Correlation between copy number variations of arm-level result and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1D21WPK
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/C1D21WPK
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 8 molecular subtypes across 492 patients, 331 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',  '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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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',  'MRNASEQ_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' 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',  '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',  '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',  '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',  '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',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 331 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
3p gain 40 (8%) 452 1e-05
(0.000119) 		0.0103
(0.0305) 		0.00472
(0.0162) 		0.00036
(0.00222) 		0.021
(0.0514) 		0.00531
(0.0176) 		0.00361
(0.0134) 		0.00027
(0.00175)
3q gain 54 (11%) 438 1e-05
(0.000119) 		0.0076
(0.0234) 		0.00123
(0.00592) 		0.00129
(0.00607) 		0.00433
(0.0151) 		0.00377
(0.0138) 		0.0147
(0.039) 		2e-05
(0.000194)
7p gain 102 (21%) 390 1e-05
(0.000119) 		1e-05
(0.000119) 		1e-05
(0.000119) 		2e-05
(0.000194) 		0.0186
(0.0476) 		1e-05
(0.000119) 		0.0003
(0.00192) 		0.0017
(0.0075)
7q gain 95 (19%) 397 1e-05
(0.000119) 		1e-05
(0.000119) 		1e-05
(0.000119) 		7e-05
(0.00056) 		0.0243
(0.0579) 		4e-05
(0.000351) 		0.0004
(0.00242) 		0.00524
(0.0175)
8q gain 124 (25%) 368 1e-05
(0.000119) 		1e-05
(0.000119) 		3e-05
(0.000274) 		3e-05
(0.000274) 		0.00046
(0.00268) 		1e-05
(0.000119) 		2e-05
(0.000194) 		2e-05
(0.000194)
20p gain 26 (5%) 466 1e-05
(0.000119) 		0.0208
(0.0513) 		0.0223
(0.0537) 		0.0364
(0.0762) 		0.00213
(0.00885) 		0.00394
(0.0142) 		0.0296
(0.0673) 		0.00454
(0.0157)
21q gain 21 (4%) 471 1e-05
(0.000119) 		0.0386
(0.0789) 		0.00156
(0.00717) 		0.0264
(0.062) 		0.0137
(0.0376) 		0.00347
(0.0131) 		0.0124
(0.0349) 		0.0292
(0.0669)
1p loss 22 (4%) 470 1e-05
(0.000119) 		0.00057
(0.00317) 		0.00122
(0.00592) 		0.00019
(0.00131) 		0.0251
(0.0594) 		0.00364
(0.0135) 		0.0196
(0.0496) 		0.0132
(0.0367)
4p loss 24 (5%) 468 1e-05
(0.000119) 		0.0189
(0.0481) 		0.00375
(0.0138) 		0.0295
(0.0673) 		0.00152
(0.00705) 		0.00258
(0.0105) 		4e-05
(0.000351) 		7e-05
(0.00056)
6q loss 40 (8%) 452 1e-05
(0.000119) 		0.0358
(0.0761) 		0.00036
(0.00222) 		0.00124
(0.00592) 		0.013
(0.0362) 		0.0477
(0.0934) 		0.00407
(0.0144) 		0.00207
(0.00866)
10q loss 43 (9%) 449 1e-05
(0.000119) 		0.00086
(0.00451) 		0.00201
(0.00846) 		0.00051
(0.00291) 		0.0391
(0.0792) 		0.00125
(0.00593) 		0.00174
(0.00757) 		7e-05
(0.00056)
15q loss 36 (7%) 456 1e-05
(0.000119) 		0.00166
(0.00738) 		0.00068
(0.00369) 		0.00648
(0.0205) 		0.0001
(0.000744) 		0.00751
(0.0232) 		0.00116
(0.00567) 		0.00013
(0.000945)
18q loss 101 (21%) 391 1e-05
(0.000119) 		0.00629
(0.0202) 		0.00339
(0.013) 		0.0223
(0.0537) 		0.0068
(0.0214) 		0.0034
(0.013) 		0.0154
(0.0405) 		1e-05
(0.000119)
8p gain 71 (14%) 421 1e-05
(0.000119) 		1e-05
(0.000119) 		7e-05
(0.00056) 		0.00046
(0.00268) 		0.125
(0.184) 		0.00512
(0.0172) 		0.00196
(0.00831) 		0.00231
(0.00948)
6p loss 25 (5%) 467 1e-05
(0.000119) 		0.0147
(0.039) 		0.00032
(0.00203) 		0.00298
(0.0117) 		0.0581
(0.108) 		0.0316
(0.0696) 		0.0141
(0.0383) 		0.00402
(0.0143)
10p loss 41 (8%) 451 1e-05
(0.000119) 		0.00011
(0.000809) 		0.00026
(0.0017) 		0.0001
(0.000744) 		0.0842
(0.143) 		5e-05
(0.000427) 		0.0113
(0.0324) 		5e-05
(0.000427)
16q loss 107 (22%) 385 1e-05
(0.000119) 		0.00069
(0.00371) 		0.0306
(0.0688) 		0.0304
(0.0688) 		0.0839
(0.143) 		0.00054
(0.00306) 		0.00422
(0.0148) 		8e-05
(0.000617)
17p loss 76 (15%) 416 1e-05
(0.000119) 		0.00157
(0.00717) 		0.00014
(0.000985) 		0.00171
(0.0075) 		0.0978
(0.157) 		0.0318
(0.0696) 		0.0225
(0.0541) 		8e-05
(0.000617)
17q loss 20 (4%) 472 1e-05
(0.000119) 		0.0101
(0.0304) 		0.00092
(0.00479) 		0.0357
(0.0761) 		0.0124
(0.0349) 		0.0452
(0.0895) 		0.0306
(0.0688) 		0.144
(0.206)
18p loss 68 (14%) 424 1e-05
(0.000119) 		0.005
(0.0169) 		0.00325
(0.0126) 		0.0491
(0.0953) 		0.0584
(0.108) 		0.0299
(0.0679) 		0.0103
(0.0305) 		0.00567
(0.0184)
xp loss 39 (8%) 453 1e-05
(0.000119) 		2e-05
(0.000194) 		0.00049
(0.00283) 		4e-05
(0.000351) 		1e-05
(0.000119) 		0.0355
(0.0761) 		0.00556
(0.0182) 		0.0984
(0.157)
