Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1V40SN7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1V40SN7
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 504 patients, 202 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

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

  • 4p gain cnv correlated to 'MIRSEQ_CNMF'.

  • 4q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

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

  • 14q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 22q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

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

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

  • 8p loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

  • xq loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 202 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
14q loss 211 (42%) 293 3.12e-05
(0.0228) 		4.31e-05
(0.0314) 		1.46e-18
(1.28e-15) 		6.21e-08
(5.02e-05) 		1.01e-13
(8.71e-11) 		1.28e-07
(0.000102) 		1.02e-19
(9.01e-17) 		1.49e-15
(1.29e-12) 		6.27e-11
(5.26e-08) 		0.911
(1.00) 		0.00107
(0.688) 		0.000317
(0.219)
12q gain 119 (24%) 385 0.0129
(1.00) 		0.0142
(1.00) 		5.47e-14
(4.72e-11) 		0.000118
(0.0841) 		3.78e-14
(3.27e-11) 		0.000288
(0.2) 		8.9e-12
(7.54e-09) 		7.91e-12
(6.71e-09) 		1.43e-10
(1.19e-07) 		0.0308
(1.00) 		1.81e-07
(0.000144) 		0.00028
(0.195)
2p loss 14 (3%) 490 3.58e-05
(0.0262) 		6.3e-05
(0.0454) 		8.84e-07
(0.000691) 		0.668
(1.00) 		4.58e-05
(0.0333) 		2.35e-06
(0.00181) 		2.11e-07
(0.000167) 		4.8e-09
(3.94e-06) 		5.54e-05
(0.0402) 		2.12e-14
(1.84e-11) 		0.0593
(1.00) 		0.0399
(1.00)
6p loss 100 (20%) 404 0.0113
(1.00) 		0.00282
(1.00) 		1.14e-17
(9.99e-15) 		0.000723
(0.478) 		1.01e-06
(0.000786) 		0.000234
(0.164) 		7.62e-08
(6.14e-05) 		1.66e-07
(0.000133) 		2.33e-11
(1.96e-08) 		4.61e-06
(0.00351) 		3.04e-08
(2.47e-05) 		3.08e-05
(0.0226)
9p loss 144 (29%) 360 0.00417
(1.00) 		0.000533
(0.362) 		8.23e-44
(7.3e-41) 		5.75e-19
(5.05e-16) 		1.5e-05
(0.0112) 		0.00109
(0.705) 		1.4e-22
(1.23e-19) 		2.7e-23
(2.39e-20) 		2.13e-13
(1.83e-10) 		7.65e-05
(0.0548) 		2.07e-08
(1.69e-05) 		2.96e-05
(0.0218)
9q loss 147 (29%) 357 0.0101
(1.00) 		0.00143
(0.915) 		5.71e-44
(5.08e-41) 		1.8e-18
(1.58e-15) 		1.06e-06
(0.00082) 		0.00159
(1.00) 		4.98e-24
(4.42e-21) 		9.3e-24
(8.24e-21) 		1.64e-15
(1.42e-12) 		0.000165
(0.116) 		2.63e-08
(2.14e-05) 		3.11e-06
(0.00238)
18p loss 91 (18%) 413 0.0574
(1.00) 		0.135
(1.00) 		2.15e-13
(1.85e-10) 		2.68e-07
(0.000212) 		3.07e-08
(2.49e-05) 		0.00183
(1.00) 		8.18e-18
(7.15e-15) 		4.86e-16
(4.23e-13) 		7.12e-11
(5.97e-08) 		6.24e-07
(0.000489) 		1.01e-07
(8.12e-05) 		7.96e-05
(0.0569)
18q loss 93 (18%) 411 0.0468
(1.00) 		0.0649
(1.00) 		3.81e-13
(3.26e-10) 		1.97e-06
(0.00152) 		1.99e-07
(0.000158) 		0.0067
(1.00) 		7.34e-17
(6.4e-14) 		7.86e-16
(6.84e-13) 		2.1e-10
(1.75e-07) 		3.51e-07
(0.000276) 		3.04e-08
(2.47e-05) 		9.28e-06
(0.007)
8q gain 59 (12%) 445 0.226
(1.00) 		0.325
(1.00) 		7.56e-18
(6.62e-15) 		2.94e-06
(0.00225) 		7e-05
(0.0502) 		0.0155
(1.00) 		3.8e-11
(3.2e-08) 		5.42e-10
(4.51e-07) 		1.96e-09
(1.62e-06) 		0.00479
(1.00) 		3.74e-06
(0.00285) 		5.27e-06
(0.004)
20p gain 110 (22%) 394 0.116
(1.00) 		0.163
(1.00) 		1.09e-21
(9.61e-19) 		5.62e-05
(0.0407) 		1.07e-07
(8.59e-05) 		0.00174
(1.00) 		3.96e-13
(3.39e-10) 		2.01e-11
(1.69e-08) 		2.03e-10
(1.69e-07) 		0.000253
(0.177) 		7.8e-07
(0.00061) 		0.00329
(1.00)
20q gain 113 (22%) 391 0.0457
(1.00) 		0.0675
(1.00) 		4.64e-23
(4.1e-20) 		5.62e-05
(0.0407) 		6.76e-09
(5.54e-06) 		0.000896
(0.586) 		7.97e-15
(6.91e-12) 		2.08e-12
(1.77e-09) 		1.96e-11
(1.66e-08) 		0.000145
(0.102) 		3.23e-07
(0.000255) 		0.00197
(1.00)
2q loss 14 (3%) 490 0.000249
(0.174) 		0.000389
(0.267) 		8.84e-07
(0.000691) 		1
(1.00) 		0.000316
(0.219) 		2.35e-06
(0.00181) 		2.11e-07
(0.000167) 		6.68e-08
(5.38e-05) 		8.16e-06
(0.00616) 		1.23e-12
(1.05e-09) 		0.0593
(1.00) 		0.0399
(1.00)
12p gain 118 (23%) 386 0.0129
(1.00) 		0.0142
(1.00) 		6.21e-14
(5.36e-11) 		0.000174
(0.122) 		1.34e-12
(1.14e-09) 		0.00103
(0.669) 		6.53e-12
(5.55e-09) 		1.76e-11
(1.49e-08) 		1e-09
(8.33e-07) 		0.024
(1.00) 		4.88e-07
(0.000383) 		0.000575
(0.388)
13q loss 69 (14%) 435 0.00304
(1.00) 		0.00455
(1.00) 		3.81e-10
(3.17e-07) 		0.000737
(0.487) 		7.66e-06
(0.0058) 		0.00307
(1.00) 		1.21e-05
(0.00907) 		2.17e-07
(0.000172) 		1.04e-06
(0.000807) 		1.66e-05
(0.0124) 		0.0163
(1.00) 		0.000294
(0.204)
17p loss 46 (9%) 458 0.000135
(0.096) 		0.000271
(0.189) 		8.36e-09
(6.84e-06) 		0.14
(1.00) 		0.00511
(1.00) 		0.00163
(1.00) 		2.08e-07
(0.000165) 		1e-07
(8.05e-05) 		1.55e-08
(1.26e-05) 		6.22e-08
(5.02e-05) 		0.0566
(1.00) 		0.307
(1.00)
3q gain 57 (11%) 447 0.0122
(1.00) 		0.0188
(1.00) 		3.7e-09
(3.04e-06) 		0.0125
(1.00) 		0.000872
(0.571) 		1.03e-06
(0.000801) 		9.97e-05
(0.071) 		4.46e-05
(0.0325) 		3.48e-08
(2.82e-05) 		6.14e-07
(0.000481) 		0.00148
(0.943) 		0.16
(1.00)
6q loss 127 (25%) 377 0.0475
(1.00) 		0.0212
(1.00) 		3.53e-17
(3.08e-14) 		0.0434
(1.00) 		9.82e-06
(0.00739) 		0.00277
(1.00) 		0.000332
(0.229) 		0.00173
(1.00) 		1.08e-07
(8.68e-05) 		0.000336
(0.231) 		1.75e-05
(0.013) 		0.00506
(1.00)
17q loss 28 (6%) 476 0.000618
(0.413) 		0.000912
(0.595) 		2.95e-06
(0.00226) 		0.585
(1.00) 		0.157
(1.00) 		0.0237
(1.00) 		8.58e-05
(0.0613) 		3.11e-05
(0.0228) 		6.34e-06
(0.00481) 		4.63e-07
(0.000364) 		0.117
(1.00) 		0.335
(1.00)
8p gain 30 (6%) 474 1.16e-08
(9.46e-06) 		0.000964
(0.627) 		0.00453
(1.00) 		0.271
(1.00) 		7.9e-06
(0.00597) 		2.73e-05
(0.0202) 		3.31e-06
(0.00253) 		0.00595
(1.00) 		0.00272
(1.00) 		0.00144
(0.92)
3p loss 364 (72%) 140 0.00349
(1.00) 		0.000663
(0.441) 		4.72e-22
(4.17e-19) 		0.0207
(1.00) 		0.0284
(1.00) 		0.0139
(1.00) 		9.09e-07
(0.000708) 		1.84e-11
(1.56e-08) 		0.127
(1.00) 		1.81e-05
(0.0134) 		0.131
(1.00) 		0.000713
