Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1RV0N0C
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/C1RV0N0C
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 499 patients, 278 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',  'MRNASEQ_CNMF',  'MRNASEQ_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',  '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',  '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',  'RPPA_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 'CN_CNMF',  'METHLYATION_CNMF',  '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, 278 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
7q gain 20 (4%) 479 1e-05
(0.000109) 		1e-05
(0.000109) 		0.141
(0.236) 		0.0159
(0.0418) 		0.00011
(0.000656) 		4e-05
(0.000299) 		7e-05
(0.000469) 		1e-05
(0.000109) 		0.643
(0.761) 		0.00094
(0.00388)
17p gain 16 (3%) 483 1e-05
(0.000109) 		1e-05
(0.000109) 		0.322
(0.456) 		0.03
(0.0692) 		2e-05
(0.000182) 		1e-05
(0.000109) 		1e-05
(0.000109) 		1e-05
(0.000109) 		0.357
(0.503) 		0.00027
(0.00134)
17q gain 18 (4%) 481 1e-05
(0.000109) 		1e-05
(0.000109) 		0.699
(0.813) 		0.0171
(0.0434) 		1e-05
(0.000109) 		1e-05
(0.000109) 		1e-05
(0.000109) 		1e-05
(0.000109) 		0.513
(0.655) 		0.00023
(0.00117)
13q loss 14 (3%) 485 0.00147
(0.00556) 		0.0155
(0.0413) 		0.00732
(0.0223) 		0.131
(0.221) 		0.00508
(0.0163) 		0.00884
(0.0258) 		0.00117
(0.0046) 		0.00056
(0.0025) 		0.104
(0.186) 		0.0122
(0.0337)
22q loss 89 (18%) 410 1e-05
(0.000109) 		1e-05
(0.000109) 		0.407
(0.554) 		0.51
(0.653) 		1e-05
(0.000109) 		1e-05
(0.000109) 		0.00052
(0.00238) 		3e-05
(0.000239) 		0.00016
(0.000866) 		0.00039
(0.00186)
5p gain 21 (4%) 478 1e-05
(0.000109) 		0.0021
(0.00751) 		0.126
(0.214) 		0.261
(0.389) 		0.00557
(0.0175) 		6e-05
(0.000407) 		0.001
(0.00407) 		0.00011
(0.000656) 		0.601
(0.734) 		0.00384
(0.013)
5q gain 17 (3%) 482 1e-05
(0.000109) 		6e-05
(0.000407) 		0.268
(0.395) 		0.0902
(0.173) 		0.00021
(0.00108) 		3e-05
(0.000239) 		0.0002
(0.00105) 		3e-05
(0.000239) 		0.838
(0.947) 		0.00479
(0.0156)
7p gain 18 (4%) 481 1e-05
(0.000109) 		8e-05
(0.000519) 		0.237
(0.36) 		0.0582
(0.121) 		0.0006
(0.00262) 		0.0002
(0.00105) 		0.00049
(0.00229) 		4e-05
(0.000299) 		0.574
(0.713) 		0.00524
(0.0166)
12p gain 14 (3%) 485 1e-05
(0.000109) 		1e-05
(0.000109) 		0.767
(0.886) 		0.0892
(0.172) 		1e-05
(0.000109) 		1e-05
(0.000109) 		5e-05
(0.000355) 		1e-05
(0.000109) 		0.553
(0.693) 		0.00308
(0.0106)
12q gain 15 (3%) 484 1e-05
(0.000109) 		1e-05
(0.000109) 		0.765
(0.885) 		0.0886
(0.171) 		1e-05
(0.000109) 		1e-05
(0.000109) 		2e-05
(0.000182) 		1e-05
(0.000109) 		0.382
(0.53) 		0.00101
(0.00408)
14q gain 11 (2%) 488 1e-05
(0.000109) 		0.00013
(0.000752) 		0.483
(0.624) 		0.169
(0.277) 		0.00057
(0.00253) 		0.0001
(0.000634) 		0.00074
(0.00316) 		6e-05
(0.000407) 		0.852
(0.955) 		0.0018
(0.00652)
16p gain 15 (3%) 484 1e-05
(0.000109) 		2e-05
(0.000182) 		0.7
(0.813) 		0.085
(0.166) 		6e-05
(0.000407) 		5e-05
(0.000355) 		0.00012
(0.000708) 		1e-05
(0.000109) 		0.464
(0.603) 		0.00086
(0.0036)
16q gain 13 (3%) 486 1e-05
(0.000109) 		0.00015
(0.000843) 		0.448
(0.595) 		0.293
(0.424) 		0.00094
(0.00388) 		0.00031
(0.00151) 		0.00168
(0.00619) 		8e-05
(0.000519) 		0.617
(0.748) 		0.00815
(0.0242)
19p gain 8 (2%) 491 1e-05
(0.000109) 		0.00017
(0.000912) 		0.00055
(0.00248) 		0.00016
(0.000866) 		8e-05
(0.000519) 		2e-05
(0.000182) 		0.452
(0.596) 		0.0233
(0.0556)
19q gain 10 (2%) 489 1e-05
(0.000109) 		2e-05
(0.000182) 		0.367
(0.514) 		0.0696
(0.139) 		5e-05
(0.000355) 		4e-05
(0.000299) 		2e-05
(0.000182) 		1e-05
(0.000109) 		0.637
(0.757) 		0.00152
(0.00571)
2p loss 10 (2%) 489 1e-05
(0.000109) 		3e-05
(0.000239) 		0.635
(0.755) 		0.0941
(0.176) 		0.00011
(0.000656) 		5e-05
(0.000355) 		2e-05
(0.000182) 		1e-05
(0.000109) 		0.263
(0.39) 		0.00038
(0.00182)
2q loss 10 (2%) 489 1e-05
(0.000109) 		2e-05
(0.000182) 		0.58
(0.717) 		0.0929
(0.174) 		0.0001
(0.000634) 		3e-05
(0.000239) 		1e-05
(0.000109) 		1e-05
(0.000109) 		0.261
(0.389) 		0.00048
(0.00227)
6q loss 7 (1%) 492 1e-05
(0.000109) 		0.0021
(0.00751) 		0.102
(0.184) 		0.578
(0.716) 		0.0317
(0.0729) 		0.0188
(0.0461) 		0.00538
(0.017) 		0.00084
(0.00357) 		1
(1.00) 		0.0106
(0.0299)
8p loss 4 (1%) 495 0.00011
(0.000656) 		0.018
(0.0454) 		0.036
(0.0817) 		0.0468
(0.102) 		0.00849
(0.0249) 		0.00431
(0.0144) 		0.11
(0.193) 		0.0188
(0.0461)
8q loss 4 (1%) 495 0.00016
(0.000866) 		0.0182
(0.0456) 		0.0364
(0.0817) 		0.0458
(0.1) 		0.00817
(0.0242) 		0.00433
(0.0144) 		0.111
(0.193) 		0.0187
(0.0461)
10p loss 7 (1%) 492 1e-05
(0.000109) 		0.0117
(0.0324) 		0.365
(0.513) 		0.446
(0.595) 		0.0211
(0.0508) 		0.016
(0.0418) 		0.0048
(0.0156) 		0.00086
(0.0036) 		1
(1.00) 		0.00973
(0.028)
11p loss 7 (1%) 492 1e-05
(0.000109) 		0.0112
(0.0311) 		0.782
(0.898) 		0.959
(1.00) 		0.00757
(0.0229) 		0.0185
(0.0459) 		0.00488
(0.0157) 		0.00074
(0.00316) 		0.799
(0.91) 		0.0104
(0.0293)
11q loss 9 (2%) 490 2e-05
(0.000182) 		0.0166
(0.0427) 		0.606
(0.739) 		0.83
(0.94) 		0.0166
(0.0427) 		0.0193
(0.0467) 		0.00051
(0.00237) 		0.00216
(0.00763) 		0.907
(1.00) 		0.00282
(0.00979)
15q loss 8 (2%) 491 0.00011
(0.000656) 		0.00021
(0.00108) 		0.153
(0.254) 		0.0961
(0.178) 		0.00053
(0.00241) 		0.00026
(0.0013) 		0.00011
(0.000656) 		4e-05
(0.000299) 		0.409
(0.556) 		0.00147
(0.00556)
19p loss 5 (1%) 494 0.0085
(0.0249) 		0.0065
(0.0202) 		0.119
(0.205) 		0.26
(0.389) 		0.016
(0.0418) 		0.0147
(0.0391) 		0.00247
(0.00867) 		0.00112
(0.00446) 		0.109
(0.193) 		0.00129
(0.00501)
1q gain 25 (5%) 474 1e-05
(0.000109) 		0.0189
(0.0462) 		0.0509
(0.107) 		0.0537
(0.112) 		0.00052
