Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1QZ2932
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QZ2932
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 59 arm-level events and 10 molecular subtypes across 501 patients, 279 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',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 13q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

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

  • xq gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

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

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • xp loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 59 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 279 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1q gain 26 (5%) 475 1e-05
(0.000105) 		0.0161
(0.0413) 		0.00302
(0.0102) 		0.0645
(0.129) 		0.00144
(0.00548) 		4e-05
(0.000288) 		0.087
(0.167) 		0.0493
(0.105) 		0.0146
(0.0384) 		0.0154
(0.0401)
7q gain 20 (4%) 481 1e-05
(0.000105) 		1e-05
(0.000105) 		0.572
(0.711) 		0.0132
(0.0355) 		0.00013
(0.000737) 		2e-05
(0.000182) 		5e-05
(0.000347) 		1e-05
(0.000105) 		0.612
(0.748) 		0.00089
(0.00365)
17p gain 16 (3%) 485 1e-05
(0.000105) 		1e-05
(0.000105) 		0.537
(0.676) 		0.0278
(0.0642) 		1e-05
(0.000105) 		1e-05
(0.000105) 		2e-05
(0.000182) 		1e-05
(0.000105) 		0.362
(0.509) 		0.00027
(0.00132)
17q gain 18 (4%) 483 1e-05
(0.000105) 		1e-05
(0.000105) 		0.636
(0.763) 		0.016
(0.0412) 		1e-05
(0.000105) 		1e-05
(0.000105) 		1e-05
(0.000105) 		1e-05
(0.000105) 		0.512
(0.653) 		0.00017
(0.00092)
6q loss 7 (1%) 494 4e-05
(0.000288) 		0.00234
(0.00827) 		0.0124
(0.0341) 		0.575
(0.712) 		0.028
(0.0642) 		0.018
(0.044) 		0.00489
(0.0155) 		0.00064
(0.00278) 		1
(1.00) 		0.00979
(0.0279)
22q loss 89 (18%) 412 1e-05
(0.000105) 		1e-05
(0.000105) 		0.12
(0.204) 		0.502
(0.643) 		1e-05
(0.000105) 		1e-05
(0.000105) 		0.00042
(0.00197) 		4e-05
(0.000288) 		0.00018
(0.000957) 		0.00026
(0.00128)
5p gain 21 (4%) 480 1e-05
(0.000105) 		0.00187
(0.00685) 		0.529
(0.671) 		0.233
(0.356) 		0.00532
(0.0167) 		7e-05
(0.000459) 		0.0012
(0.00475) 		0.00013
(0.000737) 		0.598
(0.734) 		0.0033
(0.0111)
5q gain 17 (3%) 484 1e-05
(0.000105) 		3e-05
(0.000242) 		0.849
(0.957) 		0.0791
(0.153) 		0.00017
(0.00092) 		4e-05
(0.000288) 		0.00012
(0.00073) 		2e-05
(0.000182) 		0.839
(0.956) 		0.00419
(0.0137)
7p gain 18 (4%) 483 1e-05
(0.000105) 		5e-05
(0.000347) 		0.662
(0.789) 		0.0526
(0.11) 		0.00065
(0.00278) 		0.0001
(0.000628) 		0.00038
(0.00181) 		2e-05
(0.000182) 		0.576
(0.712) 		0.00555
(0.0172)
12p gain 14 (3%) 487 1e-05
(0.000105) 		1e-05
(0.000105) 		0.852
(0.957) 		0.0798
(0.154) 		1e-05
(0.000105) 		1e-05
(0.000105) 		5e-05
(0.000347) 		1e-05
(0.000105) 		0.556
(0.695) 		0.00242
(0.00845)
12q gain 15 (3%) 486 1e-05
(0.000105) 		1e-05
(0.000105) 		0.85
(0.957) 		0.0813
(0.156) 		1e-05
(0.000105) 		1e-05
(0.000105) 		3e-05
(0.000242) 		2e-05
(0.000182) 		0.386
(0.537) 		0.00098
(0.00399)
14q gain 11 (2%) 490 1e-05
(0.000105) 		0.00019
(0.001) 		1
(1.00) 		0.159
(0.262) 		0.00057
(0.00257) 		0.00012
(0.00073) 		0.00074
(0.00314) 		0.0001
(0.000628) 		0.851
(0.957) 		0.00217
(0.00771)
16p gain 15 (3%) 486 1e-05
(0.000105) 		4e-05
(0.000288) 		0.633
(0.763) 		0.0799
(0.154) 		0.00017
(0.00092) 		3e-05
(0.000242) 		0.00011
(0.000683) 		3e-05
(0.000242) 		0.435
(0.584) 		0.00078
(0.00326)
16q gain 13 (3%) 488 1e-05
(0.000105) 		0.00017
(0.00092) 		0.796
(0.922) 		0.277
(0.404) 		0.00088
(0.00363) 		0.00025
(0.00125) 		0.00163
(0.00601) 		0.00013
(0.000737) 		0.62
(0.755) 		0.00756
(0.0225)
19p gain 8 (2%) 493 1e-05
(0.000105) 		0.0002
(0.00104) 		0.00043
(0.002) 		0.00023
(0.00116) 		0.00013
(0.000737) 		3e-05
(0.000242) 		0.453
(0.599) 		0.0223
(0.0527)
19q gain 10 (2%) 491 1e-05
(0.000105) 		2e-05
(0.000182) 		0.636
(0.763) 		0.0635
(0.128) 		3e-05
(0.000242) 		4e-05
(0.000288) 		1e-05
(0.000105) 		1e-05
(0.000105) 		0.638
(0.763) 		0.00159
(0.00594)
2p loss 10 (2%) 491 1e-05
(0.000105) 		4e-05
(0.000288) 		0.775
(0.911) 		0.0915
(0.171) 		7e-05
(0.000459) 		3e-05
(0.000242) 		1e-05
(0.000105) 		2e-05
(0.000182) 		0.234
(0.356) 		0.00044
(0.00203)
2q loss 10 (2%) 491 1e-05
(0.000105) 		3e-05
(0.000242) 		0.773
(0.911) 		0.0896
(0.17) 		6e-05
(0.000407) 		6e-05
(0.000407) 		1e-05
(0.000105) 		1e-05
(0.000105) 		0.232
(0.356) 		0.00056
(0.00256)
8p loss 4 (1%) 497 0.0001
(0.000628) 		0.0173
(0.0428) 		0.0364
(0.0814) 		0.0494
(0.105) 		0.00777
(0.0229) 		0.00422
(0.0137) 		0.108
(0.191) 		0.0189
(0.0453)
8q loss 4 (1%) 497 0.00013
(0.000737) 		0.0174
(0.0428) 		0.0362
(0.0812) 		0.0458
(0.0992) 		0.00774
(0.0229) 		0.00421
(0.0137) 		0.111
(0.194) 		0.0187
(0.0451)
10p loss 7 (1%) 494 1e-05
(0.000105) 		0.0116
(0.0322) 		0.496
(0.637) 		0.42
(0.566) 		0.0206
(0.0489) 		0.0154
(0.0401) 		0.00474
(0.0152) 		0.00063
(0.00277) 		1
(1.00) 		0.0112
(0.0313)
11p loss 7 (1%) 494 1e-05
(0.000105) 		0.011
(0.0309) 		0.495
(0.637) 		0.959
(1.00) 		0.00648
(0.0199) 		0.0175
(0.0429) 		0.00494
(0.0156) 		0.00059
(0.00262) 		0.801
(0.923) 		0.0107
(0.0303)
11q loss 9 (2%) 492 1e-05
(0.000105) 		0.0173
(0.0428) 		0.321
(0.454) 		0.814
(0.936) 		0.0158
(0.0408) 		0.0184
(0.0447) 		0.00057
(0.00257) 		0.00247
(0.00857) 		0.909
(1.00) 		0.00255
(0.0088)
13q loss 14 (3%) 487 0.00161
(0.00597) 		0.0148
(0.0387) 		0.0626
(0.127) 		0.138
(0.232) 		0.00534
(0.0167) 		0.00799
(0.0233) 		0.00105
(0.00421) 		0.00041
(0.00194) 		0.102
(0.182) 		0.0127
(0.0346)
15q loss 8 (2%) 493 0.00014
(0.000787) 		0.0002
(0.00104) 		0.193
(0.306) 		0.09
(0.17) 		0.00059
(0.00262) 		0.00026
(0.00128) 		7e-05
(0.000459) 		2e-05
(0.000182) 		0.411
(0.561) 		0.00195
(0.00706)
19p loss 5 (1%) 496 0.00932
(0.0269) 		0.00657
(0.02) 		0.324
(0.457) 		0.237
