Correlation between copy number variations of arm-level result and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1KP81GZ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KP81GZ
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 10 molecular subtypes across 492 patients, 352 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p gain cnv correlated to 'CN_CNMF'.

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

  • 5q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

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

  • 8p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 9p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 11q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 4q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 13q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF'.

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

  • 16p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 19p loss cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 20q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 352 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type 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
3p gain 40 (8%) 452 1e-05
(0.000143) 		0.0102
(0.036) 		0.0406
(0.0961) 		0.0268
(0.0742) 		0.00468
(0.0195) 		0.00039
(0.00288) 		0.0216
(0.0627) 		0.00509
(0.0208) 		0.00371
(0.0163) 		0.00025
(0.00198)
3q gain 54 (11%) 438 1e-05
(0.000143) 		0.00754
(0.0278) 		0.027
(0.0742) 		0.0258
(0.0725) 		0.00112
(0.00654) 		0.0013
(0.00727) 		0.00529
(0.0213) 		0.00391
(0.0171) 		0.0148
(0.0472) 		2e-05
(0.000262)
8q gain 124 (25%) 368 1e-05
(0.000143) 		1e-05
(0.000143) 		0.00013
(0.00116) 		0.00038
(0.00284) 		5e-05
(0.000548) 		3e-05
(0.000358) 		0.00046
(0.00323) 		1e-05
(0.000143) 		1e-05
(0.000143) 		3e-05
(0.000358)
6q loss 40 (8%) 452 1e-05
(0.000143) 		0.0347
(0.0872) 		0.0262
(0.0731) 		0.028
(0.0758) 		0.00031
(0.00238) 		0.00092
(0.00575) 		0.0129
(0.0431) 		0.0482
(0.11) 		0.00438
(0.0183) 		0.00198
(0.01)
18q loss 101 (21%) 391 1e-05
(0.000143) 		0.00629
(0.0243) 		0.00037
(0.00279) 		0.0014
(0.00762) 		0.00332
(0.0151) 		0.0215
(0.0627) 		0.00725
(0.0269) 		0.00334
(0.0151) 		0.0151
(0.0477) 		1e-05
(0.000143)
8p gain 71 (14%) 421 1e-05
(0.000143) 		1e-05
(0.000143) 		8e-05
(0.00078) 		0.00048
(0.00325) 		6e-05
(0.000615) 		0.00048
(0.00325) 		0.126
(0.213) 		0.00591
(0.0231) 		0.00207
(0.0103) 		0.00187
(0.00965)
4p loss 24 (5%) 468 1e-05
(0.000143) 		0.0181
(0.0551) 		0.0376
(0.0917) 		0.128
(0.215) 		0.0043
(0.0181) 		0.0286
(0.0774) 		0.00131
(0.00728) 		0.00259
(0.0126) 		4e-05
(0.000464) 		7e-05
(7e-04)
18p loss 68 (14%) 424 1e-05
(0.000143) 		0.00548
(0.0219) 		0.0101
(0.0358) 		0.0032
(0.0149) 		0.00329
(0.0151) 		0.0489
(0.111) 		0.0582
(0.126) 		0.0302
(0.0803) 		0.0102
(0.036) 		0.00505
(0.0207)
7p gain 102 (21%) 390 1e-05
(0.000143) 		1e-05
(0.000143) 		0.229
(0.326) 		0.299
(0.407) 		1e-05
(0.000143) 		3e-05
(0.000358) 		0.0184
(0.0557) 		5e-05
(0.000548) 		0.00023
(0.00186) 		0.00168
(0.00895)
7q gain 95 (19%) 397 1e-05
(0.000143) 		1e-05
(0.000143) 		0.303
(0.411) 		0.64
(0.72) 		1e-05
(0.000143) 		4e-05
(0.000464) 		0.0242
(0.0687) 		9e-05
(0.000857) 		0.0004
(0.00288) 		0.00549
(0.0219)
20p gain 26 (5%) 466 1e-05
(0.000143) 		0.0222
(0.0644) 		0.221
(0.319) 		0.146
(0.237) 		0.0233
(0.0665) 		0.0367
(0.0901) 		0.00203
(0.0101) 		0.00401
(0.0173) 		0.0313
(0.0817) 		0.00407
(0.0174)
21q gain 21 (4%) 471 1e-05
(0.000143) 		0.0388
(0.0924) 		0.541
(0.639) 		0.843
(0.898) 		0.00179
(0.00935) 		0.0268
(0.0742) 		0.0145
(0.0469) 		0.00321
(0.0149) 		0.0121
(0.0413) 		0.0292
(0.0784)
1p loss 22 (4%) 470 1e-05
(0.000143) 		0.00057
(0.0038) 		0.541
(0.639) 		0.869
(0.913) 		0.00117
(0.00673) 		0.00026
(0.00204) 		0.0252
(0.0711) 		0.00361
(0.016) 		0.0204
(0.0608) 		0.013
(0.0432)
10q loss 43 (9%) 449 1e-05
(0.000143) 		0.00078
(0.00495) 		0.352
(0.46) 		0.163
(0.253) 		0.00221
(0.0108) 		0.0004
(0.00288) 		0.0384
(0.092) 		0.00125
(0.00704) 		0.00178
(0.00935) 		0.00012
(0.00108)
15q loss 36 (7%) 456 1e-05
(0.000143) 		0.0018
(0.00935) 		0.14
(0.23) 		0.408
(0.519) 		0.00067
(0.00439) 		0.00616
(0.0239) 		0.00012
(0.00108) 		0.00726
(0.0269) 		0.00116
(0.00672) 		0.00018
(0.00155)
17p loss 76 (15%) 416 1e-05
(0.000143) 		0.00122
(0.00692) 		0.0223
(0.0645) 		0.154
(0.246) 		0.00012
(0.00108) 		0.00168
(0.00895) 		0.0989
(0.183) 		0.0319
(0.0826) 		0.0225
(0.0646) 		7e-05
(7e-04)
5p gain 23 (5%) 469 1e-05
(0.000143) 		0.0591
(0.128) 		0.0275
(0.0752) 		0.191
(0.283) 		0.00882
(0.0319) 		0.0614
(0.132) 		0.00122
(0.00692) 		0.00152
(0.00822) 		0.00191
(0.00979) 		0.00403
(0.0173)
6p loss 25 (5%) 467 1e-05
(0.000143) 		0.0153
(0.0481) 		0.168
(0.26) 		0.0575
(0.126) 		0.00027
(0.0021) 		0.00283
(0.0135) 		0.0576
(0.126) 		0.0313
(0.0817) 		0.0144
(0.0469) 		0.00354
(0.0159)
10p loss 41 (8%) 451 1e-05
(0.000143) 		5e-05
(0.000548) 		0.21
(0.306) 		0.315
(0.423) 		0.0002
(0.00167) 		6e-05
(0.000615) 		0.0838
(0.166) 		6e-05
(0.000615) 		0.0114
(0.0393) 		0.00014
(0.00123)
16q loss 107 (22%) 385 1e-05
(0.000143) 		0.00075
(0.0048) 		0.968
(0.995) 		0.954
(0.984) 		0.0301
(0.0802) 		0.0309
(0.0811) 		0.0812
(0.162) 		0.00045
(0.00319) 		0.00428
(0.0181) 		8e-05
(0.00078)
17q loss 20 (4%) 472 1e-05
(0.000143) 		0.0108
(0.0375) 		0.592
(0.677) 		0.527
(0.625) 		0.00095
(0.00589) 		0.0358
(0.0885) 		0.0127
(0.0427) 		0.0466
(0.107) 		0.0306
(0.0808) 		0.146
(0.238)
xp loss 39 (8%) 453 1e-05
(0.000143) 		3e-05
(0.000358) 		0.113
(0.195) 		0.0846
(0.166) 		0.00041
(0.00293) 		5e-05
(0.000548) 		1e-05
(0.000143) 		0.0359
(0.0885) 		0.00573
(0.0226) 		0.0963
(0.18)
xq loss 39 (8%) 453 1e-05
(0.000143) 		1e-05
(0.000143) 		0.113
(0.195) 		0.0833
(0.165) 		0.0004
(0.00288) 		0.00011
(0.00104) 		1e-05
(0.000143) 		0.0346
(0.0872) 		0.00592
(0.0231) 		0.0958
(0.18)
20q gain 28 (6%) 464 1e-05
(0.000143) 		0.0196
(0.0592) 		0.342
(0.448) 		0.034
(0.0864) 		0.0551
(0.123) 		0.125
(0.212) 		0.0114
(0.0393) 		0.0079
(0.029) 		0.1
(0.184) 		0.00929
(0.0335)
5q loss 22 (4%) 470 1e-05
(0.000143) 		0.00279
(0.0134) 		0.103
(0.184) 		0.285
(0.392) 		0.012
(0.041) 		0.002
(0.0101) 		0.0573
(0.126) 		0.00112
(0.00654) 		0.111
(0.193) 		0.027
(0.0742)
8p loss 168 (34%) 324 1e-05
(0.000143) 		1e-05
(0.000143) 		0.848
(0.899) 		0.387
(0.499) 		1e-05
(0.000143) 		1e-05
(0.000143) 		0.00035
(0.00267) 		0.0799
(0.16) 		0.058
(0.126) 		0.0316
(0.0821)
1q gain 26 (5%) 466 1e-05
(0.000143) 		0.142
(0.233) 		0.0422
(0.0985) 		0.211
(0.307) 		0.00016
(0.00139) 		0.00054
(0.00363) 		0.0975
(0.181) 		0.0332
(0.0852) 		0.502
(0.607) 		0.195
(0.289)
9q gain 50 (10%) 442 1e-05
(0.000143) 		0.118
(0.202) 		0.295
(0.403) 		0.0917
(0.176) 		0.0154
(0.0484) 		0.19
(0.282) 		0.357
(0.464) 		0.0109
(0.0376) 		0.00702
(0.0264) 		0.0139
(0.0456)
10p gain 15 (3%) 477 6e-05
(0.000615) 		0.0344
(0.0871) 		0.545
(0.642) 		0.801
(0.863) 		0.105
(0.186) 		0.0337
(0.0859) 		0.574
(0.665) 		0.0135
(0.0445) 		0.172
(0.265) 		0.0007
(0.00452)
2q loss 18 (4%) 474 0.00012
(0.00108) 		0.0207
(0.0609) 		0.478
(0.589) 		0.886
(0.928) 		0.723
(0.792) 		0.485
(0.595) 		0.127
(0.214) 		0.0349
(0.0872) 		0.00855
(0.0312) 		0.00099
(0.00609)
4q loss 17 (3%) 475 1e-05
(0.000143) 		0.154
(0.246) 		0.593
(0.678) 		0.827
(0.887) 		0.0065
(0.0248) 		0.105
(0.186) 		0.202
(0.296) 		0.0484
(0.111) 		0.0147
(0.0471) 		0.00504
(0.0207)
9p loss 21 (4%) 471 1e-05
(0.000143) 		0.285
(0.392) 		0.00721
(0.0269) 		0.00528
(0.0213) 		0.00423
(0.018) 		0.0225
(0.0646) 		0.263
(0.367) 		0.242
(0.344) 		0.107
(0.188) 		0.0633
(0.134)
12p loss 48 (10%) 444 1e-05
(0.000143) 		0.298
(0.407) 		0.138
(0.229) 		0.525
(0.624) 		0.0495
(0.113) 		0.418
(0.528) 		0.456
(0.568) 		0.0167
(0.0515) 		0.00697
(0.0263) 		0.00277
(0.0133)
13q loss 77 (16%) 415 1e-05
(0.000143) 		0.331
(0.438) 		0.499
(0.605) 		0.0125
(0.0424) 		0.0417
(0.0977) 		0.0649
(0.137) 		0.182
(0.274) 		0.0407
(0.0961) 		0.227
(0.324) 		0.0002
(0.00167)
22q loss 47 (10%) 445 1e-05
(0.000143) 		0.213
(0.309) 		0.0887
(0.172) 		0.373
(0.482) 		0.0181
(0.0551) 		0.0469
(0.108) 		0.0691
(0.144) 		0.029
(0.078) 		0.148
(0.24) 		0.00022
(0.0018)
1p gain 16 (3%) 476 1e-05