(0.00238) 		3e-05
(0.000239) 		0.126
(0.214) 		0.0877
(0.17) 		0.0275
(0.0644) 		0.0283
(0.0659)
4p gain 5 (1%) 494 4e-05
(0.000299) 		0.00652
(0.0202) 		0.0164
(0.0425) 		0.0138
(0.0375) 		0.0408
(0.0905) 		0.0139
(0.0377) 		1
(1.00) 		0.0761
(0.149)
4q gain 5 (1%) 494 2e-05
(0.000182) 		0.00664
(0.0205) 		0.0166
(0.0427) 		0.0136
(0.0373) 		0.0421
(0.093) 		0.0143
(0.0384) 		1
(1.00) 		0.0768
(0.15)
20p gain 12 (2%) 487 1e-05
(0.000109) 		0.00032
(0.00155) 		0.446
(0.595) 		0.104
(0.186) 		0.00288
(0.00994) 		0.00114
(0.00451) 		0.00422
(0.0142) 		0.0007
(0.00304) 		0.914
(1.00) 		0.0946
(0.176)
20q gain 12 (2%) 487 1e-05
(0.000109) 		0.00028
(0.00138) 		0.444
(0.595) 		0.103
(0.185) 		0.00275
(0.0096) 		0.00107
(0.00429) 		0.00448
(0.0147) 		0.00058
(0.00255) 		0.914
(1.00) 		0.0947
(0.176)
3q loss 4 (1%) 495 0.00015
(0.000843) 		0.0183
(0.0457) 		0.368
(0.515) 		0.446
(0.595) 		0.0353
(0.0804) 		0.0476
(0.102) 		0.00811
(0.0242) 		0.00429
(0.0144) 		1
(1.00) 		0.0664
(0.133)
9p loss 19 (4%) 480 1e-05
(0.000109) 		0.0369
(0.0824) 		0.942
(1.00) 		0.65
(0.766) 		0.0331
(0.0756) 		0.0623
(0.127) 		0.00901
(0.0262) 		0.00766
(0.0231) 		0.286
(0.414) 		0.00384
(0.013)
10q loss 6 (1%) 493 2e-05
(0.000182) 		0.0362
(0.0817) 		0.0515
(0.108) 		0.0463
(0.101) 		0.0143
(0.0384) 		0.00517
(0.0165) 		1
(1.00) 		0.0286
(0.0664)
11p gain 6 (1%) 493 0.00167
(0.00619) 		0.0364
(0.0817) 		0.883
(0.988) 		0.305
(0.438) 		0.053
(0.111) 		0.0457
(0.1) 		0.00924
(0.0267) 		0.0071
(0.0218) 		0.471
(0.61) 		0.0973
(0.179)
xq loss 3 (1%) 496 0.0476
(0.102) 		0.0482
(0.103) 		0.0656
(0.133) 		0.201
(0.311) 		0.0983
(0.18) 		0.172
(0.279) 		0.0274
(0.0644) 		0.0179
(0.0454) 		0.11
(0.193) 		0.019
(0.0462)
3p loss 3 (1%) 496 0.00146
(0.00556) 		0.0495
(0.105) 		0.0997
(0.182) 		0.172
(0.279) 		0.0273
(0.0643) 		0.016
(0.0418) 		1
(1.00) 		0.191
(0.301)
9q loss 25 (5%) 474 1e-05
(0.000109) 		0.102
(0.184) 		0.573
(0.713) 		0.116
(0.199) 		0.175
(0.283) 		0.0603
(0.124) 		0.01
(0.0286) 		0.00712
(0.0218) 		0.28
(0.407) 		0.0044
(0.0145)
11q gain 5 (1%) 494 0.00016
(0.000866) 		0.0596
(0.123) 		0.885
(0.989) 		0.303
(0.436) 		0.11
(0.193) 		0.127
(0.214) 		0.0272
(0.0643) 		0.0226
(0.0541) 		0.309
(0.442) 		0.276
(0.402)
13q gain 5 (1%) 494 3e-05
(0.000239) 		0.0184
(0.0457) 		0.63
(0.755) 		0.219
(0.336) 		0.0479
(0.103) 		0.101
(0.183) 		0.235
(0.358) 		0.0724
(0.144) 		0.843
(0.948) 		0.197
(0.307)
xp gain 8 (2%) 491 1e-05
(0.000109) 		0.00216
(0.00763) 		0.776
(0.893) 		0.516
(0.658) 		0.0474
(0.102) 		0.0594
(0.123) 		0.184
(0.294) 		0.0723
(0.144) 		0.8
(0.91) 		0.183
(0.294)
1q loss 3 (1%) 496 0.00145
(0.00556) 		0.0502
(0.106) 		0.101
(0.183) 		0.171
(0.279) 		0.0272
(0.0643) 		0.0168
(0.043) 		1
(1.00) 		0.191
(0.301)
xq gain 9 (2%) 490 1e-05
(0.000109) 		0.011
(0.0308) 		0.774
(0.892) 		0.517
(0.658) 		0.0976
(0.179) 		0.144
(0.239) 		0.28
(0.407) 		0.137
(0.23) 		0.909
(1.00) 		0.397
(0.544)
6p loss 4 (1%) 495 0.00021
(0.00108) 		0.0455
(0.1) 		0.459
(0.599) 		0.412
(0.559) 		0.116
(0.199) 		0.0663
(0.133) 		0.401
(0.547) 		0.197
(0.307)
21q loss 8 (2%) 491 0.00096
(0.00393) 		0.16
(0.265) 		0.633
(0.755) 		0.221
(0.338) 		0.709
(0.821) 		0.429
(0.577) 		0.092
(0.174) 		0.03
(0.0692) 		0.464
(0.603) 		0.0555
(0.115)
1p gain 4 (1%) 495 0.00984
(0.0282) 		0.616
(0.748) 		0.6
(0.734) 		0.615
(0.748) 		0.269
(0.396) 		0.139
(0.232) 		0.652
(0.766) 		0.373
(0.52)
3p gain 3 (1%) 496 0.00129
(0.00501) 		0.55
(0.691) 		0.493
(0.633) 		0.587
(0.725) 		0.303
(0.436) 		0.189
(0.3) 		1
(1.00) 		0.191
(0.301)
8p gain 6 (1%) 493 0.00015
(0.000843) 		0.414
(0.559) 		1
(1.00) 		0.645
(0.761) 		0.595
(0.732) 		0.539
(0.679) 		0.452
(0.596) 		0.453
(0.596) 		1
(1.00) 		1
(1.00)
8q gain 7 (1%) 492 3e-05
(0.000239) 		0.2
(0.311) 		1
(1.00) 		0.645
(0.761) 		0.827
(0.939) 		0.519
(0.659) 		0.799
(0.91) 		0.632
(0.755) 		0.899
(0.998) 		0.894
(0.997)
9p gain 3 (1%) 496 0.00158
(0.0059) 		0.548
(0.689) 		0.492
(0.633) 		0.589
(0.725) 		1
(1.00) 		1
(1.00) 		0.414
(0.559) 		0.634
(0.755)
9q gain 4 (1%) 495 0.0104
(0.0293) 		0.791
(0.905) 		0.898
(0.998) 		0.38
(0.529) 		0.839
(0.947) 		1
(1.00) 		0.166
(0.273) 		0.568
(0.71)
18p gain 6 (1%) 493 3e-05
(0.000239) 		0.0924
(0.174) 		0.127
(0.214) 		0.267
(0.395) 		0.253
(0.381) 		0.112
(0.195) 		0.455
(0.597) 		0.396
(0.544)
18q gain 6 (1%) 493 1e-05
(0.000109) 		0.093
(0.174) 		0.126
(0.214) 		0.266
(0.395) 		0.257
(0.386) 		0.111
(0.193) 		0.458
(0.599) 		0.399
(0.546)
21q gain 5 (1%) 494 0.00024
(0.00121) 		0.168
(0.275) 		0.235
(0.358) 		0.493
(0.633) 		0.449
(0.596) 		0.311
(0.444) 		0.694
(0.81) 		0.685
(0.8)
1p loss 4 (1%) 495 0.00013
(0.000752) 		0.185
(0.294) 		0.24
(0.364) 		0.319
(0.452) 		0.114
(0.197) 		0.0656
(0.133) 		0.843
(0.948) 		0.195
(0.306)
17p loss 8 (2%) 491 0.0129
(0.0355) 		0.415
(0.559) 		0.634
(0.755) 		0.393
(0.542) 		0.634
(0.755) 		0.6
(0.734) 		0.0919
(0.174) 		0.162
(0.266) 		0.126
(0.214) 		0.207
(0.32)
18p loss 4 (1%) 495 0.00174
(0.00634) 		0.183
(0.294) 		0.631
(0.755) 		0.393
(0.542) 		0.24
(0.364) 		0.318
(0.452) 		0.0743
(0.146) 		0.0911
(0.174) 		0.531
(0.671) 		0.274
(0.402)
18q loss 4 (1%) 495 0.00173
(0.00634) 		0.185
(0.294) 		0.631
(0.755) 		0.393
(0.542) 		0.241
(0.364) 		0.318
(0.452) 		0.074
(0.146) 		0.093
(0.174) 		0.53
(0.671) 		0.275
(0.402)
xp loss 4 (1%) 495 0.107
(0.189) 		0.184
(0.294) 		0.0655
(0.133) 		0.2
(0.311) 		0.459
(0.599) 		0.219
(0.336) 		0.0738
(0.146) 		0.0923
(0.174) 		0.037
(0.0824) 		0.097
(0.179)
17q loss 4 (1%) 495 0.105
(0.187) 		0.792
(0.905) 		0.9
(0.998) 		0.668
(0.783) 		0.469
(0.608) 		0.57
(0.71) 		0.331
(0.467) 		0.683
(0.799)
'1p gain' versus 'CN_CNMF'