xq loss 39 (8%) 453 1e-05
(0.000119) 		2e-05
(0.000194) 		0.00041
(0.00245) 		6e-05
(0.000505) 		1e-05
(0.000119) 		0.0363
(0.0762) 		0.00548
(0.0181) 		0.0982
(0.157)
5p gain 23 (5%) 469 1e-05
(0.000119) 		0.0588
(0.109) 		0.00926
(0.0278) 		0.0612
(0.112) 		0.0014
(0.00654) 		0.00163
(0.0073) 		0.00193
(0.00823) 		0.00395
(0.0142)
5q loss 22 (4%) 470 1e-05
(0.000119) 		0.00293
(0.0116) 		0.0124
(0.0349) 		0.00216
(0.00892) 		0.0579
(0.108) 		0.00111
(0.00546) 		0.109
(0.164) 		0.027
(0.0627)
8p loss 168 (34%) 324 1e-05
(0.000119) 		1e-05
(0.000119) 		1e-05
(0.000119) 		1e-05
(0.000119) 		0.00044
(0.00261) 		0.0793
(0.136) 		0.0578
(0.108) 		0.0309
(0.0688)
9q gain 50 (10%) 442 1e-05
(0.000119) 		0.117
(0.173) 		0.0148
(0.0392) 		0.196
(0.258) 		0.358
(0.424) 		0.0106
(0.0308) 		0.00707
(0.022) 		0.0136
(0.0375)
10p gain 15 (3%) 477 8e-05
(0.000617) 		0.0348
(0.0751) 		0.103
(0.159) 		0.0334
(0.0727) 		0.575
(0.625) 		0.0135
(0.0375) 		0.173
(0.236) 		0.00082
(0.00434)
17p gain 8 (2%) 484 0.0145
(0.039) 		0.912
(0.928) 		0.0491
(0.0953) 		0.665
(0.702) 		0.0212
(0.0517) 		0.0162
(0.0422) 		0.608
(0.652) 		0.00361
(0.0134)
20q gain 28 (6%) 464 1e-05
(0.000119) 		0.0199
(0.0502) 		0.0565
(0.107) 		0.126
(0.185) 		0.0112
(0.0323) 		0.00787
(0.0241) 		0.101
(0.158) 		0.00896
(0.027)
2q loss 18 (4%) 474 0.00014
(0.000985) 		0.0205
(0.0509) 		0.724
(0.755) 		0.484
(0.552) 		0.127
(0.186) 		0.0349
(0.0751) 		0.00882
(0.0269) 		0.001
(0.00504)
4q loss 17 (3%) 475 1e-05
(0.000119) 		0.155
(0.218) 		0.00638
(0.0204) 		0.103
(0.159) 		0.201
(0.263) 		0.0466
(0.0919) 		0.0144
(0.0388) 		0.00521
(0.0175)
12p loss 48 (10%) 444 1e-05
(0.000119) 		0.296
(0.365) 		0.0485
(0.0947) 		0.422
(0.489) 		0.455
(0.524) 		0.0164
(0.0428) 		0.00684
(0.0215) 		0.00272
(0.0109)
22q loss 47 (10%) 445 1e-05
(0.000119) 		0.21
(0.273) 		0.0187
(0.0476) 		0.0475
(0.0933) 		0.0688
(0.122) 		0.0278
(0.0643) 		0.149
(0.211) 		0.00024
(0.0016)
1p gain 16 (3%) 476 2e-05
(0.000194) 		0.203
(0.265) 		0.0107
(0.0309) 		0.00062
(0.00342) 		0.309
(0.377) 		0.0413
(0.0828) 		0.848
(0.872) 		0.177
(0.239)
1q gain 26 (5%) 466 1e-05
(0.000119) 		0.142
(0.203) 		0.00014
(0.000985) 		0.00056
(0.00314) 		0.0975
(0.157) 		0.0324
(0.0708) 		0.503
(0.566) 		0.194
(0.257)
16p gain 31 (6%) 461 1e-05
(0.000119) 		0.264
(0.331) 		0.0697
(0.123) 		0.318
(0.386) 		0.155
(0.218) 		0.00398
(0.0142) 		0.0263
(0.0618) 		0.0124
(0.0349)
2p loss 16 (3%) 476 9e-05
(0.000686) 		0.00486
(0.0165) 		0.481
(0.549) 		0.354
(0.421) 		0.133
(0.193) 		0.0874
(0.146) 		0.00389
(0.0141) 		0.00345
(0.0131)
5p loss 12 (2%) 480 2e-05
(0.000194) 		0.173
(0.236) 		0.0376
(0.0782) 		0.00562
(0.0184) 		0.866
(0.886) 		0.00319
(0.0124) 		0.51
(0.567) 		0.104
(0.16)
8q loss 24 (5%) 468 0.0289
(0.0666) 		0.001
(0.00504) 		0.0105
(0.0307) 		0.0249
(0.0591) 		0.101
(0.159) 		0.992
(1.00) 		0.219
(0.284) 		0.246
(0.312)
13q loss 77 (16%) 415 1e-05
(0.000119) 		0.33
(0.396) 		0.0419
(0.0839) 		0.0656
(0.118) 		0.184
(0.245) 		0.0408
(0.0822) 		0.225
(0.289) 		0.00016
(0.00111)
2p gain 10 (2%) 482 0.00095
(0.00486) 		0.0755
(0.131) 		0.00706
(0.022) 		0.143
(0.204) 		0.114
(0.169) 		0.0359
(0.0761) 		0.168
(0.23) 		0.188
(0.249)
10q gain 14 (3%) 478 0.00021
(0.00141) 		0.0581
(0.108) 		0.131
(0.191) 		0.0316
(0.0696) 		0.588
(0.636) 		0.0883
(0.146) 		0.27
(0.335) 		0.00192
(0.00823)
11p gain 26 (5%) 466 1e-05
(0.000119) 		0.0537
(0.103) 		0.0923
(0.152) 		0.0142
(0.0386) 		0.598
(0.646) 		0.0539
(0.103) 		0.0356
(0.0761) 		0.177
(0.239)
11q gain 29 (6%) 463 1e-05
(0.000119) 		0.0727
(0.127) 		0.0309
(0.0688) 		0.0381
(0.0787) 		0.689
(0.723) 		0.0502
(0.0967) 		0.084
(0.143) 		0.123
(0.181)
12p gain 14 (3%) 478 3e-05
(0.000274) 		0.183
(0.245) 		0.0875
(0.146) 		0.115
(0.171) 		0.361
(0.427) 		0.00094
(0.00485) 		0.0233
(0.0557) 		0.206
(0.269)
12q gain 17 (3%) 475 0.00039
(0.00238) 		0.0828
(0.141) 		0.198
(0.26) 		0.112
(0.168) 		0.784
(0.813) 		0.0203
(0.0506) 		0.0154
(0.0405) 		0.0964
(0.156)
17q gain 11 (2%) 481 0.00035
(0.0022) 		0.799
(0.826) 		0.0166
(0.0429) 		0.216
(0.28) 		0.0908
(0.15) 		0.11
(0.166) 		0.472
(0.541) 		0.00067
(0.00366)
xp gain 7 (1%) 485 0.00082
(0.00434) 		0.0648
(0.117) 		0.101
(0.158) 		0.0928
(0.153) 		0.51
(0.567) 		0.045
(0.0895) 		0.00615
(0.0199) 		0.0868
(0.145)
xq gain 7 (1%) 485 0.00106
(0.00526) 		0.0645
(0.116) 		0.099
(0.158) 		0.0942
(0.155) 		0.508
(0.567) 		0.0456
(0.09) 		0.0064
(0.0204) 		0.0864
(0.145)
9p loss 21 (4%) 471 1e-05
(0.000119) 		0.283
(0.351) 		0.00415
(0.0146) 		0.0211
(0.0514) 		0.267
