Correlation between copy number variations of arm-level result and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1PG1QQK
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/C1PG1QQK
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 82 arm-level events and 12 molecular subtypes across 615 patients, 335 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 4q gain cnv correlated to 'CN_CNMF'.

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

  • 5q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 7q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 8q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

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

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

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 18q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 19q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

  • xp gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 2q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

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

  • 12q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 16q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

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

  • 17q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'RPPA_CNMF'.

  • 21q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 335 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 465 (76%) 150 1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.00325
(0.0182) 		0.00533
(0.0272) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.0158
(0.0617) 		0.0005
(0.00378) 		0.00054
(0.00406) 		0.019
(0.0706)
18p loss 379 (62%) 236 1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.0307
(0.102) 		0.0486
(0.144) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.00734
(0.0344) 		0.00902
(0.0398) 		0.00011
(0.00109) 		0.00105
(0.00705)
18q loss 409 (67%) 206 1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.0427
(0.131) 		0.097
(0.244) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.00102
(0.00692) 		0.00605
(0.0301) 		0.0001
(0.001) 		0.0004
(0.00323)
7p gain 349 (57%) 266 0.0005
(0.00378) 		1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.0085
(0.0385) 		0.00786
(0.0361) 		2e-05
(0.000249) 		1e-05
(0.000139) 		0.00583
(0.0293) 		0.179
(0.372) 		0.0279
(0.094) 		0.089
(0.229)
17p loss 341 (55%) 274 2e-05
(0.000249) 		5e-05
(0.000566) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.12
(0.28) 		0.00799
(0.0366) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.0356
(0.113) 		0.0236
(0.0824) 		0.0286
(0.0957) 		0.383
(0.614)
14q loss 207 (34%) 408 0.00026
(0.0023) 		7e-05
(0.000749) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.00277
(0.0158) 		0.182
(0.377) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.135
(0.305) 		0.119
(0.277) 		0.0365
(0.115) 		0.0444
(0.134)
2p gain 123 (20%) 492 0.0212
(0.0765) 		0.00483
(0.025) 		0.00163
(0.0102) 		0.00116
(0.00756) 		0.62
(0.818) 		0.566
(0.775) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.0324
(0.106) 		0.00134
(0.00856) 		0.988
(1.00) 		0.969
(1.00)
3q gain 98 (16%) 517 0.0337
(0.108) 		0.00199
(0.0121) 		1e-05
(0.000139) 		0.0327
(0.106) 		0.126
(0.29) 		0.0201
(0.0737) 		0.0928
(0.236) 		0.0039
(0.0208) 		0.0443
(0.134) 		0.548
(0.76) 		0.0206
(0.0752) 		0.0506
(0.148)
7q gain 311 (51%) 304 0.00021
(0.00193) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.00049
(0.00377) 		0.119
(0.277) 		0.0264
(0.0898) 		0.0001
(0.001) 		1e-05
(0.000139) 		0.0106
(0.0453) 		0.196
(0.398) 		0.0773
(0.205) 		0.436
(0.665)
13q gain 368 (60%) 247 1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.24
(0.451) 		0.381
(0.613) 		1e-05
(0.000139) 		1e-05
(0.000139) 		0.00039
(0.0032) 		0.437
(0.665) 		0.0144
(0.0574) 		0.0709
(0.194)
17q gain 110 (18%) 505 0.0191
(0.0706) 		0.007
(0.0333) 		1e-05
(0.000139) 		0.00275
(0.0157) 		0.243
(0.455) 		0.841
(0.943) 		2e-05
(0.000249) 		2e-05
(0.000249) 		0.0046
(0.0242) 		0.0424
(0.13) 		0.864
(0.958) 		0.28
(0.499)
8p loss 218 (35%) 397 0.00889
(0.0396) 		0.00581
(0.0293) 		1e-05
(0.000139) 		0.00056
(0.00411) 		0.442
(0.666) 		0.0261
(0.0896) 		0.0064
(0.0309) 		1e-05
(0.000139) 		0.663
(0.849) 		0.24
(0.451) 		0.00247
(0.0146) 		0.471
(0.692)
2q gain 121 (20%) 494 0.0126
(0.0519) 		0.00144
(0.00908) 		6e-05
(0.000656) 		0.00036
(0.00298) 		0.649
(0.841) 		0.856
(0.954) 		0.00029
(0.00253) 		1e-05
(0.000139) 		0.0932
(0.236) 		0.0083
(0.0378) 		0.938
(1.00) 		0.817
(0.936)
18q gain 19 (3%) 596 0.0357
(0.113) 		0.703
(0.868) 		0.0122
(0.0506) 		0.0086
(0.0386) 		0.396
(0.628) 		0.00713
(0.0336) 		0.00297
(0.0168) 		9e-05
(0.000922) 		0.0928
(0.236) 		0.0154
(0.0608) 		0.672
(0.853) 		0.83
(0.94)
20p gain 352 (57%) 263 0.00024
(0.00219) 		3e-05
(0.000351) 		1e-05
(0.000139) 		0.00034
(0.00286) 		0.0218
(0.078) 		0.0856
(0.222) 		0.00601
(0.03) 		1e-05
(0.000139) 		0.37
(0.604) 		0.108
(0.264) 		0.667
(0.85) 		0.103
(0.255)
9q loss 78 (13%) 537 0.0486
(0.144) 		0.0132
(0.0542) 		0.00043
(0.00338) 		0.00026
(0.0023) 		0.902
(0.985) 		0.208
(0.416) 		0.00012
(0.00118) 		0.00106
(0.00705) 		0.439
(0.666) 		0.0109
(0.0465) 		0.798
(0.925) 		0.327
(0.555)
10q loss 112 (18%) 503 0.023
(0.0809) 		0.251
(0.465) 		1e-05
(0.000139) 		0.0064
(0.0309) 		0.0184
(0.0693) 		0.46
(0.68) 		0.0025
(0.0146) 		2e-05
(0.000249) 		0.555
(0.768) 		0.445
(0.667) 		0.0466
(0.141) 		0.266
(0.483)
6p gain 124 (20%) 491 0.0148
(0.0589) 		0.00048
(0.00375) 		1e-05
(0.000139) 		0.183
(0.378) 		0.853
(0.952) 		0.967
(1.00) 		0.382
(0.613) 		0.0353
(0.113) 		0.459
(0.68) 		0.71
(0.872) 		0.0251
(0.087) 		0.0336
(0.108)
11p gain 85 (14%) 530 0.0121
(0.0505) 		0.0053
(0.0272) 		1e-05
(0.000139) 		5e-05
(0.000566) 		0.655
(0.843) 		0.633
(0.827) 		0.00478
(0.0249) 		0.00034
(0.00286) 		0.333
(0.561) 		0.406
(0.639) 		0.786
(0.919) 		0.972
(1.00)
11q gain 77 (13%) 538 0.017
(0.0656) 		0.00097
(0.00667) 		1e-05
(0.000139) 		6e-05
(0.000656) 		0.195
(0.397) 		0.374
(0.607) 		3e-05
(0.000351) 		3e-05
(0.000351) 		0.3
(0.524) 		0.0605
(0.17) 		0.299
(0.523) 		0.179
(0.372)
16p gain 147 (24%) 468 0.00608
(0.0301) 		0.00392
(0.0208) 		1e-05
(0.000139) 		0.0117
(0.0491) 		0.143
(0.314) 		0.667
(0.85) 		0.00055
(0.00407) 		2e-05
(0.000249) 		0.491
(0.71) 		0.442
(0.666) 		0.224
(0.436) 		0.183
(0.378)
16q gain 145 (24%) 470 0.00861
(0.0386) 		0.00381
(0.0206) 		1e-05