P value = 0.00984 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
1P GAIN MUTATED 3 1 0
1P GAIN WILD-TYPE 53 359 83

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 56 360 83
1Q GAIN MUTATED 17 7 1
1Q GAIN WILD-TYPE 39 353 82

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
1Q GAIN MUTATED 18 2 5
1Q GAIN WILD-TYPE 258 152 64

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0024

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
1Q GAIN MUTATED 17 2 4 2
1Q GAIN WILD-TYPE 151 153 54 114

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
1Q GAIN MUTATED 16 2 1 2 4
1Q GAIN WILD-TYPE 88 132 85 93 74

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

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.064

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 145
1Q GAIN MUTATED 13 5 3
1Q GAIN WILD-TYPE 146 159 142

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.066

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
1Q GAIN MUTATED 13 2 6
1Q GAIN WILD-TYPE 151 124 172

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.005

Table S8.  Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
3P GAIN MUTATED 3 0 0
3P GAIN WILD-TYPE 53 360 83

Figure S8.  Get High-res Image Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S9.  Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
4P GAIN MUTATED 5 0 0
4P GAIN WILD-TYPE 51 360 83

Figure S9.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.02

Table S10.  Gene #4: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
4P GAIN MUTATED 0 5 0
4P GAIN WILD-TYPE 276 149 69

Figure S10.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

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

Table S11.  Gene #4: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
4P GAIN MUTATED 0 5 0 0
4P GAIN WILD-TYPE 168 150 58 116

Figure S11.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.038

Table S12.  Gene #4: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
4P GAIN MUTATED 0 5 0 0 0
4P GAIN WILD-TYPE 104 129 86 95 78

Figure S12.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.09

Table S13.  Gene #4: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
4P GAIN MUTATED 1 4 0
4P GAIN WILD-TYPE 180 147 166

Figure S13.  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 = 0.038

Table S14.  Gene #4: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
4P GAIN MUTATED 1 4 0
4P GAIN WILD-TYPE 177 124 192

Figure S14.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

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

Table S15.  Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
4Q GAIN MUTATED 5 0 0
4Q GAIN WILD-TYPE 51 360 83

Figure S15.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00664 (Fisher's exact test), Q value = 0.021

Table S16.  Gene #5: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
4Q GAIN MUTATED 0 5 0
4Q GAIN WILD-TYPE 276 149 69

Figure S16.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
4Q GAIN MUTATED 0 5 0 0
4Q GAIN WILD-TYPE 168 150 58 116

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

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S18.  Gene #5: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
4Q GAIN MUTATED 0 5 0 0 0
4Q GAIN WILD-TYPE 104 129 86 95 78