(0.000143) 		0.204
(0.298) 		0.0911
(0.175) 		0.279
(0.384) 		0.00977
(0.035) 		0.00062
(0.0041) 		0.312
(0.421) 		0.0419
(0.098) 		0.848
(0.899) 		0.175
(0.267)
16p gain 31 (6%) 461 1e-05
(0.000143) 		0.265
(0.369) 		0.56
(0.652) 		0.859
(0.907) 		0.0702
(0.145) 		0.318
(0.426) 		0.155
(0.246) 		0.00398
(0.0173) 		0.0262
(0.0731) 		0.0127
(0.0427)
17p gain 8 (2%) 484 0.0147
(0.0471) 		0.911
(0.946) 		0.334
(0.441) 		1
(1.00) 		0.0501
(0.113) 		0.663
(0.739) 		0.0208
(0.061) 		0.0165
(0.0513) 		0.606
(0.687) 		0.00361
(0.016)
2p loss 16 (3%) 476 9e-05
(0.000857) 		0.00517
(0.021) 		0.176
(0.267) 		0.591
(0.677) 		0.481
(0.591) 		0.353
(0.461) 		0.134
(0.223) 		0.0874
(0.17) 		0.00367
(0.0162) 		0.00332
(0.0151)
5p loss 12 (2%) 480 2e-05
(0.000262) 		0.17
(0.262) 		0.911
(0.946) 		0.551
(0.647) 		0.0388
(0.0924) 		0.00557
(0.0221) 		0.864
(0.91) 		0.00291
(0.0138) 		0.51
(0.609) 		0.103
(0.184)
8q loss 24 (5%) 468 0.0295
(0.0789) 		0.00112
(0.00654) 		0.712
(0.782) 		0.416
(0.527) 		0.0104
(0.0365) 		0.0249
(0.0704) 		0.103
(0.184) 		0.992
(1.00) 		0.216
(0.312) 		0.248
(0.352)
2p gain 10 (2%) 482 0.00104
(0.0063) 		0.0765
(0.155) 		0.425
(0.535) 		0.446
(0.559) 		0.00675
(0.0256) 		0.143
(0.233) 		0.113
(0.195) 		0.0365
(0.0897) 		0.165
(0.256) 		0.188
(0.281)
10q gain 14 (3%) 478 0.00025
(0.00198) 		0.0572
(0.126) 		0.0723
(0.149) 		0.0926
(0.176) 		0.129
(0.215) 		0.0323
(0.0831) 		0.585
(0.673) 		0.0864
(0.168) 		0.273
(0.377) 		0.00197
(0.01)
11p gain 26 (5%) 466 1e-05
(0.000143) 		0.0553
(0.123) 		1
(1.00) 		0.454
(0.566) 		0.0943
(0.179) 		0.0146
(0.047) 		0.6
(0.683) 		0.0536
(0.12) 		0.0356
(0.0885) 		0.177
(0.269)
11q gain 29 (6%) 463 1e-05
(0.000143) 		0.0736
(0.151) 		0.955
(0.985) 		0.406
(0.518) 		0.0306
(0.0808) 		0.0383
(0.092) 		0.69
(0.761) 		0.0509
(0.114) 		0.0846
(0.166) 		0.125
(0.212)
12p gain 14 (3%) 478 2e-05
(0.000262) 		0.185
(0.276) 		0.781
(0.844) 		0.487
(0.595) 		0.0889
(0.172) 		0.114
(0.195) 		0.364
(0.473) 		0.00106
(0.00638) 		0.0238
(0.0678) 		0.207
(0.303)
12q gain 17 (3%) 475 0.00048
(0.00325) 		0.0827
(0.165) 		0.48
(0.59) 		0.622
(0.702) 		0.2
(0.294) 		0.111
(0.193) 		0.781
(0.844) 		0.0198
(0.0597) 		0.0157
(0.0492) 		0.096
(0.18)
17q gain 11 (2%) 481 0.00047
(0.00325) 		0.803
(0.863) 		0.779
(0.843) 		0.957
(0.986) 		0.0172
(0.0529) 		0.216
(0.312) 		0.0903
(0.174) 		0.11
(0.193) 		0.476
(0.587) 		0.00068
(0.00442)
19p gain 12 (2%) 480 1e-05
(0.000143) 		0.159
(0.248) 		0.015
(0.0477) 		0.298
(0.406) 		0.0357
(0.0885) 		0.342
(0.448) 		0.14
(0.229) 		0.0861
(0.168) 		0.514
(0.613) 		0.122
(0.207)
xp gain 7 (1%) 485 0.00107
(0.00639) 		0.0661
(0.139) 		1
(1.00) 		0.838
(0.895) 		0.102
(0.184) 		0.0921
(0.176) 		0.51
(0.609) 		0.0444
(0.103) 		0.00638
(0.0244) 		0.0858
(0.168)
xq gain 7 (1%) 485 0.00104
(0.0063) 		0.0661
(0.139) 		1
(1.00) 		0.838
(0.895) 		0.101
(0.184) 		0.0924
(0.176) 		0.507
(0.609) 		0.0461
(0.106) 		0.00638
(0.0244) 		0.086
(0.168)
19p loss 17 (3%) 475 0.00021
(0.00173) 		0.0571
(0.126) 		0.646
(0.722) 		0.253
(0.356) 		0.305
(0.412) 		0.159
(0.248) 		0.131
(0.219) 		0.158
(0.248) 		0.003
(0.0141) 		0.00996
(0.0356)
19q loss 17 (3%) 475 0.00019
(0.00162) 		0.0549
(0.122) 		0.644
(0.722) 		0.255
(0.357) 		0.304
(0.411) 		0.16
(0.248) 		0.131
(0.219) 		0.159
(0.248) 		0.00268
(0.013) 		0.0107
(0.0374)
21q loss 24 (5%) 468 3e-05
(0.000358) 		0.0683
(0.142) 		0.153
(0.246) 		0.158
(0.248) 		0.00324
(0.015) 		0.323
(0.43) 		0.571
(0.663) 		0.103
(0.184) 		0.425
(0.535) 		0.0414
(0.0974)
5q gain 12 (2%) 480 2e-05
(0.000262) 		0.171
(0.264) 		0.588
(0.675) 		0.579
(0.669) 		0.0349
(0.0872) 		0.23
(0.327) 		0.38
(0.491) 		0.159
(0.248) 		0.123
(0.209) 		0.324
(0.43)
6p gain 10 (2%) 482 0.00136
(0.00745) 		0.159
(0.248) 		0.174
(0.266) 		0.404
(0.517) 		0.139
(0.229) 		0.272
(0.377) 		0.67
(0.743) 		0.106
(0.187) 		0.0177
(0.0542) 		0.0745
(0.152)
6q gain 6 (1%) 486 0.0202
(0.0607) 		0.79
(0.852) 		0.828
(0.887) 		0.913
(0.948) 		0.102
(0.184) 		0.582
(0.671) 		0.196
(0.289) 		0.0392
(0.0931) 		0.27
(0.374) 		0.568
(0.661)
9p gain 34 (7%) 458 1e-05
(0.000143) 		0.1
(0.184) 		0.703
(0.774) 		0.128
(0.215) 		0.0785
(0.158) 		0.0984
(0.182) 		0.485
(0.595) 		0.111
(0.193) 		0.0161
(0.0501) 		0.18
(0.272)
19q gain 12 (2%) 480 1e-05
(0.000143) 		0.102
(0.184) 		0.152
(0.245) 		0.109
(0.192) 		0.0383
(0.092) 		0.367
(0.475) 		0.218
(0.315) 		0.0615
(0.132) 		0.507
(0.609) 		0.155
(0.246)
1q loss 6 (1%) 486 0.0204
(0.0608) 		0.154
(0.246) 		0.679
(0.752) 		0.473
(0.585) 		0.0432
(0.101) 		0.0949
(0.179) 		0.101
(0.184) 		0.102
(0.184) 		0.0511
(0.114) 		0.393
(0.506)
3p loss 9 (2%) 483 0.0337
(0.0859) 		0.313
(0.421) 		0.518
(0.617) 		0.205
(0.3) 		0.106
(0.187) 		0.0382
(0.092) 		0.104
(0.186) 		0.411
(0.521) 		0.0503
(0.114) 		0.195
(0.289)
9q loss 10 (2%) 482 0.00134
(0.00739) 		0.34
(0.446) 		0.197
(0.291) 		0.15
(0.242) 		0.262
(0.367) 		0.227
(0.324) 		0.615
(0.695) 		0.55
(0.647) 		0.52
(0.618) 		0.0373
(0.0913)
11q loss 5 (1%) 487 0.0135
(0.0445) 		0.0694
(0.144) 		1
(1.00) 		0.889
(0.928) 		0.0621
(0.133) 		0.302
(0.41) 		0.634
(0.714) 		0.185
(0.276) 		0.0205
(0.0608) 		0.288
(0.395)
12q loss 20 (4%) 472 3e-05
(0.000358) 		0.181
(0.274) 		0.504
(0.608) 		0.333
(0.44) 		0.253
(0.357) 		0.264
(0.368) 		1
(1.00) 		0.051
(0.114) 		0.0683
(0.142) 		0.00877
(0.0319)
16p loss 32 (7%) 460 0.00169
(0.00895) 		0.336
(0.442) 		1
(1.00) 		0.139
(0.229) 		0.49
(0.596) 		0.379
(0.49) 		0.645
(0.722) 		0.319
(0.426) 		0.224
(0.321) 		0.0308
(0.0811)
20q loss 9 (2%) 483 0.0275
(0.0752) 		0.0787
(0.158) 		1
(1.00) 		0.772
(0.839) 		0.0941
(0.179) 		0.0382
(0.092) 		0.0733
(0.15) 		0.06
(0.129) 		1
(1.00) 		0.503
(0.607)
2q gain 7 (1%) 485 0.00092
(0.00575) 		0.469
(0.581) 		0.849
(0.899) 		0.688
(0.761) 		0.102
(0.184) 		0.555
(0.65) 		0.51
(0.609) 		0.0625
(0.133) 		0.176
(0.267) 		0.159
(0.248)
4p gain 9 (2%) 483 0.0277
(0.0754) 		0.847
(0.899) 		0.148
(0.24) 		0.417
(0.527) 		0.489
(0.596) 		0.766
(0.835) 		0.917
(0.95) 		0.414
(0.525) 		0.605
(0.686) 		0.576
(0.667)
13q gain 8 (2%) 484 0.0144
(0.0469) 		0.139
(0.229) 		0.0961
(0.18) 		0.849
(0.899) 		0.605
(0.686) 		0.663
(0.739) 		0.822
(0.883) 		0.558
(0.651) 		0.739
(0.807) 		0.868
(0.913)
14q gain 10 (2%) 482 6e-05
(0.000615) 		0.158
(0.248) 		0.468
(0.58) 		0.779
(0.843) 		0.0826
(0.165) 		0.229
(0.326) 		0.113
(0.195) 		0.254
(0.357) 		0.493
(0.598) 		0.465
(0.578)
15q gain 6 (1%) 486 0.0207
(0.0609) 		1
(1.00) 		0.427
(0.536) 		0.889
(0.928) 		0.877
(0.921) 		0.669
(0.743) 		0.777
(0.843) 		0.18
(0.272) 		0.706
(0.776) 		0.321
(0.429)
16q gain 8 (2%) 484 0.0833
(0.165) 		0.5
(0.606) 		0.58
(0.669) 		0.771
(0.839) 		0.605
(0.686) 		0.903
(0.942) 		0.102
(0.184) 		0.0129
(0.0431) 		0.646
(0.722) 		0.543
(0.641)
18p gain 18 (4%) 474 2e-05
(0.000262) 		0.357
(0.464) 		0.738
(0.807) 		0.953
(0.984) 		0.139
(0.229) 		0.507
(0.609) 		0.688
(0.761) 		0.613
(0.693) 		0.726
(0.794) 		0.45
(0.562)
18q gain 9 (2%) 483 0.0049
(0.0203) 		1
(1.00) 		0.111
(0.193) 		1
(1.00) 		0.104
(0.185) 		0.91
(0.946) 		0.642
(0.721) 		0.438
(0.549) 		0.451
(0.562) 		0.665
(0.739)
3q loss 5 (1%) 487 0.304
(0.411) 		1
(1.00) 		0.331
(0.438) 		0.251
(0.355) 		0.157
(0.248) 		0.0322
(0.0831)
11p loss 8 (2%) 484 0.00214
(0.0106) 		0.0778
(0.157) 		0.597
(0.681) 		0.702
(0.774) 		0.266
(0.369) 		0.117
(0.201) 		0.322
(0.43) 		0.26
(0.364) 		0.114
(0.196) 		0.102
(0.184)
14q loss 25 (5%) 467 1e-05
(0.000143) 		0.0581
(0.126) 		0.182
(0.274) 		0.84
(0.896) 		0.0763
(0.155) 		0.0973
(0.181) 		0.404
(0.517) 		0.0648
(0.137) 		0.0971
(0.181) 		0.0681
(0.142)
20p loss 19 (4%) 473 0.0377
(0.0917) 		0.0629
(0.134) 		1
(1.00) 		0.953
(0.984) 		0.222
(0.319) 		0.182
(0.274) 		0.491
(0.596) 		0.185
(0.276) 		1
(1.00) 		0.583
(0.671)
4q gain 10 (2%) 482 0.0738
(0.151) 		0.487
(0.595) 		0.273
(0.377) 		0.403
(0.517) 		1
(1.00) 		0.558
(0.651) 		0.852
(0.901) 		0.176
(0.267) 		0.154
(0.246) 		0.0718
(0.148)
22q gain 4 (1%) 488 0.0947
(0.179) 		0.551
(0.647) 		1
(1.00) 		0.889
(0.928) 		0.558
(0.651) 		0.224
(0.321) 		0.325
(0.431) 		0.407
(0.519) 		0.404
(0.517) 		0.159
(0.248)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
1P GAIN MUTATED 2 14 0
1P GAIN WILD-TYPE 271 120 85

