00) 		0.00603
(1.00) 		0.0908
(1.00) 		0.114
(1.00) 		0.116
(1.00) 		0.114
(1.00)
16q loss 16 (3%) 512 0.0378
(1.00) 		0.91
(1.00) 		0.185
(1.00) 		0.158
(1.00) 		0.115
(1.00) 		0.0135
(1.00) 		0.0643
(1.00) 		0.0083
(1.00) 		0.0712
(1.00) 		0.0289
(1.00)
19q loss 4 (1%) 524 0.0113
(1.00) 		0.918
(1.00) 		0.17
(1.00) 		0.428
(1.00) 		0.0523
(1.00) 		0.83
(1.00) 		0.084
(1.00)
20p loss 8 (2%) 520 0.175
(1.00) 		1
(1.00) 		0.0299
(1.00) 		1
(1.00) 		0.0763
(1.00) 		0.0892
(1.00) 		0.0191
(1.00) 		0.232
(1.00)
20q loss 3 (1%) 525 0.165
(1.00) 		0.104
(1.00) 		0.162
(1.00) 		0.0578
(1.00) 		0.0291
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1P GAIN MUTATED 2 1 21
1P GAIN WILD-TYPE 236 134 134

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
1P GAIN MUTATED 7 3 13
1P GAIN WILD-TYPE 154 234 112

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1Q GAIN MUTATED 6 2 43
1Q GAIN WILD-TYPE 232 133 112

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
1Q GAIN MUTATED 1 15 33
1Q GAIN WILD-TYPE 105 207 162

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
1Q GAIN MUTATED 3 13 33
1Q GAIN WILD-TYPE 121 191 149

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2P GAIN MUTATED 15 14 48
2P GAIN WILD-TYPE 223 121 107

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S7.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2Q GAIN MUTATED 18 14 47
2Q GAIN WILD-TYPE 220 121 108

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

'3p gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.19

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3P GAIN MUTATED 1 9 9
3P GAIN WILD-TYPE 237 126 146

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
3P GAIN MUTATED 3 1 15
3P GAIN WILD-TYPE 121 203 167

Figure S9.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3Q GAIN MUTATED 7 15 39
3Q GAIN WILD-TYPE 231 120 116

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
3Q GAIN MUTATED 7 12 36
3Q GAIN WILD-TYPE 114 184 94

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
3Q GAIN MUTATED 12 11 38
3Q GAIN WILD-TYPE 94 211 157

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
3Q GAIN MUTATED 20 11 30
3Q GAIN WILD-TYPE 141 226 95

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
3Q GAIN MUTATED 8 10 42
3Q GAIN WILD-TYPE 116 194 140

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
4P GAIN MUTATED 7 0 5
4P GAIN WILD-TYPE 99 222 190

Figure S15.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S16.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
4P GAIN MUTATED 2 0 11
4P GAIN WILD-TYPE 122 204 171

Figure S16.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.18

Table S17.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
4Q GAIN MUTATED 7 0 5
4Q GAIN WILD-TYPE 99 222 190

Figure S17.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S18.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
4Q GAIN MUTATED 2 0 11
4Q GAIN WILD-TYPE 122 204 171

Figure S18.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
5P GAIN MUTATED 73 43 77
5P GAIN WILD-TYPE 165 92 78

Figure S19.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
7P GAIN MUTATED 39 46 86
7P GAIN WILD-TYPE 199 89 69

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
7P GAIN MUTATED 23 30 31 35 19 11
7P GAIN WILD-TYPE 85 32 44 45 60 32

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S22.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
7P GAIN MUTATED 31 53 85
7P GAIN WILD-TYPE 75 169 110

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S23.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
7Q GAIN MUTATED 39 47 86
7Q GAIN WILD-TYPE 199 88 69

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
7Q GAIN MUTATED 23 30 31 35 21 10
7Q GAIN WILD-TYPE 85 32 44 45 58 33

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
7Q GAIN MUTATED 32 53 85
7Q GAIN WILD-TYPE 74 169 110

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

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S26.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
8P GAIN MUTATED 1 8 22
8P GAIN WILD-TYPE 237 127 133

Figure S26.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S27.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
8P GAIN MUTATED 2 4 16
8P GAIN WILD-TYPE 126 72 94