Figure S18.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.093

Table S19.  Gene #5: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
4Q GAIN MUTATED 1 4 0
4Q GAIN WILD-TYPE 180 147 166

Figure S19.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.038

Table S20.  Gene #5: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
4Q GAIN MUTATED 1 4 0
4Q GAIN WILD-TYPE 177 124 192

Figure S20.  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 S21.  Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
5P GAIN MUTATED 21 0 0
5P GAIN WILD-TYPE 35 360 83

Figure S21.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0075

Table S22.  Gene #6: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
5P GAIN MUTATED 5 14 2
5P GAIN WILD-TYPE 271 140 67

Figure S22.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
5P GAIN MUTATED 5 14 1 1
5P GAIN WILD-TYPE 163 141 57 115

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
5P GAIN MUTATED 6 14 0 1 0
5P GAIN WILD-TYPE 98 120 86 94 78

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

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0041

Table S25.  Gene #6: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
5P GAIN MUTATED 7 13 1
5P GAIN WILD-TYPE 174 138 165

Figure S25.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S26.  Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
5P GAIN MUTATED 7 13 1
5P GAIN WILD-TYPE 171 115 191

Figure S26.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.013

Table S27.  Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
5P GAIN MUTATED 8 9 1
5P GAIN WILD-TYPE 156 117 177

Figure S27.  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 S28.  Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
5Q GAIN MUTATED 17 0 0
5Q GAIN WILD-TYPE 39 360 83

Figure S28.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

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

Table S29.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
5Q GAIN MUTATED 2 14 1
5Q GAIN WILD-TYPE 274 140 68

Figure S29.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
5Q GAIN MUTATED 2 14 0 1
5Q GAIN WILD-TYPE 166 141 58 115

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S31.  Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
5Q GAIN MUTATED 2 14 0 1 0
5Q GAIN WILD-TYPE 102 120 86 94 78

Figure S31.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 178 138 165

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

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S33.  Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 175 115 191

Figure S33.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.016

Table S34.  Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
5Q GAIN MUTATED 4 9 1
5Q GAIN WILD-TYPE 160 117 177

Figure S34.  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 S35.  Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
7P GAIN MUTATED 18 0 0
7P GAIN WILD-TYPE 38 360 83

Figure S35.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00052

Table S36.  Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
7P GAIN MUTATED 2 14 2
7P GAIN WILD-TYPE 274 140 67

Figure S36.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0026

Table S37.  Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
7P GAIN MUTATED 2 14 1 1
7P GAIN WILD-TYPE 166 141 57 115

Figure S37.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S38.  Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
7P GAIN MUTATED 2 14 1 1 0
7P GAIN WILD-TYPE 102 120 85 94 78

Figure S38.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 177 138 165

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 174 115 191

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

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S41.  Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
7P GAIN MUTATED 5 9 1
7P GAIN WILD-TYPE 159 117 177

Figure S41.  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 S42.  Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
7Q GAIN MUTATED 19 0 1
7Q GAIN WILD-TYPE 37 360 82

Figure S42.  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 S43.  Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
7Q GAIN MUTATED 2 16 2
7Q GAIN WILD-TYPE 274 138 67

Figure S43.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.042

Table S44.  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 47 27 9
7Q GAIN MUTATED 4 1 0 2 0 5 0
7Q GAIN WILD-TYPE 42 27 33 27 47 22 9

Figure S44.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S45.  Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
7Q GAIN MUTATED 2 16 1 1
7Q GAIN WILD-TYPE 166 139 57 115

Figure S45.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S46.  Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
7Q GAIN MUTATED 2 16 1 1 0
7Q GAIN WILD-TYPE 102 118 85 94 78

Figure S46.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00047

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 177 136 165

Figure S47.  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 S48.  Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 174 113 191

Figure S48.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0039

Table S49.  Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
7Q GAIN MUTATED 5 11 1
7Q GAIN WILD-TYPE 159 115 177

Figure S49.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00084

Table S50.  Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
8P GAIN MUTATED 5 1 0
8P GAIN WILD-TYPE 51 359 83

Figure S50.  Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

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

Table S51.  Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
8Q GAIN MUTATED 6 1 0
8Q GAIN WILD-TYPE 50 359 83

Figure S51.  Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0059

Table S52.  Gene #12: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
9P GAIN MUTATED 3 0 0
9P GAIN WILD-TYPE 53 360 83

Figure S52.  Get High-res Image Gene #12: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.029

Table S53.  Gene #13: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
9Q GAIN MUTATED 3 1 0
9Q GAIN WILD-TYPE 53 359 83

Figure S53.  Get High-res Image Gene #13: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0062

Table S54.  Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
11P GAIN MUTATED 4 1 1
11P GAIN WILD-TYPE 52 359 82

Figure S54.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.082

Table S55.  Gene #14: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
11P GAIN MUTATED 1 5 0
11P GAIN WILD-TYPE 275 149 69

Figure S55.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.1

Table S56.  Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
11P GAIN MUTATED 0 5 0 1 0
11P GAIN WILD-TYPE 104 129 86 94 78

Figure S56.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.027

Table S57.  Gene #14: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
11P GAIN MUTATED 0 5 1
11P GAIN WILD-TYPE 181 146 165

Figure S57.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0071 (Fisher's exact test), Q value = 0.022

Table S58.  Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11P GAIN MUTATED 0 5 1
11P GAIN WILD-TYPE 178 123 191

Figure S58.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00087

Table S59.  Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
11Q GAIN MUTATED 4 0 1
11Q GAIN WILD-TYPE 52 360 82

Figure S59.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.064

Table S60.  Gene #15: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
11Q GAIN MUTATED 0 4 1
11Q GAIN WILD-TYPE 181 147 165

Figure S60.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.054

Table S61.  Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11Q GAIN MUTATED 0 4 1
11Q GAIN WILD-TYPE 178 124 191

Figure S61.  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 S62.  Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
12P GAIN MUTATED 13 0 1
12P GAIN WILD-TYPE 43 360 82

Figure S62.  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 S63.  Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
12P GAIN MUTATED 1 13 0
12P GAIN WILD-TYPE 275 141 69

Figure S63.  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 S64.  Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
12P GAIN MUTATED 0 13 0 1
12P GAIN WILD-TYPE 168 142 58 115

Figure S64.  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 S65.  Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
12P GAIN MUTATED 0 13 0 1 0
12P GAIN WILD-TYPE 104 121 86 94 78

Figure S65.  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 = 0.00036

Table S66.  Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
12P GAIN MUTATED 1 12 1
12P GAIN WILD-TYPE 180 139 165

Figure S66.  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 S67.  Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
12P GAIN MUTATED 1 12 1
12P GAIN WILD-TYPE 177 116 191

Figure S67.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.011

Table S68.  Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
12P GAIN MUTATED 2 8 1
12P GAIN WILD-TYPE 162 118 177

Figure S68.  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 S69.  Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
12Q GAIN MUTATED 14 0 1
12Q GAIN WILD-TYPE 42 360 82

Figure S69.  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 S70.  Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
12Q GAIN MUTATED 1 14 0
12Q GAIN WILD-TYPE 275 140 69