(0.000139) 		0.00991
(0.0428) 		0.231
(0.443) 		0.475
(0.694) 		0.00106
(0.00705) 		4e-05
(0.000463) 		0.786
(0.919) 		0.479
(0.699) 		0.107
(0.263) 		0.123
(0.285)
4p loss 198 (32%) 417 0.0223
(0.0791) 		0.00767
(0.0356) 		1e-05
(0.000139) 		0.00115
(0.00754) 		0.474
(0.694) 		0.296
(0.523) 		0.00067
(0.00478) 		9e-05
(0.000922) 		0.0811
(0.212) 		0.442
(0.666) 		0.199
(0.403) 		0.918
(0.992)
4q loss 191 (31%) 424 0.0421
(0.13) 		0.0743
(0.202) 		1e-05
(0.000139) 		0.00014
(0.00135) 		0.757
(0.904) 		0.591
(0.794) 		0.00354
(0.0195) 		8e-05
(0.000837) 		0.105
(0.26) 		0.136
(0.305) 		0.0395
(0.123) 		0.502
(0.721)
10p loss 102 (17%) 513 0.0113
(0.0477) 		0.185
(0.381) 		1e-05
(0.000139) 		0.0248
(0.0864) 		0.0175
(0.0667) 		0.409
(0.639) 		0.0112
(0.0475) 		0.00034
(0.00286) 		0.21
(0.417) 		0.361
(0.595) 		0.057
(0.164) 		0.247
(0.46)
15q loss 229 (37%) 386 0.00013
(0.00127) 		0.00165
(0.0102) 		1e-05
(0.000139) 		0.00069
(0.00485) 		0.239
(0.451) 		0.778
(0.918) 		2e-05
(0.000249) 		1e-05
(0.000139) 		0.819
(0.937) 		0.682
(0.856) 		0.0808
(0.211) 		0.209
(0.417)
21q loss 194 (32%) 421 0.0171
(0.0656) 		0.022
(0.0782) 		1e-05
(0.000139) 		0.0137
(0.0553) 		0.703
(0.868) 		0.537
(0.749) 		2e-05
(0.000249) 		0.00367
(0.0201) 		0.137
(0.307) 		0.146
(0.32) 		0.806
(0.93) 		0.185
(0.381)
8q gain 315 (51%) 300 0.329
(0.556) 		0.108
(0.264) 		1e-05
(0.000139) 		0.0628
(0.176) 		0.0596
(0.168) 		0.0774
(0.205) 		0.00224
(0.0134) 		0.021
(0.0762) 		0.291
(0.516) 		0.00966
(0.0419) 		0.109
(0.264) 		0.044
(0.134)
19q gain 114 (19%) 501 0.0498
(0.147) 		0.00377
(0.0205) 		0.00021
(0.00193) 		0.116
(0.274) 		0.031
(0.102) 		0.494
(0.712) 		0.402
(0.634) 		0.00099
(0.00676) 		0.218
(0.428) 		1
(1.00) 		0.166
(0.351) 		0.0855
(0.222)
1p loss 138 (22%) 477 0.0752
(0.202) 		0.0263
(0.0898) 		1e-05
(0.000139) 		0.00134
(0.00856) 		0.951
(1.00) 		0.894
(0.978) 		0.00146
(0.00915) 		0.00016
(0.00151) 		0.347
(0.576) 		0.0673
(0.187) 		0.765
(0.909) 		0.317
(0.541)
5q loss 121 (20%) 494 0.00903
(0.0398) 		0.0284
(0.0955) 		1e-05
(0.000139) 		0.11
(0.264) 		0.144
(0.316) 		0.101
(0.251) 		0.0311
(0.102) 		0.00083
(0.00575) 		0.537
(0.749) 		0.663
(0.849) 		0.69
(0.861) 		0.675
(0.855)
19p loss 64 (10%) 551 0.375
(0.607) 		0.475
(0.694) 		0.00042
(0.00333) 		0.459
(0.68) 		0.694
(0.865) 		0.249
(0.462) 		0.0497
(0.147) 		0.0439
(0.134) 		0.156
(0.336) 		0.00623
(0.0305) 		0.292
(0.516) 		0.00955
(0.0418)
20p loss 68 (11%) 547 0.112
(0.267) 		0.0189
(0.0704) 		3e-05
(0.000351) 		0.00222
(0.0133) 		0.831
(0.94) 		0.949
(1.00) 		0.142
(0.314) 		0.00021
(0.00193) 		0.836
(0.94) 		0.387
(0.618) 		0.0745
(0.202) 		0.00231
(0.0137)
22q loss 203 (33%) 412 0.00513
(0.0264) 		0.00034
(0.00286) 		1e-05
(0.000139) 		0.118
(0.277) 		0.777
(0.918) 		0.798
(0.925) 		0.0178
(0.0676) 		1e-05
(0.000139) 		0.977
(1.00) 		0.0693
(0.191) 		0.46
(0.68) 		0.418
(0.646)
3p gain 72 (12%) 543 0.0136
(0.0553) 		0.0778
(0.205) 		1e-05
(0.000139) 		0.219
(0.43) 		0.121
(0.283) 		0.0233
(0.0817) 		0.906
(0.988) 		0.03
(0.0998) 		0.107
(0.262) 		0.437
(0.665) 		0.0997
(0.249) 		0.272
(0.489)
6q gain 111 (18%) 504 0.159
(0.343) 		0.00109
(0.0072) 		1e-05
(0.000139) 		0.193
(0.394) 		0.827
(0.94) 		0.741
(0.89) 		0.435
(0.665) 		0.138
(0.307) 		0.357
(0.589) 		0.892
(0.977) 		0.00922
(0.0405) 		0.0478
(0.143)
18p gain 33 (5%) 582 0.309
(0.534) 		0.37
(0.604) 		0.00168
(0.0103) 		0.00062
(0.00449) 		0.605
(0.805) 		0.0583
(0.167) 		0.0271
(0.092) 		0.00061
(0.00445) 		0.396
(0.628) 		0.0785
(0.207) 		0.76
(0.906) 		0.977
(1.00)
19p gain 104 (17%) 511 0.328
(0.556) 		0.0194
(0.0713) 		1e-05
(0.000139) 		0.08
(0.21) 		0.159
(0.342) 		0.772
(0.914) 		0.256
(0.471) 		6e-05
(0.000656) 		0.0422
(0.13) 		0.729
(0.885) 		0.515
(0.732) 		0.0884
(0.228)
1q loss 79 (13%) 536 0.311
(0.535) 		0.299
(0.523) 		0.00015
(0.00143) 		0.415
(0.644) 		0.868
(0.961) 		0.817
(0.936) 		8e-05
(0.000837) 		0.00067
(0.00478) 		0.718
(0.878) 		0.00674
(0.0324) 		0.165
(0.35) 		0.155
(0.336)
9p loss 77 (13%) 538 0.489
(0.709) 		0.202
(0.406) 		0.00083
(0.00575) 		0.00207
(0.0125) 		0.843
(0.943) 		0.471
(0.692) 		0.00029
(0.00253) 		0.0173
(0.0664) 		0.211
(0.418) 		0.112
(0.267) 		0.676
(0.855) 		0.717
(0.877)
13q loss 20 (3%) 595 0.298
(0.523) 		0.0157
(0.0617) 		0.0139
(0.0563) 		0.679
(0.855) 		0.296
(0.523) 		0.00683
(0.0326) 		0.701
(0.868) 		0.141
(0.312) 		0.733
(0.888) 		0.787
(0.919) 		0.0142
(0.0569) 		0.409
(0.639)
1p gain 50 (8%) 565 0.204
(0.409) 		0.454
(0.678) 		0.0405
(0.126) 		0.644
(0.837) 		0.0185
(0.0693) 		0.0185
(0.0693) 		0.978
(1.00) 		0.627
(0.824) 		0.389
(0.62) 		0.315
(0.539) 		0.194
(0.395) 		0.589
(0.793)
5p gain 105 (17%) 510 0.498
(0.716) 		0.129
(0.295) 		0.0004
(0.00323) 		0.912
(0.989) 		0.165
(0.35) 		0.13
(0.297) 		0.0133
(0.0544) 		0.0328
(0.106) 		0.752
(0.901) 		0.392
(0.624) 		0.454
(0.678) 		0.557
(0.769)
5q gain 66 (11%) 549 0.782
(0.919) 		0.596
(0.797) 		0.00069
(0.00485) 		0.597
(0.798) 		0.737
(0.888) 		0.714
(0.876) 		0.126
(0.29) 		0.0131
(0.0541) 		0.651
(0.842) 		0.00311
(0.0175) 		0.997
(1.00) 		1
(1.00)
8p gain 170 (28%) 445 0.924
(0.994) 		0.531
(0.746) 		1e-05
(0.000139) 		0.862
(0.957) 		0.232
(0.444) 		0.43
(0.66) 		0.00332
(0.0185) 		0.0478
(0.143) 		0.199
(0.403) 		0.267
(0.483) 		0.398
(0.63) 		0.122
(0.283)
12p gain 127 (21%) 488 0.355
(0.587) 		0.364
(0.597) 		0.00469
(0.0245) 		0.00269
(0.0156) 		0.459
(0.68) 		0.239
(0.451) 		0.641
(0.834) 		0.0166
(0.0644) 		0.414
(0.643) 		0.786
(0.919) 		0.564
(0.773) 		0.485
(0.707)
12q gain 111 (18%) 504 0.252
(0.465) 		0.35
(0.581) 		0.00272
(0.0157) 		0.00137
(0.0087) 		0.423
(0.651) 		0.255
(0.469) 		0.424
(0.651) 		0.00629
(0.0306) 		0.236
(0.449) 		0.444
(0.667) 		0.652
(0.842) 		0.639
(0.834)
xp gain 99 (16%) 516 0.037
(0.116) 		0.109
(0.264) 		7e-05
(0.000749) 		0.0499
(0.147) 		0.318
(0.541) 		0.0995
(0.249) 		0.307
(0.532) 		0.279
(0.499) 		0.23
(0.442) 		0.933
(0.998) 		0.862
(0.957) 		0.559
(0.769)
2p loss 17 (3%) 598 1
(1.00) 		0.616
(0.817) 		0.00049
(0.00377) 		0.0313
(0.103) 		0.347
(0.576) 		0.806
(0.93) 		0.0589
(0.168) 		0.00773
(0.0357) 		0.0961
(0.242) 		0.229
(0.442)
2q loss 14 (2%) 601 0.677
(0.855) 		0.245
(0.458) 		0.0154
(0.0608) 		0.186
(0.381) 		0.255
(0.469) 		0.373
(0.607) 		0.112
(0.267) 		0.00557
(0.0283) 		0.0913
(0.233) 		0.0216
(0.0777)
12p loss 71 (12%) 544 0.0667
(0.185) 		0.0143
(0.0572) 		1e-05
(0.000139) 		0.0904
(0.232) 		0.874
(0.965) 		0.579