(0.473)
22q loss 39 (8%) 465 0.0101
(1.00) 		0.0155
(1.00) 		1.49e-08
(1.22e-05) 		0.00695
(1.00) 		0.00423
(1.00) 		0.0358
(1.00) 		2.17e-06
(0.00167) 		1.06e-05
(0.00795) 		1.91e-05
(0.0142) 		0.045
(1.00) 		0.0307
(1.00) 		0.185
(1.00)
1q gain 50 (10%) 454 0.41
(1.00) 		0.411
(1.00) 		1.21e-14
(1.05e-11) 		0.0369
(1.00) 		0.0875
(1.00) 		0.0312
(1.00) 		5.7e-05
(0.0411) 		0.000761
(0.502) 		2.46e-05
(0.0182) 		0.659
(1.00) 		0.0945
(1.00) 		0.0258
(1.00)
15q loss 35 (7%) 469 0.118
(1.00) 		0.127
(1.00) 		4.08e-11
(3.43e-08) 		0.00787
(1.00) 		0.042
(1.00) 		0.414
(1.00) 		7.51e-06
(0.00569) 		1.08e-05
(0.00811) 		0.0015
(0.951) 		0.0359
(1.00) 		0.000913
(0.595) 		0.14
(1.00)
3p gain 18 (4%) 486 0.0536
(1.00) 		0.0623
(1.00) 		0.00155
(0.982) 		0.585
(1.00) 		0.00734
(1.00) 		0.00332
(1.00) 		0.0163
(1.00) 		0.00267
(1.00) 		3.74e-05
(0.0273) 		1.08e-05
(0.00808) 		0.0025
(1.00) 		0.155
(1.00)
7p gain 167 (33%) 337 0.416
(1.00) 		0.577
(1.00) 		3.99e-13
(3.41e-10) 		0.00627
(1.00) 		1.61e-05
(0.012) 		0.00178
(1.00) 		0.000572
(0.387) 		0.00286
(1.00) 		0.00877
(1.00) 		0.153
(1.00) 		0.0382
(1.00) 		0.393
(1.00)
7q gain 168 (33%) 336 0.416
(1.00) 		0.577
(1.00) 		2.17e-12
(1.85e-09) 		0.0156
(1.00) 		2.78e-05
(0.0205) 		0.000692
(0.459) 		0.000653
(0.436) 		0.0028
(1.00) 		0.00588
(1.00) 		0.0742
(1.00) 		0.108
(1.00) 		0.308
(1.00)
19p gain 50 (10%) 454 0.226
(1.00) 		0.325
(1.00) 		5.73e-10
(4.76e-07) 		0.00494
(1.00) 		0.00924
(1.00) 		0.0794
(1.00) 		0.00376
(1.00) 		0.0115
(1.00) 		0.000167
(0.118) 		0.00409
(1.00) 		0.00648
(1.00) 		0.779
(1.00)
19q gain 56 (11%) 448 0.102
(1.00) 		0.149
(1.00) 		7.33e-12
(6.22e-09) 		0.000654
(0.436) 		0.00184
(1.00) 		0.0101
(1.00) 		0.00173
(1.00) 		0.00515
(1.00) 		6.43e-05
(0.0463) 		0.000491
(0.335) 		0.00176
(1.00) 		0.618
(1.00)
21q gain 50 (10%) 454 0.269
(1.00) 		0.28
(1.00) 		3.09e-07
(0.000243) 		0.00867
(1.00) 		0.0011
(0.707) 		0.509
(1.00) 		0.000483
(0.33) 		9.78e-05
(0.0697) 		0.0144
(1.00) 		1
(1.00) 		0.029
(1.00) 		0.0321
(1.00)
1p loss 58 (12%) 446 0.00175
(1.00) 		0.00063
(0.421) 		1.31e-09
(1.08e-06) 		0.469
(1.00) 		0.000606
(0.406) 		0.187
(1.00) 		0.138
(1.00) 		0.000966
(0.627) 		0.189
(1.00) 		8.63e-11
(7.22e-08) 		0.0911
(1.00) 		0.00845
(1.00)
1q loss 37 (7%) 467 0.0217
(1.00) 		0.0298
(1.00) 		1.05e-09
(8.72e-07) 		0.289
(1.00) 		0.013
(1.00) 		0.0787
(1.00) 		0.00488
(1.00) 		0.0005
(0.34) 		0.208
(1.00) 		1.23e-10
(1.03e-07) 		0.0856
(1.00) 		0.0509
(1.00)
21q loss 55 (11%) 449 0.026
(1.00) 		0.0306
(1.00) 		2.15e-07
(0.00017) 		0.0241
(1.00) 		0.0277
(1.00) 		0.00788
(1.00) 		0.00633
(1.00) 		0.000416
(0.285) 		0.0249
(1.00) 		3.26e-05
(0.0239) 		0.156
(1.00) 		0.0575
(1.00)
xq loss 48 (10%) 456 0.0719
(1.00) 		0.0331
(1.00) 		0.000204
(0.143) 		0.0266
(1.00) 		0.195
(1.00) 		0.00763
(1.00) 		0.0654
(1.00) 		0.00477
(1.00) 		0.0862
(1.00) 		6.52e-05
(0.0469) 		0.0189
(1.00) 		0.0142
(1.00)
1p gain 22 (4%) 482 1
(1.00) 		1
(1.00) 		9.47e-07
(0.000737) 		0.00164
(1.00) 		0.00183
(1.00) 		0.0106
(1.00) 		0.0316
(1.00) 		0.00541
(1.00) 		0.00056
(0.38) 		0.632
(1.00) 		0.117
(1.00) 		0.00728
(1.00)
2p gain 75 (15%) 429 0.561
(1.00) 		0.4
(1.00) 		2.17e-09
(1.79e-06) 		0.201
(1.00) 		0.0118
(1.00) 		0.871
(1.00) 		0.216
(1.00) 		0.0537
(1.00) 		0.742
(1.00) 		0.398
(1.00) 		0.0342
(1.00) 		0.521
(1.00)
2q gain 76 (15%) 428 0.561
(1.00) 		0.4
(1.00) 		1.76e-07
(0.00014) 		0.3
(1.00) 		0.0115
(1.00) 		0.934
(1.00) 		0.191
(1.00) 		0.0488
(1.00) 		0.822
(1.00) 		0.398
(1.00) 		0.0871
(1.00) 		0.334
(1.00)
4p gain 13 (3%) 491 0.067
(1.00) 		0.377
(1.00) 		0.253
(1.00) 		0.00175
(1.00) 		0.000418
(0.286) 		0.000791
(0.521) 		0.000145
(0.103) 		0.0195
(1.00) 		0.0162
(1.00) 		0.199
(1.00)
4q gain 13 (3%) 491 0.267
(1.00) 		0.449
(1.00) 		0.253
(1.00) 		0.0201
(1.00) 		0.000418
(0.286) 		0.00769
(1.00) 		0.000145
(0.103) 		0.0312
(1.00) 		0.0162
(1.00) 		0.199
(1.00)
5p gain 185 (37%) 319 0.835
(1.00) 		0.778
(1.00) 		0.000161
(0.114) 		0.23
(1.00) 		0.118
(1.00) 		0.0964
(1.00) 		0.0362
(1.00) 		0.00495
(1.00) 		0.16
(1.00) 		0.836
(1.00) 		0.198
(1.00) 		0.951
(1.00)
10q gain 12 (2%) 492 0.000287
(0.199) 		0.0822
(1.00) 		0.0673
(1.00) 		0.546
(1.00) 		0.0164
(1.00) 		0.00919
(1.00) 		0.0584
(1.00) 		0.378
(1.00) 		0.439
(1.00) 		0.0971
(1.00)
11p gain 30 (6%) 474 0.232
(1.00) 		0.252
(1.00) 		3.3e-06
(0.00253) 		0.308
(1.00) 		0.195
(1.00) 		0.246
(1.00) 		0.217
(1.00) 		0.279
(1.00) 		0.282
(1.00) 		0.042
(1.00) 		0.268
(1.00) 		0.555
(1.00)
11q gain 28 (6%) 476 0.341
(1.00) 		0.539
(1.00) 		0.000125
(0.0886) 		0.188
(1.00) 		0.423
(1.00) 		0.513
(1.00) 		0.463
(1.00) 		0.542
(1.00) 		0.612
(1.00) 		0.0308
(1.00) 		0.603
(1.00) 		0.919
(1.00)
14q gain 16 (3%) 488 0.769
(1.00) 		0.783
(1.00) 		0.000569
(0.385) 		0.328
(1.00) 		0.0121
(1.00) 		0.007
(1.00) 		0.00837
(1.00) 		0.0596
(1.00) 		0.00196
(1.00) 		5.45e-05
(0.0396) 		0.439
(1.00) 		0.29
(1.00)
16q gain 98 (19%) 406 0.233
(1.00) 		0.218
(1.00) 		0.000275
(0.191) 		0.227
(1.00) 		0.0023
(1.00) 		0.0635
(1.00) 		0.0276
(1.00) 		0.00335
(1.00) 		0.00847
(1.00) 		0.129
(1.00) 		0.0492
(1.00) 		0.305
(1.00)
17p gain 24 (5%) 480 0.0186
(1.00) 		0.0349
(1.00) 		3.52e-06
(0.00269) 		0.727
(1.00) 		0.329
(1.00) 		0.0734
(1.00) 		0.243
(1.00) 		0.0817
(1.00) 		0.272
(1.00) 		0.00331
(1.00) 		0.259
(1.00) 		0.0666
(1.00)
17q gain 30 (6%) 474 0.0692
(1.00) 		0.0988
(1.00) 		2.58e-05
(0.0191) 		0.394
(1.00) 		0.493
(1.00) 		0.0761
(1.00) 		0.184
(1.00) 		0.0254
(1.00) 		0.111
(1.00) 		0.000947
(0.617) 		0.131
(1.00) 		0.0212
(1.00)
22q gain 40 (8%) 464 0.327
(1.00) 		0.0289
(1.00) 		1.73e-05
(0.0129) 		0.679
(1.00) 		0.378
(1.00) 		0.581
(1.00) 		0.068
(1.00) 		0.186
(1.00) 		0.0326
(1.00) 		0.23
(1.00) 		0.0188
(1.00) 		0.274
(1.00)
4p loss 71 (14%) 433 0.531
(1.00) 		0.389
(1.00) 		1.02e-09
(8.48e-07) 		0.00136
(0.869) 		0.0845
(1.00) 		0.336