Figure S70.  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 S71.  Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
12Q GAIN MUTATED 0 14 0 1
12Q GAIN WILD-TYPE 168 141 58 115

Figure S71.  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 S72.  Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
12Q GAIN MUTATED 0 14 0 1 0
12Q GAIN WILD-TYPE 104 120 86 94 78

Figure S72.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

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

Table S73.  Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 180 138 165

Figure S73.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S74.  Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 177 115 191

Figure S74.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0041

Table S75.  Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
12Q GAIN MUTATED 2 9 1
12Q GAIN WILD-TYPE 162 117 177

Figure S75.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

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

Table S76.  Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
13Q GAIN MUTATED 5 0 0
13Q GAIN WILD-TYPE 51 360 83

Figure S76.  Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.046

Table S77.  Gene #18: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
13Q GAIN MUTATED 0 4 1
13Q GAIN WILD-TYPE 276 150 68

Figure S77.  Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.1

Table S78.  Gene #18: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
13Q GAIN MUTATED 0 4 1 0
13Q GAIN WILD-TYPE 168 151 57 116

Figure S78.  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 S79.  Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
14Q GAIN MUTATED 10 0 1
14Q GAIN WILD-TYPE 46 360 82

Figure S79.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00075

Table S80.  Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
14Q GAIN MUTATED 1 10 0
14Q GAIN WILD-TYPE 275 144 69

Figure S80.  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 = 0.0025

Table S81.  Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
14Q GAIN MUTATED 1 10 0 0
14Q GAIN WILD-TYPE 167 145 58 116

Figure S81.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S82.  Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
14Q GAIN MUTATED 0 10 0 0 1
14Q GAIN WILD-TYPE 104 124 86 95 77

Figure S82.  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 = 0.0032

Table S83.  Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 179 142 166

Figure S83.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S84.  Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 176 119 192

Figure S84.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0065

Table S85.  Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
14Q GAIN MUTATED 3 7 0
14Q GAIN WILD-TYPE 161 119 178

Figure S85.  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 S86.  Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
16P GAIN MUTATED 14 0 1
16P GAIN WILD-TYPE 42 360 82

Figure S86.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

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

Table S87.  Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
16P GAIN MUTATED 1 13 1
16P GAIN WILD-TYPE 275 141 68

Figure S87.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

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

Table S88.  Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
16P GAIN MUTATED 1 13 0 1
16P GAIN WILD-TYPE 167 142 58 115

Figure S88.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S89.  Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
16P GAIN MUTATED 1 13 0 1 0
16P GAIN WILD-TYPE 103 121 86 94 78

Figure S89.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00071

Table S90.  Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 179 139 165

Figure S90.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S91.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 176 116 191

Figure S91.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0036

Table S92.  Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
16P GAIN MUTATED 3 10 1
16P GAIN WILD-TYPE 161 116 177

Figure S92.  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 S93.  Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
16Q GAIN MUTATED 13 0 0
16Q GAIN WILD-TYPE 43 360 83

Figure S93.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00084

Table S94.  Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
16Q GAIN MUTATED 1 11 1
16Q GAIN WILD-TYPE 275 143 68

Figure S94.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0039

Table S95.  Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
16Q GAIN MUTATED 1 11 0 1
16Q GAIN WILD-TYPE 167 144 58 115

Figure S95.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S96.  Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
16Q GAIN MUTATED 1 11 0 1 0
16Q GAIN WILD-TYPE 103 123 86 94 78

Figure S96.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0062

Table S97.  Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
16Q GAIN MUTATED 2 10 1
16Q GAIN WILD-TYPE 179 141 165

Figure S97.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00052

Table S98.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
16Q GAIN MUTATED 2 10 1
16Q GAIN WILD-TYPE 176 118 191

Figure S98.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00815 (Fisher's exact test), Q value = 0.024

Table S99.  Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
16Q GAIN MUTATED 3 8 1
16Q GAIN WILD-TYPE 161 118 177

Figure S99.  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 S100.  Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
17P GAIN MUTATED 12 2 2
17P GAIN WILD-TYPE 44 358 81

Figure S100.  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 S101.  Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
17P GAIN MUTATED 1 15 0
17P GAIN WILD-TYPE 275 139 69

Figure S101.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.069

Table S102.  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 47 27 9
17P GAIN MUTATED 1 1 0 2 0 4 0
17P GAIN WILD-TYPE 45 27 33 27 47 23 9

Figure S102.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

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

Table S103.  Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
17P GAIN MUTATED 0 15 0 1
17P GAIN WILD-TYPE 168 140 58 115

Figure S103.  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 S104.  Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
17P GAIN MUTATED 0 15 0 1 0
17P GAIN WILD-TYPE 104 119 86 94 78

Figure S104.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

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

Table S105.  Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 180 137 165

Figure S105.  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 S106.  Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 177 114 191

Figure S106.  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 S107.  Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
17P GAIN MUTATED 2 10 1
17P GAIN WILD-TYPE 162 116 177

Figure S107.  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 S108.  Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
17Q GAIN MUTATED 13 2 3
17Q GAIN WILD-TYPE 43 358 80

Figure S108.  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 S109.  Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
17Q GAIN MUTATED 2 16 0
17Q GAIN WILD-TYPE 274 138 69

Figure S109.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.043

Table S110.  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 47 27 9
17Q GAIN MUTATED 1 1 0 3 0 4 0
17Q GAIN WILD-TYPE 45 27 33 26 47 23 9

Figure S110.  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 S111.  Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
17Q GAIN MUTATED 1 16 0 1
17Q GAIN WILD-TYPE 167 139 58 115

Figure S111.  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 S112.  Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
17Q GAIN MUTATED 1 16 0 1 0
17Q GAIN WILD-TYPE 103 118 86 94 78

Figure S112.  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 S113.  Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 179 136 165

Figure S113.  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 S114.  Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 176 113 191

Figure S114.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S115.  Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
17Q GAIN MUTATED 3 11 1
17Q GAIN WILD-TYPE 161 115 177

Figure S115.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

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

Table S116.  Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
18P GAIN MUTATED 5 0 1
18P GAIN WILD-TYPE 51 360 82

Figure S116.  Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

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

Table S117.  Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
18Q GAIN MUTATED 5 0 1
18Q GAIN WILD-TYPE 51 360 82

Figure S117.  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 S118.  Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
19P GAIN MUTATED 8 0 0
19P GAIN WILD-TYPE 48 360 83

Figure S118.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00091

Table S119.  Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 276 146 69

Figure S119.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0025

Table S120.  Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
19P GAIN MUTATED 0 8 0 0
19P GAIN WILD-TYPE 168 147 58 116

Figure S120.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00087

Table S121.  Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
19P GAIN MUTATED 0 8 0 0 0
19P GAIN WILD-TYPE 104 126 86 95 78

Figure S121.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00052

Table S122.  Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 181 143 166

Figure S122.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S123.  Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 178 120 192

Figure S123.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S124.  Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
19P GAIN MUTATED 1 4 0
19P GAIN WILD-TYPE 163 122 178

Figure S124.  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 S125.  Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
19Q GAIN MUTATED 10 0 0
19Q GAIN WILD-TYPE 46 360 83

Figure S125.  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 S126.  Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 276 144 69