(0.786) 		0.0949
(0.24) 		0.00042
(0.00333) 		0.82
(0.937) 		0.82
(0.937) 		0.28
(0.5) 		0.261
(0.477)
12q loss 71 (12%) 544 0.125
(0.288) 		0.0258
(0.0892) 		1e-05
(0.000139) 		0.14
(0.31) 		0.618
(0.817) 		0.836
(0.94) 		0.0656
(0.183) 		3e-05
(0.000351) 		0.223
(0.435) 		0.872
(0.964) 		0.418
(0.646) 		0.411
(0.64)
17q loss 96 (16%) 519 0.892
(0.977) 		0.6
(0.8) 		0.00131
(0.00848) 		0.512
(0.731) 		0.836
(0.94) 		0.0183
(0.0693) 		0.83
(0.94) 		0.029
(0.0969) 		0.732
(0.888) 		0.517
(0.733) 		0.715
(0.876) 		0.961
(1.00)
xq loss 80 (13%) 535 0.956
(1.00) 		0.771
(0.914) 		0.132
(0.299) 		0.0327
(0.106) 		0.0665
(0.185) 		0.491
(0.71) 		0.442
(0.666) 		0.377
(0.609) 		0.0487
(0.144) 		0.829
(0.94) 		0.457
(0.68) 		0.00766
(0.0356)
1q gain 117 (19%) 498 0.738
(0.888) 		0.806
(0.93) 		0.0104
(0.0448) 		0.3
(0.524) 		0.161
(0.346) 		0.0203
(0.0743) 		0.913
(0.989) 		0.339
(0.569) 		0.172
(0.362) 		0.138
(0.307) 		0.56
(0.77) 		0.409
(0.639)
4p gain 20 (3%) 595 0.815
(0.936) 		0.569
(0.778) 		0.00706
(0.0334) 		0.216
(0.426) 		0.154
(0.334) 		0.174
(0.364) 		0.0111
(0.0472) 		0.162
(0.346) 		0.579
(0.786) 		0.508
(0.727) 		0.675
(0.855) 		0.132
(0.299)
10p gain 49 (8%) 566 0.111
(0.267) 		0.111
(0.266) 		0.00388
(0.0208) 		0.793
(0.923) 		0.106
(0.262) 		0.0483
(0.144) 		0.518
(0.733) 		0.815
(0.936) 		0.509
(0.728) 		0.301
(0.524) 		0.542
(0.754) 		0.466
(0.687)
5p loss 86 (14%) 529 0.377
(0.609) 		0.696
(0.866) 		0.00036
(0.00298) 		0.0719
(0.196) 		0.746
(0.894) 		0.641
(0.834) 		0.736
(0.888) 		0.00339
(0.0187) 		0.956
(1.00) 		0.264
(0.481) 		0.454
(0.678) 		0.943
(1.00)
6p loss 46 (7%) 569 0.556
(0.769) 		0.0219
(0.078) 		0.521
(0.736) 		0.67
(0.852) 		0.0685
(0.189) 		0.076
(0.203) 		0.593
(0.796) 		0.0333
(0.107) 		0.458
(0.68) 		0.938
(1.00) 		0.532
(0.746) 		0.771
(0.914)
8q loss 37 (6%) 578 0.91
(0.989) 		0.781
(0.919) 		0.00429
(0.0227) 		0.681
(0.855) 		0.956
(1.00) 		0.227
(0.44) 		0.58
(0.786) 		0.646
(0.838) 		0.27
(0.488) 		0.584
(0.789) 		0.0514
(0.15) 		0.039
(0.122)
16q loss 44 (7%) 571 0.0261
(0.0896) 		0.586
(0.79) 		0.00864
(0.0386) 		0.737
(0.888) 		0.24
(0.451) 		0.239
(0.451) 		0.784
(0.919) 		0.564
(0.773) 		0.576
(0.785) 		0.553
(0.767) 		0.275
(0.494) 		0.869
(0.961)
xp loss 91 (15%) 524 0.925
(0.994) 		0.367
(0.6) 		0.0762
(0.203) 		0.411
(0.64) 		0.00623
(0.0305) 		0.137
(0.307) 		0.889
(0.976) 		0.952
(1.00) 		0.0992
(0.249) 		0.559
(0.769) 		0.504
(0.723) 		0.0337
(0.108)
4q gain 21 (3%) 594 0.228
(0.442) 		0.213
(0.421) 		0.0229
(0.0809) 		0.678
(0.855) 		0.115
(0.272) 		0.515
(0.732) 		0.0584
(0.167) 		0.221
(0.434) 		0.331
(0.557) 		0.364
(0.597) 		0.879
(0.968) 		1
(1.00)
9p gain 123 (20%) 492 0.538
(0.75) 		0.586
(0.79) 		0.00251
(0.0146) 		0.811
(0.933) 		0.128
(0.293) 		0.261
(0.477) 		0.92
(0.992) 		0.382
(0.613) 		0.978
(1.00) 		0.923
(0.994) 		0.63
(0.825) 		0.788
(0.919)
14q gain 43 (7%) 572 0.736
(0.888) 		0.4
(0.631) 		0.0164
(0.0639) 		0.798
(0.925) 		0.789
(0.919) 		0.828
(0.94) 		0.596
(0.797) 		0.606
(0.805) 		0.881
(0.968) 		0.89
(0.977) 		0.782
(0.919) 		0.344
(0.574)
21q gain 34 (6%) 581 0.313
(0.536) 		0.264
(0.481) 		0.00055
(0.00407) 		0.488
(0.709) 		0.486
(0.708) 		0.255
(0.469) 		0.679
(0.855) 		0.107
(0.263) 		0.407
(0.639) 		0.968
(1.00) 		0.461
(0.681) 		0.742
(0.89)
22q gain 23 (4%) 592 0.117
(0.277) 		0.136
(0.305) 		0.00963
(0.0419) 		0.311
(0.535) 		0.861
(0.957) 		0.692
(0.863) 		0.11
(0.264) 		0.28
(0.499) 		0.688
(0.861) 		0.918
(0.992) 		0.842
(0.943) 		1
(1.00)
xq gain 107 (17%) 508 0.141
(0.312) 		0.265
(0.481) 		0.00025
(0.00226) 		0.308
(0.533) 		0.0868
(0.225) 		0.056
(0.161) 		0.687
(0.86) 		0.375
(0.607) 		0.339
(0.569) 		0.925
(0.994) 		0.698
(0.868) 		0.878
(0.967)
11p loss 75 (12%) 540 0.955
(1.00) 		1
(1.00) 		0.0215
(0.0776) 		0.188
(0.385) 		0.498
(0.716) 		0.606
(0.805) 		0.531
(0.746) 		0.125
(0.288) 		0.913
(0.989) 		0.233
(0.446) 		0.658
(0.846) 		0.853
(0.952)
11q loss 93 (15%) 522 0.846
(0.945) 		0.685
(0.859) 		0.0275
(0.0929) 		0.0533
(0.155) 		0.957
(1.00) 		0.702
(0.868) 		0.811
(0.933) 		0.171
(0.36) 		0.805
(0.93) 		0.416
(0.645) 		0.278
(0.498) 		0.286
(0.509)
19q loss 55 (9%) 560 0.665
(0.85) 		0.147
(0.321) 		0.00179
(0.0109) 		0.708
(0.872) 		0.119
(0.277) 		0.434
(0.663) 		0.111
(0.267) 		0.0913
(0.233) 		0.226
(0.439) 		0.0756
(0.203) 		0.721
(0.88) 		0.0524
(0.153)
20q loss 6 (1%) 609 0.581
(0.787) 		0.825
(0.94) 		0.0413
(0.128) 		1
(1.00) 		0.207
(0.415) 		0.646
(0.838) 		0.408
(0.639) 		0.532
(0.746)
9q gain 101 (16%) 514 0.657
(0.845) 		0.833
(0.94) 		0.0545
(0.158) 		0.97
(1.00) 		0.0707
(0.194) 		0.212
(0.419) 		0.948
(1.00) 		0.762
(0.908) 		0.625
(0.824) 		0.306
(0.532) 		0.933
(0.998) 		0.833
(0.94)
10q gain 29 (5%) 586 0.912
(0.989) 		0.258
(0.473) 		0.0584
(0.167) 		0.0718
(0.196) 		0.169
(0.358) 		0.709
(0.872) 		0.42
(0.647) 		0.6
(0.8) 		0.519
(0.734) 		0.659
(0.846) 		0.179
(0.372) 		0.955
(1.00)
15q gain 15 (2%) 600 0.298
(0.523) 		0.152
(0.331) 		0.0608
(0.171) 		0.545
(0.757) 		0.174
(0.364) 		0.209
(0.417) 		0.927
(0.995) 		0.929
(0.996) 		1
(1.00) 		0.728
(0.885)
17p gain 38 (6%) 577 0.442
(0.666) 		0.162
(0.346) 		0.756
(0.904) 		0.966
(1.00) 		0.2
(0.403) 		1
(1.00) 		0.193
(0.394) 		0.0778
(0.205) 		0.169
(0.357) 		0.72
(0.879) 		0.0747
(0.202) 		0.939
(1.00)
3p loss 70 (11%) 545 0.361
(0.594) 		0.837
(0.94) 		0.489
(0.709) 		0.668
(0.85) 		0.535
(0.749) 		0.628
(0.824) 		0.433
(0.663) 		0.765
(0.909) 		0.773
(0.915) 		0.398
(0.63) 		0.384
(0.615) 		0.353
(0.585)
3q loss 45 (7%) 570 0.248
(0.462) 		0.246
(0.46) 		0.904
(0.987) 		0.617
(0.817) 		0.321
(0.545) 		0.957
(1.00) 		0.705
(0.869) 		0.232
(0.444) 		0.576
(0.785) 		0.341
(0.571) 		0.654
(0.843) 		0.786
(0.919)
6q loss 69 (11%) 546 0.442
(0.666) 		0.312
(0.536) 		0.317
(0.541) 		0.58
(0.786) 		0.229
(0.442) 		0.155
(0.335) 		0.101
(0.25) 		0.0595
(0.168) 		0.514
(0.732) 		0.514
(0.732) 		0.135
(0.305) 		0.531
(0.746)
7p loss 3 (0%) 612 0.618
(0.817) 		0.629
(0.825) 		0.153
(0.333)
7q loss 5 (1%) 610 0.627
(0.824) 		1
(1.00) 		1
(1.00) 		0.739
(0.888) 		0.875
(0.965) 		0.701
(0.868) 		1
(1.00) 		0.222
(0.434)
16p loss 41 (7%) 574 0.0751
(0.202) 		0.372
(0.605) 		0.33
(0.557) 		0.912
(0.989) 		0.344
(0.574) 		0.24
(0.451) 		0.729
(0.885) 		0.291
(0.516) 		0.834
(0.94) 		0.236
(0.449) 		0.307
(0.532) 		0.953
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1P GAIN MUTATED 13 24 13
1P GAIN WILD-TYPE 240 185 140