Figure S27.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S28.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
8P GAIN MUTATED 4 3 24
8P GAIN WILD-TYPE 102 219 171

Figure S28.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S29.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
8P GAIN MUTATED 8 5 18
8P GAIN WILD-TYPE 153 232 107

Figure S29.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S30.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
8P GAIN MUTATED 3 3 25
8P GAIN WILD-TYPE 121 201 157

Figure S30.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S31.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
8Q GAIN MUTATED 3 13 46
8Q GAIN WILD-TYPE 235 122 109

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S32.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
8Q GAIN MUTATED 3 11 26
8Q GAIN WILD-TYPE 125 65 84

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S33.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
8Q GAIN MUTATED 3 18 14 11 7 2
8Q GAIN WILD-TYPE 105 44 61 69 72 41

Figure S33.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S34.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
8Q GAIN MUTATED 5 6 50
8Q GAIN WILD-TYPE 101 216 145

Figure S34.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S35.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
8Q GAIN MUTATED 11 10 40
8Q GAIN WILD-TYPE 150 227 85

Figure S35.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S36.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
8Q GAIN MUTATED 8 7 45
8Q GAIN WILD-TYPE 116 197 137

Figure S36.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S37.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
8Q GAIN MUTATED 20 22 9 9
8Q GAIN WILD-TYPE 124 112 186 28

Figure S37.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.09

Table S38.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10P GAIN MUTATED 1 4 12
10P GAIN WILD-TYPE 237 131 143

Figure S38.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S39.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10Q GAIN MUTATED 0 3 9
10Q GAIN WILD-TYPE 238 132 146

Figure S39.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S40.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11P GAIN MUTATED 2 12 17
11P GAIN WILD-TYPE 236 123 138

Figure S40.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S41.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11Q GAIN MUTATED 3 12 14
11Q GAIN WILD-TYPE 235 123 141

Figure S41.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S42.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
12P GAIN MUTATED 22 34 65
12P GAIN WILD-TYPE 216 101 90

Figure S42.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S43.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
12P GAIN MUTATED 16 18 42
12P GAIN WILD-TYPE 112 58 68

Figure S43.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S44.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
12P GAIN MUTATED 7 31 28 17 15 6
12P GAIN WILD-TYPE 101 31 47 63 64 37

Figure S44.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S45.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
12P GAIN MUTATED 26 27 51
12P GAIN WILD-TYPE 95 169 79

Figure S45.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S46.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
12P GAIN MUTATED 18 23 79
12P GAIN WILD-TYPE 88 199 116

Figure S46.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S47.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
12P GAIN MUTATED 30 31 59
12P GAIN WILD-TYPE 131 206 66

Figure S47.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S48.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
12P GAIN MUTATED 20 24 75
12P GAIN WILD-TYPE 104 180 107

Figure S48.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S49.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
12P GAIN MUTATED 33 46 24 16
12P GAIN WILD-TYPE 111 88 171 21

Figure S49.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S50.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
12Q GAIN MUTATED 22 34 66
12Q GAIN WILD-TYPE 216 101 89

Figure S50.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S51.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
12Q GAIN MUTATED 16 18 42
12Q GAIN WILD-TYPE 112 58 68

Figure S51.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S52.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
12Q GAIN MUTATED 7 33 28 17 14 6
12Q GAIN WILD-TYPE 101 29 47 63 65 37

Figure S52.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S53.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
12Q GAIN MUTATED 26 26 53
12Q GAIN WILD-TYPE 95 170 77

Figure S53.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S54.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
12Q GAIN MUTATED 19 23 79
12Q GAIN WILD-TYPE 87 199 116

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S55.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
12Q GAIN MUTATED 30 31 60
12Q GAIN WILD-TYPE 131 206 65

Figure S55.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S56.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
12Q GAIN MUTATED 19 24 77
12Q GAIN WILD-TYPE 105 180 105

Figure S56.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S57.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
12Q GAIN MUTATED 32 48 24 16
12Q GAIN WILD-TYPE 112 86 171 21

Figure S57.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S58.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
16P GAIN MUTATED 30 29 48
16P GAIN WILD-TYPE 208 106 107

Figure S58.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S59.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
16Q GAIN MUTATED 26 29 44
16Q GAIN WILD-TYPE 212 106 111