Figure S126.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S127.  Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
19Q GAIN MUTATED 0 10 0 0
19Q GAIN WILD-TYPE 168 145 58 116

Figure S127.  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 = 3e-04

Table S128.  Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
19Q GAIN MUTATED 0 10 0 0 0
19Q GAIN WILD-TYPE 104 124 86 95 78

Figure S128.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

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

Table S129.  Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 181 141 166

Figure S129.  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 S130.  Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 178 118 192

Figure S130.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.0057

Table S131.  Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
19Q GAIN MUTATED 1 6 0
19Q GAIN WILD-TYPE 163 120 178

Figure S131.  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 S132.  Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
20P GAIN MUTATED 12 0 0
20P GAIN WILD-TYPE 44 360 83

Figure S132.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S133.  Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
20P GAIN MUTATED 1 10 1
20P GAIN WILD-TYPE 275 144 68

Figure S133.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.0099

Table S134.  Gene #28: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
20P GAIN MUTATED 1 10 0 1
20P GAIN WILD-TYPE 167 145 58 115

Figure S134.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0045

Table S135.  Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
20P GAIN MUTATED 1 10 0 1 0
20P GAIN WILD-TYPE 103 124 86 94 78

Figure S135.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00422 (Fisher's exact test), Q value = 0.014

Table S136.  Gene #28: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
20P GAIN MUTATED 2 9 1
20P GAIN WILD-TYPE 179 142 165

Figure S136.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.003

Table S137.  Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
20P GAIN MUTATED 2 9 1
20P GAIN WILD-TYPE 176 119 191

Figure S137.  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 S138.  Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
20Q GAIN MUTATED 12 0 0
20Q GAIN WILD-TYPE 44 360 83

Figure S138.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0014

Table S139.  Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
20Q GAIN MUTATED 1 10 1
20Q GAIN WILD-TYPE 275 144 68

Figure S139.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.0096

Table S140.  Gene #29: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
20Q GAIN MUTATED 1 10 0 1
20Q GAIN WILD-TYPE 167 145 58 115

Figure S140.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0043

Table S141.  Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
20Q GAIN MUTATED 1 10 0 1 0
20Q GAIN WILD-TYPE 103 124 86 94 78

Figure S141.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.015

Table S142.  Gene #29: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
20Q GAIN MUTATED 2 9 1
20Q GAIN WILD-TYPE 179 142 165

Figure S142.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0026

Table S143.  Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
20Q GAIN MUTATED 2 9 1
20Q GAIN WILD-TYPE 176 119 191

Figure S143.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S144.  Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
21Q GAIN MUTATED 4 0 1
21Q GAIN WILD-TYPE 52 360 82

Figure S144.  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 S145.  Gene #31: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
XP GAIN MUTATED 8 0 0
XP GAIN WILD-TYPE 48 360 83

Figure S145.  Get High-res Image Gene #31: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0076

Table S146.  Gene #31: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
XP GAIN MUTATED 0 6 2
XP GAIN WILD-TYPE 276 148 67

Figure S146.  Get High-res Image Gene #31: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.1

Table S147.  Gene #31: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
XP GAIN MUTATED 1 6 1 0
XP GAIN WILD-TYPE 167 149 57 116

Figure S147.  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 S148.  Gene #32: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
XQ GAIN MUTATED 8 1 0
XQ GAIN WILD-TYPE 48 359 83

Figure S148.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.031

Table S149.  Gene #32: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
XQ GAIN MUTATED 1 6 2
XQ GAIN WILD-TYPE 275 148 67

Figure S149.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00075

Table S150.  Gene #33: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
1P LOSS MUTATED 4 0 0
1P LOSS WILD-TYPE 52 360 83

Figure S150.  Get High-res Image Gene #33: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0056

Table S151.  Gene #34: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
1Q LOSS MUTATED 3 0 0
1Q LOSS WILD-TYPE 53 360 83

Figure S151.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.064

Table S152.  Gene #34: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 181 148 166

Figure S152.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.043

Table S153.  Gene #34: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 178 125 192

Figure S153.  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 S154.  Gene #35: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
2P LOSS MUTATED 9 0 1
2P LOSS WILD-TYPE 47 360 82

Figure S154.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

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

Table S155.  Gene #35: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 276 144 69

Figure S155.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S156.  Gene #35: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
2P LOSS MUTATED 0 10 0 0
2P LOSS WILD-TYPE 168 145 58 116

Figure S156.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S157.  Gene #35: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
2P LOSS MUTATED 0 10 0 0 0
2P LOSS WILD-TYPE 104 124 86 95 78

Figure S157.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

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

Table S158.  Gene #35: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 181 141 166

Figure S158.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S159.  Gene #35: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 178 118 192

Figure S159.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S160.  Gene #35: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
2P LOSS MUTATED 1 7 0
2P LOSS WILD-TYPE 163 119 178

Figure S160.  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 S161.  Gene #36: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
2Q LOSS MUTATED 10 0 0
2Q LOSS WILD-TYPE 46 360 83

Figure S161.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

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

Table S162.  Gene #36: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 276 144 69

Figure S162.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

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

Table S163.  Gene #36: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
2Q LOSS MUTATED 0 10 0 0
2Q LOSS WILD-TYPE 168 145 58 116

Figure S163.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S164.  Gene #36: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
2Q LOSS MUTATED 0 10 0 0 0
2Q LOSS WILD-TYPE 104 124 86 95 78

Figure S164.  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 S165.  Gene #36: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 181 141 166

Figure S165.  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 S166.  Gene #36: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 178 118 192

Figure S166.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0023

Table S167.  Gene #36: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
2Q LOSS MUTATED 1 7 0
2Q LOSS WILD-TYPE 163 119 178

Figure S167.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0056

Table S168.  Gene #37: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
3P LOSS MUTATED 3 0 0
3P LOSS WILD-TYPE 53 360 83

Figure S168.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.1

Table S169.  Gene #37: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 276 151 69

Figure S169.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.064

Table S170.  Gene #37: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 181 148 166

Figure S170.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.042

Table S171.  Gene #37: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 178 125 192

Figure S171.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00084

Table S172.  Gene #38: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
3Q LOSS MUTATED 4 0 0
3Q LOSS WILD-TYPE 52 360 83

Figure S172.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.046

Table S173.  Gene #38: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 276 150 69

Figure S173.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.08

Table S174.  Gene #38: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
3Q LOSS MUTATED 0 4 0 0
3Q LOSS WILD-TYPE 168 151 58 116

Figure S174.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.1

Table S175.  Gene #38: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
3Q LOSS MUTATED 0 4 0 0 0
3Q LOSS WILD-TYPE 104 130 86 95 78

Figure S175.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00811 (Fisher's exact test), Q value = 0.024

Table S176.  Gene #38: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 181 147 166

Figure S176.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.014

Table S177.  Gene #38: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 178 124 192

Figure S177.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

Table S178.  Gene #39: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
6P LOSS MUTATED 4 0 0
6P LOSS WILD-TYPE 52 360 83

Figure S178.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.1

Table S179.  Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
6P LOSS MUTATED 0 3 1
6P LOSS WILD-TYPE 276 151 68