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.069

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
1P GAIN MUTATED 7 18 6 4
1P GAIN WILD-TYPE 90 160 33 133

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
1P GAIN MUTATED 7 26 2
1P GAIN WILD-TYPE 45 276 95

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

'1q gain' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.045

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1Q GAIN MUTATED 35 52 30
1Q GAIN WILD-TYPE 218 157 123

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.074

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
1Q GAIN MUTATED 13 66 10
1Q GAIN WILD-TYPE 39 236 87

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.077

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
2P GAIN MUTATED 3 11 16 2
2P GAIN WILD-TYPE 40 51 53 39

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.025

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
2P GAIN MUTATED 2 10 8 12
2P GAIN WILD-TYPE 47 31 68 37

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.01

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2P GAIN MUTATED 34 55 34
2P GAIN WILD-TYPE 219 154 119

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0076

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
2P GAIN MUTATED 19 52 18
2P GAIN WILD-TYPE 77 112 111

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

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

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
2P GAIN MUTATED 52 15 25 30
2P GAIN WILD-TYPE 96 126 105 163

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2P GAIN MUTATED 25 14 8 12 28 31 4
2P GAIN WILD-TYPE 55 72 56 45 62 107 93

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
2P GAIN MUTATED 52 16 35
2P GAIN WILD-TYPE 159 79 197

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0086

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
2P GAIN MUTATED 42 40 21
2P GAIN WILD-TYPE 186 99 150

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.052

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
2Q GAIN MUTATED 3 13 16 2
2Q GAIN WILD-TYPE 40 49 53 39

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0091

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
2Q GAIN MUTATED 2 12 8 12
2Q GAIN WILD-TYPE 47 29 68 37

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00066

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2Q GAIN MUTATED 30 56 35
2Q GAIN WILD-TYPE 223 153 118

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.003

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
2Q GAIN MUTATED 16 52 17
2Q GAIN WILD-TYPE 80 112 112

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0025

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
2Q GAIN MUTATED 46 16 25 33
2Q GAIN WILD-TYPE 102 125 105 160

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2Q GAIN MUTATED 22 15 5 12 29 32 5
2Q GAIN WILD-TYPE 58 71 59 45 61 106 92

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0083 (Fisher's exact test), Q value = 0.038

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
2Q GAIN MUTATED 41 37 22
2Q GAIN WILD-TYPE 187 102 149

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.055

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
3P GAIN MUTATED 1 10 11 1
3P GAIN WILD-TYPE 42 52 58 40

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
3P GAIN MUTATED 13 44 15
3P GAIN WILD-TYPE 240 165 138

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.082

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
3P GAIN MUTATED 10 37 5
3P GAIN WILD-TYPE 42 265 92

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.1

Table S24.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
3P GAIN MUTATED 7 13 3 6 18 19 6
3P GAIN WILD-TYPE 73 73 61 51 72 119 91

Figure S24.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.11

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
3Q GAIN MUTATED 3 11 15 2
3Q GAIN WILD-TYPE 40 51 54 39

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00199 (Fisher's exact test), Q value = 0.012

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
3Q GAIN MUTATED 2 6 8 15
3Q GAIN WILD-TYPE 47 35 68 34

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
3Q GAIN MUTATED 14 58 26
3Q GAIN WILD-TYPE 239 151 127

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.11

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
3Q GAIN MUTATED 13 38 16
3Q GAIN WILD-TYPE 83 126 113

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.074

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
3Q GAIN MUTATED 14 47 9
3Q GAIN WILD-TYPE 38 255 88

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.021

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
3Q GAIN MUTATED 10 17 4 9 24 26 8
3Q GAIN WILD-TYPE 70 69 60 48 66 112 89

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.13

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
3Q GAIN MUTATED 45 11 32
3Q GAIN WILD-TYPE 166 84 200

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.075

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
3Q GAIN MUTATED 6 3 8 4 8 0
3Q GAIN WILD-TYPE 18 17 20 24 10 17

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.00706 (Fisher's exact test), Q value = 0.033

Table S33.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4P GAIN MUTATED 2 11 7
4P GAIN WILD-TYPE 251 198 146

Figure S33.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.047

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
4P GAIN MUTATED 11 2 1 6
4P GAIN WILD-TYPE 137 139 129 187

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

'4q gain' versus 'CN_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.081

Table S35.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4Q GAIN MUTATED 3 11 7
4Q GAIN WILD-TYPE 250 198 146

Figure S35.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0032

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5P GAIN MUTATED 26 50 29
5P GAIN WILD-TYPE 227 159 124

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

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.054

Table S37.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
5P GAIN MUTATED 30 12 25 38
5P GAIN WILD-TYPE 118 129 105 155

Figure S37.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.11

Table S38.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5P GAIN MUTATED 15 9 8 6 24 30 13
5P GAIN WILD-TYPE 65 77 56 51 66 108 84

Figure S38.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0048

Table S39.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5Q GAIN MUTATED 16 36 14
5Q GAIN WILD-TYPE 237 173 139

Figure S39.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.054

Table S40.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5Q GAIN MUTATED 8 11 1 2 14 21 9
5Q GAIN WILD-TYPE 72 75 63 55 76 117 88

Figure S40.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.017

Table S41.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
5Q GAIN MUTATED 24 5 25
5Q GAIN WILD-TYPE 204 134 146

Figure S41.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.059

Table S42.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
6P GAIN MUTATED 9 11 20 2
6P GAIN WILD-TYPE 34 51 49 39

Figure S42.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0037

Table S43.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
6P GAIN MUTATED 5 10 8 19
6P GAIN WILD-TYPE 44 31 68 30

Figure S43.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

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

Table S44.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
6P GAIN MUTATED 22 66 36
6P GAIN WILD-TYPE 231 143 117

Figure S44.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.11

Table S45.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
6P GAIN MUTATED 15 15 6 16 23 35 14
6P GAIN WILD-TYPE 65 71 58 41 67 103 83

Figure S45.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.087

Table S46.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
6P GAIN MUTATED 6 2 13 4 6 2
6P GAIN WILD-TYPE 18 18 15 24 12 15

Figure S46.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.11

Table S47.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
6P GAIN MUTATED 8 6 7 12
6P GAIN WILD-TYPE 47 9 27 19

Figure S47.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0072

Table S48.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
6Q GAIN MUTATED 5 8 5 16
6Q GAIN WILD-TYPE 44 33 71 33

Figure S48.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

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

Table S49.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
6Q GAIN MUTATED 18 60 33
6Q GAIN WILD-TYPE 235 149 120

Figure S49.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00922 (Fisher's exact test), Q value = 0.041

Table S50.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
6Q GAIN MUTATED 7 1 12 3 6 2
6Q GAIN WILD-TYPE 17 19 16 25 12 15

Figure S50.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.14

Table S51.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
6Q GAIN MUTATED 8 5 6 12
6Q GAIN WILD-TYPE 47 10 28 19

Figure S51.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MRNA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0038

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
7P GAIN MUTATED 14 41 38 13
7P GAIN WILD-TYPE 29 21 31 28

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

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

Table S53.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
7P GAIN MUTATED 12 27 30 37
7P GAIN WILD-TYPE 37 14 46 12

Figure S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

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

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
7P GAIN MUTATED 86 159 104
7P GAIN WILD-TYPE 167 50 49

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

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

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
7P GAIN MUTATED 53 123 62
7P GAIN WILD-TYPE 43 41 67

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.039

Table S56.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
7P GAIN MUTATED 66 99 25 64
7P GAIN WILD-TYPE 31 79 14 73

Figure S56.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00786 (Fisher's exact test), Q value = 0.036

Table S57.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
7P GAIN MUTATED 37 173 44
7P GAIN WILD-TYPE 15 129 53

Figure S57.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S58.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
7P GAIN MUTATED 108 63 76 100
7P GAIN WILD-TYPE 40 78 54 93

Figure S58.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S59.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
7P GAIN MUTATED 50 50 14 41 72 90 30
7P GAIN WILD-TYPE 30 36 50 16 18 48 67

Figure S59.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00583 (Fisher's exact test), Q value = 0.029

Table S60.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
7P GAIN MUTATED 138 53 117
7P GAIN WILD-TYPE 73 42 115

Figure S60.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.094

Table S61.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
7P GAIN MUTATED 16 11 22 20 15 6
7P GAIN WILD-TYPE 8 9 6 8 3 11

Figure S61.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0019

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
7Q GAIN MUTATED 9 36 35 12
7Q GAIN WILD-TYPE 34 26 34 29

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
7Q GAIN MUTATED 9 22 26 35
7Q GAIN WILD-TYPE 40 19 50 14

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

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

Table S64.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
7Q GAIN MUTATED 82 140 89
7Q GAIN WILD-TYPE 171 69 64

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0038

Table S65.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
7Q GAIN MUTATED 47 108 57
7Q GAIN WILD-TYPE 49 56 72

Figure S65.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.09

Table S66.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
7Q GAIN MUTATED 34 148 41
7Q GAIN WILD-TYPE 18 154 56

Figure S66.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S67.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
7Q GAIN MUTATED 97 56 66 90
7Q GAIN WILD-TYPE 51 85 64 103

Figure S67.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S68.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
7Q GAIN MUTATED 46 46 13 36 63 79 26
7Q GAIN WILD-TYPE 34 40 51 21 27 59 71

Figure S68.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.045

Table S69.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
7Q GAIN MUTATED 124 48 103
7Q GAIN WILD-TYPE 87 47 129

Figure S69.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'CN_CNMF'

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

Table S70.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8P GAIN MUTATED 54 48 68
8P GAIN WILD-TYPE 199 161 85

Figure S70.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.018

Table S71.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
8P GAIN MUTATED 53 33 43 39
8P GAIN WILD-TYPE 95 108 87 154

Figure S71.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
8P GAIN MUTATED 25 23 22 16 33 25 24
8P GAIN WILD-TYPE 55 63 42 41 57 113 73

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

'8q gain' versus 'CN_CNMF'

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

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8Q GAIN MUTATED 81 95 139
8Q GAIN WILD-TYPE 172 114 14

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.013

Table S74.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
8Q GAIN MUTATED 88 55 74 95
8Q GAIN WILD-TYPE 60 86 56 98

Figure S74.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.076

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
8Q GAIN MUTATED 46 38 29 30 58 72 39
8Q GAIN WILD-TYPE 34 48 35 27 32 66 58

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00966 (Fisher's exact test), Q value = 0.042

Table S76.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
8Q GAIN MUTATED 112 87 79
8Q GAIN WILD-TYPE 116 52 92

Figure S76.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.13

Table S77.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
8Q GAIN MUTATED 28 10 19 25
8Q GAIN WILD-TYPE 27 5 15 6