Figure S59.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S60.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17P GAIN MUTATED 1 10 15
17P GAIN WILD-TYPE 237 125 140

Figure S60.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S61.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17Q GAIN MUTATED 3 11 19
17Q GAIN WILD-TYPE 235 124 136

Figure S61.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S62.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19P GAIN MUTATED 4 19 28
19P GAIN WILD-TYPE 234 116 127

Figure S62.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S63.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
19P GAIN MUTATED 7 3 24
19P GAIN WILD-TYPE 121 73 86

Figure S63.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S64.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
19P GAIN MUTATED 14 13 24
19P GAIN WILD-TYPE 147 224 101

Figure S64.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S65.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
19P GAIN MUTATED 10 8 32
19P GAIN WILD-TYPE 114 196 150

Figure S65.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S66.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19Q GAIN MUTATED 4 19 34
19Q GAIN WILD-TYPE 234 116 121

Figure S66.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S67.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
19Q GAIN MUTATED 7 3 27
19Q GAIN WILD-TYPE 121 73 83

Figure S67.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.16

Table S68.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
19Q GAIN MUTATED 6 13 15 13 4 1
19Q GAIN WILD-TYPE 102 49 60 67 75 42

Figure S68.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S69.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
19Q GAIN MUTATED 14 14 28
19Q GAIN WILD-TYPE 147 223 97

Figure S69.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S70.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
19Q GAIN MUTATED 10 9 36
19Q GAIN WILD-TYPE 114 195 146

Figure S70.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
20P GAIN MUTATED 10 39 63
20P GAIN WILD-TYPE 228 96 92

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

'20p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S72.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
20P GAIN MUTATED 12 16 37
20P GAIN WILD-TYPE 116 60 73

Figure S72.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S73.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
20P GAIN MUTATED 7 30 17 20 18 6
20P GAIN WILD-TYPE 101 32 58 60 61 37

Figure S73.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S74.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
20P GAIN MUTATED 19 28 51
20P GAIN WILD-TYPE 102 168 79

Figure S74.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S75.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
20P GAIN MUTATED 18 18 76
20P GAIN WILD-TYPE 88 204 119

Figure S75.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S76.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
20P GAIN MUTATED 23 23 66
20P GAIN WILD-TYPE 138 214 59

Figure S76.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S77.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
20P GAIN MUTATED 25 18 68
20P GAIN WILD-TYPE 99 186 114

Figure S77.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S78.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
20P GAIN MUTATED 36 33 22 20
20P GAIN WILD-TYPE 108 101 173 17

Figure S78.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S79.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
20P GAIN MUTATED 6 3 3 18
20P GAIN WILD-TYPE 32 18 45 17

Figure S79.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S80.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
20Q GAIN MUTATED 10 38 67
20Q GAIN WILD-TYPE 228 97 88

Figure S80.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S81.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
20Q GAIN MUTATED 12 16 37
20Q GAIN WILD-TYPE 116 60 73

Figure S81.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S82.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
20Q GAIN MUTATED 7 32 19 20 17 6
20Q GAIN WILD-TYPE 101 30 56 60 62 37

Figure S82.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S83.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
20Q GAIN MUTATED 20 28 53
20Q GAIN WILD-TYPE 101 168 77

Figure S83.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S84.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
20Q GAIN MUTATED 17 18 80
20Q GAIN WILD-TYPE 89 204 115

Figure S84.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S85.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
20Q GAIN MUTATED 23 23 69
20Q GAIN WILD-TYPE 138 214 56

Figure S85.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S86.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
20Q GAIN MUTATED 25 18 71
20Q GAIN WILD-TYPE 99 186 111

Figure S86.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S87.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
20Q GAIN MUTATED 38 34 22 20
20Q GAIN WILD-TYPE 106 100 173 17

Figure S87.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S88.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
20Q GAIN MUTATED 6 3 3 19
20Q GAIN WILD-TYPE 32 18 45 16

Figure S88.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S89.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
21Q GAIN MUTATED 12 7 31
21Q GAIN WILD-TYPE 226 128 124

Figure S89.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S90.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
21Q GAIN MUTATED 7 11 32
21Q GAIN WILD-TYPE 99 211 163