(0.333) 		0.245
(0.312) 		0.107
(0.163) 		0.0619
(0.113)
12q loss 20 (4%) 472 3e-05
(0.000274) 		0.179
(0.241) 		0.251
(0.318) 		0.265
(0.331) 		1
(1.00) 		0.0493
(0.0953) 		0.0671
(0.119) 		0.00892
(0.027)
19p loss 17 (3%) 475 0.00021
(0.00141) 		0.0558
(0.106) 		0.307
(0.376) 		0.158
(0.219) 		0.134
(0.195) 		0.158
(0.219) 		0.00292
(0.0116) 		0.0104
(0.0307)
19q loss 17 (3%) 475 0.00025
(0.00165) 		0.0561
(0.106) 		0.304
(0.372) 		0.16
(0.219) 		0.133
(0.193) 		0.157
(0.219) 		0.00294
(0.0116) 		0.0104
(0.0306)
21q loss 24 (5%) 468 2e-05
(0.000194) 		0.0667
(0.119) 		0.00361
(0.0134) 		0.323
(0.39) 		0.572
(0.623) 		0.103
(0.159) 		0.422
(0.489) 		0.0404
(0.0815)
5q gain 12 (2%) 480 2e-05
(0.000194) 		0.173
(0.236) 		0.0363
(0.0762) 		0.23
(0.293) 		0.373
(0.439) 		0.158
(0.219) 		0.124
(0.182) 		0.325
(0.391)
6p gain 10 (2%) 482 0.00158
(0.00717) 		0.157
(0.219) 		0.139
(0.2) 		0.268
(0.333) 		0.672
(0.708) 		0.106
(0.162) 		0.017
(0.0436) 		0.0746
(0.13)
6q gain 6 (1%) 486 0.0206
(0.0509) 		0.791
(0.82) 		0.103
(0.159) 		0.579
(0.628) 		0.196
(0.258) 		0.0391
(0.0792) 		0.27
(0.335) 		0.564
(0.616)
9p gain 34 (7%) 458 1e-05
(0.000119) 		0.1
(0.158) 		0.0785
(0.135) 		0.0955
(0.156) 		0.486
(0.553) 		0.111
(0.167) 		0.0166
(0.0429) 		0.179
(0.241)
19p gain 12 (2%) 480 1e-05
(0.000119) 		0.159
(0.219) 		0.0365
(0.0762) 		0.343
(0.409) 		0.14
(0.2) 		0.0858
(0.144) 		0.515
(0.571) 		0.119
(0.176)
19q gain 12 (2%) 480 1e-05
(0.000119) 		0.104
(0.16) 		0.0391
(0.0792) 		0.367
(0.434) 		0.219
(0.284) 		0.0609
(0.112) 		0.508
(0.567) 		0.154
(0.218)
1q loss 6 (1%) 486 0.0206
(0.0509) 		0.152
(0.216) 		0.0425
(0.0847) 		0.0962
(0.156) 		0.1
(0.158) 		0.102
(0.159) 		0.0516
(0.099) 		0.394
(0.462)
3p loss 9 (2%) 483 0.0336
(0.073) 		0.315
(0.384) 		0.105
(0.16) 		0.0385
(0.0789) 		0.104
(0.159) 		0.412
(0.48) 		0.0509
(0.0978) 		0.196
(0.258)
9q loss 10 (2%) 482 0.00163
(0.0073) 		0.342
(0.408) 		0.264
(0.331) 		0.228
(0.292) 		0.616
(0.658) 		0.548
(0.605) 		0.52
(0.576) 		0.0364
(0.0762)
11q loss 5 (1%) 487 0.0137
(0.0376) 		0.0704
(0.124) 		0.0614
(0.112) 		0.3
(0.369) 		0.632
(0.675) 		0.187
(0.249) 		0.0218
(0.0529) 		0.291
(0.36)
16p loss 32 (7%) 460 0.00175
(0.00757) 		0.334
(0.4) 		0.492
(0.555) 		0.38
(0.447) 		0.646
(0.687) 		0.319
(0.387) 		0.223
(0.287) 		0.0316
(0.0696)
20q loss 9 (2%) 483 0.0271
(0.0629) 		0.0791
(0.136) 		0.0956
(0.156) 		0.0381
(0.0787) 		0.0734
(0.128) 		0.0607
(0.112) 		1
(1.00) 		0.504
(0.566)
2q gain 7 (1%) 485 0.00103
(0.00515) 		0.465
(0.534) 		0.101
(0.158) 		0.553
(0.608) 		0.508
(0.567) 		0.0623
(0.113) 		0.177
(0.239) 		0.159
(0.219)
4p gain 9 (2%) 483 0.0269
(0.0627) 		0.845
(0.871) 		0.489
(0.553) 		0.768
(0.799) 		0.915
(0.929) 		0.415
(0.483) 		0.605
(0.65) 		0.572
(0.623)
13q gain 8 (2%) 484 0.0144
(0.0389) 		0.137
(0.198) 		0.606
(0.651) 		0.662
(0.701) 		0.821
(0.848) 		0.563
(0.616) 		0.741
(0.772) 		0.865
(0.886)
14q gain 10 (2%) 482 2e-05
(0.000194) 		0.159
(0.219) 		0.0856
(0.144) 		0.226
(0.289) 		0.113
(0.169) 		0.256
(0.323) 		0.489
(0.553) 		0.466
(0.534)
15q gain 6 (1%) 486 0.0201
(0.0504) 		1
(1.00) 		0.877
(0.897) 		0.665
(0.702) 		0.777
(0.807) 		0.182
(0.244) 		0.706
(0.739) 		0.321
(0.389)
16q gain 8 (2%) 484 0.0849
(0.143) 		0.5
(0.564) 		0.604
(0.65) 		0.904
(0.922) 		0.102
(0.159) 		0.0124
(0.0349) 		0.647
(0.687) 		0.543
(0.6)
18p gain 18 (4%) 474 1e-05
(0.000119) 		0.356
(0.423) 		0.139
(0.2) 		0.508
(0.567) 		0.688
(0.723) 		0.609
(0.652) 		0.723
(0.755) 		0.45
(0.519)
18q gain 9 (2%) 483 0.00473
(0.0162) 		1
(1.00) 		0.106
(0.162) 		0.909
(0.926) 		0.64
(0.682) 		0.444
(0.514) 		0.446
(0.515) 		0.665
(0.702)
3q loss 5 (1%) 487 0.304
(0.372) 		1
(1.00) 		0.328
(0.394) 		0.249
(0.316) 		0.152
(0.216) 		0.0317
(0.0696)
11p loss 8 (2%) 484 0.0024
(0.00978) 		0.0809
(0.139) 		0.265
(0.331) 		0.117
(0.173) 		0.322
(0.39) 		0.26
(0.328) 		0.113
(0.169) 		0.102
(0.159)
14q loss 25 (5%) 467 2e-05
(0.000194) 		0.0576
(0.108) 		0.0758
(0.131) 		0.0981
(0.157) 		0.405
(0.474) 		0.0641
(0.116) 		0.0988
(0.158) 		0.0669
(0.119)
20p loss 19 (4%) 473 0.0383
(0.0788) 		0.0635
(0.115) 		0.223
(0.287) 		0.184
(0.245) 		0.489
(0.553) 		0.183
(0.245) 		1
(1.00) 		0.583
(0.631)
4q gain 10 (2%) 482 0.0729
(0.128) 		0.486
(0.553) 		1
(1.00) 		0.555
(0.608) 		0.854
(0.877) 		0.177
(0.239) 		0.154
(0.218) 		0.0696
(0.123)
22q gain 4 (1%) 488 0.0955
(0.156) 		0.551
(0.607) 		0.555
(0.608) 		0.222
(0.286) 		0.325
(0.391) 		0.406
(0.474) 		0.404
(0.474) 		0.159
(0.219)
'1p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