Figure S179.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

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

Table S180.  Gene #40: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
6Q LOSS MUTATED 6 1 0
6Q LOSS WILD-TYPE 50 359 83

Figure S180.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0075

Table S181.  Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
6Q LOSS MUTATED 0 6 1
6Q LOSS WILD-TYPE 276 148 68

Figure S181.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.073

Table S182.  Gene #40: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
6Q LOSS MUTATED 1 6 0 0
6Q LOSS WILD-TYPE 167 149 58 116

Figure S182.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
6Q LOSS MUTATED 1 6 0 0 0
6Q LOSS WILD-TYPE 103 128 86 95 78

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

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00538 (Fisher's exact test), Q value = 0.017

Table S184.  Gene #40: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 180 145 166

Figure S184.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0036

Table S185.  Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 177 122 192

Figure S185.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.03

Table S186.  Gene #40: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
6Q LOSS MUTATED 2 5 0
6Q LOSS WILD-TYPE 162 121 178

Figure S186.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S187.  Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 52 360 83

Figure S187.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.045

Table S188.  Gene #41: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 276 150 69

Figure S188.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.082

Table S189.  Gene #41: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
8P LOSS MUTATED 0 4 0 0
8P LOSS WILD-TYPE 168 151 58 116

Figure S189.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.1

Table S190.  Gene #41: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
8P LOSS MUTATED 0 4 0 0 0
8P LOSS WILD-TYPE 104 130 86 95 78

Figure S190.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00849 (Fisher's exact test), Q value = 0.025

Table S191.  Gene #41: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 181 147 166

Figure S191.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00431 (Fisher's exact test), Q value = 0.014

Table S192.  Gene #41: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 178 124 192

Figure S192.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.046

Table S193.  Gene #41: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
8P LOSS MUTATED 0 3 0
8P LOSS WILD-TYPE 164 123 178

Figure S193.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00087

Table S194.  Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 52 360 83

Figure S194.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.046

Table S195.  Gene #42: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 276 150 69

Figure S195.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.082

Table S196.  Gene #42: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
8Q LOSS MUTATED 0 4 0 0
8Q LOSS WILD-TYPE 168 151 58 116

Figure S196.  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 = 0.1

Table S197.  Gene #42: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
8Q LOSS MUTATED 0 4 0 0 0
8Q LOSS WILD-TYPE 104 130 86 95 78

Figure S197.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.024

Table S198.  Gene #42: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 181 147 166

Figure S198.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.014

Table S199.  Gene #42: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 178 124 192

Figure S199.  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 = 0.046

Table S200.  Gene #42: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
8Q LOSS MUTATED 0 3 0
8Q LOSS WILD-TYPE 164 123 178

Figure S200.  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 S201.  Gene #43: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
9P LOSS MUTATED 15 2 2
9P LOSS WILD-TYPE 41 358 81

Figure S201.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.082

Table S202.  Gene #43: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
9P LOSS MUTATED 6 11 2
9P LOSS WILD-TYPE 270 143 67

Figure S202.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.076

Table S203.  Gene #43: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
9P LOSS MUTATED 2 11 3 3
9P LOSS WILD-TYPE 166 144 55 113

Figure S203.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00901 (Fisher's exact test), Q value = 0.026

Table S204.  Gene #43: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
9P LOSS MUTATED 8 10 1
9P LOSS WILD-TYPE 173 141 165

Figure S204.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00766 (Fisher's exact test), Q value = 0.023

Table S205.  Gene #43: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
9P LOSS MUTATED 7 10 2
9P LOSS WILD-TYPE 171 118 190

Figure S205.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.013

Table S206.  Gene #43: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
9P LOSS MUTATED 7 9 1
9P LOSS WILD-TYPE 157 117 177

Figure S206.  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 S207.  Gene #44: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
9Q LOSS MUTATED 20 3 2
9Q LOSS WILD-TYPE 36 357 81

Figure S207.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.029

Table S208.  Gene #44: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
9Q LOSS MUTATED 12 11 2
9Q LOSS WILD-TYPE 169 140 164

Figure S208.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00712 (Fisher's exact test), Q value = 0.022

Table S209.  Gene #44: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
9Q LOSS MUTATED 11 11 3
9Q LOSS WILD-TYPE 167 117 189

Figure S209.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0044 (Fisher's exact test), Q value = 0.015

Table S210.  Gene #44: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
9Q LOSS MUTATED 11 10 2
9Q LOSS WILD-TYPE 153 116 176

Figure S210.  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 S211.  Gene #45: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
10P LOSS MUTATED 7 0 0
10P LOSS WILD-TYPE 49 360 83

Figure S211.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.032

Table S212.  Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 275 148 69

Figure S212.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

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

Table S213.  Gene #45: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
10P LOSS MUTATED 0 6 0 1
10P LOSS WILD-TYPE 168 149 58 115

Figure S213.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.042

Table S214.  Gene #45: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
10P LOSS MUTATED 0 6 0 1 0
10P LOSS WILD-TYPE 104 128 86 94 78

Figure S214.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.016

Table S215.  Gene #45: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 180 145 166

Figure S215.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0036

Table S216.  Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 177 122 192

Figure S216.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.028

Table S217.  Gene #45: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
10P LOSS MUTATED 2 5 0
10P LOSS WILD-TYPE 162 121 178

Figure S217.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

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

Table S218.  Gene #46: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
10Q LOSS MUTATED 6 0 0
10Q LOSS WILD-TYPE 50 360 83

Figure S218.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.082

Table S219.  Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 275 149 69

Figure S219.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S220.  Gene #46: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
10Q LOSS MUTATED 0 5 0 1 0
10Q LOSS WILD-TYPE 104 129 86 94 78

Figure S220.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.038

Table S221.  Gene #46: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 180 146 166

Figure S221.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00517 (Fisher's exact test), Q value = 0.016

Table S222.  Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 177 123 192

Figure S222.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.066

Table S223.  Gene #46: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
10Q LOSS MUTATED 2 4 0
10Q LOSS WILD-TYPE 162 122 178

Figure S223.  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 S224.  Gene #47: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
11P LOSS MUTATED 6 0 1
11P LOSS WILD-TYPE 50 360 82

Figure S224.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.031

Table S225.  Gene #47: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 275 148 69

Figure S225.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00757 (Fisher's exact test), Q value = 0.023

Table S226.  Gene #47: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
11P LOSS MUTATED 0 6 1 0
11P LOSS WILD-TYPE 168 149 57 116

Figure S226.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.046

Table S227.  Gene #47: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
11P LOSS MUTATED 1 6 0 0 0
11P LOSS WILD-TYPE 103 128 86 95 78

Figure S227.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.016

Table S228.  Gene #47: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 180 145 166

Figure S228.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0032

Table S229.  Gene #47: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 177 122 192

Figure S229.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.029

Table S230.  Gene #47: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
11P LOSS MUTATED 2 5 0
11P LOSS WILD-TYPE 162 121 178

Figure S230.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

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

Table S231.  Gene #48: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
11Q LOSS MUTATED 7 1 1
11Q LOSS WILD-TYPE 49 359 82