Figure S77.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.015

Table S78.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
9P GAIN MUTATED 36 57 30
9P GAIN WILD-TYPE 217 152 123

Figure S78.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.00388 (Fisher's exact test), Q value = 0.021

Table S79.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10P GAIN MUTATED 10 25 14
10P GAIN WILD-TYPE 243 184 139

Figure S79.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.14

Table S80.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
10P GAIN MUTATED 9 20 8
10P GAIN WILD-TYPE 43 282 89

Figure S80.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.05

Table S81.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
11P GAIN MUTATED 2 11 13 1
11P GAIN WILD-TYPE 41 51 56 40

Figure S81.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.027

Table S82.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
11P GAIN MUTATED 1 8 7 11
11P GAIN WILD-TYPE 48 33 69 38

Figure S82.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

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

Table S83.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11P GAIN MUTATED 13 42 30
11P GAIN WILD-TYPE 240 167 123

Figure S83.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00057

Table S84.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
11P GAIN MUTATED 12 39 7
11P GAIN WILD-TYPE 84 125 122

Figure S84.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00478 (Fisher's exact test), Q value = 0.025

Table S85.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
11P GAIN MUTATED 32 10 17 26
11P GAIN WILD-TYPE 116 131 113 167

Figure S85.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0029

Table S86.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
11P GAIN MUTATED 17 9 1 9 17 26 6
11P GAIN WILD-TYPE 63 77 63 48 73 112 91

Figure S86.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.066

Table S87.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
11Q GAIN MUTATED 3 8 15 1
11Q GAIN WILD-TYPE 40 54 54 40

Figure S87.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0067

Table S88.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
11Q GAIN MUTATED 1 7 6 13
11Q GAIN WILD-TYPE 48 34 70 36

Figure S88.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

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

Table S89.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11Q GAIN MUTATED 7 39 31
11Q GAIN WILD-TYPE 246 170 122

Figure S89.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00066

Table S90.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
11Q GAIN MUTATED 9 35 6
11Q GAIN WILD-TYPE 87 129 123

Figure S90.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00035

Table S91.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
11Q GAIN MUTATED 32 5 15 25
11Q GAIN WILD-TYPE 116 136 115 168

Figure S91.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00035

Table S92.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
11Q GAIN MUTATED 17 6 0 7 18 24 5
11Q GAIN WILD-TYPE 63 80 64 50 72 114 92

Figure S92.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.025

Table S93.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12P GAIN MUTATED 63 28 36
12P GAIN WILD-TYPE 190 181 117

Figure S93.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.016

Table S94.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
12P GAIN MUTATED 20 19 35
12P GAIN WILD-TYPE 76 145 94

Figure S94.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.064

Table S95.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12P GAIN MUTATED 13 24 16 7 14 23 30
12P GAIN WILD-TYPE 67 62 48 50 76 115 67

Figure S95.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.016

Table S96.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12Q GAIN MUTATED 58 23 30
12Q GAIN WILD-TYPE 195 186 123

Figure S96.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0087

Table S97.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
12Q GAIN MUTATED 17 15 32
12Q GAIN WILD-TYPE 79 149 97

Figure S97.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00629 (Fisher's exact test), Q value = 0.031

Table S98.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12Q GAIN MUTATED 13 23 13 5 10 20 27
12Q GAIN WILD-TYPE 67 63 51 52 80 118 70

Figure S98.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CNMF'

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

Table S99.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
13Q GAIN MUTATED 16 46 51 14
13Q GAIN WILD-TYPE 27 16 18 27

Figure S99.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S100.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
13Q GAIN MUTATED 12 29 48 38
13Q GAIN WILD-TYPE 37 12 28 11

Figure S100.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

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

Table S101.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
13Q GAIN MUTATED 87 184 97
13Q GAIN WILD-TYPE 166 25 56

Figure S101.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

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

Table S102.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
13Q GAIN MUTATED 52 127 60
13Q GAIN WILD-TYPE 44 37 69

Figure S102.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

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

Table S103.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
13Q GAIN MUTATED 110 61 72 122
13Q GAIN WILD-TYPE 38 80 58 71

Figure S103.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S104.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
13Q GAIN MUTATED 57 48 14 43 66 103 34
13Q GAIN WILD-TYPE 23 38 50 14 24 35 63

Figure S104.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0032

Table S105.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
13Q GAIN MUTATED 149 48 130
13Q GAIN WILD-TYPE 62 47 102

Figure S105.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.057

Table S106.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
13Q GAIN MUTATED 21 9 23 19 14 9
13Q GAIN WILD-TYPE 3 11 5 9 4 8

Figure S106.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.064

Table S107.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
14Q GAIN MUTATED 14 10 19
14Q GAIN WILD-TYPE 239 199 134

Figure S107.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.03

Table S108.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
16P GAIN MUTATED 6 21 24 5
16P GAIN WILD-TYPE 37 41 45 36

Figure S108.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00392 (Fisher's exact test), Q value = 0.021

Table S109.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
16P GAIN MUTATED 5 13 18 20
16P GAIN WILD-TYPE 44 28 58 29

Figure S109.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

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

Table S110.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16P GAIN MUTATED 17 88 42
16P GAIN WILD-TYPE 236 121 111

Figure S110.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.049

Table S111.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
16P GAIN MUTATED 19 50 21
16P GAIN WILD-TYPE 77 114 108

Figure S111.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0041

Table S112.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
16P GAIN MUTATED 47 19 25 55
16P GAIN WILD-TYPE 101 122 105 138

Figure S112.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S113.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
16P GAIN MUTATED 15 19 4 14 30 49 15
16P GAIN WILD-TYPE 65 67 60 43 60 89 82

Figure S113.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 0.00861 (Fisher's exact test), Q value = 0.039

Table S114.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
16Q GAIN MUTATED 5 19 23 5
16Q GAIN WILD-TYPE 38 43 46 36

Figure S114.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.021

Table S115.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
16Q GAIN MUTATED 4 13 17 18
16Q GAIN WILD-TYPE 45 28 59 31

Figure S115.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

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

Table S116.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16Q GAIN MUTATED 16 90 39
16Q GAIN WILD-TYPE 237 119 114

Figure S116.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.043

Table S117.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
16Q GAIN MUTATED 20 51 21
16Q GAIN WILD-TYPE 76 113 108

Figure S117.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.007

Table S118.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
16Q GAIN MUTATED 47 19 26 52
16Q GAIN WILD-TYPE 101 122 104 141

Figure S118.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S119.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
16Q GAIN MUTATED 16 19 4 13 32 46 14
16Q GAIN WILD-TYPE 64 67 60 44 58 92 83

Figure S119.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.071

Table S120.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17Q GAIN MUTATED 3 16 14 3
17Q GAIN WILD-TYPE 40 46 55 38

Figure S120.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.007 (Fisher's exact test), Q value = 0.033

Table S121.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
17Q GAIN MUTATED 3 12 9 12
17Q GAIN WILD-TYPE 46 29 67 37

Figure S121.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

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

Table S122.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17Q GAIN MUTATED 22 47 41
17Q GAIN WILD-TYPE 231 162 112

Figure S122.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.016

Table S123.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
17Q GAIN MUTATED 12 45 18
17Q GAIN WILD-TYPE 84 119 111

Figure S123.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S124.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
17Q GAIN MUTATED 47 14 15 34
17Q GAIN WILD-TYPE 101 127 115 159

Figure S124.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S125.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
17Q GAIN MUTATED 25 16 3 7 19 33 7
17Q GAIN WILD-TYPE 55 70 61 50 71 105 90

Figure S125.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.024

Table S126.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
17Q GAIN MUTATED 49 8 38
17Q GAIN WILD-TYPE 162 87 194

Figure S126.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.13

Table S127.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
17Q GAIN MUTATED 38 34 23
17Q GAIN WILD-TYPE 190 105 148

Figure S127.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.01

Table S128.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18P GAIN MUTATED 16 3 14
18P GAIN WILD-TYPE 237 206 139

Figure S128.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0045

Table S129.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
18P GAIN MUTATED 8 2 14
18P GAIN WILD-TYPE 88 162 115

Figure S129.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.092

Table S130.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18P GAIN MUTATED 4 12 11 6
18P GAIN WILD-TYPE 144 129 119 187

Figure S130.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0044

Table S131.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18P GAIN MUTATED 1 3 11 3 6 2 7
18P GAIN WILD-TYPE 79 83 53 54 84 136 90

Figure S131.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.11

Table S132.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q GAIN MUTATED 1 0 0 2
18Q GAIN WILD-TYPE 42 62 69 39

Figure S132.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.051

Table S133.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18Q GAIN MUTATED 12 1 6
18Q GAIN WILD-TYPE 241 208 147

Figure S133.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0086 (Fisher's exact test), Q value = 0.039

Table S134.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
18Q GAIN MUTATED 6 1 8
18Q GAIN WILD-TYPE 90 163 121

Figure S134.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.034

Table S135.  Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
18Q GAIN MUTATED 6 7 5
18Q GAIN WILD-TYPE 46 295 92

Figure S135.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00297 (Fisher's exact test), Q value = 0.017

Table S136.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18Q GAIN MUTATED 1 7 9 2
18Q GAIN WILD-TYPE 147 134 121 191

Figure S136.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00092

Table S137.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18Q GAIN MUTATED 0 1 8 1 5 0 4
18Q GAIN WILD-TYPE 80 85 56 56 85 138 93

Figure S137.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.061

Table S138.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
18Q GAIN MUTATED 14 1 4
18Q GAIN WILD-TYPE 214 138 167

Figure S138.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.071

Table S139.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
19P GAIN MUTATED 2 10 9 10
19P GAIN WILD-TYPE 47 31 67 39

Figure S139.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

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

Table S140.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19P GAIN MUTATED 19 54 31
19P GAIN WILD-TYPE 234 155 122

Figure S140.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00066

Table S141.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
19P GAIN MUTATED 11 19 3 13 23 29 5
19P GAIN WILD-TYPE 69 67 61 44 67 109 92