(0.36) 		0.0167
(0.0419) 		0.0129
(0.0349) 		0.00239
(0.00839) 		0.00107
(0.00427) 		0.0874
(0.167) 		0.00145
(0.00548)
4p gain 5 (1%) 496 1e-05
(0.000105) 		0.00668
(0.0202) 		0.0165
(0.0419) 		0.0125
(0.0341) 		0.0416
(0.0915) 		0.0139
(0.0373) 		1
(1.00) 		0.0754
(0.147)
4q gain 5 (1%) 496 1e-05
(0.000105) 		0.00659
(0.02) 		0.0163
(0.0417) 		0.0125
(0.0341) 		0.0411
(0.0908) 		0.0142
(0.038) 		1
(1.00) 		0.078
(0.152)
20p gain 12 (2%) 489 1e-05
(0.000105) 		0.00029
(0.0014) 		0.794
(0.922) 		0.0944
(0.173) 		0.0026
(0.00892) 		0.00079
(0.00328) 		0.00424
(0.0137) 		0.00075
(0.00316) 		0.915
(1.00) 		0.0955
(0.174)
20q gain 12 (2%) 489 1e-05
(0.000105) 		0.00031
(0.00149) 		0.795
(0.922) 		0.0926
(0.171) 		0.00277
(0.00945) 		0.00103
(0.00416) 		0.00406
(0.0135) 		0.00065
(0.00278) 		0.912
(1.00) 		0.0947
(0.173)
3q loss 4 (1%) 497 0.00022
(0.00113) 		0.0174
(0.0428) 		0.496
(0.637) 		0.424
(0.569) 		0.0358
(0.0805) 		0.0459
(0.0992) 		0.00794
(0.0233) 		0.00394
(0.0132) 		1
(1.00) 		0.0675
(0.135)
9p loss 19 (4%) 482 1e-05
(0.000105) 		0.0379
(0.084) 		0.242
(0.365) 		0.648
(0.774) 		0.031
(0.0701) 		0.0615
(0.125) 		0.0087
(0.0253) 		0.00712
(0.0213) 		0.3
(0.433) 		0.00422
(0.0137)
10q loss 6 (1%) 495 1e-05
(0.000105) 		0.0292
(0.0663) 		0.0532
(0.11) 		0.0456
(0.0992) 		0.0144
(0.0382) 		0.00445
(0.0143) 		1
(1.00) 		0.028
(0.0642)
11p gain 6 (1%) 495 0.00123
(0.00481) 		0.0279
(0.0642) 		0.781
(0.914) 		0.299
(0.432) 		0.0527
(0.11) 		0.0447
(0.098) 		0.00946
(0.0271) 		0.00645
(0.0199) 		0.469
(0.611) 		0.0965
(0.175)
1q loss 3 (1%) 498 0.00132
(0.00509) 		0.0478
(0.103) 		0.0997
(0.179) 		0.151
(0.252) 		0.0266
(0.0624) 		0.0167
(0.0419) 		1
(1.00) 		0.192
(0.305)
3p loss 3 (1%) 498 0.00123
(0.00481) 		0.0494
(0.105) 		0.1
(0.179) 		0.153
(0.254) 		0.0267
(0.0624) 		0.0168
(0.042) 		1
(1.00) 		0.193
(0.306)
9q loss 25 (5%) 476 1e-05
(0.000105) 		0.104
(0.184) 		0.172
(0.279) 		0.114
(0.196) 		0.172
(0.279) 		0.0609
(0.124) 		0.00933
(0.0269) 		0.00704
(0.0212) 		0.278
(0.404) 		0.00488
(0.0155)
11q gain 5 (1%) 496 0.00013
(0.000737) 		0.0602
(0.123) 		0.78
(0.914) 		0.301
(0.433) 		0.111
(0.194) 		0.125
(0.212) 		0.0267
(0.0624) 		0.0214
(0.0506) 		0.31
(0.444) 		0.273
(0.401)
13q gain 5 (1%) 496 2e-05
(0.000182) 		0.0187
(0.0451) 		0.385
(0.537) 		0.213
(0.329) 		0.0486
(0.104) 		0.103
(0.183) 		0.236
(0.359) 		0.0724
(0.144) 		0.845
(0.957) 		0.196
(0.306)
xp gain 8 (2%) 493 1e-05
(0.000105) 		0.00191
(0.00696) 		0.838
(0.956) 		0.504
(0.644) 		0.045
(0.0984) 		0.0565
(0.116) 		0.178
(0.288) 		0.0737
(0.146) 		0.8
(0.923) 		0.184
(0.295)
xq loss 3 (1%) 498 0.0503
(0.106) 		0.0506
(0.106) 		0.277
(0.404) 		0.196
(0.306) 		0.0994
(0.179) 		0.151
(0.251) 		0.0281
(0.0642) 		0.0166
(0.0419) 		0.11
(0.194) 		0.019
(0.0454)
xq gain 9 (2%) 492 1e-05
(0.000105) 		0.0114
(0.0316) 		0.839
(0.956) 		0.503
(0.644) 		0.0974
(0.176) 		0.14
(0.235) 		0.281
(0.407) 		0.134
(0.226) 		0.909
(1.00) 		0.397
(0.545)
6p loss 4 (1%) 497 0.00018
(0.000957) 		0.0463
(0.0997) 		0.458
(0.601) 		0.396
(0.545) 		0.113
(0.195) 		0.0641
(0.129) 		0.399
(0.545) 		0.196
(0.306)
21q loss 8 (2%) 493 0.00065
(0.00278) 		0.162
(0.266) 		0.381
(0.533) 		0.214
(0.329) 		0.713
(0.841) 		0.418
(0.564) 		0.0912
(0.171) 		0.0287
(0.0654) 		0.464
(0.607) 		0.0554
(0.114)
1p gain 5 (1%) 496 0.00146
(0.00549) 		0.842
(0.957) 		0.922
(1.00) 		0.882
(0.989) 		0.108
(0.191) 		0.0513
(0.107) 		0.274
(0.402) 		0.142
(0.238)
3p gain 3 (1%) 498 0.00134
(0.00513) 		0.55
(0.69) 		0.494
(0.637) 		0.589
(0.725) 		0.304
(0.436) 		0.188
(0.3) 		1
(1.00) 		0.194
(0.306)
8p gain 6 (1%) 495 0.00013
(0.000737) 		0.416
(0.564) 		0.454
(0.599) 		0.632
(0.763) 		0.597
(0.734) 		0.534
(0.673) 		0.451
(0.599) 		0.451
(0.599) 		1
(1.00) 		1
(1.00)
8q gain 7 (1%) 494 4e-05
(0.000288) 		0.201
(0.313) 		0.455
(0.599) 		0.627
(0.763) 		0.826
(0.948) 		0.522
(0.664) 		0.8
(0.923) 		0.63
(0.763) 		0.9
(1.00) 		0.895
(1.00)
9p gain 3 (1%) 498 0.0013
(0.00505) 		0.553
(0.693) 		0.494
(0.637) 		0.588
(0.725) 		1
(1.00) 		1
(1.00) 		0.418
(0.564) 		0.632
(0.763)
9q gain 4 (1%) 497 0.0107
(0.0303) 		0.79
(0.922) 		0.902
(1.00) 		0.364
(0.51) 		0.838
(0.956) 		1
(1.00) 		0.166
(0.273) 		0.571
(0.711)
18p gain 6 (1%) 495 1e-05
(0.000105) 		0.0926
(0.171) 		0.121
(0.206) 		0.268
(0.397) 		0.255
(0.381) 		0.113
(0.195) 		0.454
(0.599) 		0.396
(0.545)
18q gain 6 (1%) 495 4e-05
(0.000288) 		0.0918
(0.171) 		0.119
(0.204) 		0.265
(0.394) 		0.256
(0.381) 		0.111
(0.194) 		0.454
(0.599) 		0.399
(0.545)
21q gain 5 (1%) 496 0.00023
(0.00116) 		0.168
(0.275) 		0.241
(0.365) 		0.491
(0.637) 		0.453
(0.599) 		0.311
(0.444) 		0.692
(0.818) 		0.683
(0.81)
1p loss 4 (1%) 497 0.0001
(0.000628) 		0.184
(0.295) 		0.244
(0.367) 		0.316
(0.45) 		0.114
(0.196) 		0.0646
(0.129) 		0.846
(0.957) 		0.195
(0.306)
17p loss 8 (2%) 493 0.0144
(0.0382) 		0.414
(0.563) 		1
(1.00) 		0.389
(0.538) 		0.636
(0.763) 		0.601
(0.736) 		0.0922
(0.171) 		0.16
(0.264) 		0.126
(0.213) 		0.205
(0.318)
18p loss 4 (1%) 497 0.002
(0.0072) 		0.183
(0.295) 		1
(1.00) 		0.389
(0.538) 		0.245
(0.367) 		0.317
(0.451) 		0.0741
(0.146) 		0.0922
(0.171) 		0.533
(0.673) 		0.273
(0.401)
18q loss 4 (1%) 497 0.00214
(0.00765) 		0.185
(0.295) 		1
(1.00) 		0.387
(0.537) 		0.245
(0.367) 		0.32
(0.453) 		0.0743
(0.146) 		0.0902
(0.17) 		0.532
(0.673) 		0.273
(0.401)
xp loss 4 (1%) 497 0.113
(0.195) 		0.184
(0.295) 		0.279
(0.405) 		0.196
(0.306) 		0.458
(0.601) 		0.209
(0.323) 		0.0747
(0.146) 		0.0921
(0.171) 		0.0375
(0.0835) 		0.0952
(0.174)
17q loss 4 (1%) 497 0.114
(0.196) 		0.792
(0.922) 		0.9
(1.00) 		0.665
(0.791) 		0.467
(0.609) 		0.568
(0.709) 		0.332
(0.467) 		0.684
(0.81)
'1p gain' versus 'CN_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
1P GAIN MUTATED 4 1 0
1P GAIN WILD-TYPE 52 355 89