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00977 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
1P GAIN MUTATED 0 8 8
1P GAIN WILD-TYPE 146 163 166

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0041

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
1P GAIN MUTATED 0 13 3
1P GAIN WILD-TYPE 171 192 112

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.098

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
1P GAIN MUTATED 1 4 1 9 1
1P GAIN WILD-TYPE 146 94 58 119 55

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
1Q GAIN MUTATED 5 21 0
1Q GAIN WILD-TYPE 268 113 85

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

'1q gain' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.099

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
1Q GAIN MUTATED 5 1 15
1Q GAIN WILD-TYPE 118 67 141

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0014

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
1Q GAIN MUTATED 0 10 16
1Q GAIN WILD-TYPE 146 161 158

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0036

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
1Q GAIN MUTATED 1 15 10
1Q GAIN WILD-TYPE 170 190 105

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.085

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
1Q GAIN MUTATED 4 4 3 14 1
1Q GAIN WILD-TYPE 143 94 56 114 55

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0063

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
2P GAIN MUTATED 1 8 1
2P GAIN WILD-TYPE 272 126 84

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.026

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
2P GAIN MUTATED 0 8 2
2P GAIN WILD-TYPE 146 163 172

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.09

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
2P GAIN MUTATED 0 4 0 5 1
2P GAIN WILD-TYPE 147 94 59 123 55

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0057

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
2Q GAIN MUTATED 0 6 1
2Q GAIN WILD-TYPE 273 128 84

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S14.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
3P GAIN MUTATED 3 32 5
3P GAIN WILD-TYPE 270 102 80

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.036

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
3P GAIN MUTATED 7 22 11
3P GAIN WILD-TYPE 153 143 156

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
3P GAIN MUTATED 7 2 19
3P GAIN WILD-TYPE 116 66 137

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.074

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
3P GAIN MUTATED 2 13 4 9
3P GAIN WILD-TYPE 72 100 88 59

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.019

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
3P GAIN MUTATED 5 23 12
3P GAIN WILD-TYPE 141 148 162

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0029

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
3P GAIN MUTATED 4 27 9
3P GAIN WILD-TYPE 167 178 106

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.063

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
3P GAIN MUTATED 8 8 23
3P GAIN WILD-TYPE 150 139 160

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00509 (Fisher's exact test), Q value = 0.021

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
3P GAIN MUTATED 7 6 2 21 3
3P GAIN WILD-TYPE 140 92 57 107 53

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.016

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
3P GAIN MUTATED 0 15 3 6
3P GAIN WILD-TYPE 62 91 57 84

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.002

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
3P GAIN MUTATED 2 2 11 7 0 2
3P GAIN WILD-TYPE 68 39 29 75 25 58

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
3Q GAIN MUTATED 9 37 8
3Q GAIN WILD-TYPE 264 97 77

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00754 (Fisher's exact test), Q value = 0.028

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
3Q GAIN MUTATED 9 27 18
3Q GAIN WILD-TYPE 151 138 149