Figure S90.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.19

Table S91.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
21Q GAIN MUTATED 13 13 24
21Q GAIN WILD-TYPE 148 224 101

Figure S91.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S92.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
22Q GAIN MUTATED 5 13 22
22Q GAIN WILD-TYPE 233 122 133

Figure S92.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S93.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1P LOSS MUTATED 5 27 25
1P LOSS WILD-TYPE 233 108 130

Figure S93.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S94.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1Q LOSS MUTATED 1 23 12
1Q LOSS WILD-TYPE 237 112 143

Figure S94.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S95.  Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2P LOSS MUTATED 0 1 6
2P LOSS WILD-TYPE 33 23 7

Figure S95.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S96.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2P LOSS MUTATED 0 12 2
2P LOSS WILD-TYPE 238 123 153

Figure S96.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S97.  Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
2P LOSS MUTATED 0 2 0 7 0 0
2P LOSS WILD-TYPE 108 60 75 73 79 43

Figure S97.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S98.  Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
2P LOSS MUTATED 0 0 9
2P LOSS WILD-TYPE 121 196 121

Figure S98.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S99.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
2P LOSS MUTATED 12 0 2
2P LOSS WILD-TYPE 94 222 193

Figure S99.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S100.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
2P LOSS MUTATED 12 0 2
2P LOSS WILD-TYPE 149 237 123

Figure S100.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S101.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
2P LOSS MUTATED 1 0 13
2P LOSS WILD-TYPE 123 204 169

Figure S101.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S102.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
2P LOSS MUTATED 1 12 1 0
2P LOSS WILD-TYPE 143 122 194 37

Figure S102.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.23

Table S103.  Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2Q LOSS MUTATED 0 1 5
2Q LOSS WILD-TYPE 33 23 8

Figure S103.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S104.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2Q LOSS MUTATED 0 11 3
2Q LOSS WILD-TYPE 238 124 152

Figure S104.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S105.  Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
2Q LOSS MUTATED 0 0 9
2Q LOSS WILD-TYPE 121 196 121

Figure S105.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S106.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
2Q LOSS MUTATED 12 0 2
2Q LOSS WILD-TYPE 94 222 193

Figure S106.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S107.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
2Q LOSS MUTATED 11 0 3
2Q LOSS WILD-TYPE 150 237 122

Figure S107.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S108.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
2Q LOSS MUTATED 0 0 14
2Q LOSS WILD-TYPE 124 204 168

Figure S108.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S109.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
2Q LOSS MUTATED 1 13 0 0
2Q LOSS WILD-TYPE 143 121 195 37

Figure S109.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S110.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3P LOSS MUTATED 203 41 136
3P LOSS WILD-TYPE 35 94 19

Figure S110.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S111.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
3P LOSS MUTATED 51 184 142
3P LOSS WILD-TYPE 55 38 53

Figure S111.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S112.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
3P LOSS MUTATED 95 192 90
3P LOSS WILD-TYPE 66 45 35

Figure S112.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S113.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
4P LOSS MUTATED 9 16 47
4P LOSS WILD-TYPE 229 119 108

Figure S113.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S114.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
4P LOSS MUTATED 11 8 31
4P LOSS WILD-TYPE 117 68 79

Figure S114.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S115.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
4P LOSS MUTATED 9 31 31
4P LOSS WILD-TYPE 152 206 94

Figure S115.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S116.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
4Q LOSS MUTATED 5 14 46
4Q LOSS WILD-TYPE 233 121 109

Figure S116.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S117.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
4Q LOSS MUTATED 9 6 30
4Q LOSS WILD-TYPE 119 70 80

Figure S117.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S118.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
4Q LOSS MUTATED 5 22 38
4Q LOSS WILD-TYPE 101 200 157

Figure S118.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S119.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
4Q LOSS MUTATED 7 26 32
4Q LOSS WILD-TYPE 154 211 93

Figure S119.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S120.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
6P LOSS MUTATED 11 26 63
6P LOSS WILD-TYPE 227 109 92

Figure S120.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S121.  Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
6P LOSS MUTATED 9 12 31
6P LOSS WILD-TYPE 119 64 79

Figure S121.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.09

Table S122.  Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
6P LOSS MUTATED 17 26 15 18 7 5
6P LOSS WILD-TYPE 91 36 60 62 72 38