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
1Q GAIN MUTATED 18 7 1
1Q GAIN WILD-TYPE 38 349 88

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.041

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
1Q GAIN MUTATED 19 2 5
1Q GAIN WILD-TYPE 258 152 65

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

'1q gain' versus 'RPPA_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 79 81
1Q GAIN MUTATED 0 9 2
1Q GAIN WILD-TYPE 61 70 79

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0055

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
1Q GAIN MUTATED 17 2 4 3
1Q GAIN WILD-TYPE 151 153 55 114

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
1Q GAIN MUTATED 16 2 1 3 4
1Q GAIN WILD-TYPE 89 132 85 93 74

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.1

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
1Q GAIN MUTATED 15 3 8
1Q GAIN WILD-TYPE 164 125 185

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.038

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
1Q GAIN MUTATED 14 5 3
1Q GAIN WILD-TYPE 146 159 143

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
1Q GAIN MUTATED 14 2 6
1Q GAIN WILD-TYPE 151 124 173

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0051

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
3P GAIN MUTATED 3 0 0
3P GAIN WILD-TYPE 53 356 89

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

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S11.  Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
4P GAIN MUTATED 5 0 0
4P GAIN WILD-TYPE 51 356 89

Figure S11.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.02

Table S12.  Gene #4: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
4P GAIN MUTATED 0 5 0
4P GAIN WILD-TYPE 277 149 70

Figure S12.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.042

Table S13.  Gene #4: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
4P GAIN MUTATED 0 5 0 0
4P GAIN WILD-TYPE 168 150 59 117

Figure S13.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.034

Table S14.  Gene #4: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
4P GAIN MUTATED 0 5 0 0 0
4P GAIN WILD-TYPE 105 129 86 96 78

Figure S14.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
4P GAIN MUTATED 1 4 0
4P GAIN WILD-TYPE 181 147 167

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

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.037

Table S16.  Gene #4: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
4P GAIN MUTATED 1 4 0
4P GAIN WILD-TYPE 178 124 193

Figure S16.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S17.  Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
4Q GAIN MUTATED 5 0 0
4Q GAIN WILD-TYPE 51 356 89

Figure S17.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00659 (Fisher's exact test), Q value = 0.02

Table S18.  Gene #5: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
4Q GAIN MUTATED 0 5 0
4Q GAIN WILD-TYPE 277 149 70

Figure S18.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.042

Table S19.  Gene #5: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
4Q GAIN MUTATED 0 5 0 0
4Q GAIN WILD-TYPE 168 150 59 117