(1.00) 		0.00203
(1.00) 		0.0536
(1.00) 		0.862
(1.00) 		0.323
(1.00) 		0.154
(1.00) 		0.299
(1.00)
4q loss 65 (13%) 439 0.387
(1.00) 		0.346
(1.00) 		3.38e-13
(2.9e-10) 		0.000529
(0.36) 		0.051
(1.00) 		0.199
(1.00) 		0.00081
(0.532) 		0.00211
(1.00) 		0.418
(1.00) 		0.165
(1.00) 		0.0654
(1.00) 		0.124
(1.00)
8p loss 135 (27%) 369 0.354
(1.00) 		0.426
(1.00) 		2.7e-05
(0.0199) 		0.216
(1.00) 		0.233
(1.00) 		0.277
(1.00) 		0.117
(1.00) 		0.243
(1.00) 		0.0726
(1.00) 		0.394
(1.00) 		0.0594
(1.00) 		0.243
(1.00)
10p loss 66 (13%) 438 0.173
(1.00) 		0.239
(1.00) 		2.28e-09
(1.87e-06) 		0.0553
(1.00) 		0.764
(1.00) 		0.349
(1.00) 		0.0827
(1.00) 		0.215
(1.00) 		0.0301
(1.00) 		0.00115
(0.736) 		0.0324
(1.00) 		0.471
(1.00)
10q loss 86 (17%) 418 0.315
(1.00) 		0.36
(1.00) 		5.2e-09
(4.27e-06) 		0.00715
(1.00) 		0.99
(1.00) 		0.149
(1.00) 		0.0698
(1.00) 		0.213
(1.00) 		0.0722
(1.00) 		0.0175
(1.00) 		0.0524
(1.00) 		0.287
(1.00)
11p loss 18 (4%) 486 7.79e-05
(0.0558) 		0.0473
(1.00) 		0.14
(1.00) 		0.553
(1.00) 		0.198
(1.00) 		0.157
(1.00) 		0.175
(1.00) 		0.0455
(1.00) 		0.106
(1.00) 		0.0151
(1.00)
11q loss 23 (5%) 481 0.189
(1.00) 		0.207
(1.00) 		1.81e-06
(0.0014) 		0.0143
(1.00) 		0.101
(1.00) 		0.418
(1.00) 		0.0193
(1.00) 		0.0141
(1.00) 		0.0373
(1.00) 		0.109
(1.00) 		0.0284
(1.00) 		0.0529
(1.00)
5q gain 199 (39%) 305 0.292
(1.00) 		0.212
(1.00) 		0.0123
(1.00) 		0.389
(1.00) 		0.404
(1.00) 		0.0747
(1.00) 		0.163
(1.00) 		0.0214
(1.00) 		0.7
(1.00) 		0.408
(1.00) 		0.54
(1.00) 		0.799
(1.00)
6p gain 10 (2%) 494 0.322
(1.00) 		0.34
(1.00) 		0.0505
(1.00) 		0.252
(1.00) 		0.494
(1.00) 		0.687
(1.00) 		0.716
(1.00) 		0.457
(1.00) 		0.22
(1.00) 		0.0374
(1.00)
6q gain 8 (2%) 496 0.101
(1.00) 		0.569
(1.00) 		0.00515
(1.00) 		0.427
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.904
(1.00) 		0.533
(1.00) 		0.178
(1.00) 		0.112
(1.00)
9p gain 14 (3%) 490 0.108
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.861
(1.00) 		0.437
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.0175
(1.00) 		0.832
(1.00) 		0.915
(1.00)
9q gain 12 (2%) 492 0.00468
(1.00) 		0.835
(1.00) 		0.568
(1.00) 		0.291
(1.00) 		0.247
(1.00) 		0.559
(1.00) 		0.759
(1.00) 		0.0227
(1.00) 		0.699
(1.00) 		0.89
(1.00)
10p gain 16 (3%) 488 0.000823
(0.54) 		0.113
(1.00) 		0.159
(1.00) 		0.366
(1.00) 		0.00243
(1.00) 		0.000581
(0.392) 		0.0942
(1.00) 		0.471
(1.00) 		0.471
(1.00) 		0.276
(1.00)
13q gain 22 (4%) 482 0.309
(1.00) 		0.0104
(1.00) 		0.648
(1.00) 		0.569
(1.00) 		0.0724
(1.00) 		0.302
(1.00) 		0.35
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.189
(1.00)
15q gain 26 (5%) 478 1
(1.00) 		1
(1.00) 		0.00124
(0.792) 		0.599
(1.00) 		0.452
(1.00) 		0.15
(1.00) 		0.661
(1.00) 		0.902
(1.00) 		0.773
(1.00) 		0.237
(1.00) 		0.655
(1.00) 		0.788
(1.00)
16p gain 106 (21%) 398 0.282
(1.00) 		0.337
(1.00) 		0.000601
(0.404) 		0.399
(1.00) 		0.00147
(0.933) 		0.0498
(1.00) 		0.0304
(1.00) 		0.0011
(0.705) 		0.03
(1.00) 		0.0957
(1.00) 		0.212
(1.00) 		0.221
(1.00)
18p gain 25 (5%) 479 0.312
(1.00) 		0.252
(1.00) 		0.0856
(1.00) 		0.405
(1.00) 		0.832
(1.00) 		0.191
(1.00) 		0.184
(1.00) 		0.822
(1.00) 		0.83
(1.00) 		0.605
(1.00) 		0.331
(1.00) 		0.14
(1.00)
18q gain 25 (5%) 479 0.312
(1.00) 		0.252
(1.00) 		0.125
(1.00) 		0.413
(1.00) 		0.733
(1.00) 		0.51
(1.00) 		0.184
(1.00) 		0.822
(1.00) 		0.874
(1.00) 		0.605
(1.00) 		0.331
(1.00) 		0.14
(1.00)
xq gain 27 (5%) 477 0.414
(1.00) 		0.425
(1.00) 		0.147
(1.00) 		0.723
(1.00) 		0.00478
(1.00) 		0.00446
(1.00) 		0.229
(1.00) 		0.342
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.185
(1.00) 		0.233
(1.00)
3q loss 101 (20%) 403 0.923
(1.00) 		0.852
(1.00) 		0.00101
(0.656) 		0.473
(1.00) 		0.347
(1.00) 		0.0847
(1.00) 		0.0481
(1.00) 		0.0736
(1.00) 		0.606
(1.00) 		0.388
(1.00) 		0.0759
(1.00) 		0.139
(1.00)
5p loss 7 (1%) 497 0.0195
(1.00) 		0.291
(1.00) 		0.657
(1.00) 		0.287
(1.00) 		0.027
(1.00) 		0.0308
(1.00) 		0.0301
(1.00) 		0.00874
(1.00)
5q loss 6 (1%) 498 0.0415
(1.00) 		0.534
(1.00) 		0.471
(1.00) 		0.626
(1.00) 		0.0461
(1.00) 		0.0496
(1.00) 		0.065
(1.00) 		0.00108
(0.695)
7p loss 3 (1%) 501 0.34
(1.00) 		0.166
(1.00) 		0.134
(1.00) 		0.0527
(1.00) 		0.28
(1.00) 		0.0524
(1.00) 		0.199
(1.00)
7q loss 4 (1%) 500 0.126
(1.00) 		0.363
(1.00) 		0.098
(1.00) 		1
(1.00) 		0.0505
(1.00) 		0.0925
(1.00) 		0.294
(1.00) 		0.397
(1.00) 		0.0524
(1.00) 		0.199
(1.00)
8q loss 65 (13%) 439 0.647
(1.00) 		0.747
(1.00) 		0.0446
(1.00) 		0.144
(1.00) 		0.299
(1.00) 		0.63
(1.00) 		0.782
(1.00) 		0.673
(1.00) 		0.544
(1.00) 		0.883
(1.00) 		0.0768
(1.00) 		0.171
(1.00)
12p loss 3 (1%) 501 0.183
(1.00) 		0.432
(1.00) 		0.38
(1.00) 		0.47
(1.00) 		0.439
(1.00)
12q loss 4 (1%) 500 0.462
(1.00) 		0.525
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.808
(1.00) 		0.229
(1.00) 		0.751
(1.00)
16p loss 9 (2%) 495 0.126
(1.00) 		0.631
(1.00) 		0.036
(1.00) 		0.837
(1.00) 		0.115
(1.00) 		0.0219
(1.00) 		0.102
(1.00) 		0.0618
(1.00) 		0.453
(1.00) 		0.0735
(1.00)
16q loss 14 (3%) 490 0.00483
(1.00) 		0.344
(1.00) 		0.0576
(1.00) 		0.595
(1.00) 		0.149
(1.00) 		0.00371
(1.00) 		0.115
(1.00) 		0.0144
(1.00) 		0.504
(1.00) 		0.155
(1.00)
19p loss 11 (2%) 493 0.000615
(0.412) 		0.0604
(1.00) 		0.00059
(0.397) 		0.000788
(0.519) 		0.188
(1.00) 		0.0222
(1.00) 		0.237
(1.00) 		0.436
(1.00) 		0.162
(1.00) 		0.11
(1.00)
19q loss 4 (1%) 500 0.0161
(1.00) 		0.89
(1.00) 		0.168
(1.00) 		0.436
(1.00) 		0.393
(1.00) 		0.826
(1.00) 		1
(1.00)
20p loss 8 (2%) 496 0.342
(1.00) 		1
(1.00) 		0.0582
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.105
(1.00) 		0.0111
(1.00) 		0.076
(1.00)
20q loss 3 (1%) 501 0.34
(1.00) 		0.166
(1.00) 		0.134
(1.00) 		0.0527
(1.00) 		0.0535
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 9.47e-07 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
1P GAIN MUTATED 19 1 2
1P GAIN WILD-TYPE 152 211 119