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 = 0.0107 (Fisher's exact test), Q value = 0.031

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #3: '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 #3: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0034

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #4: '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 #4: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.083

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #6: '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 #6: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

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 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00098

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0031

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #4: '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 S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.071

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

'2p gain' versus 'CN_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0049

Table S9.  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 S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00706 (Fisher's exact test), Q value = 0.022

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #3: '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 S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.076

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #6: '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 S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0051

Table S12.  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 S12.  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 = 0.00012

Table S13.  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 S13.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.03

Table S14.  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 S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 0.016

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #3: '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 S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #4: '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 S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.051

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #5: '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 S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.018

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #6: '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 S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.013

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #7: '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 S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0017

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #8: '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 S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S21.  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 S21.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0076 (Fisher's exact test), Q value = 0.023

Table S22.  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 S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0059

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #3: '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 S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0061

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #4: '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 S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.015

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #5: '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 S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00377 (Fisher's exact test), Q value = 0.014

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

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.039

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #7: '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 S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #8: '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 S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.063

Table S29.  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 S29.  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 = 0.00012

Table S30.  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 S30.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.028

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #3: '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 S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0065

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #5: '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 S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0073

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #6: '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 S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.0082

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #7: '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 S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00395 (Fisher's exact test), Q value = 0.014

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #8: '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 S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S36.  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 S36.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.076

Table S37.  Gene #10: '5q gain' versus Molecular Subtype #3: '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 S37.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0072

Table S38.  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 S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.044

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #7: '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 S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.051

Table S40.  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 S40.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.079