Figure S19.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.034

Table S20.  Gene #5: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
4Q GAIN MUTATED 0 5 0 0 0
4Q GAIN WILD-TYPE 105 129 86 96 78

Figure S20.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.091

Table S21.  Gene #5: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
4Q GAIN MUTATED 1 4 0
4Q GAIN WILD-TYPE 181 147 167

Figure S21.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.038

Table S22.  Gene #5: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
4Q GAIN MUTATED 1 4 0
4Q GAIN WILD-TYPE 178 124 193

Figure S22.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S23.  Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
5P GAIN MUTATED 21 0 0
5P GAIN WILD-TYPE 35 356 89

Figure S23.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0069

Table S24.  Gene #6: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
5P GAIN MUTATED 5 14 2
5P GAIN WILD-TYPE 272 140 68

Figure S24.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.017

Table S25.  Gene #6: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
5P GAIN MUTATED 5 14 1 1
5P GAIN WILD-TYPE 163 141 58 116

Figure S25.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00046

Table S26.  Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
5P GAIN MUTATED 6 14 0 1 0
5P GAIN WILD-TYPE 99 120 86 95 78

Figure S26.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0048

Table S27.  Gene #6: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
5P GAIN MUTATED 7 13 1
5P GAIN WILD-TYPE 175 138 166

Figure S27.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S28.  Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
5P GAIN MUTATED 7 13 1
5P GAIN WILD-TYPE 172 115 192

Figure S28.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.011

Table S29.  Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
5P GAIN MUTATED 8 9 1
5P GAIN WILD-TYPE 157 117 178

Figure S29.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S30.  Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
5Q GAIN MUTATED 17 0 0
5Q GAIN WILD-TYPE 39 356 89

Figure S30.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S31.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
5Q GAIN MUTATED 2 14 1
5Q GAIN WILD-TYPE 275 140 69

Figure S31.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00092

Table S32.  Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
5Q GAIN MUTATED 2 14 0 1
5Q GAIN WILD-TYPE 166 141 59 116

Figure S32.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S33.  Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
5Q GAIN MUTATED 2 14 0 1 0
5Q GAIN WILD-TYPE 103 120 86 95 78

Figure S33.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00073

Table S34.  Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 179 138 166

Figure S34.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S35.  Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 176 115 192

Figure S35.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.014

Table S36.  Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
5Q GAIN MUTATED 4 9 1
5Q GAIN WILD-TYPE 161 117 178

Figure S36.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S37.  Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
7P GAIN MUTATED 18 0 0
7P GAIN WILD-TYPE 38 356 89

Figure S37.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00035

Table S38.  Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
7P GAIN MUTATED 2 14 2
7P GAIN WILD-TYPE 275 140 68

Figure S38.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0028

Table S39.  Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
7P GAIN MUTATED 2 14 1 1
7P GAIN WILD-TYPE 166 141 58 116

Figure S39.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00063

Table S40.  Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
7P GAIN MUTATED 2 14 1 1 0
7P GAIN WILD-TYPE 103 120 85 95 78

Figure S40.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0018

Table S41.  Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 178 138 166

Figure S41.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S42.  Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 175 115 192

Figure S42.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00555 (Fisher's exact test), Q value = 0.017

Table S43.  Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
7P GAIN MUTATED 5 9 1
7P GAIN WILD-TYPE 160 117 178

Figure S43.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S44.  Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
7Q GAIN MUTATED 19 0 1
7Q GAIN WILD-TYPE 37 356 88

Figure S44.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S45.  Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
7Q GAIN MUTATED 2 16 2
7Q GAIN WILD-TYPE 275 138 68

Figure S45.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.036

Table S46.  Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
7Q GAIN MUTATED 4 1 0 2 0 5 0
7Q GAIN WILD-TYPE 42 27 33 27 49 22 9

Figure S46.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S47.  Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
7Q GAIN MUTATED 2 16 1 1
7Q GAIN WILD-TYPE 166 139 58 116

Figure S47.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S48.  Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
7Q GAIN MUTATED 2 16 1 1 0
7Q GAIN WILD-TYPE 103 118 85 95 78

Figure S48.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00035

Table S49.  Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 178 136 166

Figure S49.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S50.  Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 175 113 192

Figure S50.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0036

Table S51.  Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
7Q GAIN MUTATED 5 11 1
7Q GAIN WILD-TYPE 160 115 178

Figure S51.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S52.  Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8P GAIN MUTATED 5 1 0
8P GAIN WILD-TYPE 51 355 89

Figure S52.  Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S53.  Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8Q GAIN MUTATED 6 1 0
8Q GAIN WILD-TYPE 50 355 89

Figure S53.  Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.005

Table S54.  Gene #12: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
9P GAIN MUTATED 3 0 0
9P GAIN WILD-TYPE 53 356 89

Figure S54.  Get High-res Image Gene #12: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.03

Table S55.  Gene #13: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
9Q GAIN MUTATED 3 1 0
9Q GAIN WILD-TYPE 53 355 89

Figure S55.  Get High-res Image Gene #13: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0048

Table S56.  Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11P GAIN MUTATED 4 1 1
11P GAIN WILD-TYPE 52 355 88

Figure S56.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.064

Table S57.  Gene #14: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
11P GAIN MUTATED 1 5 0
11P GAIN WILD-TYPE 276 149 70

Figure S57.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.098

Table S58.  Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
11P GAIN MUTATED 0 5 0 1 0
11P GAIN WILD-TYPE 105 129 86 95 78

Figure S58.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00946 (Fisher's exact test), Q value = 0.027

Table S59.  Gene #14: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
11P GAIN MUTATED 0 5 1
11P GAIN WILD-TYPE 182 146 166

Figure S59.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00645 (Fisher's exact test), Q value = 0.02

Table S60.  Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
11P GAIN MUTATED 0 5 1
11P GAIN WILD-TYPE 179 123 192

Figure S60.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S61.  Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11Q GAIN MUTATED 4 0 1
11Q GAIN WILD-TYPE 52 356 88

Figure S61.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.062

Table S62.  Gene #15: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
11Q GAIN MUTATED 0 4 1
11Q GAIN WILD-TYPE 182 147 166

Figure S62.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.051

Table S63.  Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
11Q GAIN MUTATED 0 4 1
11Q GAIN WILD-TYPE 179 124 192

Figure S63.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S64.  Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
12P GAIN MUTATED 13 0 1
12P GAIN WILD-TYPE 43 356 88

Figure S64.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S65.  Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
12P GAIN MUTATED 1 13 0
12P GAIN WILD-TYPE 276 141 70

Figure S65.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S66.  Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
12P GAIN MUTATED 0 13 0 1
12P GAIN WILD-TYPE 168 142 59 116

Figure S66.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S67.  Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
12P GAIN MUTATED 0 13 0 1 0
12P GAIN WILD-TYPE 105 121 86 95 78

Figure S67.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00035

Table S68.  Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
12P GAIN MUTATED 1 12 1
12P GAIN WILD-TYPE 181 139 166

Figure S68.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S69.  Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
12P GAIN MUTATED 1 12 1
12P GAIN WILD-TYPE 178 116 192