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

'1q gain' versus 'CN_CNMF'

P value = 1.21e-14 (Fisher's exact test), Q value = 1e-11

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
1Q GAIN MUTATED 43 5 2
1Q GAIN WILD-TYPE 128 207 119

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Fisher's exact test), Q value = 0.041

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
1Q GAIN MUTATED 14 31 2
1Q GAIN WILD-TYPE 191 158 102

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.018

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
1Q GAIN MUTATED 3 15 30
1Q GAIN WILD-TYPE 115 188 135

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 2.17e-09 (Fisher's exact test), Q value = 1.8e-06

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
2P GAIN MUTATED 49 12 14
2P GAIN WILD-TYPE 122 200 107

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1.76e-07 (Fisher's exact test), Q value = 0.00014

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
2Q GAIN MUTATED 47 15 14
2Q GAIN WILD-TYPE 124 197 107

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
3P GAIN MUTATED 2 1 15
3P GAIN WILD-TYPE 116 202 150

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0081

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
3P GAIN MUTATED 3 8 7
3P GAIN WILD-TYPE 261 32 175

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 3.7e-09 (Fisher's exact test), Q value = 3e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
3Q GAIN MUTATED 37 5 15
3Q GAIN WILD-TYPE 134 207 106

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

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.03e-06 (Fisher's exact test), Q value = 8e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
3Q GAIN MUTATED 9 14 28
3Q GAIN WILD-TYPE 177 138 81

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 9.97e-05 (Fisher's exact test), Q value = 0.071

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
3Q GAIN MUTATED 11 36 10
3Q GAIN WILD-TYPE 194 153 94

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.032

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
3Q GAIN MUTATED 10 37 10
3Q GAIN WILD-TYPE 205 169 67

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 3.48e-08 (Fisher's exact test), Q value = 2.8e-05

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
3Q GAIN MUTATED 8 9 39
3Q GAIN WILD-TYPE 110 194 126

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.14e-07 (Fisher's exact test), Q value = 0.00048

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
3Q GAIN MUTATED 14 13 29
3Q GAIN WILD-TYPE 250 27 153

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.1

Table S15.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
4P GAIN MUTATED 2 0 11
4P GAIN WILD-TYPE 116 203 154

Figure S15.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.1

Table S16.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
4Q GAIN MUTATED 2 0 11
4Q GAIN WILD-TYPE 116 203 154

Figure S16.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.11

Table S17.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
5P GAIN MUTATED 83 59 43
5P GAIN WILD-TYPE 88 153 78

Figure S17.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.99e-13 (Fisher's exact test), Q value = 3.4e-10

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
7P GAIN MUTATED 86 33 48
7P GAIN WILD-TYPE 85 179 73

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 1.61e-05 (Chi-square test), Q value = 0.012

Table S19.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
7P GAIN MUTATED 21 19 34 34 11 30
7P GAIN WILD-TYPE 79 69 50 41 32 27

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.17e-12 (Fisher's exact test), Q value = 1.8e-09

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
7Q GAIN MUTATED 84 34 50
7Q GAIN WILD-TYPE 87 178 71

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 2.78e-05 (Chi-square test), Q value = 0.02

Table S21.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
7Q GAIN MUTATED 21 21 34 34 10 30
7Q GAIN WILD-TYPE 79 67 50 41 33 27

Figure S21.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.16e-08 (Fisher's exact test), Q value = 9.5e-06

Table S22.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
8P GAIN MUTATED 23 0 7
8P GAIN WILD-TYPE 148 212 114

Figure S22.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 7.9e-06 (Fisher's exact test), Q value = 0.006

Table S23.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
8P GAIN MUTATED 2 23 5
8P GAIN WILD-TYPE 203 166 99

Figure S23.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.02

Table S24.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
8P GAIN MUTATED 3 24 3
8P GAIN WILD-TYPE 212 182 74

Figure S24.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 3.31e-06 (Fisher's exact test), Q value = 0.0025

Table S25.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
8P GAIN MUTATED 4 3 23
8P GAIN WILD-TYPE 114 200 142