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.074

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
3Q GAIN MUTATED 9 4 25
3Q GAIN WILD-TYPE 114 64 131

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.072

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
3Q GAIN MUTATED 3 16 7 12
3Q GAIN WILD-TYPE 71 97 85 56

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0065

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
3Q GAIN MUTATED 6 28 20
3Q GAIN WILD-TYPE 140 143 154

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0073

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
3Q GAIN MUTATED 8 33 13
3Q GAIN WILD-TYPE 163 172 102

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.021

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
3Q GAIN MUTATED 12 10 31
3Q GAIN WILD-TYPE 146 137 152

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.017

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
3Q GAIN MUTATED 10 10 4 26 3
3Q GAIN WILD-TYPE 137 88 55 102 53

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.047

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
3Q GAIN MUTATED 1 17 6 7
3Q GAIN WILD-TYPE 61 89 54 83

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00026

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
3Q GAIN MUTATED 2 3 14 9 1 2
3Q GAIN WILD-TYPE 68 38 26 73 24 58

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.075

Table S34.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
4P GAIN MUTATED 2 6 1
4P GAIN WILD-TYPE 271 128 84

Figure S34.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
5P GAIN MUTATED 2 21 0
5P GAIN WILD-TYPE 271 113 85

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.075

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
5P GAIN MUTATED 2 2 13
5P GAIN WILD-TYPE 121 66 143

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.032

Table S37.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
5P GAIN MUTATED 1 10 12
5P GAIN WILD-TYPE 145 161 162

Figure S37.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0069

Table S38.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
5P GAIN MUTATED 4 2 17
5P GAIN WILD-TYPE 154 145 166

Figure S38.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.0082

Table S39.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
5P GAIN MUTATED 4 3 0 15 1
5P GAIN WILD-TYPE 143 95 59 113 55

Figure S39.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0098

Table S40.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
5P GAIN MUTATED 1 12 0 2
5P GAIN WILD-TYPE 61 94 60 88

Figure S40.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00403 (Fisher's exact test), Q value = 0.017

Table S41.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
5P GAIN MUTATED 2 0 5 8 0 0
5P GAIN WILD-TYPE 68 41 35 74 25 60

Figure S41.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00026

Table S42.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
5Q GAIN MUTATED 1 11 0
5Q GAIN WILD-TYPE 272 123 85

Figure S42.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.087

Table S43.  Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
5Q GAIN MUTATED 0 5 7
5Q GAIN WILD-TYPE 146 166 167

Figure S43.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0075

Table S44.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
6P GAIN MUTATED 2 8 0
6P GAIN WILD-TYPE 271 126 85

Figure S44.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.054

Table S45.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
6P GAIN MUTATED 0 7 0 1
6P GAIN WILD-TYPE 62 99 60 89

Figure S45.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.061

Table S46.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
6Q GAIN MUTATED 1 5 0
6Q GAIN WILD-TYPE 272 129 85

Figure S46.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.093

Table S47.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
6Q GAIN MUTATED 0 1 0 5 0
6Q GAIN WILD-TYPE 147 97 59 123 56

Figure S47.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
7P GAIN MUTATED 13 67 22
7P GAIN WILD-TYPE 260 67 63

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
7P GAIN MUTATED 14 60 28
7P GAIN WILD-TYPE 146 105 139

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
7P GAIN MUTATED 10 64 28
7P GAIN WILD-TYPE 136 107 146

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
7P GAIN MUTATED 21 64 17
7P GAIN WILD-TYPE 150 141 98

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.056

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
7P GAIN MUTATED 22 31 48
7P GAIN WILD-TYPE 136 116 135

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S53.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
7P GAIN MUTATED 16 28 15 38 4
7P GAIN WILD-TYPE 131 70 44 90 52

Figure S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0019

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
7P GAIN MUTATED 4 36 11 18
7P GAIN WILD-TYPE 58 70 49 72

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.009

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
7P GAIN MUTATED 6 12 13 25 2 11
7P GAIN WILD-TYPE 64 29 27 57 23 49

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
7Q GAIN MUTATED 13 61 21
7Q GAIN WILD-TYPE 260 73 64

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
7Q GAIN MUTATED 11 58 26
7Q GAIN WILD-TYPE 149 107 141

Figure S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S58.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
7Q GAIN MUTATED 10 59 26
7Q GAIN WILD-TYPE 136 112 148

Figure S58.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00046

Table S59.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
7Q GAIN MUTATED 20 59 16
7Q GAIN WILD-TYPE 151 146 99

Figure S59.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.069

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
7Q GAIN MUTATED 20 30 44
7Q GAIN WILD-TYPE 138 117 139

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00086

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
7Q GAIN MUTATED 14 27 14 35 4
7Q GAIN WILD-TYPE 133 71 45 93 52

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0029

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
7Q GAIN MUTATED 4 35 11 16
7Q GAIN WILD-TYPE 58 71 49 74

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.022

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
7Q GAIN MUTATED 6 11 12 24 2 11
7Q GAIN WILD-TYPE 64 30 28 58 23 49

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S64.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
8P GAIN MUTATED 13 49 9
8P GAIN WILD-TYPE 260 85 76

Figure S64.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S65.  Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
8P GAIN MUTATED 10 47 14
8P GAIN WILD-TYPE 150 118 153

Figure S65.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00078

Table S66.  Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
8P GAIN MUTATED 10 4 38
8P GAIN WILD-TYPE 113 64 118

Figure S66.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0033

Table S67.  Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
8P GAIN MUTATED 7 15 8 22
8P GAIN WILD-TYPE 67 98 84 46

Figure S67.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S68.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
8P GAIN MUTATED 13 42 16
8P GAIN WILD-TYPE 133 129 158

Figure S68.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0033

Table S69.  Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8P GAIN MUTATED 15 45 11
8P GAIN WILD-TYPE 156 160 104

Figure S69.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00591 (Fisher's exact test), Q value = 0.023

Table S70.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
8P GAIN MUTATED 11 15 10 29 5
8P GAIN WILD-TYPE 136 83 49 99 51

Figure S70.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.01

Table S71.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
8P GAIN MUTATED 3 27 7 11
8P GAIN WILD-TYPE 59 79 53 79

Figure S71.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.0097

Table S72.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
8P GAIN MUTATED 4 6 6 24 2 6
8P GAIN WILD-TYPE 66 35 34 58 23 54

Figure S72.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
8Q GAIN MUTATED 36 77 11
8Q GAIN WILD-TYPE 237 57 74

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S74.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
8Q GAIN MUTATED 21 68 35
8Q GAIN WILD-TYPE 139 97 132

Figure S74.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0012

Table S75.  Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
8Q GAIN MUTATED 24 8 56
8Q GAIN WILD-TYPE 99 60 100

Figure S75.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0028

Table S76.  Gene #16: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
8Q GAIN MUTATED 12 25 20 31
8Q GAIN WILD-TYPE 62 88 72 37

Figure S76.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S77.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
8Q GAIN MUTATED 21 63 40
8Q GAIN WILD-TYPE 125 108 134

Figure S77.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S78.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8Q GAIN MUTATED 26 73 25
8Q GAIN WILD-TYPE 145 132 90

Figure S78.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0032

Table S79.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
8Q GAIN MUTATED 29 29 64
8Q GAIN WILD-TYPE 129 118 119

Figure S79.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S80.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
8Q GAIN MUTATED 17 24 18 54 9
8Q GAIN WILD-TYPE 130 74 41 74 47

Figure S80.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S81.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
8Q GAIN MUTATED 6 46 11 18
8Q GAIN WILD-TYPE 56 60 49 72

Figure S81.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S82.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
8Q GAIN MUTATED 8 9 13 37 3 11
8Q GAIN WILD-TYPE 62 32 27 45 22 49

Figure S82.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S83.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
9P GAIN MUTATED 4 30 0
9P GAIN WILD-TYPE 269 104 85

Figure S83.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.05

Table S84.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
9P GAIN MUTATED 2 13 1 3
9P GAIN WILD-TYPE 60 93 59 87

Figure S84.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S85.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
9Q GAIN MUTATED 8 42 0
9Q GAIN WILD-TYPE 265 92 85

Figure S85.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.048

Table S86.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
9Q GAIN MUTATED 7 18 25
9Q GAIN WILD-TYPE 139 153 149

Figure S86.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.038

Table S87.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
9Q GAIN MUTATED 10 7 5 24 3
9Q GAIN WILD-TYPE 137 91 54 104 53

Figure S87.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.026

Table S88.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
9Q GAIN MUTATED 2 18 3 5
9Q GAIN WILD-TYPE 60 88 57 85

Figure S88.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.046

Table S89.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
9Q GAIN MUTATED 3 1 8 12 1 3
9Q GAIN WILD-TYPE 67 40 32 70 24 57

Figure S89.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S90.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
10P GAIN MUTATED 3 12 0
10P GAIN WILD-TYPE 270 122 85

Figure S90.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.087

Table S91.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
10P GAIN MUTATED 1 9 5
10P GAIN WILD-TYPE 159 156 162

Figure S91.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.086

Table S92.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10P GAIN MUTATED 1 10 4
10P GAIN WILD-TYPE 170 195 111

Figure S92.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.044

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
10P GAIN MUTATED 1 1 1 8 4
10P GAIN WILD-TYPE 146 97 58 120 52

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0045

Table S94.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
10P GAIN MUTATED 1 0 8 3 0 2
10P GAIN WILD-TYPE 69 41 32 79 25 58

Figure S94.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.002

Table S95.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
10Q GAIN MUTATED 3 11 0
10Q GAIN WILD-TYPE 270 123 85

Figure S95.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.083

Table S96.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10Q GAIN MUTATED 1 10 3
10Q GAIN WILD-TYPE 170 195 112