Figure S141.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.13

Table S142.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
19P GAIN MUTATED 41 19 27
19P GAIN WILD-TYPE 170 76 205

Figure S142.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MRNA_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.15

Table S143.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
19Q GAIN MUTATED 2 15 10 6
19Q GAIN WILD-TYPE 41 47 59 35

Figure S143.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00377 (Fisher's exact test), Q value = 0.02

Table S144.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
19Q GAIN MUTATED 1 11 14 7
19Q GAIN WILD-TYPE 48 30 62 42

Figure S144.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0019

Table S145.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19Q GAIN MUTATED 29 55 30
19Q GAIN WILD-TYPE 224 154 123

Figure S145.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.1

Table S146.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
19Q GAIN MUTATED 27 35 7 17
19Q GAIN WILD-TYPE 70 143 32 120

Figure S146.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0068

Table S147.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
19Q GAIN MUTATED 14 21 4 12 24 30 8
19Q GAIN WILD-TYPE 66 65 60 45 66 108 89

Figure S147.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0022

Table S148.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20P GAIN MUTATED 16 40 51 18
20P GAIN WILD-TYPE 27 22 18 23

Figure S148.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00035

Table S149.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20P GAIN MUTATED 13 27 50 35
20P GAIN WILD-TYPE 36 14 26 14

Figure S149.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

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

Table S150.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20P GAIN MUTATED 110 154 88
20P GAIN WILD-TYPE 143 55 65

Figure S150.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0029

Table S151.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
20P GAIN MUTATED 52 112 59
20P GAIN WILD-TYPE 44 52 70

Figure S151.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.078

Table S152.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
20P GAIN MUTATED 63 102 23 62
20P GAIN WILD-TYPE 34 76 16 75

Figure S152.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.03

Table S153.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
20P GAIN MUTATED 96 65 70 118
20P GAIN WILD-TYPE 52 76 60 75

Figure S153.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
20P GAIN MUTATED 53 47 16 44 55 97 37
20P GAIN WILD-TYPE 27 39 48 13 35 41 60

Figure S154.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

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

Table S155.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20Q GAIN MUTATED 18 60 63 22
20Q GAIN WILD-TYPE 25 2 6 19

Figure S155.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S156.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20Q GAIN MUTATED 15 39 61 48
20Q GAIN WILD-TYPE 34 2 15 1

Figure S156.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S157.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20Q GAIN MUTATED 128 206 131
20Q GAIN WILD-TYPE 125 3 22

Figure S157.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

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

Table S158.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
20Q GAIN MUTATED 64 158 74
20Q GAIN WILD-TYPE 32 6 55

Figure S158.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.018

Table S159.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
20Q GAIN MUTATED 79 141 32 87
20Q GAIN WILD-TYPE 18 37 7 50

Figure S159.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00533 (Fisher's exact test), Q value = 0.027

Table S160.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
20Q GAIN MUTATED 46 230 63
20Q GAIN WILD-TYPE 6 72 34

Figure S160.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

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

Table S161.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
20Q GAIN MUTATED 143 78 91 150
20Q GAIN WILD-TYPE 5 63 39 43

Figure S161.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S162.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
20Q GAIN MUTATED 73 62 18 50 82 132 45
20Q GAIN WILD-TYPE 7 24 46 7 8 6 52

Figure S162.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.062

Table S163.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
20Q GAIN MUTATED 173 67 166
20Q GAIN WILD-TYPE 38 28 66

Figure S163.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0038

Table S164.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
20Q GAIN MUTATED 166 121 119
20Q GAIN WILD-TYPE 62 18 52

Figure S164.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0041

Table S165.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
20Q GAIN MUTATED 23 16 27 23 16 8
20Q GAIN WILD-TYPE 1 4 1 5 2 9

Figure S165.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.071

Table S166.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
20Q GAIN MUTATED 40 15 29 29
20Q GAIN WILD-TYPE 15 0 5 2

Figure S166.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0041

Table S167.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
21Q GAIN MUTATED 4 15 15
21Q GAIN WILD-TYPE 249 194 138

Figure S167.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00963 (Fisher's exact test), Q value = 0.042

Table S168.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
22Q GAIN MUTATED 3 13 7
22Q GAIN WILD-TYPE 250 196 146

Figure S168.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'MRNA_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.12

Table S169.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
XP GAIN MUTATED 2 15 9 8
XP GAIN WILD-TYPE 41 47 60 33

Figure S169.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00075

Table S170.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
XP GAIN MUTATED 22 46 31
XP GAIN WILD-TYPE 231 163 122

Figure S170.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.15

Table S171.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
XP GAIN MUTATED 9 34 19
XP GAIN WILD-TYPE 87 130 110

Figure S171.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0023

Table S172.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
XQ GAIN MUTATED 26 44 37
XQ GAIN WILD-TYPE 227 165 116

Figure S172.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.09

Table S173.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
1P LOSS MUTATED 6 14 12 14
1P LOSS WILD-TYPE 43 27 64 35

Figure S173.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S174.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1P LOSS MUTATED 32 75 31
1P LOSS WILD-TYPE 221 134 122

Figure S174.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0086

Table S175.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
1P LOSS MUTATED 17 53 20
1P LOSS WILD-TYPE 79 111 109

Figure S175.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0092

Table S176.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
1P LOSS MUTATED 43 16 33 45
1P LOSS WILD-TYPE 105 125 97 148

Figure S176.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0015

Table S177.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
1P LOSS MUTATED 24 14 5 13 29 40 12
1P LOSS WILD-TYPE 56 72 59 44 61 98 85

Figure S177.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S178.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1Q LOSS MUTATED 17 41 21
1Q LOSS WILD-TYPE 236 168 132

Figure S178.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00084

Table S179.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
1Q LOSS MUTATED 30 5 18 25
1Q LOSS WILD-TYPE 118 136 112 168

Figure S179.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0048

Table S180.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
1Q LOSS MUTATED 16 5 3 6 19 23 6
1Q LOSS WILD-TYPE 64 81 61 51 71 115 91

Figure S180.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00674 (Fisher's exact test), Q value = 0.032

Table S181.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
1Q LOSS MUTATED 22 28 16
1Q LOSS WILD-TYPE 206 111 155

Figure S181.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0038

Table S182.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2P LOSS MUTATED 1 13 3
2P LOSS WILD-TYPE 252 196 150

Figure S182.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.1

Table S183.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
2P LOSS MUTATED 0 5 0
2P LOSS WILD-TYPE 96 159 129

Figure S183.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 0.036

Table S184.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2P LOSS MUTATED 0 0 0 2 3 4 8
2P LOSS WILD-TYPE 80 86 64 55 87 134 89

Figure S184.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.061

Table S185.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2Q LOSS MUTATED 2 10 2
2Q LOSS WILD-TYPE 251 199 151

Figure S185.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00557 (Fisher's exact test), Q value = 0.028

Table S186.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2Q LOSS MUTATED 0 0 0 1 2 3 8
2Q LOSS WILD-TYPE 80 86 64 56 88 135 89

Figure S186.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.078

Table S187.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
2Q LOSS MUTATED 2 2 9
2Q LOSS WILD-TYPE 226 137 162

Figure S187.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.079

Table S188.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
4P LOSS MUTATED 13 24 28 6
4P LOSS WILD-TYPE 30 38 41 35

Figure S188.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.036

Table S189.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
4P LOSS MUTATED 11 13 21 26
4P LOSS WILD-TYPE 38 28 55 23

Figure S189.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

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

Table S190.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4P LOSS MUTATED 44 107 47
4P LOSS WILD-TYPE 209 102 106

Figure S190.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0075

Table S191.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
4P LOSS MUTATED 25 69 30
4P LOSS WILD-TYPE 71 95 99

Figure S191.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0048

Table S192.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
4P LOSS MUTATED 62 28 42 65
4P LOSS WILD-TYPE 86 113 88 128

Figure S192.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00092

Table S193.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
4P LOSS MUTATED 33 22 7 20 37 54 24
4P LOSS WILD-TYPE 47 64 57 37 53 84 73

Figure S193.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.13

Table S194.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
4Q LOSS MUTATED 12 23 26 6
4Q LOSS WILD-TYPE 31 39 43 35

Figure S194.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'CN_CNMF'

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

Table S195.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4Q LOSS MUTATED 38 103 50
4Q LOSS WILD-TYPE 215 106 103

Figure S195.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S196.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
4Q LOSS MUTATED 27 69 25
4Q LOSS WILD-TYPE 69 95 104

Figure S196.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.019

Table S197.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
4Q LOSS MUTATED 58 28 40 64
4Q LOSS WILD-TYPE 90 113 90 129

Figure S197.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00084

Table S198.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
4Q LOSS MUTATED 32 21 6 21 35 51 24
4Q LOSS WILD-TYPE 48 65 58 36 55 87 73

Figure S198.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.12

Table S199.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
4Q LOSS MUTATED 12 5 15 9 8 2
4Q LOSS WILD-TYPE 12 15 13 19 10 15

Figure S199.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.003

Table S200.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5P LOSS MUTATED 20 33 33
5P LOSS WILD-TYPE 233 176 120

Figure S200.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00339 (Fisher's exact test), Q value = 0.019

Table S201.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5P LOSS MUTATED 14 13 1 15 10 21 12
5P LOSS WILD-TYPE 66 73 63 42 80 117 85

Figure S201.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.00903 (Fisher's exact test), Q value = 0.04

Table S202.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
5Q LOSS MUTATED 7 14 17 1
5Q LOSS WILD-TYPE 36 48 52 40

Figure S202.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.096

Table S203.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
5Q LOSS MUTATED 7 13 8 11
5Q LOSS WILD-TYPE 42 28 68 38

Figure S203.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

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

Table S204.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5Q LOSS MUTATED 23 49 49
5Q LOSS WILD-TYPE 230 160 104

Figure S204.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.1

Table S205.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
5Q LOSS MUTATED 39 18 28 36
5Q LOSS WILD-TYPE 109 123 102 157

Figure S205.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0058

Table S206.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5Q LOSS MUTATED 20 12 4 19 21 32 13
5Q LOSS WILD-TYPE 60 74 60 38 69 106 84