Figure S25.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 7.56e-18 (Fisher's exact test), Q value = 6.6e-15

Table S26.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
8Q GAIN MUTATED 46 0 13
8Q GAIN WILD-TYPE 125 212 108

Figure S26.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2.94e-06 (Fisher's exact test), Q value = 0.0023

Table S27.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
8Q GAIN MUTATED 25 3 9
8Q GAIN WILD-TYPE 75 111 67

Figure S27.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 7e-05 (Chi-square test), Q value = 0.05

Table S28.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
8Q GAIN MUTATED 4 10 15 8 1 16
8Q GAIN WILD-TYPE 96 78 69 67 42 41

Figure S28.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 3.8e-11 (Fisher's exact test), Q value = 3.2e-08

Table S29.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
8Q GAIN MUTATED 6 46 6
8Q GAIN WILD-TYPE 199 143 98

Figure S29.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.42e-10 (Fisher's exact test), Q value = 4.5e-07

Table S30.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
8Q GAIN MUTATED 8 47 3
8Q GAIN WILD-TYPE 207 159 74

Figure S30.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1.96e-09 (Fisher's exact test), Q value = 1.6e-06

Table S31.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
8Q GAIN MUTATED 8 8 41
8Q GAIN WILD-TYPE 110 195 124

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.74e-06 (Fisher's exact test), Q value = 0.0028

Table S32.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
8Q GAIN MUTATED 2 2 19
8Q GAIN WILD-TYPE 51 93 59

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.27e-06 (Fisher's exact test), Q value = 0.004

Table S33.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
8Q GAIN MUTATED 0 15 8
8Q GAIN WILD-TYPE 86 54 63

Figure S33.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.000287 (Fisher's exact test), Q value = 0.2

Table S34.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
10Q GAIN MUTATED 10 0 2
10Q GAIN WILD-TYPE 161 212 119

Figure S34.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 3.3e-06 (Fisher's exact test), Q value = 0.0025

Table S35.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
11P GAIN MUTATED 18 1 11
11P GAIN WILD-TYPE 153 211 110

Figure S35.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.089

Table S36.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
11Q GAIN MUTATED 15 2 11
11Q GAIN WILD-TYPE 156 210 110

Figure S36.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 6.21e-14 (Fisher's exact test), Q value = 5.4e-11

Table S37.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
12P GAIN MUTATED 70 17 31
12P GAIN WILD-TYPE 101 195 90

Figure S37.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.000174 (Fisher's exact test), Q value = 0.12

Table S38.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
12P GAIN MUTATED 37 15 22
12P GAIN WILD-TYPE 63 99 54

Figure S38.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 1.34e-12 (Chi-square test), Q value = 1.1e-09

Table S39.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
12P GAIN MUTATED 4 17 31 14 6 31
12P GAIN WILD-TYPE 96 71 53 61 37 26

Figure S39.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 6.53e-12 (Fisher's exact test), Q value = 5.5e-09

Table S40.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
12P GAIN MUTATED 22 77 18
12P GAIN WILD-TYPE 183 112 86

Figure S40.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-11 (Fisher's exact test), Q value = 1.5e-08

Table S41.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
12P GAIN MUTATED 24 81 12
12P GAIN WILD-TYPE 191 125 65

Figure S41.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-09 (Fisher's exact test), Q value = 8.3e-07

Table S42.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
12P GAIN MUTATED 22 26 68
12P GAIN WILD-TYPE 96 177 97

Figure S42.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.88e-07 (Fisher's exact test), Q value = 0.00038

Table S43.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
12P GAIN MUTATED 9 8 33
12P GAIN WILD-TYPE 44 87 45

Figure S43.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 5.47e-14 (Fisher's exact test), Q value = 4.7e-11

Table S44.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
12Q GAIN MUTATED 70 17 32
12Q GAIN WILD-TYPE 101 195 89

Figure S44.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.084

Table S45.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
12Q GAIN MUTATED 38 15 21
12Q GAIN WILD-TYPE 62 99 55

Figure S45.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 3.78e-14 (Chi-square test), Q value = 3.3e-11

Table S46.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
12Q GAIN MUTATED 4 16 31 14 6 33
12Q GAIN WILD-TYPE 96 72 53 61 37 24

Figure S46.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000288 (Fisher's exact test), Q value = 0.2

Table S47.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
12Q GAIN MUTATED 26 44 34
12Q GAIN WILD-TYPE 160 108 75

Figure S47.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 8.9e-12 (Fisher's exact test), Q value = 7.5e-09

Table S48.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
12Q GAIN MUTATED 22 77 19
12Q GAIN WILD-TYPE 183 112 85

Figure S48.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.91e-12 (Fisher's exact test), Q value = 6.7e-09

Table S49.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
12Q GAIN MUTATED 24 82 12
12Q GAIN WILD-TYPE 191 124 65

Figure S49.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.43e-10 (Fisher's exact test), Q value = 1.2e-07

Table S50.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
12Q GAIN MUTATED 21 26 70
12Q GAIN WILD-TYPE 97 177 95

Figure S50.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.81e-07 (Fisher's exact test), Q value = 0.00014

Table S51.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
12Q GAIN MUTATED 9 8 34
12Q GAIN WILD-TYPE 44 87 44

Figure S51.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
12Q GAIN MUTATED 9 26 16
12Q GAIN WILD-TYPE 77 43 55

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

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.04

Table S53.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
14Q GAIN MUTATED 3 7 5
14Q GAIN WILD-TYPE 261 33 177

Figure S53.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.000275 (Fisher's exact test), Q value = 0.19

Table S54.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
16Q GAIN MUTATED 45 24 29
16Q GAIN WILD-TYPE 126 188 92

Figure S54.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 3.52e-06 (Fisher's exact test), Q value = 0.0027

Table S55.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
17P GAIN MUTATED 15 0 9
17P GAIN WILD-TYPE 156 212 112

Figure S55.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 2.58e-05 (Fisher's exact test), Q value = 0.019

Table S56.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
17Q GAIN MUTATED 19 2 9
17Q GAIN WILD-TYPE 152 210 112

Figure S56.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 5.73e-10 (Fisher's exact test), Q value = 4.8e-07

Table S57.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
19P GAIN MUTATED 31 2 17
19P GAIN WILD-TYPE 140 210 104

Figure S57.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
19P GAIN MUTATED 11 9 29
19P GAIN WILD-TYPE 107 194 136

Figure S58.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 7.33e-12 (Fisher's exact test), Q value = 6.2e-09

Table S59.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
19Q GAIN MUTATED 37 2 17
19Q GAIN WILD-TYPE 134 210 104

Figure S59.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.046

Table S60.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
19Q GAIN MUTATED 12 10 32
19Q GAIN WILD-TYPE 106 193 133

Figure S60.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.09e-21 (Fisher's exact test), Q value = 9.6e-19

Table S61.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
20P GAIN MUTATED 68 6 36
20P GAIN WILD-TYPE 103 206 85

Figure S61.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 5.62e-05 (Fisher's exact test), Q value = 0.041

Table S62.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
20P GAIN MUTATED 34 11 18
20P GAIN WILD-TYPE 66 103 58

Figure S62.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1.07e-07 (Chi-square test), Q value = 8.6e-05

Table S63.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
20P GAIN MUTATED 7 21 19 18 5 28
20P GAIN WILD-TYPE 93 67 65 57 38 29

Figure S63.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.96e-13 (Fisher's exact test), Q value = 3.4e-10

Table S64.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
20P GAIN MUTATED 18 75 17
20P GAIN WILD-TYPE 187 114 87

Figure S64.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-11 (Fisher's exact test), Q value = 1.7e-08

Table S65.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
20P GAIN MUTATED 21 77 12
20P GAIN WILD-TYPE 194 129 65

Figure S65.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.03e-10 (Fisher's exact test), Q value = 1.7e-07

Table S66.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
20P GAIN MUTATED 27 19 63
20P GAIN WILD-TYPE 91 184 102

Figure S66.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000253 (Fisher's exact test), Q value = 0.18

Table S67.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
20P GAIN MUTATED 41 14 54
20P GAIN WILD-TYPE 223 26 128

Figure S67.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.8e-07 (Fisher's exact test), Q value = 0.00061

Table S68.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
20P GAIN MUTATED 10 6 30
20P GAIN WILD-TYPE 43 89 48

Figure S68.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 4.64e-23 (Fisher's exact test), Q value = 4.1e-20