Figure S122.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S123.  Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
6P LOSS MUTATED 22 20 46
6P LOSS WILD-TYPE 99 176 84

Figure S123.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S124.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
6P LOSS MUTATED 16 20 61
6P LOSS WILD-TYPE 90 202 134

Figure S124.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S125.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
6P LOSS MUTATED 23 23 51
6P LOSS WILD-TYPE 138 214 74

Figure S125.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S126.  Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
6P LOSS MUTATED 14 17 65
6P LOSS WILD-TYPE 110 187 117

Figure S126.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S127.  Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
6P LOSS MUTATED 26 40 14 16
6P LOSS WILD-TYPE 118 94 181 21

Figure S127.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S128.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
6Q LOSS MUTATED 27 26 75
6Q LOSS WILD-TYPE 211 109 80

Figure S128.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S129.  Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
6Q LOSS MUTATED 28 28 21 20 7 7
6Q LOSS WILD-TYPE 80 34 54 60 72 36

Figure S129.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S130.  Gene #52: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
6Q LOSS MUTATED 33 30 48
6Q LOSS WILD-TYPE 88 166 82

Figure S130.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.18

Table S131.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
6Q LOSS MUTATED 18 41 66
6Q LOSS WILD-TYPE 88 181 129

Figure S131.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S132.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
6Q LOSS MUTATED 32 42 51
6Q LOSS WILD-TYPE 129 195 74

Figure S132.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S133.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
6Q LOSS MUTATED 20 33 71
6Q LOSS WILD-TYPE 104 171 111

Figure S133.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S134.  Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
6Q LOSS MUTATED 31 46 30 17
6Q LOSS WILD-TYPE 113 88 165 20

Figure S134.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S135.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
8P LOSS MUTATED 43 30 64
8P LOSS WILD-TYPE 195 105 91

Figure S135.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S136.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
9P LOSS MUTATED 10 32 107
9P LOSS WILD-TYPE 228 103 48

Figure S136.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S137.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
9P LOSS MUTATED 6 20 67
9P LOSS WILD-TYPE 122 56 43

Figure S137.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S138.  Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
9P LOSS MUTATED 18 36 29 21 20 10
9P LOSS WILD-TYPE 90 26 46 59 59 33

Figure S138.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S139.  Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
9P LOSS MUTATED 33 43 58
9P LOSS WILD-TYPE 88 153 72

Figure S139.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S140.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
9P LOSS MUTATED 14 26 107
9P LOSS WILD-TYPE 92 196 88

Figure S140.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S141.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
9P LOSS MUTATED 36 35 76
9P LOSS WILD-TYPE 125 202 49

Figure S141.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S142.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
9P LOSS MUTATED 27 26 91
9P LOSS WILD-TYPE 97 178 91

Figure S142.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S143.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
9P LOSS MUTATED 43 53 24 24
9P LOSS WILD-TYPE 101 81 171 13

Figure S143.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S144.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
9Q LOSS MUTATED 11 32 107
9Q LOSS WILD-TYPE 227 103 48

Figure S144.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S145.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
9Q LOSS MUTATED 6 21 64
9Q LOSS WILD-TYPE 122 55 46

Figure S145.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S146.  Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
9Q LOSS MUTATED 17 36 32 21 20 10
9Q LOSS WILD-TYPE 91 26 43 59 59 33

Figure S146.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S147.  Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
9Q LOSS MUTATED 36 43 57
9Q LOSS WILD-TYPE 85 153 73

Figure S147.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S148.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
9Q LOSS MUTATED 14 26 108
9Q LOSS WILD-TYPE 92 196 87

Figure S148.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S149.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
9Q LOSS MUTATED 38 34 76
9Q LOSS WILD-TYPE 123 203 49

Figure S149.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S150.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
9Q LOSS MUTATED 26 25 93
9Q LOSS WILD-TYPE 98 179 89

Figure S150.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S151.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
9Q LOSS MUTATED 42 55 23 24
9Q LOSS WILD-TYPE 102 79 172 13

Figure S151.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S152.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10P LOSS MUTATED 9 23 35
10P LOSS WILD-TYPE 229 112 120

Figure S152.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S153.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10Q LOSS MUTATED 17 27 45
10Q LOSS WILD-TYPE 221 108 110