Figure S96.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.01

Table S97.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
10Q GAIN MUTATED 0 0 6 2 0 2
10Q GAIN WILD-TYPE 70 41 34 80 25 58

Figure S97.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S98.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
11P GAIN MUTATED 3 21 2
11P GAIN WILD-TYPE 270 113 83

Figure S98.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.047

Table S99.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
11P GAIN MUTATED 4 18 4
11P GAIN WILD-TYPE 167 187 111

Figure S99.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.089

Table S100.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
11P GAIN MUTATED 1 11 2 2
11P GAIN WILD-TYPE 61 95 58 88

Figure S100.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S101.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
11Q GAIN MUTATED 3 24 2
11Q GAIN WILD-TYPE 270 110 83

Figure S101.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.081

Table S102.  Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
11Q GAIN MUTATED 3 15 11
11Q GAIN WILD-TYPE 143 156 163

Figure S102.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.092

Table S103.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
11Q GAIN MUTATED 6 19 4
11Q GAIN WILD-TYPE 165 186 111

Figure S103.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00026

Table S104.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
12P GAIN MUTATED 2 12 0
12P GAIN WILD-TYPE 271 122 85

Figure S104.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0064

Table S105.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12P GAIN MUTATED 1 1 1 11 0
12P GAIN WILD-TYPE 146 97 58 117 56

Figure S105.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.068

Table S106.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
12P GAIN MUTATED 0 8 1 1
12P GAIN WILD-TYPE 62 98 59 89

Figure S106.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0033

Table S107.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
12Q GAIN MUTATED 5 12 0
12Q GAIN WILD-TYPE 268 122 85

Figure S107.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.06

Table S108.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12Q GAIN MUTATED 3 1 3 10 0
12Q GAIN WILD-TYPE 144 97 56 118 56

Figure S108.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.049

Table S109.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
12Q GAIN MUTATED 1 10 1 1
12Q GAIN WILD-TYPE 61 96 59 89

Figure S109.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.047

Table S110.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
13Q GAIN MUTATED 2 6 0
13Q GAIN WILD-TYPE 271 128 85

Figure S110.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S111.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
14Q GAIN MUTATED 0 9 1
14Q GAIN WILD-TYPE 273 125 84

Figure S111.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.061

Table S112.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
15Q GAIN MUTATED 1 5 0
15Q GAIN WILD-TYPE 272 129 85

Figure S112.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S113.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
16P GAIN MUTATED 8 23 0
16P GAIN WILD-TYPE 265 111 85

Figure S113.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.017

Table S114.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
16P GAIN MUTATED 2 4 6 14 4
16P GAIN WILD-TYPE 145 94 53 114 52

Figure S114.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.073

Table S115.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
16P GAIN MUTATED 0 9 2 9
16P GAIN WILD-TYPE 62 97 58 81

Figure S115.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.043

Table S116.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
16P GAIN MUTATED 1 1 7 5 0 6
16P GAIN WILD-TYPE 69 40 33 77 25 54

Figure S116.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.043

Table S117.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
16Q GAIN MUTATED 0 0 1 6 1
16Q GAIN WILD-TYPE 147 98 58 122 55

Figure S117.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.047

Table S118.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
17P GAIN MUTATED 2 6 0
17P GAIN WILD-TYPE 271 128 85

Figure S118.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.061

Table S119.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
17P GAIN MUTATED 6 0 2
17P GAIN WILD-TYPE 152 147 181

Figure S119.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.051

Table S120.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
17P GAIN MUTATED 1 0 4 3 0
17P GAIN WILD-TYPE 146 98 55 125 56

Figure S120.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.016

Table S121.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
17P GAIN MUTATED 0 0 4 1 1 0
17P GAIN WILD-TYPE 70 41 36 81 24 60

Figure S121.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0033

Table S122.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
17Q GAIN MUTATED 2 9 0
17Q GAIN WILD-TYPE 271 125 85

Figure S122.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.053

Table S123.  Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
17Q GAIN MUTATED 0 3 8
17Q GAIN WILD-TYPE 146 168 166

Figure S123.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0044

Table S124.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
17Q GAIN MUTATED 1 0 6 1 1 0
17Q GAIN WILD-TYPE 69 41 34 81 24 60

Figure S124.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00026

Table S125.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
18P GAIN MUTATED 3 15 0
18P GAIN WILD-TYPE 270 119 85

Figure S125.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.02

Table S126.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
18Q GAIN MUTATED 2 7 0
18Q GAIN WILD-TYPE 271 127 85

Figure S126.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S127.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
19P GAIN MUTATED 0 12 0
19P GAIN WILD-TYPE 273 122 85

Figure S127.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.048

Table S128.  Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
19P GAIN MUTATED 0 1 8
19P GAIN WILD-TYPE 123 67 148

Figure S128.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.089

Table S129.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
19P GAIN MUTATED 0 5 7
19P GAIN WILD-TYPE 146 166 167

Figure S129.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S130.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
19Q GAIN MUTATED 0 12 0
19Q GAIN WILD-TYPE 273 122 85

Figure S130.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.092

Table S131.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
19Q GAIN MUTATED 0 6 6
19Q GAIN WILD-TYPE 146 165 168

Figure S131.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S132.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
20P GAIN MUTATED 3 22 1
20P GAIN WILD-TYPE 270 112 84

Figure S132.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S133.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
20P GAIN MUTATED 3 14 9
20P GAIN WILD-TYPE 157 151 158

Figure S133.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.066

Table S134.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
20P GAIN MUTATED 2 11 13
20P GAIN WILD-TYPE 144 160 161

Figure S134.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.09

Table S135.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
20P GAIN MUTATED 4 17 5
20P GAIN WILD-TYPE 167 188 110

Figure S135.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.01

Table S136.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
20P GAIN MUTATED 4 3 18
20P GAIN WILD-TYPE 154 144 165

Figure S136.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00401 (Fisher's exact test), Q value = 0.017

Table S137.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
20P GAIN MUTATED 3 5 1 15 1
20P GAIN WILD-TYPE 144 93 58 113 55

Figure S137.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.082

Table S138.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
20P GAIN MUTATED 0 10 2 3
20P GAIN WILD-TYPE 62 96 58 87

Figure S138.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00407 (Fisher's exact test), Q value = 0.017

Table S139.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
20P GAIN MUTATED 1 0 7 5 0 2
20P GAIN WILD-TYPE 69 41 33 77 25 58

Figure S139.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S140.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
20Q GAIN MUTATED 3 24 1
20Q GAIN WILD-TYPE 270 110 84

Figure S140.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.059

Table S141.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
20Q GAIN MUTATED 4 16 8
20Q GAIN WILD-TYPE 156 149 159

Figure S141.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.086

Table S142.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
20Q GAIN MUTATED 3 9 2 9
20Q GAIN WILD-TYPE 71 104 90 59

Figure S142.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.039

Table S143.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
20Q GAIN MUTATED 4 6 18
20Q GAIN WILD-TYPE 154 141 165

Figure S143.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.029

Table S144.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
20Q GAIN MUTATED 4 7 1 15 1
20Q GAIN WILD-TYPE 143 91 58 113 55

Figure S144.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00929 (Fisher's exact test), Q value = 0.033

Table S145.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
20Q GAIN MUTATED 1 1 8 4 1 3
20Q GAIN WILD-TYPE 69 40 32 78 24 57

Figure S145.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S146.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
21Q GAIN MUTATED 0 21 0
21Q GAIN WILD-TYPE 273 113 85

Figure S146.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.092

Table S147.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
21Q GAIN MUTATED 2 11 8
21Q GAIN WILD-TYPE 158 154 159

Figure S147.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0094

Table S148.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
21Q GAIN MUTATED 0 11 10
21Q GAIN WILD-TYPE 146 160 164

Figure S148.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.074

Table S149.  Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
21Q GAIN MUTATED 2 13 6
21Q GAIN WILD-TYPE 169 192 109

Figure S149.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.047

Table S150.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
21Q GAIN MUTATED 2 5 14
21Q GAIN WILD-TYPE 156 142 169

Figure S150.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.015

Table S151.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
21Q GAIN MUTATED 1 3 2 13 2
21Q GAIN WILD-TYPE 146 95 57 115 54

Figure S151.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.041

Table S152.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
21Q GAIN MUTATED 0 11 1 5
21Q GAIN WILD-TYPE 62 95 59 85

Figure S152.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.078

Table S153.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
21Q GAIN MUTATED 1 1 6 7 0 2
21Q GAIN WILD-TYPE 69 40 34 75 25 58

Figure S153.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0064

Table S154.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
XP GAIN MUTATED 0 6 1
XP GAIN WILD-TYPE 273 128 84

Figure S154.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.1

Table S155.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XP GAIN MUTATED 0 2 0 5 0
XP GAIN WILD-TYPE 147 96 59 123 56

Figure S155.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00638 (Fisher's exact test), Q value = 0.024

Table S156.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
XP GAIN MUTATED 0 6 0 0
XP GAIN WILD-TYPE 62 100 60 90

Figure S156.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0063

Table S157.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
XQ GAIN MUTATED 0 6 1
XQ GAIN WILD-TYPE 273 128 84

Figure S157.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.11

Table S158.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XQ GAIN MUTATED 0 2 0 5 0
XQ GAIN WILD-TYPE 147 96 59 123 56

Figure S158.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00638 (Fisher's exact test), Q value = 0.024

Table S159.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
XQ GAIN MUTATED 0 6 0 0
XQ GAIN WILD-TYPE 62 100 60 90

Figure S159.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S160.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
1P LOSS MUTATED 1 20 1
1P LOSS WILD-TYPE 272 114 84

Figure S160.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0038

Table S161.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
1P LOSS MUTATED 0 11 11
1P LOSS WILD-TYPE 160 154 156

Figure S161.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0067

Table S162.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
1P LOSS MUTATED 0 11 11
1P LOSS WILD-TYPE 146 160 163