Figure S206.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.078

Table S207.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
6P LOSS MUTATED 5 0 11 2
6P LOSS WILD-TYPE 44 41 65 47

Figure S207.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.11

Table S208.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
6P LOSS MUTATED 7 3 4 1 12 7 12
6P LOSS WILD-TYPE 73 83 60 56 78 131 85

Figure S208.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00889 (Fisher's exact test), Q value = 0.04

Table S209.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
8P LOSS MUTATED 12 31 31 9
8P LOSS WILD-TYPE 31 31 38 32

Figure S209.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.029

Table S210.  Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
8P LOSS MUTATED 9 20 31 23
8P LOSS WILD-TYPE 40 21 45 26

Figure S210.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

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

Table S211.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8P LOSS MUTATED 36 103 79
8P LOSS WILD-TYPE 217 106 74

Figure S211.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0041

Table S212.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
8P LOSS MUTATED 29 74 31
8P LOSS WILD-TYPE 67 90 98

Figure S212.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.09

Table S213.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
8P LOSS MUTATED 24 106 24
8P LOSS WILD-TYPE 28 196 73

Figure S213.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0064 (Fisher's exact test), Q value = 0.031

Table S214.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
8P LOSS MUTATED 58 34 45 80
8P LOSS WILD-TYPE 90 107 85 113

Figure S214.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S215.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
8P LOSS MUTATED 28 26 8 23 40 66 26
8P LOSS WILD-TYPE 52 60 56 34 50 72 71

Figure S215.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.015

Table S216.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
8P LOSS MUTATED 14 5 9 10 11 1
8P LOSS WILD-TYPE 10 15 19 18 7 16

Figure S216.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.00429 (Fisher's exact test), Q value = 0.023

Table S217.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8Q LOSS MUTATED 7 21 9
8Q LOSS WILD-TYPE 246 188 144

Figure S217.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.12

Table S218.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
8Q LOSS MUTATED 9 0 4 0
8Q LOSS WILD-TYPE 46 15 30 31

Figure S218.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0058

Table S219.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
9P LOSS MUTATED 17 34 26
9P LOSS WILD-TYPE 236 175 127

Figure S219.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.012

Table S220.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
9P LOSS MUTATED 10 34 9
9P LOSS WILD-TYPE 86 130 120

Figure S220.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0025

Table S221.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
9P LOSS MUTATED 31 7 19 20
9P LOSS WILD-TYPE 117 134 111 173

Figure S221.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.066

Table S222.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
9P LOSS MUTATED 13 9 2 12 15 19 7
9P LOSS WILD-TYPE 67 77 62 45 75 119 90

Figure S222.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.14

Table S223.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
9Q LOSS MUTATED 3 11 11 1
9Q LOSS WILD-TYPE 40 51 58 40

Figure S223.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.054

Table S224.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
9Q LOSS MUTATED 2 10 6 8
9Q LOSS WILD-TYPE 47 31 70 41

Figure S224.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0034

Table S225.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
9Q LOSS MUTATED 17 38 23
9Q LOSS WILD-TYPE 236 171 130

Figure S225.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0023

Table S226.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
9Q LOSS MUTATED 11 35 7
9Q LOSS WILD-TYPE 85 129 122

Figure S226.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S227.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
9Q LOSS MUTATED 30 6 21 21
9Q LOSS WILD-TYPE 118 135 109 172

Figure S227.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.007

Table S228.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
9Q LOSS MUTATED 10 7 2 12 19 22 6
9Q LOSS WILD-TYPE 70 79 62 45 71 116 91

Figure S228.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.047

Table S229.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
9Q LOSS MUTATED 26 28 15
9Q LOSS WILD-TYPE 202 111 156

Figure S229.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.048

Table S230.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
10P LOSS MUTATED 3 4 17 4
10P LOSS WILD-TYPE 40 58 52 37

Figure S230.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'CN_CNMF'

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

Table S231.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10P LOSS MUTATED 20 47 35
10P LOSS WILD-TYPE 233 162 118

Figure S231.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.086

Table S232.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
10P LOSS MUTATED 15 41 17
10P LOSS WILD-TYPE 81 123 112

Figure S232.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.067

Table S233.  Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
10P LOSS MUTATED 17 33 12 14
10P LOSS WILD-TYPE 80 145 27 123

Figure S233.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.047

Table S234.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
10P LOSS MUTATED 36 14 22 29
10P LOSS WILD-TYPE 112 127 108 164

Figure S234.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0029

Table S235.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
10P LOSS MUTATED 16 10 3 11 28 23 10
10P LOSS WILD-TYPE 64 76 61 46 62 115 87

Figure S235.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.081

Table S236.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
10Q LOSS MUTATED 5 6 19 4
10Q LOSS WILD-TYPE 38 56 50 37

Figure S236.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'CN_CNMF'

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

Table S237.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10Q LOSS MUTATED 16 53 43
10Q LOSS WILD-TYPE 237 156 110

Figure S237.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0064 (Fisher's exact test), Q value = 0.031

Table S238.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
10Q LOSS MUTATED 14 45 18
10Q LOSS WILD-TYPE 82 119 111

Figure S238.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.069

Table S239.  Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
10Q LOSS MUTATED 20 32 14 18
10Q LOSS WILD-TYPE 77 146 25 119

Figure S239.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.015

Table S240.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
10Q LOSS MUTATED 40 14 22 35
10Q LOSS WILD-TYPE 108 127 108 158

Figure S240.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S241.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
10Q LOSS MUTATED 18 10 1 10 32 26 14
10Q LOSS WILD-TYPE 62 76 63 47 58 112 83

Figure S241.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.14

Table S242.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
10Q LOSS MUTATED 4 3 10 6 6 0
10Q LOSS WILD-TYPE 20 17 18 22 12 17

Figure S242.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.078

Table S243.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11P LOSS MUTATED 22 36 17
11P LOSS WILD-TYPE 231 173 136

Figure S243.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.093

Table S244.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11Q LOSS MUTATED 28 42 23
11Q LOSS WILD-TYPE 225 167 130

Figure S244.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.057

Table S245.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
12P LOSS MUTATED 0 5 9 8
12P LOSS WILD-TYPE 49 36 67 41

Figure S245.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

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

Table S246.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12P LOSS MUTATED 6 44 21
12P LOSS WILD-TYPE 247 165 132

Figure S246.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0033

Table S247.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12P LOSS MUTATED 16 3 2 8 15 21 6
12P LOSS WILD-TYPE 64 83 62 49 75 117 91

Figure S247.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.089

Table S248.  Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
12Q LOSS MUTATED 0 4 9 7
12Q LOSS WILD-TYPE 49 37 67 42

Figure S248.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

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

Table S249.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12Q LOSS MUTATED 8 42 21
12Q LOSS WILD-TYPE 245 167 132

Figure S249.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00035

Table S250.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12Q LOSS MUTATED 18 2 3 8 15 20 5
12Q LOSS WILD-TYPE 62 84 61 49 75 118 92

Figure S250.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.062

Table S251.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
13Q LOSS MUTATED 5 0 2 0
13Q LOSS WILD-TYPE 44 41 74 49

Figure S251.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.056

Table S252.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
13Q LOSS MUTATED 8 2 10
13Q LOSS WILD-TYPE 245 207 143

Figure S252.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00683 (Fisher's exact test), Q value = 0.033

Table S253.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
13Q LOSS MUTATED 5 9 0
13Q LOSS WILD-TYPE 47 293 97

Figure S253.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.057

Table S254.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
13Q LOSS MUTATED 0 4 1 0 1 0
13Q LOSS WILD-TYPE 24 16 27 28 17 17

Figure S254.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0023

Table S255.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
14Q LOSS MUTATED 10 29 33 6
14Q LOSS WILD-TYPE 33 33 36 35

Figure S255.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00075

Table S256.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
14Q LOSS MUTATED 6 20 27 25
14Q LOSS WILD-TYPE 43 21 49 24

Figure S256.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

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

Table S257.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
14Q LOSS MUTATED 33 141 33
14Q LOSS WILD-TYPE 220 68 120

Figure S257.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

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

Table S258.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
14Q LOSS MUTATED 27 78 23
14Q LOSS WILD-TYPE 69 86 106

Figure S258.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.016

Table S259.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
14Q LOSS MUTATED 35 74 12 30
14Q LOSS WILD-TYPE 62 104 27 107

Figure S259.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

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

Table S260.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
14Q LOSS MUTATED 77 25 28 76
14Q LOSS WILD-TYPE 71 116 102 117

Figure S260.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S261.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
14Q LOSS MUTATED 35 26 3 21 37 65 19
14Q LOSS WILD-TYPE 45 60 61 36 53 73 78

Figure S261.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.12

Table S262.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
14Q LOSS MUTATED 13 5 12 14 9 2
14Q LOSS WILD-TYPE 11 15 16 14 9 15

Figure S262.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.13

Table S263.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
14Q LOSS MUTATED 15 6 17 17
14Q LOSS WILD-TYPE 40 9 17 14

Figure S263.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S264.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
15Q LOSS MUTATED 11 32 36 7
15Q LOSS WILD-TYPE 32 30 33 34

Figure S264.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.01

Table S265.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
15Q LOSS MUTATED 11 22 26 27
15Q LOSS WILD-TYPE 38 19 50 22

Figure S265.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

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

Table S266.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
15Q LOSS MUTATED 38 124 67
15Q LOSS WILD-TYPE 215 85 86

Figure S266.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0048

Table S267.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
15Q LOSS MUTATED 33 77 33
15Q LOSS WILD-TYPE 63 87 96

Figure S267.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S268.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
15Q LOSS MUTATED 71 31 46 80
15Q LOSS WILD-TYPE 77 110 84 113

Figure S268.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S269.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
15Q LOSS MUTATED 35 27 2 23 46 64 31
15Q LOSS WILD-TYPE 45 59 62 34 44 74 66

Figure S269.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.09

Table S270.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
16Q LOSS MUTATED 5 7 2 0
16Q LOSS WILD-TYPE 38 55 67 41