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #6: '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 S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S42.  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 S42.  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 = 0.00012

Table S43.  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 S43.  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 = 0.00012

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #3: '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 S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #4: '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 S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.048

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #5: '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 S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #6: '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 S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0019

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #7: '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 S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0017 (Fisher's exact test), Q value = 0.0075

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #8: '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 S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S50.  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 S50.  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 = 0.00012

Table S51.  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 S51.  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 = 0.00012

Table S52.  Gene #14: '7q gain' versus Molecular Subtype #3: '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 S52.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S53.  Gene #14: '7q gain' versus Molecular Subtype #4: '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 S53.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.058

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #5: '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 S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #6: '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 S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0024

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #7: '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 S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00524 (Fisher's exact test), Q value = 0.017

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #8: '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 S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S58.  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 S58.  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 = 0.00012

Table S59.  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 S59.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S60.  Gene #15: '8p gain' versus Molecular Subtype #3: '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 S60.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0027

Table S61.  Gene #15: '8p gain' versus Molecular Subtype #4: '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 S61.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00512 (Fisher's exact test), Q value = 0.017

Table S62.  Gene #15: '8p gain' versus Molecular Subtype #6: '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 S62.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0083

Table S63.  Gene #15: '8p gain' versus Molecular Subtype #7: '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 S63.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0095

Table S64.  Gene #15: '8p gain' versus Molecular Subtype #8: '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 S64.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S65.  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 S65.  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 = 0.00012

Table S66.  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 S66.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00027

Table S67.  Gene #16: '8q gain' versus Molecular Subtype #3: '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 S67.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00027

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #4: '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 S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0027

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #5: '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 S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #6: '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 S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S71.  Gene #16: '8q gain' versus Molecular Subtype #7: '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 S71.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S72.  Gene #16: '8q gain' versus Molecular Subtype #8: '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 S72.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S73.  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 S73.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.043

Table S74.  Gene #17: '9p gain' versus Molecular Subtype #7: '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 S74.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S75.  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 S75.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.039

Table S76.  Gene #18: '9q gain' versus Molecular Subtype #3: '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 S76.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.031

Table S77.  Gene #18: '9q gain' versus Molecular Subtype #6: '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 S77.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.022

Table S78.  Gene #18: '9q gain' versus Molecular Subtype #7: '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 S78.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.037

Table S79.  Gene #18: '9q gain' versus Molecular Subtype #8: '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 S79.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00062

Table S80.  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 S80.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.075

Table S81.  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 S81.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.073

Table S82.  Gene #19: '10p gain' versus Molecular Subtype #4: '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 S82.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.037

Table S83.  Gene #19: '10p gain' versus Molecular Subtype #6: '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 S83.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0043

Table S84.  Gene #19: '10p gain' versus Molecular Subtype #8: '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 S84.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0014

Table S85.  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 S85.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.07

Table S86.  Gene #20: '10q gain' versus Molecular Subtype #4: '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 S86.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0082

Table S87.  Gene #20: '10q gain' versus Molecular Subtype #8: '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 S87.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S88.  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 S88.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.039

Table S89.  Gene #21: '11p gain' versus Molecular Subtype #4: '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 S89.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.076

Table S90.  Gene #21: '11p gain' versus Molecular Subtype #7: '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 S90.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S91.  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 S91.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.069

Table S92.  Gene #22: '11q gain' versus Molecular Subtype #3: '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 S92.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.079

Table S93.  Gene #22: '11q gain' versus Molecular Subtype #4: '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 S93.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00027

Table S94.  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 S94.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0049

Table S95.  Gene #23: '12p gain' versus Molecular Subtype #6: '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 S95.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.056

Table S96.  Gene #23: '12p gain' versus Molecular Subtype #7: '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 S96.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0024

Table S97.  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 S97.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.051

Table S98.  Gene #24: '12q gain' versus Molecular Subtype #6: '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 S98.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.04

Table S99.  Gene #24: '12q gain' versus Molecular Subtype #7: '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 S99.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.039

Table S100.  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 S100.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S101.  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 S101.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.05

Table S102.  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 S102.  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 = 0.00012

Table S103.  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 S103.  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 = 0.014

Table S104.  Gene #28: '16p gain' versus Molecular Subtype #6: '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 S104.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.062

Table S105.  Gene #28: '16p gain' versus Molecular Subtype #7: '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 S105.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.035

Table S106.  Gene #28: '16p gain' versus Molecular Subtype #8: '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 S106.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.035

Table S107.  Gene #29: '16q gain' versus Molecular Subtype #6: '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 S107.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.039

Table S108.  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 S108.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.095

Table S109.  Gene #30: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 171 174
17P GAIN MUTATED 0 2 6
17P GAIN WILD-TYPE 146 169 168

Figure S109.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.052

Table S110.  Gene #30: '17p gain' versus Molecular Subtype #5: '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 S110.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.042

Table S111.  Gene #30: '17p gain' versus Molecular Subtype #6: '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 S111.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.013

Table S112.  Gene #30: '17p gain' versus Molecular Subtype #8: '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 S112.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0022

Table S113.  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 S113.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.043

Table S114.  Gene #31: '17q gain' versus Molecular Subtype #3: '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 S114.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0037

Table S115.  Gene #31: '17q gain' versus Molecular Subtype #8: '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 S115.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S116.  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 S116.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.00473 (Fisher's exact test), Q value = 0.016

Table S117.  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 S117.  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 = 0.00012

Table S118.  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 S118.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.076

Table S119.  Gene #34: '19p gain' versus Molecular Subtype #3: '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 S119.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S120.  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 S120.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.079

Table S121.  Gene #35: '19q gain' versus Molecular Subtype #3: '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 S121.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S122.  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 S122.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.051

Table S123.  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 S123.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.054

Table S124.  Gene #36: '20p gain' versus Molecular Subtype #3: '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 S124.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.076

Table S125.  Gene #36: '20p gain' versus Molecular Subtype #4: '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 S125.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0089