Figure S162.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.002

Table S163.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
1P LOSS MUTATED 0 13 9
1P LOSS WILD-TYPE 171 192 106

Figure S163.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.071

Table S164.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
1P LOSS MUTATED 2 6 13
1P LOSS WILD-TYPE 156 141 170

Figure S164.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.016

Table S165.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
1P LOSS MUTATED 1 3 4 12 1
1P LOSS WILD-TYPE 146 95 55 116 55

Figure S165.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.061

Table S166.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
1P LOSS MUTATED 0 11 4 3
1P LOSS WILD-TYPE 62 95 56 87

Figure S166.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.043

Table S167.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
1P LOSS MUTATED 0 1 5 8 0 4
1P LOSS WILD-TYPE 70 40 35 74 25 56

Figure S167.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.061

Table S168.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
1Q LOSS MUTATED 1 5 0
1Q LOSS WILD-TYPE 272 129 85

Figure S168.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.1

Table S169.  Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
1Q LOSS MUTATED 0 5 1
1Q LOSS WILD-TYPE 146 166 173

Figure S169.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00086

Table S170.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
2P LOSS MUTATED 2 12 2
2P LOSS WILD-TYPE 271 122 83

Figure S170.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00517 (Fisher's exact test), Q value = 0.021

Table S171.  Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
2P LOSS MUTATED 0 9 7
2P LOSS WILD-TYPE 160 156 160

Figure S171.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.016

Table S172.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
2P LOSS MUTATED 0 11 1 2
2P LOSS WILD-TYPE 62 95 59 88

Figure S172.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00332 (Fisher's exact test), Q value = 0.015

Table S173.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
2P LOSS MUTATED 0 0 2 10 0 2
2P LOSS WILD-TYPE 70 41 38 72 25 58

Figure S173.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S174.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
2Q LOSS MUTATED 3 13 2
2Q LOSS WILD-TYPE 270 121 83

Figure S174.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.061

Table S175.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
2Q LOSS MUTATED 1 10 7
2Q LOSS WILD-TYPE 159 155 160

Figure S175.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.087

Table S176.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
2Q LOSS MUTATED 3 2 0 10 3
2Q LOSS WILD-TYPE 144 96 59 118 53

Figure S176.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.031

Table S177.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
2Q LOSS MUTATED 0 11 1 3
2Q LOSS WILD-TYPE 62 95 59 87

Figure S177.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0061

Table S178.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
2Q LOSS MUTATED 0 0 1 11 0 3
2Q LOSS WILD-TYPE 70 41 39 71 25 57

Figure S178.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.086

Table S179.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
3P LOSS MUTATED 3 6 0
3P LOSS WILD-TYPE 270 128 85

Figure S179.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.092

Table S180.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
3P LOSS MUTATED 0 5 4
3P LOSS WILD-TYPE 171 200 111

Figure S180.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.083

Table S181.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
3Q LOSS MUTATED 0 3 1 0 0
3Q LOSS WILD-TYPE 147 95 58 128 56

Figure S181.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S182.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
4P LOSS MUTATED 2 21 1
4P LOSS WILD-TYPE 271 113 84

Figure S182.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.055

Table S183.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
4P LOSS MUTATED 2 12 10
4P LOSS WILD-TYPE 158 153 157

Figure S183.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.092

Table S184.  Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
4P LOSS MUTATED 2 2 12
4P LOSS WILD-TYPE 121 66 144

Figure S184.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.018

Table S185.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
4P LOSS MUTATED 1 9 14
4P LOSS WILD-TYPE 145 162 160

Figure S185.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.077

Table S186.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
4P LOSS MUTATED 3 12 9
4P LOSS WILD-TYPE 168 193 106

Figure S186.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0073

Table S187.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
4P LOSS MUTATED 6 1 16
4P LOSS WILD-TYPE 152 146 167

Figure S187.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.013

Table S188.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
4P LOSS MUTATED 6 1 2 14 0
4P LOSS WILD-TYPE 141 97 57 114 56

Figure S188.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00046

Table S189.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
4P LOSS MUTATED 0 14 3 0
4P LOSS WILD-TYPE 62 92 57 90

Figure S189.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 7e-04

Table S190.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
4P LOSS MUTATED 1 0 7 9 0 0
4P LOSS WILD-TYPE 69 41 33 73 25 60

Figure S190.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S191.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
4Q LOSS MUTATED 2 15 0
4Q LOSS WILD-TYPE 271 119 85

Figure S191.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.025

Table S192.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
4Q LOSS MUTATED 0 8 9
4Q LOSS WILD-TYPE 146 163 165

Figure S192.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.11

Table S193.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
4Q LOSS MUTATED 3 1 1 10 1
4Q LOSS WILD-TYPE 144 97 58 118 55

Figure S193.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.047

Table S194.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
4Q LOSS MUTATED 0 9 2 1
4Q LOSS WILD-TYPE 62 97 58 89

Figure S194.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.021

Table S195.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
4Q LOSS MUTATED 2 0 6 4 0 0
4Q LOSS WILD-TYPE 68 41 34 78 25 60

Figure S195.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00026

Table S196.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
5P LOSS MUTATED 1 11 0
5P LOSS WILD-TYPE 272 123 85

Figure S196.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.092

Table S197.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
5P LOSS MUTATED 0 6 6
5P LOSS WILD-TYPE 146 165 168

Figure S197.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00557 (Fisher's exact test), Q value = 0.022

Table S198.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
5P LOSS MUTATED 0 6 6
5P LOSS WILD-TYPE 171 199 109

Figure S198.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.014

Table S199.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
5P LOSS MUTATED 0 1 4 6 0
5P LOSS WILD-TYPE 147 97 55 122 56

Figure S199.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S200.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
5Q LOSS MUTATED 0 22 0
5Q LOSS WILD-TYPE 273 112 85

Figure S200.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.013

Table S201.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
5Q LOSS MUTATED 1 13 8
5Q LOSS WILD-TYPE 159 152 159

Figure S201.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.041

Table S202.  Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
5Q LOSS MUTATED 1 11 10
5Q LOSS WILD-TYPE 145 160 164

Figure S202.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.01

Table S203.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
5Q LOSS MUTATED 1 15 6
5Q LOSS WILD-TYPE 170 190 109

Figure S203.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0065

Table S204.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
5Q LOSS MUTATED 1 2 5 12 1
5Q LOSS WILD-TYPE 146 96 54 116 55

Figure S204.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.074

Table S205.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
5Q LOSS MUTATED 0 0 3 7 0 2
5Q LOSS WILD-TYPE 70 41 37 75 25 58

Figure S205.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S206.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
6P LOSS MUTATED 4 21 0
6P LOSS WILD-TYPE 269 113 85

Figure S206.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.048

Table S207.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
6P LOSS MUTATED 2 11 12
6P LOSS WILD-TYPE 158 154 155

Figure S207.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0021

Table S208.  Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
6P LOSS MUTATED 0 10 15
6P LOSS WILD-TYPE 146 161 159

Figure S208.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.013

Table S209.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
6P LOSS MUTATED 2 12 11
6P LOSS WILD-TYPE 169 193 104

Figure S209.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.082

Table S210.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
6P LOSS MUTATED 2 5 4 12 2
6P LOSS WILD-TYPE 145 93 55 116 54

Figure S210.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.047

Table S211.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
6P LOSS MUTATED 0 11 2 3
6P LOSS WILD-TYPE 62 95 58 87

Figure S211.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00354 (Fisher's exact test), Q value = 0.016

Table S212.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
6P LOSS MUTATED 0 0 5 8 0 3
6P LOSS WILD-TYPE 70 41 35 74 25 57

Figure S212.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S213.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
6Q LOSS MUTATED 5 32 3
6Q LOSS WILD-TYPE 268 102 82

Figure S213.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.087

Table S214.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
6Q LOSS MUTATED 6 17 17
6Q LOSS WILD-TYPE 154 148 150

Figure S214.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.073

Table S215.  Gene #53: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
6Q LOSS MUTATED 4 4 18
6Q LOSS WILD-TYPE 119 64 138

Figure S215.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.076

Table S216.  Gene #53: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
6Q LOSS MUTATED 4 8 3 11
6Q LOSS WILD-TYPE 70 105 89 57

Figure S216.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0024

Table S217.  Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
6Q LOSS MUTATED 2 19 19
6Q LOSS WILD-TYPE 144 152 155

Figure S217.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0057

Table S218.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
6Q LOSS MUTATED 4 24 12
6Q LOSS WILD-TYPE 167 181 103

Figure S218.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.043

Table S219.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
6Q LOSS MUTATED 8 8 24
6Q LOSS WILD-TYPE 150 139 159

Figure S219.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.11

Table S220.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
6Q LOSS MUTATED 5 8 7 16 4
6Q LOSS WILD-TYPE 142 90 52 112 52

Figure S220.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00438 (Fisher's exact test), Q value = 0.018

Table S221.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
6Q LOSS MUTATED 1 17 2 8
6Q LOSS WILD-TYPE 61 89 58 82

Figure S221.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.01

Table S222.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
6Q LOSS MUTATED 2 1 8 13 0 4
6Q LOSS WILD-TYPE 68 40 32 69 25 56

Figure S222.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S223.  Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
8P LOSS MUTATED 104 55 9
8P LOSS WILD-TYPE 169 79 76

Figure S223.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S224.  Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
8P LOSS MUTATED 27 56 85
8P LOSS WILD-TYPE 133 109 82

Figure S224.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S225.  Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
8P LOSS MUTATED 33 46 89
8P LOSS WILD-TYPE 113 125 85

Figure S225.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S226.  Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8P LOSS MUTATED 39 68 61
8P LOSS WILD-TYPE 132 137 54

Figure S226.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0027

Table S227.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
8P LOSS MUTATED 43 41 83
8P LOSS WILD-TYPE 115 106 100