Figure S270.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.039

Table S271.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16Q LOSS MUTATED 14 10 20
16Q LOSS WILD-TYPE 239 199 133

Figure S271.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S272.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17P LOSS MUTATED 15 44 47 15
17P LOSS WILD-TYPE 28 18 22 26

Figure S272.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00057

Table S273.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
17P LOSS MUTATED 13 27 47 34
17P LOSS WILD-TYPE 36 14 29 15

Figure S273.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

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

Table S274.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17P LOSS MUTATED 68 156 117
17P LOSS WILD-TYPE 185 53 36

Figure S274.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

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

Table S275.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
17P LOSS MUTATED 40 121 56
17P LOSS WILD-TYPE 56 43 73

Figure S275.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00799 (Fisher's exact test), Q value = 0.037

Table S276.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
17P LOSS MUTATED 38 161 46
17P LOSS WILD-TYPE 14 141 51

Figure S276.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

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

Table S277.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
17P LOSS MUTATED 104 54 70 111
17P LOSS WILD-TYPE 44 87 60 82

Figure S277.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S278.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
17P LOSS MUTATED 50 44 8 38 66 94 39
17P LOSS WILD-TYPE 30 42 56 19 24 44 58

Figure S278.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.11

Table S279.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
17P LOSS MUTATED 130 44 125
17P LOSS WILD-TYPE 81 51 107

Figure S279.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.082

Table S280.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
17P LOSS MUTATED 119 91 89
17P LOSS WILD-TYPE 109 48 82

Figure S280.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.096

Table S281.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
17P LOSS MUTATED 18 14 21 15 11 5
17P LOSS WILD-TYPE 6 6 7 13 7 12

Figure S281.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0085

Table S282.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17Q LOSS MUTATED 24 44 28
17Q LOSS WILD-TYPE 229 165 125

Figure S282.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.069

Table S283.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
17Q LOSS MUTATED 14 38 10
17Q LOSS WILD-TYPE 38 264 87

Figure S283.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.097

Table S284.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
17Q LOSS MUTATED 15 14 2 12 19 19 15
17Q LOSS WILD-TYPE 65 72 62 45 71 119 82

Figure S284.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

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

Table S285.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18P LOSS MUTATED 13 52 54 12
18P LOSS WILD-TYPE 30 10 15 29

Figure S285.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S286.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
18P LOSS MUTATED 10 35 44 42
18P LOSS WILD-TYPE 39 6 32 7

Figure S286.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

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

Table S287.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18P LOSS MUTATED 75 190 114
18P LOSS WILD-TYPE 178 19 39

Figure S287.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

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

Table S288.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
18P LOSS MUTATED 47 148 51
18P LOSS WILD-TYPE 49 16 78

Figure S288.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.1

Table S289.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
18P LOSS MUTATED 60 117 25 68
18P LOSS WILD-TYPE 37 61 14 69

Figure S289.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.14

Table S290.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 302 97
18P LOSS MUTATED 35 187 48
18P LOSS WILD-TYPE 17 115 49

Figure S290.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

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

Table S291.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18P LOSS MUTATED 133 51 72 121
18P LOSS WILD-TYPE 15 90 58 72

Figure S291.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S292.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18P LOSS MUTATED 67 50 6 39 71 108 36
18P LOSS WILD-TYPE 13 36 58 18 19 30 61

Figure S292.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00734 (Fisher's exact test), Q value = 0.034

Table S293.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
18P LOSS MUTATED 146 51 132
18P LOSS WILD-TYPE 65 44 100

Figure S293.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00902 (Fisher's exact test), Q value = 0.04

Table S294.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
18P LOSS MUTATED 131 100 98
18P LOSS WILD-TYPE 97 39 73

Figure S294.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S295.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
18P LOSS MUTATED 21 10 25 20 12 5
18P LOSS WILD-TYPE 3 10 3 8 6 12

Figure S295.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.007

Table S296.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
18P LOSS MUTATED 28 14 25 26
18P LOSS WILD-TYPE 27 1 9 5

Figure S296.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

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

Table S297.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q LOSS MUTATED 17 54 56 14
18Q LOSS WILD-TYPE 26 8 13 27

Figure S297.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S298.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
18Q LOSS MUTATED 14 36 49 42
18Q LOSS WILD-TYPE 35 5 27 7

Figure S298.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

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

Table S299.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18Q LOSS MUTATED 84 193 132
18Q LOSS WILD-TYPE 169 16 21

Figure S299.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

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

Table S300.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
18Q LOSS MUTATED 52 151 62
18Q LOSS WILD-TYPE 44 13 67

Figure S300.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.13

Table S301.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
18Q LOSS MUTATED 67 123 26 75
18Q LOSS WILD-TYPE 30 55 13 62

Figure S301.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

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

Table S302.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18Q LOSS MUTATED 133 60 82 132
18Q LOSS WILD-TYPE 15 81 48 61

Figure S302.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S303.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18Q LOSS MUTATED 67 57 9 44 75 112 43
18Q LOSS WILD-TYPE 13 29 55 13 15 26 54

Figure S303.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0069

Table S304.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
18Q LOSS MUTATED 158 52 146
18Q LOSS WILD-TYPE 53 43 86

Figure S304.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00605 (Fisher's exact test), Q value = 0.03

Table S305.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
18Q LOSS MUTATED 144 107 105
18Q LOSS WILD-TYPE 84 32 66

Figure S305.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S306.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
18Q LOSS MUTATED 21 12 26 21 14 5
18Q LOSS WILD-TYPE 3 8 2 7 4 12

Figure S306.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0032

Table S307.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
18Q LOSS MUTATED 31 14 25 29
18Q LOSS WILD-TYPE 24 1 9 2

Figure S307.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0033

Table S308.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19P LOSS MUTATED 13 25 26
19P LOSS WILD-TYPE 240 184 127

Figure S308.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.15

Table S309.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
19P LOSS MUTATED 24 9 11 20
19P LOSS WILD-TYPE 124 132 119 173

Figure S309.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.13

Table S310.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
19P LOSS MUTATED 16 4 3 5 11 15 10
19P LOSS WILD-TYPE 64 82 61 52 79 123 87

Figure S310.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00623 (Fisher's exact test), Q value = 0.03

Table S311.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
19P LOSS MUTATED 15 24 17
19P LOSS WILD-TYPE 213 115 154

Figure S311.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.042

Table S312.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
19P LOSS MUTATED 2 2 9 6
19P LOSS WILD-TYPE 53 13 25 25

Figure S312.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.011

Table S313.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19Q LOSS MUTATED 12 20 23
19Q LOSS WILD-TYPE 241 189 130

Figure S313.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.07

Table S314.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20P LOSS MUTATED 2 9 6 9
20P LOSS WILD-TYPE 47 32 70 40

Figure S314.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00035

Table S315.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20P LOSS MUTATED 12 28 28
20P LOSS WILD-TYPE 241 181 125

Figure S315.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.013

Table S316.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
20P LOSS MUTATED 6 28 7
20P LOSS WILD-TYPE 90 136 122

Figure S316.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0019

Table S317.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
20P LOSS MUTATED 8 9 0 4 18 23 6
20P LOSS WILD-TYPE 72 77 64 53 72 115 91

Figure S317.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.014

Table S318.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
20P LOSS MUTATED 3 6 3 1
20P LOSS WILD-TYPE 52 9 31 30

Figure S318.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'RPPA_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.13

Table S319.  Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
20Q LOSS MUTATED 0 0 0 4
20Q LOSS WILD-TYPE 97 178 39 133

Figure S319.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.066

Table S320.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
21Q LOSS MUTATED 10 26 23 6
21Q LOSS WILD-TYPE 33 36 46 35

Figure S320.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.078

Table S321.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
21Q LOSS MUTATED 10 19 18 18
21Q LOSS WILD-TYPE 39 22 58 31

Figure S321.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

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

Table S322.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
21Q LOSS MUTATED 54 97 43
21Q LOSS WILD-TYPE 199 112 110

Figure S322.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.055

Table S323.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
21Q LOSS MUTATED 26 67 34
21Q LOSS WILD-TYPE 70 97 95

Figure S323.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S324.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
21Q LOSS MUTATED 68 29 36 59
21Q LOSS WILD-TYPE 80 112 94 134

Figure S324.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 0.02

Table S325.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
21Q LOSS MUTATED 30 24 10 21 35 51 21
21Q LOSS WILD-TYPE 50 62 54 36 55 87 76

Figure S325.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.026

Table S326.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
22Q LOSS MUTATED 12 28 28 6
22Q LOSS WILD-TYPE 31 34 41 35

Figure S326.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0029

Table S327.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
22Q LOSS MUTATED 5 16 31 22
22Q LOSS WILD-TYPE 44 25 45 27

Figure S327.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

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

Table S328.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
22Q LOSS MUTATED 49 104 50
22Q LOSS WILD-TYPE 204 105 103

Figure S328.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.068

Table S329.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
22Q LOSS MUTATED 58 33 40 71
22Q LOSS WILD-TYPE 90 108 90 122

Figure S329.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S330.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
22Q LOSS MUTATED 30 27 5 23 35 59 23
22Q LOSS WILD-TYPE 50 59 59 34 55 79 74

Figure S330.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00623 (Fisher's exact test), Q value = 0.03

Table S331.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
XP LOSS MUTATED 13 35 7 9
XP LOSS WILD-TYPE 84 143 32 128

Figure S331.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.11

Table S332.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
XP LOSS MUTATED 3 4 8 4
XP LOSS WILD-TYPE 52 11 26 27

Figure S332.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.11

Table S333.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 164 129
XQ LOSS MUTATED 6 28 14
XQ LOSS WILD-TYPE 90 136 115

Figure S333.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.14

Table S334.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
XQ LOSS MUTATED 31 5 30
XQ LOSS WILD-TYPE 180 90 202

Figure S334.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00766 (Fisher's exact test), Q value = 0.036

Table S335.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
XQ LOSS MUTATED 3 4 9 2
XQ LOSS WILD-TYPE 52 11 25 29

Figure S335.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/COADREAD-TP/15089878/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/15117685/COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 615

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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