Table S126.  Gene #36: '20p gain' versus Molecular Subtype #5: '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 S126.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00394 (Fisher's exact test), Q value = 0.014

Table S127.  Gene #36: '20p gain' versus Molecular Subtype #6: '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 S127.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.067

Table S128.  Gene #36: '20p gain' versus Molecular Subtype #7: '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 S128.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00454 (Fisher's exact test), Q value = 0.016

Table S129.  Gene #36: '20p gain' versus Molecular Subtype #8: '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 S129.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S130.  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 S130.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.05

Table S131.  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 S131.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.032

Table S132.  Gene #37: '20q gain' versus Molecular Subtype #5: '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 S132.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00787 (Fisher's exact test), Q value = 0.024

Table S133.  Gene #37: '20q gain' versus Molecular Subtype #6: '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 S133.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00896 (Fisher's exact test), Q value = 0.027

Table S134.  Gene #37: '20q gain' versus Molecular Subtype #8: '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 S134.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S135.  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 S135.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.079

Table S136.  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 S136.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0072

Table S137.  Gene #38: '21q gain' versus Molecular Subtype #3: '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 S137.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.062

Table S138.  Gene #38: '21q gain' versus Molecular Subtype #4: '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 S138.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.038

Table S139.  Gene #38: '21q gain' versus Molecular Subtype #5: '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 S139.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00347 (Fisher's exact test), Q value = 0.013

Table S140.  Gene #38: '21q gain' versus Molecular Subtype #6: '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 S140.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.035

Table S141.  Gene #38: '21q gain' versus Molecular Subtype #7: '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 S141.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.067

Table S142.  Gene #38: '21q gain' versus Molecular Subtype #8: '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 S142.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0043

Table S143.  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 S143.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.045 (Fisher's exact test), Q value = 0.089

Table S144.  Gene #40: 'xp gain' versus Molecular Subtype #6: '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 S144.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.02

Table S145.  Gene #40: 'xp gain' versus Molecular Subtype #7: '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 S145.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0053

Table S146.  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 S146.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.09

Table S147.  Gene #41: 'xq gain' versus Molecular Subtype #6: '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 S147.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0064 (Fisher's exact test), Q value = 0.02

Table S148.  Gene #41: 'xq gain' versus Molecular Subtype #7: '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 S148.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S149.  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 S149.  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 = 0.0032

Table S150.  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 S150.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0059

Table S151.  Gene #42: '1p loss' versus Molecular Subtype #3: '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 S151.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0013

Table S152.  Gene #42: '1p loss' versus Molecular Subtype #4: '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 S152.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.059

Table S153.  Gene #42: '1p loss' versus Molecular Subtype #5: '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 S153.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00364 (Fisher's exact test), Q value = 0.013

Table S154.  Gene #42: '1p loss' versus Molecular Subtype #6: '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 S154.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.05

Table S155.  Gene #42: '1p loss' versus Molecular Subtype #7: '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 S155.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.037

Table S156.  Gene #42: '1p loss' versus Molecular Subtype #8: '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 S156.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.051

Table S157.  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 S157.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.085

Table S158.  Gene #43: '1q loss' versus Molecular Subtype #3: '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 S158.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00069

Table S159.  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 S159.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.017

Table S160.  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 S160.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.014

Table S161.  Gene #44: '2p loss' versus Molecular Subtype #7: '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 S161.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.013

Table S162.  Gene #44: '2p loss' versus Molecular Subtype #8: '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 S162.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00098

Table S163.  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 S163.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.051

Table S164.  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 S164.  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 = 0.075

Table S165.  Gene #45: '2q loss' versus Molecular Subtype #6: '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 S165.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.027

Table S166.  Gene #45: '2q loss' versus Molecular Subtype #7: '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 S166.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.005

Table S167.  Gene #45: '2q loss' versus Molecular Subtype #8: '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 S167.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.073

Table S168.  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 S168.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.079

Table S169.  Gene #46: '3p loss' versus Molecular Subtype #4: '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 S169.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.07

Table S170.  Gene #47: '3q loss' versus Molecular Subtype #6: '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 S170.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S171.  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 S171.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.048

Table S172.  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 S172.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.014

Table S173.  Gene #48: '4p loss' versus Molecular Subtype #3: '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 S173.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.067

Table S174.  Gene #48: '4p loss' versus Molecular Subtype #4: '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 S174.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.007

Table S175.  Gene #48: '4p loss' versus Molecular Subtype #5: '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 S175.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.01

Table S176.  Gene #48: '4p loss' versus Molecular Subtype #6: '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 S176.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S177.  Gene #48: '4p loss' versus Molecular Subtype #7: '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 S177.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S178.  Gene #48: '4p loss' versus Molecular Subtype #8: '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 S178.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S179.  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 S179.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00638 (Fisher's exact test), Q value = 0.02

Table S180.  Gene #49: '4q loss' versus Molecular Subtype #3: '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 S180.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.092

Table S181.  Gene #49: '4q loss' versus Molecular Subtype #6: '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 S181.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.039

Table S182.  Gene #49: '4q loss' versus Molecular Subtype #7: '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 S182.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00521 (Fisher's exact test), Q value = 0.017

Table S183.  Gene #49: '4q loss' versus Molecular Subtype #8: '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 S183.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S184.  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 S184.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.078

Table S185.  Gene #50: '5p loss' versus Molecular Subtype #3: '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 S185.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00562 (Fisher's exact test), Q value = 0.018

Table S186.  Gene #50: '5p loss' versus Molecular Subtype #4: '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 S186.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.012

Table S187.  Gene #50: '5p loss' versus Molecular Subtype #6: '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 S187.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S188.  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 S188.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.012

Table S189.  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 S189.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.035

Table S190.  Gene #51: '5q loss' versus Molecular Subtype #3: '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 S190.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.0089

Table S191.  Gene #51: '5q loss' versus Molecular Subtype #4: '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 S191.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0055