Figure S227.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.082

Table S228.  Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
8P LOSS MUTATED 16 7 18 24 5 23
8P LOSS WILD-TYPE 54 34 22 58 20 37

Figure S228.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.079

Table S229.  Gene #55: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
8Q LOSS MUTATED 11 12 1
8Q LOSS WILD-TYPE 262 122 84

Figure S229.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0065

Table S230.  Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
8Q LOSS MUTATED 1 8 15
8Q LOSS WILD-TYPE 159 157 152

Figure S230.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.037

Table S231.  Gene #55: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
8Q LOSS MUTATED 2 7 15
8Q LOSS WILD-TYPE 144 164 159

Figure S231.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.07

Table S232.  Gene #55: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8Q LOSS MUTATED 4 9 11
8Q LOSS WILD-TYPE 167 196 104

Figure S232.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S233.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
9P LOSS MUTATED 5 16 0
9P LOSS WILD-TYPE 268 118 85

Figure S233.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.027

Table S234.  Gene #56: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
9P LOSS MUTATED 2 0 12
9P LOSS WILD-TYPE 121 68 144

Figure S234.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00528 (Fisher's exact test), Q value = 0.021

Table S235.  Gene #56: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
9P LOSS MUTATED 2 1 3 8
9P LOSS WILD-TYPE 72 112 89 60

Figure S235.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.018

Table S236.  Gene #56: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
9P LOSS MUTATED 1 6 14
9P LOSS WILD-TYPE 145 165 160

Figure S236.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.065

Table S237.  Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
9P LOSS MUTATED 3 8 10
9P LOSS WILD-TYPE 168 197 105

Figure S237.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0074

Table S238.  Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
9Q LOSS MUTATED 2 8 0
9Q LOSS WILD-TYPE 271 126 85

Figure S238.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.091

Table S239.  Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
9Q LOSS MUTATED 0 0 4 3 0 1
9Q LOSS WILD-TYPE 70 41 36 79 25 59

Figure S239.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S240.  Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
10P LOSS MUTATED 9 30 2
10P LOSS WILD-TYPE 264 104 83

Figure S240.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S241.  Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
10P LOSS MUTATED 2 17 22
10P LOSS WILD-TYPE 158 148 145

Figure S241.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0017

Table S242.  Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
10P LOSS MUTATED 2 18 21
10P LOSS WILD-TYPE 144 153 153

Figure S242.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S243.  Gene #58: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10P LOSS MUTATED 3 22 16
10P LOSS WILD-TYPE 168 183 99

Figure S243.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S244.  Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
10P LOSS MUTATED 3 5 7 22 2
10P LOSS WILD-TYPE 144 93 52 106 54

Figure S244.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.039

Table S245.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
10P LOSS MUTATED 0 12 3 10
10P LOSS WILD-TYPE 62 94 57 80

Figure S245.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S246.  Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
10P LOSS MUTATED 0 0 6 13 0 6
10P LOSS WILD-TYPE 70 41 34 69 25 54

Figure S246.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S247.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
10Q LOSS MUTATED 9 31 3
10Q LOSS WILD-TYPE 264 103 82

Figure S247.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.005

Table S248.  Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
10Q LOSS MUTATED 4 17 22
10Q LOSS WILD-TYPE 156 148 145

Figure S248.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.011

Table S249.  Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
10Q LOSS MUTATED 4 16 23
10Q LOSS WILD-TYPE 142 155 151

Figure S249.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0029

Table S250.  Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10Q LOSS MUTATED 5 20 18
10Q LOSS WILD-TYPE 166 185 97

Figure S250.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.092

Table S251.  Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
10Q LOSS MUTATED 8 10 23
10Q LOSS WILD-TYPE 150 137 160

Figure S251.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.007

Table S252.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
10Q LOSS MUTATED 5 4 6 21 5
10Q LOSS WILD-TYPE 142 94 53 107 51

Figure S252.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0094

Table S253.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
10Q LOSS MUTATED 0 14 3 13
10Q LOSS WILD-TYPE 62 92 57 77

Figure S253.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S254.  Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
10Q LOSS MUTATED 1 0 9 12 0 8
10Q LOSS WILD-TYPE 69 41 31 70 25 52

Figure S254.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.011

Table S255.  Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
11P LOSS MUTATED 1 7 0
11P LOSS WILD-TYPE 272 127 85

Figure S255.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.044

Table S256.  Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
11Q LOSS MUTATED 0 4 1
11Q LOSS WILD-TYPE 273 130 84

Figure S256.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.061

Table S257.  Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
11Q LOSS MUTATED 0 5 0 0
11Q LOSS WILD-TYPE 62 101 60 90

Figure S257.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S258.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
12P LOSS MUTATED 22 26 0
12P LOSS WILD-TYPE 251 108 85

Figure S258.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.11

Table S259.  Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
12P LOSS MUTATED 11 12 25
12P LOSS WILD-TYPE 135 159 149

Figure S259.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.051

Table S260.  Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12P LOSS MUTATED 13 4 11 15 2
12P LOSS WILD-TYPE 134 94 48 113 54

Figure S260.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00697 (Fisher's exact test), Q value = 0.026

Table S261.  Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
12P LOSS MUTATED 4 20 3 5
12P LOSS WILD-TYPE 58 86 57 85

Figure S261.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.013

Table S262.  Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
12P LOSS MUTATED 3 0 7 15 3 4
12P LOSS WILD-TYPE 67 41 33 67 22 56

Figure S262.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S263.  Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
12Q LOSS MUTATED 5 15 0
12Q LOSS WILD-TYPE 268 119 85

Figure S263.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00877 (Fisher's exact test), Q value = 0.032

Table S264.  Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
12Q LOSS MUTATED 0 0 5 7 1 2
12Q LOSS WILD-TYPE 70 41 35 75 24 58

Figure S264.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S265.  Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
13Q LOSS MUTATED 19 49 9
13Q LOSS WILD-TYPE 254 85 76

Figure S265.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.042

Table S266.  Gene #64: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
13Q LOSS MUTATED 10 21 6 16
13Q LOSS WILD-TYPE 64 92 86 52

Figure S266.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.098

Table S267.  Gene #64: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
13Q LOSS MUTATED 14 30 33
13Q LOSS WILD-TYPE 132 141 141

Figure S267.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.096

Table S268.  Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
13Q LOSS MUTATED 16 15 9 30 5
13Q LOSS WILD-TYPE 131 83 50 98 51

Figure S268.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0017

Table S269.  Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
13Q LOSS MUTATED 4 5 14 21 2 6
13Q LOSS WILD-TYPE 66 36 26 61 23 54

Figure S269.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S270.  Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
14Q LOSS MUTATED 6 18 1
14Q LOSS WILD-TYPE 267 116 84

Figure S270.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S271.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
15Q LOSS MUTATED 4 30 2
15Q LOSS WILD-TYPE 269 104 83

Figure S271.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0094

Table S272.  Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
15Q LOSS MUTATED 3 18 15
15Q LOSS WILD-TYPE 157 147 152

Figure S272.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0044

Table S273.  Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
15Q LOSS MUTATED 2 20 14
15Q LOSS WILD-TYPE 144 151 160

Figure S273.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00616 (Fisher's exact test), Q value = 0.024

Table S274.  Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
15Q LOSS MUTATED 5 23 8
15Q LOSS WILD-TYPE 166 182 107

Figure S274.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S275.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
15Q LOSS MUTATED 2 10 23
15Q LOSS WILD-TYPE 156 137 160

Figure S275.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00726 (Fisher's exact test), Q value = 0.027

Table S276.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
15Q LOSS MUTATED 3 7 3 15 7
15Q LOSS WILD-TYPE 144 91 56 113 49

Figure S276.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0067

Table S277.  Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
15Q LOSS MUTATED 0 17 3 7
15Q LOSS WILD-TYPE 62 89 57 83

Figure S277.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0015

Table S278.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
15Q LOSS MUTATED 0 1 8 12 0 6
15Q LOSS WILD-TYPE 70 40 32 70 25 54

Figure S278.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.009

Table S279.  Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
16P LOSS MUTATED 11 18 3
16P LOSS WILD-TYPE 262 116 82

Figure S279.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.081

Table S280.  Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
16P LOSS MUTATED 2 3 5 14 1 3
16P LOSS WILD-TYPE 68 38 35 68 24 57

Figure S280.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S281.  Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
16Q LOSS MUTATED 40 62 5
16Q LOSS WILD-TYPE 233 72 80

Figure S281.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0048

Table S282.  Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
16Q LOSS MUTATED 19 44 44
16Q LOSS WILD-TYPE 141 121 123

Figure S282.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.08

Table S283.  Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
16Q LOSS MUTATED 21 42 44
16Q LOSS WILD-TYPE 125 129 130

Figure S283.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.081

Table S284.  Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
16Q LOSS MUTATED 26 51 30
16Q LOSS WILD-TYPE 145 154 85

Figure S284.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0032

Table S285.  Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
16Q LOSS MUTATED 20 15 18 42 10
16Q LOSS WILD-TYPE 127 83 41 86 46

Figure S285.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.018

Table S286.  Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
16Q LOSS MUTATED 6 35 12 18
16Q LOSS WILD-TYPE 56 71 48 72

Figure S286.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00078

Table S287.  Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
16Q LOSS MUTATED 7 4 15 30 3 12
16Q LOSS WILD-TYPE 63 37 25 52 22 48

Figure S287.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S288.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
17P LOSS MUTATED 21 52 3
17P LOSS WILD-TYPE 252 82 82

Figure S288.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0069

Table S289.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
17P LOSS MUTATED 12 29 35
17P LOSS WILD-TYPE 148 136 132

Figure S289.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.064

Table S290.  Gene #69: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
17P LOSS MUTATED 17 5 33
17P LOSS WILD-TYPE 106 63 123