Figure S69.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.0084

Table S70.  Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
12P GAIN MUTATED 2 8 1
12P GAIN WILD-TYPE 163 118 178

Figure S70.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S71.  Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
12Q GAIN MUTATED 14 0 1
12Q GAIN WILD-TYPE 42 356 88

Figure S71.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S72.  Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
12Q GAIN MUTATED 1 14 0
12Q GAIN WILD-TYPE 276 140 70

Figure S72.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S73.  Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
12Q GAIN MUTATED 0 14 0 1
12Q GAIN WILD-TYPE 168 141 59 116

Figure S73.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S74.  Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
12Q GAIN MUTATED 0 14 0 1 0
12Q GAIN WILD-TYPE 105 120 86 95 78

Figure S74.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S75.  Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 181 138 166

Figure S75.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S76.  Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 178 115 192

Figure S76.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.004

Table S77.  Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
12Q GAIN MUTATED 2 9 1
12Q GAIN WILD-TYPE 163 117 178

Figure S77.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S78.  Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
13Q GAIN MUTATED 5 0 0
13Q GAIN WILD-TYPE 51 356 89

Figure S78.  Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.045

Table S79.  Gene #18: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
13Q GAIN MUTATED 0 4 1
13Q GAIN WILD-TYPE 277 150 69

Figure S79.  Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.1

Table S80.  Gene #18: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
13Q GAIN MUTATED 0 4 1 0
13Q GAIN WILD-TYPE 168 151 58 117

Figure S80.  Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S81.  Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
14Q GAIN MUTATED 10 0 1
14Q GAIN WILD-TYPE 46 356 88

Figure S81.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.001

Table S82.  Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
14Q GAIN MUTATED 1 10 0
14Q GAIN WILD-TYPE 276 144 70

Figure S82.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0026

Table S83.  Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
14Q GAIN MUTATED 1 10 0 0
14Q GAIN WILD-TYPE 167 145 59 117

Figure S83.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00073

Table S84.  Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
14Q GAIN MUTATED 0 10 0 0 1
14Q GAIN WILD-TYPE 105 124 86 96 77

Figure S84.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0031

Table S85.  Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 180 142 167

Figure S85.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00063

Table S86.  Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 177 119 193

Figure S86.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0077

Table S87.  Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
14Q GAIN MUTATED 3 7 0
14Q GAIN WILD-TYPE 162 119 179

Figure S87.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S88.  Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
16P GAIN MUTATED 14 0 1
16P GAIN WILD-TYPE 42 356 88

Figure S88.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S89.  Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
16P GAIN MUTATED 1 13 1
16P GAIN WILD-TYPE 276 141 69

Figure S89.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00092

Table S90.  Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
16P GAIN MUTATED 1 13 0 1
16P GAIN WILD-TYPE 167 142 59 116

Figure S90.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S91.  Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
16P GAIN MUTATED 1 13 0 1 0
16P GAIN WILD-TYPE 104 121 86 95 78

Figure S91.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00068

Table S92.  Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 180 139 166

Figure S92.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S93.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 177 116 192

Figure S93.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0033

Table S94.  Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
16P GAIN MUTATED 3 10 1
16P GAIN WILD-TYPE 162 116 178

Figure S94.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S95.  Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
16Q GAIN MUTATED 13 0 0
16Q GAIN WILD-TYPE 43 356 89

Figure S95.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00092

Table S96.  Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
16Q GAIN MUTATED 1 11 1
16Q GAIN WILD-TYPE 276 143 69

Figure S96.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0036

Table S97.  Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
16Q GAIN MUTATED 1 11 0 1
16Q GAIN WILD-TYPE 167 144 59 116

Figure S97.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0012

Table S98.  Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
16Q GAIN MUTATED 1 11 0 1 0
16Q GAIN WILD-TYPE 104 123 86 95 78

Figure S98.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.006

Table S99.  Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
16Q GAIN MUTATED 2 10 1
16Q GAIN WILD-TYPE 180 141 166

Figure S99.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S100.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
16Q GAIN MUTATED 2 10 1
16Q GAIN WILD-TYPE 177 118 192

Figure S100.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00756 (Fisher's exact test), Q value = 0.023

Table S101.  Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
16Q GAIN MUTATED 3 8 1
16Q GAIN WILD-TYPE 162 118 178

Figure S101.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S102.  Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
17P GAIN MUTATED 12 2 2
17P GAIN WILD-TYPE 44 354 87

Figure S102.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S103.  Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
17P GAIN MUTATED 1 15 0
17P GAIN WILD-TYPE 276 139 70

Figure S103.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S104.  Gene #22: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
17P GAIN MUTATED 1 1 0 2 0 4 0
17P GAIN WILD-TYPE 45 27 33 27 49 23 9

Figure S104.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S105.  Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
17P GAIN MUTATED 0 15 0 1
17P GAIN WILD-TYPE 168 140 59 116

Figure S105.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S106.  Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
17P GAIN MUTATED 0 15 0 1 0
17P GAIN WILD-TYPE 105 119 86 95 78

Figure S106.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S107.  Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 181 137 166

Figure S107.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S108.  Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 178 114 192

Figure S108.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S109.  Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
17P GAIN MUTATED 2 10 1
17P GAIN WILD-TYPE 163 116 178

Figure S109.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S110.  Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
17Q GAIN MUTATED 13 2 3
17Q GAIN WILD-TYPE 43 354 86

Figure S110.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S111.  Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
17Q GAIN MUTATED 2 16 0
17Q GAIN WILD-TYPE 275 138 70

Figure S111.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.041

Table S112.  Gene #23: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
17Q GAIN MUTATED 1 1 0 3 0 4 0
17Q GAIN WILD-TYPE 45 27 33 26 49 23 9

Figure S112.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S113.  Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
17Q GAIN MUTATED 1 16 0 1
17Q GAIN WILD-TYPE 167 139 59 116

Figure S113.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S114.  Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
17Q GAIN MUTATED 1 16 0 1 0
17Q GAIN WILD-TYPE 104 118 86 95 78

Figure S114.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S115.  Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 180 136 166

Figure S115.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S116.  Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 177 113 192

Figure S116.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00092

Table S117.  Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
17Q GAIN MUTATED 3 11 1
17Q GAIN WILD-TYPE 162 115 178

Figure S117.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S118.  Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
18P GAIN MUTATED 5 0 1
18P GAIN WILD-TYPE 51 356 88

Figure S118.  Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S119.  Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
18Q GAIN MUTATED 5 0 1
18Q GAIN WILD-TYPE 51 356 88

Figure S119.  Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S120.  Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 48 356 89

Figure S120.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.001

Table S121.  Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 277 146 70

Figure S121.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.002

Table S122.  Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
19P GAIN MUTATED 0 8 0 0
19P GAIN WILD-TYPE 168 147 59 117

Figure S122.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S123.  Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
19P GAIN MUTATED 0 8 0 0 0
19P GAIN WILD-TYPE 105 126 86 96 78

Figure S123.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S124.  Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 182 143 167

Figure S124.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S125.  Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 179 120 193

Figure S125.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.053

Table S126.  Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
19P GAIN MUTATED 1 4 0
19P GAIN WILD-TYPE 164 122 179