Table S192.  Gene #51: '5q loss' versus Molecular Subtype #6: '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 S192.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.063

Table S193.  Gene #51: '5q loss' versus Molecular Subtype #8: '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 S193.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S194.  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 S194.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.039

Table S195.  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 S195.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.002

Table S196.  Gene #52: '6p loss' versus Molecular Subtype #3: '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 S196.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00298 (Fisher's exact test), Q value = 0.012

Table S197.  Gene #52: '6p loss' versus Molecular Subtype #4: '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 S197.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.07

Table S198.  Gene #52: '6p loss' versus Molecular Subtype #6: '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 S198.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.038

Table S199.  Gene #52: '6p loss' versus Molecular Subtype #7: '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 S199.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00402 (Fisher's exact test), Q value = 0.014

Table S200.  Gene #52: '6p loss' versus Molecular Subtype #8: '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 S200.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S201.  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 S201.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.076

Table S202.  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 S202.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S203.  Gene #53: '6q loss' versus Molecular Subtype #3: '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 S203.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0059

Table S204.  Gene #53: '6q loss' versus Molecular Subtype #4: '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 S204.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.036

Table S205.  Gene #53: '6q loss' versus Molecular Subtype #5: '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 S205.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.093

Table S206.  Gene #53: '6q loss' versus Molecular Subtype #6: '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 S206.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.014

Table S207.  Gene #53: '6q loss' versus Molecular Subtype #7: '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 S207.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.0087

Table S208.  Gene #53: '6q loss' versus Molecular Subtype #8: '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 S208.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S209.  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 S209.  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 = 0.00012

Table S210.  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 S210.  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 = 0.00012

Table S211.  Gene #54: '8p loss' versus Molecular Subtype #3: '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 S211.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S212.  Gene #54: '8p loss' versus Molecular Subtype #4: '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 S212.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0026

Table S213.  Gene #54: '8p loss' versus Molecular Subtype #5: '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 S213.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.069

Table S214.  Gene #54: '8p loss' versus Molecular Subtype #8: '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 S214.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.067

Table S215.  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 S215.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.005

Table S216.  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 S216.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.031

Table S217.  Gene #55: '8q loss' versus Molecular Subtype #3: '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 S217.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.059

Table S218.  Gene #55: '8q loss' versus Molecular Subtype #4: '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 S218.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S219.  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 S219.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.015

Table S220.  Gene #56: '9p loss' versus Molecular Subtype #3: '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 S220.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.051

Table S221.  Gene #56: '9p loss' versus Molecular Subtype #4: '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 S221.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0073

Table S222.  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 S222.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.076

Table S223.  Gene #57: '9q loss' versus Molecular Subtype #8: '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 S223.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S224.  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 S224.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00081

Table S225.  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 S225.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0017

Table S226.  Gene #58: '10p loss' versus Molecular Subtype #3: '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 S226.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00074

Table S227.  Gene #58: '10p loss' versus Molecular Subtype #4: '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 S227.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00043

Table S228.  Gene #58: '10p loss' versus Molecular Subtype #6: '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 S228.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.032

Table S229.  Gene #58: '10p loss' versus Molecular Subtype #7: '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 S229.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00043

Table S230.  Gene #58: '10p loss' versus Molecular Subtype #8: '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 S230.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S231.  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 S231.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0045

Table S232.  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 S232.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.0085

Table S233.  Gene #59: '10q loss' versus Molecular Subtype #3: '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 S233.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0029

Table S234.  Gene #59: '10q loss' versus Molecular Subtype #4: '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 S234.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.079

Table S235.  Gene #59: '10q loss' versus Molecular Subtype #5: '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 S235.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0059

Table S236.  Gene #59: '10q loss' versus Molecular Subtype #6: '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 S236.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0076

Table S237.  Gene #59: '10q loss' versus Molecular Subtype #7: '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 S237.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S238.  Gene #59: '10q loss' versus Molecular Subtype #8: '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 S238.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0098

Table S239.  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 S239.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.038

Table S240.  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 S240.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.053

Table S241.  Gene #61: '11q loss' versus Molecular Subtype #7: '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 S241.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S242.  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 S242.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.095

Table S243.  Gene #62: '12p loss' versus Molecular Subtype #3: '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 S243.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.043

Table S244.  Gene #62: '12p loss' versus Molecular Subtype #6: '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 S244.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00684 (Fisher's exact test), Q value = 0.021

Table S245.  Gene #62: '12p loss' versus Molecular Subtype #7: '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 S245.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.011

Table S246.  Gene #62: '12p loss' versus Molecular Subtype #8: '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 S246.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00027

Table S247.  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 S247.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.095

Table S248.  Gene #63: '12q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12Q LOSS MUTATED 3 4 6 5 0
12Q LOSS WILD-TYPE 144 94 53 123 56

Figure S248.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 0.027

Table S249.  Gene #63: '12q loss' versus Molecular Subtype #8: '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 S249.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S250.  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 S250.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.084

Table S251.  Gene #64: '13q loss' versus Molecular Subtype #3: '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 S251.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.082

Table S252.  Gene #64: '13q loss' versus Molecular Subtype #6: '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 S252.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0011

Table S253.  Gene #64: '13q loss' versus Molecular Subtype #8: '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 S253.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S254.  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 S254.  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 = 0.00012

Table S255.  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 S255.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0074

Table S256.  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 S256.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0037

Table S257.  Gene #66: '15q loss' versus Molecular Subtype #3: '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 S257.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00648 (Fisher's exact test), Q value = 0.021

Table S258.  Gene #66: '15q loss' versus Molecular Subtype #4: '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 S258.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00074

Table S259.  Gene #66: '15q loss' versus Molecular Subtype #5: '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 S259.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.023

Table S260.  Gene #66: '15q loss' versus Molecular Subtype #6: '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 S260.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0057

Table S261.  Gene #66: '15q loss' versus Molecular Subtype #7: '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 S261.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00095