Figure S290.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S291.  Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
17P LOSS MUTATED 10 25 41
17P LOSS WILD-TYPE 136 146 133

Figure S291.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.009

Table S292.  Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
17P LOSS MUTATED 16 31 29
17P LOSS WILD-TYPE 155 174 86

Figure S292.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.083

Table S293.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
17P LOSS MUTATED 15 11 10 30 9
17P LOSS WILD-TYPE 132 87 49 98 47

Figure S293.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.065

Table S294.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
17P LOSS MUTATED 3 23 11 15
17P LOSS WILD-TYPE 59 83 49 75

Figure S294.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 7e-04

Table S295.  Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
17P LOSS MUTATED 5 1 15 19 2 10
17P LOSS WILD-TYPE 65 40 25 63 23 50

Figure S295.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S296.  Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
17Q LOSS MUTATED 2 16 2
17Q LOSS WILD-TYPE 271 118 83

Figure S296.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.037

Table S297.  Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
17Q LOSS MUTATED 1 11 8
17Q LOSS WILD-TYPE 159 154 159

Figure S297.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0059

Table S298.  Gene #70: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
17Q LOSS MUTATED 0 7 13
17Q LOSS WILD-TYPE 146 164 161

Figure S298.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.089

Table S299.  Gene #70: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
17Q LOSS MUTATED 2 11 7
17Q LOSS WILD-TYPE 169 194 108

Figure S299.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.043

Table S300.  Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
17Q LOSS MUTATED 1 8 11
17Q LOSS WILD-TYPE 157 139 172

Figure S300.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.11

Table S301.  Gene #70: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
17Q LOSS MUTATED 1 7 2 7 3
17Q LOSS WILD-TYPE 146 91 57 121 53

Figure S301.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.081

Table S302.  Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
17Q LOSS MUTATED 0 10 2 3
17Q LOSS WILD-TYPE 62 96 58 87

Figure S302.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S303.  Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
18P LOSS MUTATED 21 43 4
18P LOSS WILD-TYPE 252 91 81

Figure S303.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.022

Table S304.  Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
18P LOSS MUTATED 11 29 28
18P LOSS WILD-TYPE 149 136 139

Figure S304.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.036

Table S305.  Gene #71: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
18P LOSS MUTATED 12 4 30
18P LOSS WILD-TYPE 111 64 126

Figure S305.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0032 (Fisher's exact test), Q value = 0.015

Table S306.  Gene #71: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
18P LOSS MUTATED 8 11 8 19
18P LOSS WILD-TYPE 66 102 84 49

Figure S306.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.015

Table S307.  Gene #71: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
18P LOSS MUTATED 9 30 29
18P LOSS WILD-TYPE 137 141 145

Figure S307.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.11

Table S308.  Gene #71: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
18P LOSS MUTATED 15 35 18
18P LOSS WILD-TYPE 156 170 97

Figure S308.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.08

Table S309.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
18P LOSS MUTATED 15 7 12 24 9
18P LOSS WILD-TYPE 132 91 47 104 47

Figure S309.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.036

Table S310.  Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
18P LOSS MUTATED 2 22 8 14
18P LOSS WILD-TYPE 60 84 52 76

Figure S310.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 0.021

Table S311.  Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
18P LOSS MUTATED 5 2 11 17 1 10
18P LOSS WILD-TYPE 65 39 29 65 24 50

Figure S311.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S312.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
18Q LOSS MUTATED 30 64 7
18Q LOSS WILD-TYPE 243 70 78

Figure S312.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00629 (Fisher's exact test), Q value = 0.024

Table S313.  Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
18Q LOSS MUTATED 20 39 42
18Q LOSS WILD-TYPE 140 126 125

Figure S313.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0028

Table S314.  Gene #72: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 123 68 156
18Q LOSS MUTATED 15 8 46
18Q LOSS WILD-TYPE 108 60 110

Figure S314.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0076

Table S315.  Gene #72: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
18Q LOSS MUTATED 10 22 12 25
18Q LOSS WILD-TYPE 64 91 80 43

Figure S315.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.015

Table S316.  Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
18Q LOSS MUTATED 17 39 45
18Q LOSS WILD-TYPE 129 132 129

Figure S316.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.063

Table S317.  Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
18Q LOSS MUTATED 24 47 30
18Q LOSS WILD-TYPE 147 158 85

Figure S317.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.027

Table S318.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
18Q LOSS MUTATED 25 23 51
18Q LOSS WILD-TYPE 133 124 132

Figure S318.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.015

Table S319.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
18Q LOSS MUTATED 21 12 17 37 12
18Q LOSS WILD-TYPE 126 86 42 91 44

Figure S319.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.048

Table S320.  Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
18Q LOSS MUTATED 6 32 11 19
18Q LOSS WILD-TYPE 56 74 49 71

Figure S320.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S321.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
18Q LOSS MUTATED 6 3 18 26 3 12
18Q LOSS WILD-TYPE 64 38 22 56 22 48

Figure S321.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0017

Table S322.  Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
19P LOSS MUTATED 2 11 4
19P LOSS WILD-TYPE 271 123 81

Figure S322.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.014

Table S323.  Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
19P LOSS MUTATED 0 9 0 1
19P LOSS WILD-TYPE 62 97 60 89

Figure S323.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00996 (Fisher's exact test), Q value = 0.036

Table S324.  Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
19P LOSS MUTATED 0 0 1 8 0 1
19P LOSS WILD-TYPE 70 41 39 74 25 59

Figure S324.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0016

Table S325.  Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
19Q LOSS MUTATED 2 11 4
19Q LOSS WILD-TYPE 271 123 81

Figure S325.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.013

Table S326.  Gene #74: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
19Q LOSS MUTATED 0 9 0 1
19Q LOSS WILD-TYPE 62 97 60 89

Figure S326.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.037

Table S327.  Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
19Q LOSS MUTATED 0 0 1 8 0 1
19Q LOSS WILD-TYPE 70 41 39 74 25 59

Figure S327.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.092

Table S328.  Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
20P LOSS MUTATED 8 10 1
20P LOSS WILD-TYPE 265 124 84

Figure S328.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.075

Table S329.  Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
20Q LOSS MUTATED 2 6 1
20Q LOSS WILD-TYPE 271 128 84

Figure S329.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.092

Table S330.  Gene #76: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
20Q LOSS MUTATED 0 5 4
20Q LOSS WILD-TYPE 171 200 111

Figure S330.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S331.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
21Q LOSS MUTATED 7 17 0
21Q LOSS WILD-TYPE 266 117 85

Figure S331.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.015

Table S332.  Gene #77: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
21Q LOSS MUTATED 2 6 16
21Q LOSS WILD-TYPE 144 165 158

Figure S332.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.097

Table S333.  Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
21Q LOSS MUTATED 1 1 6 7 0 3
21Q LOSS WILD-TYPE 69 40 34 75 25 57

Figure S333.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S334.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
22Q LOSS MUTATED 12 32 3
22Q LOSS WILD-TYPE 261 102 82

Figure S334.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.055

Table S335.  Gene #78: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
22Q LOSS MUTATED 6 20 21
22Q LOSS WILD-TYPE 140 151 153

Figure S335.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.11

Table S336.  Gene #78: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
22Q LOSS MUTATED 9 25 13
22Q LOSS WILD-TYPE 162 180 102

Figure S336.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.078

Table S337.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
22Q LOSS MUTATED 6 11 7 18 3
22Q LOSS WILD-TYPE 141 87 52 110 53

Figure S337.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0018

Table S338.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 41 40 82 25 60
22Q LOSS MUTATED 1 2 12 8 2 4
22Q LOSS WILD-TYPE 69 39 28 74 23 56

Figure S338.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S339.  Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
XP LOSS MUTATED 7 29 3
XP LOSS WILD-TYPE 266 105 82

Figure S339.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S340.  Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
XP LOSS MUTATED 1 20 18
XP LOSS WILD-TYPE 159 145 149

Figure S340.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0029

Table S341.  Gene #79: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
XP LOSS MUTATED 2 17 20
XP LOSS WILD-TYPE 144 154 154

Figure S341.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S342.  Gene #79: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
XP LOSS MUTATED 2 24 13
XP LOSS WILD-TYPE 169 181 102

Figure S342.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S343.  Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
XP LOSS MUTATED 4 4 30
XP LOSS WILD-TYPE 154 143 153

Figure S343.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.089

Table S344.  Gene #79: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XP LOSS MUTATED 6 5 5 18 4
XP LOSS WILD-TYPE 141 93 54 110 52

Figure S344.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.023

Table S345.  Gene #79: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
XP LOSS MUTATED 0 12 1 7
XP LOSS WILD-TYPE 62 94 59 83

Figure S345.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S346.  Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 134 85
XQ LOSS MUTATED 7 29 3
XQ LOSS WILD-TYPE 266 105 82

Figure S346.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S347.  Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 165 167
XQ LOSS MUTATED 1 20 18
XQ LOSS WILD-TYPE 159 145 149

Figure S347.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0029

Table S348.  Gene #80: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
XQ LOSS MUTATED 2 17 20
XQ LOSS WILD-TYPE 144 154 154

Figure S348.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.001

Table S349.  Gene #80: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
XQ LOSS MUTATED 2 24 13
XQ LOSS WILD-TYPE 169 181 102

Figure S349.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S350.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 147 183
XQ LOSS MUTATED 4 4 30
XQ LOSS WILD-TYPE 154 143 153

Figure S350.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.087

Table S351.  Gene #80: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XQ LOSS MUTATED 6 5 5 18 4
XQ LOSS WILD-TYPE 141 93 54 110 52

Figure S351.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00592 (Fisher's exact test), Q value = 0.023

Table S352.  Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 106 60 90
XQ LOSS MUTATED 0 12 1 7
XQ LOSS WILD-TYPE 62 94 59 83

Figure S352.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/19782427/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/20168456/PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

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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