Table S69.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
20Q GAIN MUTATED 72 6 35
20Q GAIN WILD-TYPE 99 206 86

Figure S69.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.62e-05 (Fisher's exact test), Q value = 0.041

Table S70.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
20Q GAIN MUTATED 34 11 18
20Q GAIN WILD-TYPE 66 103 58

Figure S70.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 6.76e-09 (Chi-square test), Q value = 5.5e-06

Table S71.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
20Q GAIN MUTATED 7 20 21 18 5 30
20Q GAIN WILD-TYPE 93 68 63 57 38 27

Figure S71.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7.97e-15 (Fisher's exact test), Q value = 6.9e-12

Table S72.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
20Q GAIN MUTATED 18 79 16
20Q GAIN WILD-TYPE 187 110 88

Figure S72.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-12 (Fisher's exact test), Q value = 1.8e-09

Table S73.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
20Q GAIN MUTATED 21 80 12
20Q GAIN WILD-TYPE 194 126 65

Figure S73.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.96e-11 (Fisher's exact test), Q value = 1.7e-08

Table S74.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
20Q GAIN MUTATED 27 19 66
20Q GAIN WILD-TYPE 91 184 99

Figure S74.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000145 (Fisher's exact test), Q value = 0.1

Table S75.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
20Q GAIN MUTATED 42 15 55
20Q GAIN WILD-TYPE 222 25 127

Figure S75.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.23e-07 (Fisher's exact test), Q value = 0.00025

Table S76.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
20Q GAIN MUTATED 10 6 31
20Q GAIN WILD-TYPE 43 89 47

Figure S76.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 3.09e-07 (Fisher's exact test), Q value = 0.00024

Table S77.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
21Q GAIN MUTATED 35 9 6
21Q GAIN WILD-TYPE 136 203 115

Figure S77.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.78e-05 (Fisher's exact test), Q value = 0.07

Table S78.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
21Q GAIN MUTATED 12 35 3
21Q GAIN WILD-TYPE 203 171 74

Figure S78.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.013

Table S79.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
22Q GAIN MUTATED 23 4 13
22Q GAIN WILD-TYPE 148 208 108

Figure S79.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.31e-09 (Fisher's exact test), Q value = 1.1e-06

Table S80.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
1P LOSS MUTATED 29 4 25
1P LOSS WILD-TYPE 142 208 96

Figure S80.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.63e-11 (Fisher's exact test), Q value = 7.2e-08

Table S81.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
1P LOSS MUTATED 20 21 17
1P LOSS WILD-TYPE 244 19 165

Figure S81.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1.05e-09 (Fisher's exact test), Q value = 8.7e-07

Table S82.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
1Q LOSS MUTATED 13 1 23
1Q LOSS WILD-TYPE 158 211 98

Figure S82.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-10 (Fisher's exact test), Q value = 1e-07

Table S83.  Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
1Q LOSS MUTATED 10 17 10
1Q LOSS WILD-TYPE 254 23 172

Figure S83.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 3.58e-05 (Fisher's exact test), Q value = 0.026

Table S84.  Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S84.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.3e-05 (Fisher's exact test), Q value = 0.045

Table S85.  Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
2P LOSS MUTATED 6 0 1
2P LOSS WILD-TYPE 8 32 23

Figure S85.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 8.84e-07 (Fisher's exact test), Q value = 0.00069

Table S86.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
2P LOSS MUTATED 2 0 12
2P LOSS WILD-TYPE 169 212 109

Figure S86.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 4.58e-05 (Chi-square test), Q value = 0.033

Table S87.  Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
2P LOSS MUTATED 0 0 0 7 0 2
2P LOSS WILD-TYPE 100 88 84 68 43 55

Figure S87.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0018

Table S88.  Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
2P LOSS MUTATED 0 0 9
2P LOSS WILD-TYPE 186 152 100

Figure S88.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 2.11e-07 (Fisher's exact test), Q value = 0.00017

Table S89.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
2P LOSS MUTATED 0 2 12
2P LOSS WILD-TYPE 205 187 92

Figure S89.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.8e-09 (Fisher's exact test), Q value = 3.9e-06

Table S90.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
2P LOSS MUTATED 0 2 12
2P LOSS WILD-TYPE 215 204 65

Figure S90.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.04

Table S91.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
2P LOSS MUTATED 2 0 12
2P LOSS WILD-TYPE 116 203 153

Figure S91.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.12e-14 (Fisher's exact test), Q value = 1.8e-11

Table S92.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
2P LOSS MUTATED 1 13 0
2P LOSS WILD-TYPE 263 27 182

Figure S92.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.17

Table S93.  Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S93.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 8.84e-07 (Fisher's exact test), Q value = 0.00069

Table S94.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
2Q LOSS MUTATED 2 0 12
2Q LOSS WILD-TYPE 169 212 109

Figure S94.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.000316 (Chi-square test), Q value = 0.22

Table S95.  Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
2Q LOSS MUTATED 0 0 0 6 0 3
2Q LOSS WILD-TYPE 100 88 84 69 43 54

Figure S95.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0018

Table S96.  Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
2Q LOSS MUTATED 0 0 9
2Q LOSS WILD-TYPE 186 152 100

Figure S96.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 2.11e-07 (Fisher's exact test), Q value = 0.00017

Table S97.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
2Q LOSS MUTATED 0 2 12
2Q LOSS WILD-TYPE 205 187 92

Figure S97.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.68e-08 (Fisher's exact test), Q value = 5.4e-05

Table S98.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
2Q LOSS MUTATED 0 3 11
2Q LOSS WILD-TYPE 215 203 66

Figure S98.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 8.16e-06 (Fisher's exact test), Q value = 0.0062

Table S99.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
2Q LOSS MUTATED 1 0 13
2Q LOSS WILD-TYPE 117 203 152

Figure S99.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-12 (Fisher's exact test), Q value = 1.1e-09

Table S100.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
2Q LOSS MUTATED 2 12 0
2Q LOSS WILD-TYPE 262 28 182

Figure S100.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 4.72e-22 (Fisher's exact test), Q value = 4.2e-19

Table S101.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
3P LOSS MUTATED 150 170 44
3P LOSS WILD-TYPE 21 42 77

Figure S101.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 9.09e-07 (Fisher's exact test), Q value = 0.00071

Table S102.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
3P LOSS MUTATED 166 139 54
3P LOSS WILD-TYPE 39 50 50

Figure S102.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-11 (Fisher's exact test), Q value = 1.6e-08

Table S103.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
3P LOSS MUTATED 173 157 29
3P LOSS WILD-TYPE 42 49 48

Figure S103.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.013

Table S104.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
3P LOSS MUTATED 207 17 126
3P LOSS WILD-TYPE 57 23 56

Figure S104.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1.02e-09 (Fisher's exact test), Q value = 8.5e-07

Table S105.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
4P LOSS MUTATED 46 9 16
4P LOSS WILD-TYPE 125 203 105

Figure S105.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 3.38e-13 (Fisher's exact test), Q value = 2.9e-10

Table S106.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
4Q LOSS MUTATED 46 4 15
4Q LOSS WILD-TYPE 125 208 106

Figure S106.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1.14e-17 (Fisher's exact test), Q value = 1e-14

Table S107.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
6P LOSS MUTATED 65 8 27
6P LOSS WILD-TYPE 106 204 94

Figure S107.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 1.01e-06 (Chi-square test), Q value = 0.00079

Table S108.  Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
6P LOSS MUTATED 17 7 17 18 4 26
6P LOSS WILD-TYPE 83 81 67 57 39 31

Figure S108.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000234 (Fisher's exact test), Q value = 0.16

Table S109.  Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
6P LOSS MUTATED 22 33 34
6P LOSS WILD-TYPE 164 119 75

Figure S109.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 7.62e-08 (Fisher's exact test), Q value = 6.1e-05

Table S110.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
6P LOSS MUTATED 20 61 16
6P LOSS WILD-TYPE 185 128 88

Figure S110.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00013

Table S111.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
6P LOSS MUTATED 20 63 14
6P LOSS WILD-TYPE 195 143 63

Figure S111.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 2.33e-11 (Fisher's exact test), Q value = 2e-08

Table S112.  Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
6P LOSS MUTATED 16 18 62
6P LOSS WILD-TYPE 102 185 103

Figure S112.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.61e-06 (Fisher's exact test), Q value = 0.0035

Table S113.  Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
6P LOSS MUTATED 34 18 44
6P LOSS WILD-TYPE 230 22 138