Figure S231.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

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

Table S232.  Gene #48: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
11Q LOSS MUTATED 2 7 0
11Q LOSS WILD-TYPE 274 147 69

Figure S232.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

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

Table S233.  Gene #48: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
11Q LOSS MUTATED 1 7 1 0
11Q LOSS WILD-TYPE 167 148 57 116

Figure S233.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.047

Table S234.  Gene #48: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
11Q LOSS MUTATED 1 7 0 0 1
11Q LOSS WILD-TYPE 103 127 86 95 77

Figure S234.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0024

Table S235.  Gene #48: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
11Q LOSS MUTATED 1 8 0
11Q LOSS WILD-TYPE 180 143 166

Figure S235.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.0076

Table S236.  Gene #48: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11Q LOSS MUTATED 1 7 1
11Q LOSS WILD-TYPE 177 121 191

Figure S236.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.0098

Table S237.  Gene #48: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
11Q LOSS MUTATED 2 6 0
11Q LOSS WILD-TYPE 162 120 178

Figure S237.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0056

Table S238.  Gene #49: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
13Q LOSS MUTATED 6 5 3
13Q LOSS WILD-TYPE 50 355 80

Figure S238.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.041

Table S239.  Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
13Q LOSS MUTATED 3 9 2
13Q LOSS WILD-TYPE 273 145 67

Figure S239.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.022

Table S240.  Gene #49: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 64 42 49
13Q LOSS MUTATED 1 1 6 1
13Q LOSS WILD-TYPE 63 63 36 48

Figure S240.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.016

Table S241.  Gene #49: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
13Q LOSS MUTATED 0 9 2 3
13Q LOSS WILD-TYPE 168 146 56 113

Figure S241.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00884 (Fisher's exact test), Q value = 0.026

Table S242.  Gene #49: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
13Q LOSS MUTATED 0 9 2 3 0
13Q LOSS WILD-TYPE 104 125 84 92 78

Figure S242.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0046

Table S243.  Gene #49: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 181 142 161

Figure S243.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0025

Table S244.  Gene #49: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 178 119 187

Figure S244.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.034

Table S245.  Gene #49: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
13Q LOSS MUTATED 1 8 4
13Q LOSS WILD-TYPE 163 118 174

Figure S245.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S246.  Gene #50: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
15Q LOSS MUTATED 5 1 2
15Q LOSS WILD-TYPE 51 359 81

Figure S246.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

Table S247.  Gene #50: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 276 146 69

Figure S247.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0024

Table S248.  Gene #50: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
15Q LOSS MUTATED 0 8 0 0
15Q LOSS WILD-TYPE 168 147 58 116

Figure S248.  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 S249.  Gene #50: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
15Q LOSS MUTATED 0 8 0 0 0
15Q LOSS WILD-TYPE 104 126 86 95 78

Figure S249.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S250.  Gene #50: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 181 143 166

Figure S250.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S251.  Gene #50: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 178 120 192

Figure S251.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.0056

Table S252.  Gene #50: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
15Q LOSS MUTATED 1 6 0
15Q LOSS WILD-TYPE 163 120 178

Figure S252.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.035

Table S253.  Gene #51: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
17P LOSS MUTATED 4 3 1
17P LOSS WILD-TYPE 52 357 82

Figure S253.  Get High-res Image Gene #51: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0063

Table S254.  Gene #53: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
18P LOSS MUTATED 3 0 1
18P LOSS WILD-TYPE 53 360 82

Figure S254.  Get High-res Image Gene #53: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0063

Table S255.  Gene #54: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
18Q LOSS MUTATED 3 0 1
18Q LOSS WILD-TYPE 53 360 82

Figure S255.  Get High-res Image Gene #54: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.025

Table S256.  Gene #55: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
19P LOSS MUTATED 3 1 1
19P LOSS WILD-TYPE 53 359 82

Figure S256.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.02

Table S257.  Gene #55: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 276 149 69

Figure S257.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.042

Table S258.  Gene #55: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
19P LOSS MUTATED 0 5 0 0
19P LOSS WILD-TYPE 168 150 58 116

Figure S258.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S259.  Gene #55: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
19P LOSS MUTATED 0 5 0 0 0
19P LOSS WILD-TYPE 104 129 86 95 78

Figure S259.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.0087

Table S260.  Gene #55: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 181 146 166

Figure S260.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0045

Table S261.  Gene #55: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 178 123 192

Figure S261.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.005

Table S262.  Gene #55: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 164 121 178

Figure S262.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0039

Table S263.  Gene #56: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
21Q LOSS MUTATED 5 2 1
21Q LOSS WILD-TYPE 51 358 82

Figure S263.  Get High-res Image Gene #56: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.069

Table S264.  Gene #56: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
21Q LOSS MUTATED 4 4 0
21Q LOSS WILD-TYPE 174 124 192

Figure S264.  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 S265.  Gene #57: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
22Q LOSS MUTATED 13 0 76
22Q LOSS WILD-TYPE 43 360 7

Figure S265.  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 S266.  Gene #57: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
22Q LOSS MUTATED 36 47 6
22Q LOSS WILD-TYPE 240 107 63

Figure S266.  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 S267.  Gene #57: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 58 116
22Q LOSS MUTATED 8 47 8 26
22Q LOSS WILD-TYPE 160 108 50 90

Figure S267.  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 S268.  Gene #57: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
22Q LOSS MUTATED 9 42 13 23 2
22Q LOSS WILD-TYPE 95 92 73 72 76

Figure S268.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0024

Table S269.  Gene #57: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
22Q LOSS MUTATED 23 43 23
22Q LOSS WILD-TYPE 158 108 143

Figure S269.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S270.  Gene #57: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
22Q LOSS MUTATED 21 40 28
22Q LOSS WILD-TYPE 157 88 164

Figure S270.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00087

Table S271.  Gene #57: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 145
22Q LOSS MUTATED 17 23 41
22Q LOSS WILD-TYPE 142 141 104

Figure S271.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0019

Table S272.  Gene #57: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
22Q LOSS MUTATED 22 37 22
22Q LOSS WILD-TYPE 142 89 156

Figure S272.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.082

Table S273.  Gene #58: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 145
XP LOSS MUTATED 0 4 0
XP LOSS WILD-TYPE 159 160 145

Figure S273.  Get High-res Image Gene #58: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.1

Table S274.  Gene #59: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 360 83
XQ LOSS MUTATED 2 1 0
XQ LOSS WILD-TYPE 54 359 83

Figure S274.  Get High-res Image Gene #59: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.1

Table S275.  Gene #59: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 276 154 69
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 276 151 69

Figure S275.  Get High-res Image Gene #59: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.064

Table S276.  Gene #59: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 151 166
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 181 148 166

Figure S276.  Get High-res Image Gene #59: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.045

Table S277.  Gene #59: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 178 125 192

Figure S277.  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 = 0.046

Table S278.  Gene #59: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 126 178
XQ LOSS MUTATED 0 3 0
XQ LOSS WILD-TYPE 164 123 178

Figure S278.  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/19782151/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/20140899/THCA-TP.transferedmergedcluster.txt

  • Number of patients = 499

  • 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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