Figure S126.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S127.  Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
19Q GAIN MUTATED 10 0 0
19Q GAIN WILD-TYPE 46 356 89

Figure S127.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S128.  Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 277 144 70

Figure S128.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S129.  Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
19Q GAIN MUTATED 0 10 0 0
19Q GAIN WILD-TYPE 168 145 59 117

Figure S129.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S130.  Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
19Q GAIN MUTATED 0 10 0 0 0
19Q GAIN WILD-TYPE 105 124 86 96 78

Figure S130.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S131.  Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 182 141 167

Figure S131.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S132.  Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 179 118 193

Figure S132.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0059

Table S133.  Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
19Q GAIN MUTATED 1 6 0
19Q GAIN WILD-TYPE 164 120 179

Figure S133.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S134.  Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
20P GAIN MUTATED 12 0 0
20P GAIN WILD-TYPE 44 356 89

Figure S134.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0014

Table S135.  Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
20P GAIN MUTATED 1 10 1
20P GAIN WILD-TYPE 276 144 69

Figure S135.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0026 (Fisher's exact test), Q value = 0.0089

Table S136.  Gene #28: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
20P GAIN MUTATED 1 10 0 1
20P GAIN WILD-TYPE 167 145 59 116

Figure S136.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0033

Table S137.  Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
20P GAIN MUTATED 1 10 0 1 0
20P GAIN WILD-TYPE 104 124 86 95 78

Figure S137.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.014

Table S138.  Gene #28: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
20P GAIN MUTATED 2 9 1
20P GAIN WILD-TYPE 180 142 166

Figure S138.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0032

Table S139.  Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
20P GAIN MUTATED 2 9 1
20P GAIN WILD-TYPE 177 119 192

Figure S139.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S140.  Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
20Q GAIN MUTATED 12 0 0
20Q GAIN WILD-TYPE 44 356 89

Figure S140.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0015

Table S141.  Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
20Q GAIN MUTATED 1 10 1
20Q GAIN WILD-TYPE 276 144 69

Figure S141.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0094

Table S142.  Gene #29: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
20Q GAIN MUTATED 1 10 0 1
20Q GAIN WILD-TYPE 167 145 59 116

Figure S142.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0042

Table S143.  Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
20Q GAIN MUTATED 1 10 0 1 0
20Q GAIN WILD-TYPE 104 124 86 95 78

Figure S143.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.014

Table S144.  Gene #29: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
20Q GAIN MUTATED 2 9 1
20Q GAIN WILD-TYPE 180 142 166

Figure S144.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0028

Table S145.  Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
20Q GAIN MUTATED 2 9 1
20Q GAIN WILD-TYPE 177 119 192

Figure S145.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S146.  Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
21Q GAIN MUTATED 4 0 1
21Q GAIN WILD-TYPE 52 356 88

Figure S146.  Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S147.  Gene #31: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
XP GAIN MUTATED 8 0 0
XP GAIN WILD-TYPE 48 356 89

Figure S147.  Get High-res Image Gene #31: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.007

Table S148.  Gene #31: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
XP GAIN MUTATED 0 6 2
XP GAIN WILD-TYPE 277 148 68

Figure S148.  Get High-res Image Gene #31: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.098

Table S149.  Gene #31: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
XP GAIN MUTATED 1 6 1 0
XP GAIN WILD-TYPE 167 149 58 117

Figure S149.  Get High-res Image Gene #31: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S150.  Gene #32: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
XQ GAIN MUTATED 8 1 0
XQ GAIN WILD-TYPE 48 355 89

Figure S150.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.032

Table S151.  Gene #32: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
XQ GAIN MUTATED 1 6 2
XQ GAIN WILD-TYPE 276 148 68

Figure S151.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00063

Table S152.  Gene #33: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
1P LOSS MUTATED 4 0 0
1P LOSS WILD-TYPE 52 356 89

Figure S152.  Get High-res Image Gene #33: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0051

Table S153.  Gene #34: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
1Q LOSS MUTATED 3 0 0
1Q LOSS WILD-TYPE 53 356 89

Figure S153.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.1

Table S154.  Gene #34: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 277 151 70

Figure S154.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.062

Table S155.  Gene #34: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 182 148 167

Figure S155.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.042

Table S156.  Gene #34: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 179 125 193

Figure S156.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S157.  Gene #35: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
2P LOSS MUTATED 9 0 1
2P LOSS WILD-TYPE 47 356 88

Figure S157.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S158.  Gene #35: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 277 144 70

Figure S158.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00046

Table S159.  Gene #35: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
2P LOSS MUTATED 0 10 0 0
2P LOSS WILD-TYPE 168 145 59 117

Figure S159.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S160.  Gene #35: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
2P LOSS MUTATED 0 10 0 0 0
2P LOSS WILD-TYPE 105 124 86 96 78

Figure S160.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S161.  Gene #35: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 182 141 167

Figure S161.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S162.  Gene #35: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 179 118 193

Figure S162.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.002

Table S163.  Gene #35: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
2P LOSS MUTATED 1 7 0
2P LOSS WILD-TYPE 164 119 179

Figure S163.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S164.  Gene #36: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 46 356 89

Figure S164.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S165.  Gene #36: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 277 144 70

Figure S165.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00041

Table S166.  Gene #36: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
2Q LOSS MUTATED 0 10 0 0
2Q LOSS WILD-TYPE 168 145 59 117

Figure S166.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00041

Table S167.  Gene #36: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
2Q LOSS MUTATED 0 10 0 0 0
2Q LOSS WILD-TYPE 105 124 86 96 78

Figure S167.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S168.  Gene #36: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 182 141 167

Figure S168.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S169.  Gene #36: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 179 118 193

Figure S169.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0026

Table S170.  Gene #36: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
2Q LOSS MUTATED 1 7 0
2Q LOSS WILD-TYPE 164 119 179

Figure S170.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0048

Table S171.  Gene #37: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
3P LOSS MUTATED 3 0 0
3P LOSS WILD-TYPE 53 356 89

Figure S171.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.1

Table S172.  Gene #37: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 277 151 70

Figure S172.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.062

Table S173.  Gene #37: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 182 148 167

Figure S173.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.042

Table S174.  Gene #37: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 179 125 193

Figure S174.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S175.  Gene #38: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
3Q LOSS MUTATED 4 0 0
3Q LOSS WILD-TYPE 52 356 89

Figure S175.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.043

Table S176.  Gene #38: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 277 150 70

Figure S176.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.081

Table S177.  Gene #38: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
3Q LOSS MUTATED 0 4 0 0
3Q LOSS WILD-TYPE 168 151 59 117

Figure S177.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.099

Table S178.  Gene #38: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
3Q LOSS MUTATED 0 4 0 0 0
3Q LOSS WILD-TYPE 105 130 86 96 78

Figure S178.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00794 (Fisher's exact test), Q value = 0.023

Table S179.  Gene #38: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 182 147 167

Figure S179.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00394 (Fisher's exact test), Q value = 0.013

Table S180.  Gene #38: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 179 124 193

Figure S180.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00096

Table S181.  Gene #39: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
6P LOSS MUTATED 4 0 0
6P LOSS WILD-TYPE 52 356 89