Table S262.  Gene #66: '15q loss' versus Molecular Subtype #8: '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 S262.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0076

Table S263.  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 S263.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.07

Table S264.  Gene #67: '16p loss' versus Molecular Subtype #8: '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 S264.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S265.  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 S265.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0037

Table S266.  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 S266.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.069

Table S267.  Gene #68: '16q loss' versus Molecular Subtype #3: '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 S267.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.069

Table S268.  Gene #68: '16q loss' versus Molecular Subtype #4: '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 S268.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0031

Table S269.  Gene #68: '16q loss' versus Molecular Subtype #6: '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 S269.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00422 (Fisher's exact test), Q value = 0.015

Table S270.  Gene #68: '16q loss' versus Molecular Subtype #7: '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 S270.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00062

Table S271.  Gene #68: '16q loss' versus Molecular Subtype #8: '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 S271.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S272.  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 S272.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0072

Table S273.  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 S273.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00098

Table S274.  Gene #69: '17p loss' versus Molecular Subtype #3: '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 S274.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0075

Table S275.  Gene #69: '17p loss' versus Molecular Subtype #4: '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 S275.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.07

Table S276.  Gene #69: '17p loss' versus Molecular Subtype #6: '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 S276.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.054

Table S277.  Gene #69: '17p loss' versus Molecular Subtype #7: '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 S277.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00062

Table S278.  Gene #69: '17p loss' versus Molecular Subtype #8: '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 S278.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S279.  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 S279.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.03

Table S280.  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 S280.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0048

Table S281.  Gene #70: '17q loss' versus Molecular Subtype #3: '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 S281.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.076

Table S282.  Gene #70: '17q loss' versus Molecular Subtype #4: '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 S282.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.035

Table S283.  Gene #70: '17q loss' versus Molecular Subtype #5: '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 S283.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.09

Table S284.  Gene #70: '17q loss' versus Molecular Subtype #6: '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 S284.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.069

Table S285.  Gene #70: '17q loss' versus Molecular Subtype #7: '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 S285.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S286.  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 S286.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.017

Table S287.  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 S287.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.013

Table S288.  Gene #71: '18p loss' versus Molecular Subtype #3: '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 S288.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.095

Table S289.  Gene #71: '18p loss' versus Molecular Subtype #4: '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 S289.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.068

Table S290.  Gene #71: '18p loss' versus Molecular Subtype #6: '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 S290.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.03

Table S291.  Gene #71: '18p loss' versus Molecular Subtype #7: '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 S291.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00567 (Fisher's exact test), Q value = 0.018

Table S292.  Gene #71: '18p loss' versus Molecular Subtype #8: '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 S292.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S293.  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 S293.  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 = 0.02

Table S294.  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 S294.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.013

Table S295.  Gene #72: '18q loss' versus Molecular Subtype #3: '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 S295.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.054

Table S296.  Gene #72: '18q loss' versus Molecular Subtype #4: '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 S296.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.021

Table S297.  Gene #72: '18q loss' versus Molecular Subtype #5: '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 S297.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0034 (Fisher's exact test), Q value = 0.013

Table S298.  Gene #72: '18q loss' versus Molecular Subtype #6: '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 S298.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.04

Table S299.  Gene #72: '18q loss' versus Molecular Subtype #7: '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 S299.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S300.  Gene #72: '18q loss' versus Molecular Subtype #8: '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 S300.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0014

Table S301.  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 S301.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.012

Table S302.  Gene #73: '19p loss' versus Molecular Subtype #7: '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 S302.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.031

Table S303.  Gene #73: '19p loss' versus Molecular Subtype #8: '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 S303.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0016

Table S304.  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 S304.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.012

Table S305.  Gene #74: '19q loss' versus Molecular Subtype #7: '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 S305.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.031

Table S306.  Gene #74: '19q loss' versus Molecular Subtype #8: '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 S306.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.079

Table S307.  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 S307.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.063

Table S308.  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 S308.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.079

Table S309.  Gene #76: '20q loss' versus Molecular Subtype #4: '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 S309.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S310.  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 S310.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.013

Table S311.  Gene #77: '21q loss' versus Molecular Subtype #3: '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 S311.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.082

Table S312.  Gene #77: '21q loss' versus Molecular Subtype #8: '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 S312.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S313.  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 S313.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.048

Table S314.  Gene #78: '22q loss' versus Molecular Subtype #3: '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 S314.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.093

Table S315.  Gene #78: '22q loss' versus Molecular Subtype #4: '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 S315.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.064

Table S316.  Gene #78: '22q loss' versus Molecular Subtype #6: '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 S316.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0016

Table S317.  Gene #78: '22q loss' versus Molecular Subtype #8: '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 S317.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S318.  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 S318.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S319.  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 S319.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0028

Table S320.  Gene #79: 'xp loss' versus Molecular Subtype #3: '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 S320.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S321.  Gene #79: 'xp loss' versus Molecular Subtype #4: '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 S321.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S322.  Gene #79: 'xp loss' versus Molecular Subtype #5: '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 S322.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.076

Table S323.  Gene #79: 'xp loss' versus Molecular Subtype #6: '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 S323.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00556 (Fisher's exact test), Q value = 0.018

Table S324.  Gene #79: 'xp loss' versus Molecular Subtype #7: '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 S324.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S325.  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 S325.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S326.  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 S326.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0025

Table S327.  Gene #80: 'xq loss' versus Molecular Subtype #3: '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 S327.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00051

Table S328.  Gene #80: 'xq loss' versus Molecular Subtype #4: '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 S328.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S329.  Gene #80: 'xq loss' versus Molecular Subtype #5: '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 S329.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.076

Table S330.  Gene #80: 'xq loss' versus Molecular Subtype #6: '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 S330.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.018

Table S331.  Gene #80: 'xq loss' versus Molecular Subtype #7: '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 S331.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: '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/15098599/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/15115159/PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 8

  • 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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