Figure S153.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S154.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11P LOSS MUTATED 0 5 13
11P LOSS WILD-TYPE 238 130 142

Figure S154.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S155.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11Q LOSS MUTATED 0 5 18
11Q LOSS WILD-TYPE 238 130 137

Figure S155.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S156.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
11Q LOSS MUTATED 4 4 15
11Q LOSS WILD-TYPE 157 233 110

Figure S156.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S157.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
13Q LOSS MUTATED 7 23 41
13Q LOSS WILD-TYPE 231 112 114

Figure S157.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S158.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
13Q LOSS MUTATED 7 15 24
13Q LOSS WILD-TYPE 121 61 86

Figure S158.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S159.  Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
13Q LOSS MUTATED 3 19 13 14 9 4
13Q LOSS WILD-TYPE 105 43 62 66 70 39

Figure S159.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S160.  Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
13Q LOSS MUTATED 14 14 34
13Q LOSS WILD-TYPE 107 182 96

Figure S160.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S161.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
13Q LOSS MUTATED 13 14 44
13Q LOSS WILD-TYPE 93 208 151

Figure S161.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S162.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
13Q LOSS MUTATED 20 11 40
13Q LOSS WILD-TYPE 141 226 85

Figure S162.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S163.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
13Q LOSS MUTATED 12 12 45
13Q LOSS WILD-TYPE 112 192 137

Figure S163.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S164.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
13Q LOSS MUTATED 17 31 9 12
13Q LOSS WILD-TYPE 127 103 186 25

Figure S164.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S165.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
14Q LOSS MUTATED 9 19 2
14Q LOSS WILD-TYPE 24 5 11

Figure S165.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S166.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
14Q LOSS MUTATED 4 7 1 11 5 0 2
14Q LOSS WILD-TYPE 7 5 3 0 8 9 8

Figure S166.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S167.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
14Q LOSS MUTATED 63 45 108
14Q LOSS WILD-TYPE 175 90 47

Figure S167.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S168.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
14Q LOSS MUTATED 25 34 64
14Q LOSS WILD-TYPE 103 42 46

Figure S168.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S169.  Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
14Q LOSS MUTATED 34 40 55 27 24 12
14Q LOSS WILD-TYPE 74 22 20 53 55 31

Figure S169.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S170.  Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
14Q LOSS MUTATED 67 59 66
14Q LOSS WILD-TYPE 54 137 64

Figure S170.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S171.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
14Q LOSS MUTATED 15 69 128
14Q LOSS WILD-TYPE 91 153 67

Figure S171.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S172.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
14Q LOSS MUTATED 66 73 73
14Q LOSS WILD-TYPE 95 164 52

Figure S172.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S173.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
14Q LOSS MUTATED 34 61 115
14Q LOSS WILD-TYPE 90 143 67

Figure S173.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S174.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
14Q LOSS MUTATED 49 80 58 23
14Q LOSS WILD-TYPE 95 54 137 14

Figure S174.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S175.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
15Q LOSS MUTATED 1 6 29
15Q LOSS WILD-TYPE 237 129 126

Figure S175.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S176.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
15Q LOSS MUTATED 1 7 28
15Q LOSS WILD-TYPE 105 215 167

Figure S176.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S177.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
15Q LOSS MUTATED 4 8 24
15Q LOSS WILD-TYPE 157 229 101

Figure S177.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.096

Table S178.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P LOSS MUTATED 0 5 6
17P LOSS WILD-TYPE 33 19 7

Figure S178.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S179.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17P LOSS MUTATED 0 5 1 0 0 0 5
17P LOSS WILD-TYPE 11 7 3 11 13 9 5

Figure S179.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S180.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17P LOSS MUTATED 2 16 28
17P LOSS WILD-TYPE 236 119 127

Figure S180.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S181.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
17P LOSS MUTATED 15 3 28
17P LOSS WILD-TYPE 91 219 167

Figure S181.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S182.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
17P LOSS MUTATED 20 3 23
17P LOSS WILD-TYPE 141 234 102

Figure S182.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S183.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
17P LOSS MUTATED 9 4 33
17P LOSS WILD-TYPE 115 200 149

Figure S183.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S184.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
17P LOSS MUTATED 13 20 6 7
17P LOSS WILD-TYPE 131 114 189 30