Figure S181.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.1

Table S182.  Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
6P LOSS MUTATED 0 3 1
6P LOSS WILD-TYPE 277 151 69

Figure S182.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S183.  Gene #40: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
6Q LOSS MUTATED 6 1 0
6Q LOSS WILD-TYPE 50 355 89

Figure S183.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.0083

Table S184.  Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
6Q LOSS MUTATED 0 6 1
6Q LOSS WILD-TYPE 277 148 69

Figure S184.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.034

Table S185.  Gene #40: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 79 81
6Q LOSS MUTATED 0 0 5
6Q LOSS WILD-TYPE 61 79 76

Figure S185.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.064

Table S186.  Gene #40: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
6Q LOSS MUTATED 1 6 0 0
6Q LOSS WILD-TYPE 167 149 59 117

Figure S186.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.044

Table S187.  Gene #40: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
6Q LOSS MUTATED 1 6 0 0 0
6Q LOSS WILD-TYPE 104 128 86 96 78

Figure S187.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.016

Table S188.  Gene #40: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 181 145 167

Figure S188.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0028

Table S189.  Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 178 122 193

Figure S189.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00979 (Fisher's exact test), Q value = 0.028

Table S190.  Gene #40: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
6Q LOSS MUTATED 2 5 0
6Q LOSS WILD-TYPE 163 121 179

Figure S190.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00063

Table S191.  Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 52 356 89

Figure S191.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.043

Table S192.  Gene #41: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 277 150 70

Figure S192.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.081

Table S193.  Gene #41: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
8P LOSS MUTATED 0 4 0 0
8P LOSS WILD-TYPE 168 151 59 117

Figure S193.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.1

Table S194.  Gene #41: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
8P LOSS MUTATED 0 4 0 0 0
8P LOSS WILD-TYPE 105 130 86 96 78

Figure S194.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00777 (Fisher's exact test), Q value = 0.023

Table S195.  Gene #41: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 182 147 167

Figure S195.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.014

Table S196.  Gene #41: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 179 124 193

Figure S196.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.045

Table S197.  Gene #41: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
8P LOSS MUTATED 0 3 0
8P LOSS WILD-TYPE 165 123 179

Figure S197.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00074

Table S198.  Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 52 356 89

Figure S198.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.043

Table S199.  Gene #42: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 277 150 70

Figure S199.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.081

Table S200.  Gene #42: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
8Q LOSS MUTATED 0 4 0 0
8Q LOSS WILD-TYPE 168 151 59 117

Figure S200.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.099

Table S201.  Gene #42: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
8Q LOSS MUTATED 0 4 0 0 0
8Q LOSS WILD-TYPE 105 130 86 96 78

Figure S201.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00774 (Fisher's exact test), Q value = 0.023

Table S202.  Gene #42: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 182 147 167

Figure S202.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.014

Table S203.  Gene #42: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 179 124 193

Figure S203.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.045

Table S204.  Gene #42: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
8Q LOSS MUTATED 0 3 0
8Q LOSS WILD-TYPE 165 123 179

Figure S204.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S205.  Gene #43: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
9P LOSS MUTATED 15 2 2
9P LOSS WILD-TYPE 41 354 87

Figure S205.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.084

Table S206.  Gene #43: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
9P LOSS MUTATED 6 11 2
9P LOSS WILD-TYPE 271 143 68

Figure S206.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.07

Table S207.  Gene #43: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
9P LOSS MUTATED 2 11 3 3
9P LOSS WILD-TYPE 166 144 56 114

Figure S207.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0087 (Fisher's exact test), Q value = 0.025

Table S208.  Gene #43: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
9P LOSS MUTATED 8 10 1
9P LOSS WILD-TYPE 174 141 166

Figure S208.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00712 (Fisher's exact test), Q value = 0.021

Table S209.  Gene #43: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
9P LOSS MUTATED 7 10 2
9P LOSS WILD-TYPE 172 118 191

Figure S209.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.014

Table S210.  Gene #43: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
9P LOSS MUTATED 7 9 1
9P LOSS WILD-TYPE 158 117 178

Figure S210.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S211.  Gene #44: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
9Q LOSS MUTATED 20 2 3
9Q LOSS WILD-TYPE 36 354 86

Figure S211.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00933 (Fisher's exact test), Q value = 0.027

Table S212.  Gene #44: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
9Q LOSS MUTATED 12 11 2
9Q LOSS WILD-TYPE 170 140 165

Figure S212.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00704 (Fisher's exact test), Q value = 0.021

Table S213.  Gene #44: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
9Q LOSS MUTATED 11 11 3
9Q LOSS WILD-TYPE 168 117 190

Figure S213.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00488 (Fisher's exact test), Q value = 0.016

Table S214.  Gene #44: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
9Q LOSS MUTATED 11 10 2
9Q LOSS WILD-TYPE 154 116 177

Figure S214.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S215.  Gene #45: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
10P LOSS MUTATED 7 0 0
10P LOSS WILD-TYPE 49 356 89

Figure S215.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.032

Table S216.  Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 276 148 70

Figure S216.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.049

Table S217.  Gene #45: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
10P LOSS MUTATED 0 6 0 1
10P LOSS WILD-TYPE 168 149 59 116

Figure S217.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218.  Gene #45: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
10P LOSS MUTATED 0 6 0 1 0
10P LOSS WILD-TYPE 105 128 86 95 78

Figure S218.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00474 (Fisher's exact test), Q value = 0.015

Table S219.  Gene #45: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 181 145 167

Figure S219.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0028

Table S220.  Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 178 122 193

Figure S220.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.031

Table S221.  Gene #45: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
10P LOSS MUTATED 2 5 0
10P LOSS WILD-TYPE 163 121 179

Figure S221.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S222.  Gene #46: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
10Q LOSS MUTATED 6 0 0
10Q LOSS WILD-TYPE 50 356 89

Figure S222.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.066

Table S223.  Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 276 149 70

Figure S223.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.099

Table S224.  Gene #46: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
10Q LOSS MUTATED 0 5 0 1 0
10Q LOSS WILD-TYPE 105 129 86 95 78

Figure S224.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.038

Table S225.  Gene #46: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 181 146 167

Figure S225.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 0.014

Table S226.  Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 178 123 193

Figure S226.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.064

Table S227.  Gene #46: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
10Q LOSS MUTATED 2 4 0
10Q LOSS WILD-TYPE 163 122 179

Figure S227.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S228.  Gene #47: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11P LOSS MUTATED 6 0 1
11P LOSS WILD-TYPE 50 356 88

Figure S228.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.031

Table S229.  Gene #47: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 276 148 70

Figure S229.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.02

Table S230.  Gene #47: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
11P LOSS MUTATED 0 6 1 0
11P LOSS WILD-TYPE 168 149 58 117

Figure S230.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.043

Table S231.  Gene #47: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
11P LOSS MUTATED 1 6 0 0 0
11P LOSS WILD-TYPE 104 128 86 96 78

Figure S231.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00494 (Fisher's exact test), Q value = 0.016

Table S232.  Gene #47: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 181 145 167