Figure S113.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05

Table S114.  Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
6P LOSS MUTATED 8 4 30
6P LOSS WILD-TYPE 45 91 48

Figure S114.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.023

Table S115.  Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
6P LOSS MUTATED 4 20 18
6P LOSS WILD-TYPE 82 49 53

Figure S115.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 3.53e-17 (Fisher's exact test), Q value = 3.1e-14

Table S116.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
6Q LOSS MUTATED 81 19 27
6Q LOSS WILD-TYPE 90 193 94

Figure S116.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 9.82e-06 (Chi-square test), Q value = 0.0074

Table S117.  Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
6Q LOSS MUTATED 28 8 24 19 6 27
6Q LOSS WILD-TYPE 72 80 60 56 37 30

Figure S117.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.000332 (Fisher's exact test), Q value = 0.23

Table S118.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
6Q LOSS MUTATED 40 66 18
6Q LOSS WILD-TYPE 165 123 86

Figure S118.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 1.08e-07 (Fisher's exact test), Q value = 8.7e-05

Table S119.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
6Q LOSS MUTATED 21 34 68
6Q LOSS WILD-TYPE 97 169 97

Figure S119.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000336 (Fisher's exact test), Q value = 0.23

Table S120.  Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
6Q LOSS MUTATED 53 20 50
6Q LOSS WILD-TYPE 211 20 132

Figure S120.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.013

Table S121.  Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
6Q LOSS MUTATED 11 13 35
6Q LOSS WILD-TYPE 42 82 43

Figure S121.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2.7e-05 (Fisher's exact test), Q value = 0.02

Table S122.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
8P LOSS MUTATED 67 39 29
8P LOSS WILD-TYPE 104 173 92

Figure S122.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 8.23e-44 (Fisher's exact test), Q value = 7.3e-41

Table S123.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
9P LOSS MUTATED 110 5 29
9P LOSS WILD-TYPE 61 207 92

Figure S123.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 5.75e-19 (Fisher's exact test), Q value = 5.1e-16

Table S124.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
9P LOSS MUTATED 59 5 24
9P LOSS WILD-TYPE 41 109 52

Figure S124.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.011

Table S125.  Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
9P LOSS MUTATED 18 24 31 18 10 32
9P LOSS WILD-TYPE 82 64 53 57 33 25

Figure S125.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.4e-22 (Fisher's exact test), Q value = 1.2e-19

Table S126.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
9P LOSS MUTATED 24 103 15
9P LOSS WILD-TYPE 181 86 89

Figure S126.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.7e-23 (Fisher's exact test), Q value = 2.4e-20

Table S127.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
9P LOSS MUTATED 24 109 9
9P LOSS WILD-TYPE 191 97 68

Figure S127.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2.13e-13 (Fisher's exact test), Q value = 1.8e-10

Table S128.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
9P LOSS MUTATED 29 28 82
9P LOSS WILD-TYPE 89 175 83

Figure S128.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.65e-05 (Fisher's exact test), Q value = 0.055

Table S129.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
9P LOSS MUTATED 54 15 70
9P LOSS WILD-TYPE 210 25 112

Figure S129.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.07e-08 (Fisher's exact test), Q value = 1.7e-05

Table S130.  Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
9P LOSS MUTATED 18 9 38
9P LOSS WILD-TYPE 35 86 40

Figure S130.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.96e-05 (Fisher's exact test), Q value = 0.022

Table S131.  Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
9P LOSS MUTATED 11 31 23
9P LOSS WILD-TYPE 75 38 48

Figure S131.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 5.71e-44 (Fisher's exact test), Q value = 5.1e-41

Table S132.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
9Q LOSS MUTATED 112 6 29
9Q LOSS WILD-TYPE 59 206 92

Figure S132.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.8e-18 (Fisher's exact test), Q value = 1.6e-15

Table S133.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
9Q LOSS MUTATED 58 5 25
9Q LOSS WILD-TYPE 42 109 51

Figure S133.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1.06e-06 (Chi-square test), Q value = 0.00082

Table S134.  Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
9Q LOSS MUTATED 17 24 34 18 10 33
9Q LOSS WILD-TYPE 83 64 50 57 33 24

Figure S134.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 4.98e-24 (Fisher's exact test), Q value = 4.4e-21

Table S135.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
9Q LOSS MUTATED 24 106 15
9Q LOSS WILD-TYPE 181 83 89

Figure S135.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.3e-24 (Fisher's exact test), Q value = 8.2e-21

Table S136.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
9Q LOSS MUTATED 24 111 10
9Q LOSS WILD-TYPE 191 95 67

Figure S136.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1.64e-15 (Fisher's exact test), Q value = 1.4e-12

Table S137.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
9Q LOSS MUTATED 28 27 86
9Q LOSS WILD-TYPE 90 176 79

Figure S137.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.12

Table S138.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
9Q LOSS MUTATED 56 16 69
9Q LOSS WILD-TYPE 208 24 113

Figure S138.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.63e-08 (Fisher's exact test), Q value = 2.1e-05

Table S139.  Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
9Q LOSS MUTATED 19 10 39
9Q LOSS WILD-TYPE 34 85 39

Figure S139.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.11e-06 (Fisher's exact test), Q value = 0.0024

Table S140.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
9Q LOSS MUTATED 11 34 23
9Q LOSS WILD-TYPE 75 35 48

Figure S140.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 2.28e-09 (Fisher's exact test), Q value = 1.9e-06

Table S141.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
10P LOSS MUTATED 35 6 25
10P LOSS WILD-TYPE 136 206 96

Figure S141.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 5.2e-09 (Fisher's exact test), Q value = 4.3e-06

Table S142.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
10Q LOSS MUTATED 46 12 28
10Q LOSS WILD-TYPE 125 200 93

Figure S142.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.79e-05 (Fisher's exact test), Q value = 0.056

Table S143.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
11P LOSS MUTATED 12 0 6
11P LOSS WILD-TYPE 159 212 115

Figure S143.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1.81e-06 (Fisher's exact test), Q value = 0.0014

Table S144.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
11Q LOSS MUTATED 17 0 6
11Q LOSS WILD-TYPE 154 212 115

Figure S144.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.81e-10 (Fisher's exact test), Q value = 3.2e-07

Table S145.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
13Q LOSS MUTATED 39 6 24
13Q LOSS WILD-TYPE 132 206 97

Figure S145.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 7.66e-06 (Chi-square test), Q value = 0.0058

Table S146.  Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
13Q LOSS MUTATED 3 10 14 13 3 19
13Q LOSS WILD-TYPE 97 78 70 62 40 38

Figure S146.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0091

Table S147.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
13Q LOSS MUTATED 13 43 13
13Q LOSS WILD-TYPE 192 146 91

Figure S147.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.17e-07 (Fisher's exact test), Q value = 0.00017

Table S148.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
13Q LOSS MUTATED 11 48 10
13Q LOSS WILD-TYPE 204 158 67

Figure S148.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00081

Table S149.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
13Q LOSS MUTATED 14 12 41
13Q LOSS WILD-TYPE 104 191 124

Figure S149.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.012

Table S150.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
13Q LOSS MUTATED 23 15 29
13Q LOSS WILD-TYPE 241 25 153

Figure S150.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000294 (Fisher's exact test), Q value = 0.2

Table S151.  Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
13Q LOSS MUTATED 4 19 11
13Q LOSS WILD-TYPE 82 50 60

Figure S151.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.023

Table S152.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S152.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.031

Table S153.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
14Q LOSS MUTATED 3 8 19
14Q LOSS WILD-TYPE 11 24 5

Figure S153.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.46e-18 (Fisher's exact test), Q value = 1.3e-15

Table S154.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
14Q LOSS MUTATED 118 52 41
14Q LOSS WILD-TYPE 53 160 80

Figure S154.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 6.21e-08 (Fisher's exact test), Q value = 5e-05

Table S155.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
14Q LOSS MUTATED 58 24 36
14Q LOSS WILD-TYPE 42 90 40

Figure S155.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1.01e-13 (Chi-square test), Q value = 8.7e-11

Table S156.  Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
14Q LOSS MUTATED 27 28 62 23 13 39
14Q LOSS WILD-TYPE 73 60 22 52 30 18

Figure S156.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.28e-07 (Fisher's exact test), Q value = 1e-04

Table S157.  Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
14Q LOSS MUTATED 53 89 50
14Q LOSS WILD-TYPE 133 63 59

Figure S157.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.02e-19 (Fisher's exact test), Q value = 9e-17