Figure S184.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S185.  Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17Q LOSS MUTATED 0 4 0 0 0 0 5
17Q LOSS WILD-TYPE 11 8 4 11 13 9 5

Figure S185.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S186.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17Q LOSS MUTATED 1 13 14
17Q LOSS WILD-TYPE 237 122 141

Figure S186.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S187.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
17Q LOSS MUTATED 12 2 14
17Q LOSS WILD-TYPE 94 220 181

Figure S187.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S188.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
17Q LOSS MUTATED 15 2 11
17Q LOSS WILD-TYPE 146 235 114

Figure S188.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S189.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
17Q LOSS MUTATED 4 2 22
17Q LOSS WILD-TYPE 120 202 160

Figure S189.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S190.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
18P LOSS MUTATED 12 25 56
18P LOSS WILD-TYPE 226 110 99

Figure S190.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S191.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
18P LOSS MUTATED 6 19 32
18P LOSS WILD-TYPE 122 57 78

Figure S191.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S192.  Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
18P LOSS MUTATED 7 24 20 16 13 3
18P LOSS WILD-TYPE 101 38 55 64 66 40

Figure S192.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S193.  Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
18P LOSS MUTATED 21 20 42
18P LOSS WILD-TYPE 100 176 88

Figure S193.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S194.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
18P LOSS MUTATED 9 11 72
18P LOSS WILD-TYPE 97 211 123

Figure S194.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S195.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
18P LOSS MUTATED 28 12 52
18P LOSS WILD-TYPE 133 225 73

Figure S195.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S196.  Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
18P LOSS MUTATED 21 11 61
18P LOSS WILD-TYPE 103 193 121

Figure S196.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S197.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
18P LOSS MUTATED 29 40 9 15
18P LOSS WILD-TYPE 115 94 186 22

Figure S197.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S198.  Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
18P LOSS MUTATED 7 4 0 10
18P LOSS WILD-TYPE 31 17 48 25

Figure S198.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S199.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
18Q LOSS MUTATED 13 25 57
18Q LOSS WILD-TYPE 225 110 98

Figure S199.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S200.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
18Q LOSS MUTATED 7 19 31
18Q LOSS WILD-TYPE 121 57 79

Figure S200.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S201.  Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
18Q LOSS MUTATED 7 24 20 17 13 5
18Q LOSS WILD-TYPE 101 38 55 63 66 38

Figure S201.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S202.  Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
18Q LOSS MUTATED 20 24 42
18Q LOSS WILD-TYPE 101 172 88

Figure S202.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S203.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
18Q LOSS MUTATED 10 12 72
18Q LOSS WILD-TYPE 96 210 123

Figure S203.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S204.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
18Q LOSS MUTATED 30 12 52
18Q LOSS WILD-TYPE 131 225 73

Figure S204.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S205.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
18Q LOSS MUTATED 22 12 61
18Q LOSS WILD-TYPE 102 192 121

Figure S205.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S206.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
18Q LOSS MUTATED 28 41 10 16
18Q LOSS WILD-TYPE 116 93 185 21

Figure S206.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S207.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19P LOSS MUTATED 0 1 10
19P LOSS WILD-TYPE 238 134 145

Figure S207.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S208.  Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
19P LOSS MUTATED 2 0 8
19P LOSS WILD-TYPE 119 196 122

Figure S208.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S209.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
19P LOSS MUTATED 0 2 9
19P LOSS WILD-TYPE 161 235 116

Figure S209.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S210.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
21Q LOSS MUTATED 6 26 23
21Q LOSS WILD-TYPE 232 109 132

Figure S210.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S211.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
22Q LOSS MUTATED 2 13 24
22Q LOSS WILD-TYPE 236 122 131

Figure S211.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S212.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
22Q LOSS MUTATED 4 5 30
22Q LOSS WILD-TYPE 102 217 165

Figure S212.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S213.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
22Q LOSS MUTATED 13 6 20
22Q LOSS WILD-TYPE 148 231 105

Figure S213.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S214.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
22Q LOSS MUTATED 2 7 30
22Q LOSS WILD-TYPE 122 197 152

Figure S214.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0087

Table S215.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
XQ LOSS MUTATED 7 10 30
XQ LOSS WILD-TYPE 231 125 125

Figure S215.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 528

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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