Figure S232.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0026

Table S233.  Gene #47: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 178 122 193

Figure S233.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.03

Table S234.  Gene #47: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
11P LOSS MUTATED 2 5 0
11P LOSS WILD-TYPE 163 121 179

Figure S234.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S235.  Gene #48: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
11Q LOSS MUTATED 7 1 1
11Q LOSS WILD-TYPE 49 355 88

Figure S235.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.043

Table S236.  Gene #48: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
11Q LOSS MUTATED 2 7 0
11Q LOSS WILD-TYPE 275 147 70

Figure S236.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.041

Table S237.  Gene #48: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
11Q LOSS MUTATED 1 7 1 0
11Q LOSS WILD-TYPE 167 148 58 117

Figure S237.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.045

Table S238.  Gene #48: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
11Q LOSS MUTATED 1 7 0 0 1
11Q LOSS WILD-TYPE 104 127 86 96 77

Figure S238.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0026

Table S239.  Gene #48: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
11Q LOSS MUTATED 1 8 0
11Q LOSS WILD-TYPE 181 143 167

Figure S239.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0086

Table S240.  Gene #48: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
11Q LOSS MUTATED 1 7 1
11Q LOSS WILD-TYPE 178 121 192

Figure S240.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.0088

Table S241.  Gene #48: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
11Q LOSS MUTATED 2 6 0
11Q LOSS WILD-TYPE 163 120 179

Figure S241.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.006

Table S242.  Gene #49: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
13Q LOSS MUTATED 6 5 3
13Q LOSS WILD-TYPE 50 351 86

Figure S242.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

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

Table S243.  Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
13Q LOSS MUTATED 3 9 2
13Q LOSS WILD-TYPE 274 145 68

Figure S243.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.017

Table S244.  Gene #49: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
13Q LOSS MUTATED 0 9 2 3
13Q LOSS WILD-TYPE 168 146 57 114

Figure S244.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00799 (Fisher's exact test), Q value = 0.023

Table S245.  Gene #49: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
13Q LOSS MUTATED 0 9 2 3 0
13Q LOSS WILD-TYPE 105 125 84 93 78

Figure S245.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0042

Table S246.  Gene #49: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 182 142 162

Figure S246.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0019

Table S247.  Gene #49: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 179 119 188

Figure S247.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.035

Table S248.  Gene #49: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
13Q LOSS MUTATED 1 8 4
13Q LOSS WILD-TYPE 164 118 175

Figure S248.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00079

Table S249.  Gene #50: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
15Q LOSS MUTATED 5 1 2
15Q LOSS WILD-TYPE 51 355 87

Figure S249.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.001

Table S250.  Gene #50: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 277 146 70

Figure S250.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0026

Table S251.  Gene #50: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
15Q LOSS MUTATED 0 8 0 0
15Q LOSS WILD-TYPE 168 147 59 117

Figure S251.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S252.  Gene #50: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
15Q LOSS MUTATED 0 8 0 0 0
15Q LOSS WILD-TYPE 105 126 86 96 78

Figure S252.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00046

Table S253.  Gene #50: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 182 143 167

Figure S253.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S254.  Gene #50: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 179 120 193

Figure S254.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0071

Table S255.  Gene #50: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
15Q LOSS MUTATED 1 6 0
15Q LOSS WILD-TYPE 164 120 179

Figure S255.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.038

Table S256.  Gene #51: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
17P LOSS MUTATED 4 3 1
17P LOSS WILD-TYPE 52 353 88

Figure S256.  Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0072

Table S257.  Gene #53: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
18P LOSS MUTATED 3 0 1
18P LOSS WILD-TYPE 53 356 88

Figure S257.  Get High-res Image Gene #53: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0077

Table S258.  Gene #54: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
18Q LOSS MUTATED 3 0 1
18Q LOSS WILD-TYPE 53 356 88

Figure S258.  Get High-res Image Gene #54: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.00932 (Fisher's exact test), Q value = 0.027

Table S259.  Gene #55: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
19P LOSS MUTATED 3 1 1
19P LOSS WILD-TYPE 53 355 88

Figure S259.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00657 (Fisher's exact test), Q value = 0.02

Table S260.  Gene #55: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 277 149 70

Figure S260.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.042

Table S261.  Gene #55: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
19P LOSS MUTATED 0 5 0 0
19P LOSS WILD-TYPE 168 150 59 117

Figure S261.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.035

Table S262.  Gene #55: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
19P LOSS MUTATED 0 5 0 0 0
19P LOSS WILD-TYPE 105 129 86 96 78

Figure S262.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.0084

Table S263.  Gene #55: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 182 146 167

Figure S263.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0043

Table S264.  Gene #55: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 179 123 193

Figure S264.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0055

Table S265.  Gene #55: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 165 121 179

Figure S265.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0028

Table S266.  Gene #56: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
21Q LOSS MUTATED 5 2 1
21Q LOSS WILD-TYPE 51 354 88

Figure S266.  Get High-res Image Gene #56: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.065

Table S267.  Gene #56: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
21Q LOSS MUTATED 4 4 0
21Q LOSS WILD-TYPE 175 124 193

Figure S267.  Get High-res Image Gene #56: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S268.  Gene #57: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
22Q LOSS MUTATED 13 0 76
22Q LOSS WILD-TYPE 43 356 13

Figure S268.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S269.  Gene #57: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
22Q LOSS MUTATED 36 47 6
22Q LOSS WILD-TYPE 241 107 64

Figure S269.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S270.  Gene #57: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
22Q LOSS MUTATED 8 47 8 26
22Q LOSS WILD-TYPE 160 108 51 91

Figure S270.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S271.  Gene #57: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
22Q LOSS MUTATED 9 42 13 23 2
22Q LOSS WILD-TYPE 96 92 73 73 76

Figure S271.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.002

Table S272.  Gene #57: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
22Q LOSS MUTATED 23 43 23
22Q LOSS WILD-TYPE 159 108 144

Figure S272.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S273.  Gene #57: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
22Q LOSS MUTATED 21 40 28
22Q LOSS WILD-TYPE 158 88 165

Figure S273.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00096

Table S274.  Gene #57: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
22Q LOSS MUTATED 17 23 41
22Q LOSS WILD-TYPE 143 141 105

Figure S274.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S275.  Gene #57: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
22Q LOSS MUTATED 22 37 22
22Q LOSS WILD-TYPE 143 89 157

Figure S275.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.083

Table S276.  Gene #58: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
XP LOSS MUTATED 0 4 0
XP LOSS WILD-TYPE 160 160 146

Figure S276.  Get High-res Image Gene #58: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.064

Table S277.  Gene #59: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 182 148 167

Figure S277.  Get High-res Image Gene #59: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.042

Table S278.  Gene #59: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 179 125 193

Figure S278.  Get High-res Image Gene #59: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.045

Table S279.  Gene #59: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 165 123 179

Figure S279.  Get High-res Image Gene #59: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/15101916/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/15125146/THCA-TP.transferedmergedcluster.txt

  • Number of patients = 501

  • Number of significantly arm-level cnvs = 59

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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