Table S158.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
14Q LOSS MUTATED 65 125 16
14Q LOSS WILD-TYPE 140 64 88

Figure S158.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.49e-15 (Fisher's exact test), Q value = 1.3e-12

Table S159.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
14Q LOSS MUTATED 65 128 13
14Q LOSS WILD-TYPE 150 78 64

Figure S159.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 6.27e-11 (Fisher's exact test), Q value = 5.3e-08

Table S160.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
14Q LOSS MUTATED 36 64 105
14Q LOSS WILD-TYPE 82 139 60

Figure S160.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000317 (Fisher's exact test), Q value = 0.22

Table S161.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
14Q LOSS MUTATED 29 44 26
14Q LOSS WILD-TYPE 57 25 45

Figure S161.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 4.08e-11 (Fisher's exact test), Q value = 3.4e-08

Table S162.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
15Q LOSS MUTATED 29 0 6
15Q LOSS WILD-TYPE 142 212 115

Figure S162.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7.51e-06 (Fisher's exact test), Q value = 0.0057

Table S163.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
15Q LOSS MUTATED 6 27 2
15Q LOSS WILD-TYPE 199 162 102

Figure S163.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0081

Table S164.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
15Q LOSS MUTATED 5 28 2
15Q LOSS WILD-TYPE 210 178 75

Figure S164.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.096

Table S165.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S165.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000271 (Fisher's exact test), Q value = 0.19

Table S166.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
17P LOSS MUTATED 6 0 5
17P LOSS WILD-TYPE 8 32 19

Figure S166.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 8.36e-09 (Fisher's exact test), Q value = 6.8e-06

Table S167.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
17P LOSS MUTATED 26 2 18
17P LOSS WILD-TYPE 145 210 103

Figure S167.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 2.08e-07 (Fisher's exact test), Q value = 0.00017

Table S168.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
17P LOSS MUTATED 3 28 15
17P LOSS WILD-TYPE 202 161 89

Figure S168.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-07 (Fisher's exact test), Q value = 8e-05

Table S169.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
17P LOSS MUTATED 4 26 16
17P LOSS WILD-TYPE 211 180 61

Figure S169.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 1.3e-05

Table S170.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
17P LOSS MUTATED 9 4 33
17P LOSS WILD-TYPE 109 199 132

Figure S170.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.22e-08 (Fisher's exact test), Q value = 5e-05

Table S171.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
17P LOSS MUTATED 12 15 19
17P LOSS WILD-TYPE 252 25 163

Figure S171.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.0023

Table S172.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
17Q LOSS MUTATED 12 1 15
17Q LOSS WILD-TYPE 159 211 106

Figure S172.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 8.58e-05 (Fisher's exact test), Q value = 0.061

Table S173.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
17Q LOSS MUTATED 2 14 12
17Q LOSS WILD-TYPE 203 175 92

Figure S173.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.023

Table S174.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
17Q LOSS MUTATED 3 13 12
17Q LOSS WILD-TYPE 212 193 65

Figure S174.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 6.34e-06 (Fisher's exact test), Q value = 0.0048

Table S175.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
17Q LOSS MUTATED 5 2 21
17Q LOSS WILD-TYPE 113 201 144

Figure S175.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.63e-07 (Fisher's exact test), Q value = 0.00036

Table S176.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
17Q LOSS MUTATED 8 12 8
17Q LOSS WILD-TYPE 256 28 174

Figure S176.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 2.15e-13 (Fisher's exact test), Q value = 1.8e-10

Table S177.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
18P LOSS MUTATED 58 10 23
18P LOSS WILD-TYPE 113 202 98

Figure S177.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2.68e-07 (Fisher's exact test), Q value = 0.00021

Table S178.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
18P LOSS MUTATED 28 5 22
18P LOSS WILD-TYPE 72 109 54

Figure S178.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 3.07e-08 (Chi-square test), Q value = 2.5e-05

Table S179.  Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
18P LOSS MUTATED 5 14 23 15 2 24
18P LOSS WILD-TYPE 95 74 61 60 41 33

Figure S179.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 8.18e-18 (Fisher's exact test), Q value = 7.2e-15

Table S180.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
18P LOSS MUTATED 10 71 9
18P LOSS WILD-TYPE 195 118 95

Figure S180.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.86e-16 (Fisher's exact test), Q value = 4.2e-13

Table S181.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
18P LOSS MUTATED 9 71 10
18P LOSS WILD-TYPE 206 135 67

Figure S181.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 7.12e-11 (Fisher's exact test), Q value = 6e-08

Table S182.  Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
18P LOSS MUTATED 25 12 54
18P LOSS WILD-TYPE 93 191 111

Figure S182.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.24e-07 (Fisher's exact test), Q value = 0.00049

Table S183.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
18P LOSS MUTATED 29 17 45
18P LOSS WILD-TYPE 235 23 137

Figure S183.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.01e-07 (Fisher's exact test), Q value = 8.1e-05

Table S184.  Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
18P LOSS MUTATED 9 4 29
18P LOSS WILD-TYPE 44 91 49

Figure S184.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.96e-05 (Fisher's exact test), Q value = 0.057

Table S185.  Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
18P LOSS MUTATED 5 22 15
18P LOSS WILD-TYPE 81 47 56

Figure S185.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 3.81e-13 (Fisher's exact test), Q value = 3.3e-10

Table S186.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
18Q LOSS MUTATED 59 11 23
18Q LOSS WILD-TYPE 112 201 98

Figure S186.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.0015

Table S187.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
18Q LOSS MUTATED 27 6 22
18Q LOSS WILD-TYPE 73 108 54

Figure S187.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 1.99e-07 (Chi-square test), Q value = 0.00016

Table S188.  Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
18Q LOSS MUTATED 5 14 23 16 4 24
18Q LOSS WILD-TYPE 95 74 61 59 39 33

Figure S188.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 7.34e-17 (Fisher's exact test), Q value = 6.4e-14

Table S189.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
18Q LOSS MUTATED 11 71 10
18Q LOSS WILD-TYPE 194 118 94

Figure S189.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.86e-16 (Fisher's exact test), Q value = 6.8e-13

Table S190.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
18Q LOSS MUTATED 9 71 12
18Q LOSS WILD-TYPE 206 135 65

Figure S190.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 2.1e-10 (Fisher's exact test), Q value = 1.8e-07

Table S191.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
18Q LOSS MUTATED 26 13 54
18Q LOSS WILD-TYPE 92 190 111

Figure S191.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.51e-07 (Fisher's exact test), Q value = 0.00028

Table S192.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
18Q LOSS MUTATED 30 18 45
18Q LOSS WILD-TYPE 234 22 137

Figure S192.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05

Table S193.  Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 95 78
18Q LOSS MUTATED 8 4 30
18Q LOSS WILD-TYPE 45 91 48

Figure S193.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.28e-06 (Fisher's exact test), Q value = 0.007

Table S194.  Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 69 71
18Q LOSS MUTATED 4 23 15
18Q LOSS WILD-TYPE 82 46 56

Figure S194.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 2.15e-07 (Fisher's exact test), Q value = 0.00017

Table S195.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
21Q LOSS MUTATED 24 6 25
21Q LOSS WILD-TYPE 147 206 96

Figure S195.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.024

Table S196.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
21Q LOSS MUTATED 20 14 20
21Q LOSS WILD-TYPE 244 26 162

Figure S196.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.49e-08 (Fisher's exact test), Q value = 1.2e-05

Table S197.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
22Q LOSS MUTATED 25 1 13
22Q LOSS WILD-TYPE 146 211 108

Figure S197.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 0.0017

Table S198.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 189 104
22Q LOSS MUTATED 6 30 3
22Q LOSS WILD-TYPE 199 159 101

Figure S198.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0079

Table S199.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 206 77
22Q LOSS MUTATED 4 28 7
22Q LOSS WILD-TYPE 211 178 70

Figure S199.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.014

Table S200.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 203 165
22Q LOSS MUTATED 4 8 27
22Q LOSS WILD-TYPE 114 195 138

Figure S200.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.14

Table S201.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 212 121
XQ LOSS MUTATED 27 8 13
XQ LOSS WILD-TYPE 144 204 108

Figure S201.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.52e-05 (Fisher's exact test), Q value = 0.047

Table S202.  Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 264 40 182
XQ LOSS MUTATED 19 13 15
XQ LOSS WILD-TYPE 245 27 167

Figure S202.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 504

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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