Correlation between copy number variations of arm-level result and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 577 patients, 272 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'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 3q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'MRNA_CNMF'.

  • 6q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

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

  • 8p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 8q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 9p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • 14q gain cnv correlated to 'MIR_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • 17p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • 17q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

  • 18q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 19p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 22q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • xq gain cnv correlated to 'MRNASEQ_CNMF'.

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

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • 4p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 4q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 5p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 7p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 8q loss cnv correlated to 'MIR_CNMF'.

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

  • 10p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 16p loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 17q loss cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 20p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xp loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • xq loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 272 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
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
7p gain 468 (81%) 109 1e-05
(0.000132) 		1e-05
(0.000132) 		0.00029
(0.00207) 		1e-05
(0.000132) 		1e-05
(0.000132) 		1e-05
(0.000132) 		0.0083
(0.036) 		0.00066
(0.00413) 		0.0155
(0.062) 		4e-05
(0.000381)
7q gain 474 (82%) 103 2e-05
(0.000231) 		1e-05
(0.000132) 		0.00109
(0.00643) 		0.00015
(0.00116) 		1e-05
(0.000132) 		4e-05
(0.000381) 		0.345
(0.551) 		0.011
(0.0461) 		0.0542
(0.16) 		0.00162
(0.00892)
10p loss 483 (84%) 94 1e-05
(0.000132) 		1e-05
(0.000132) 		0.00999
(0.0429) 		7e-05
(0.000611) 		1e-05
(0.000132) 		1e-05
(0.000132) 		0.212
(0.391) 		0.00054
(0.00357) 		0.222
(0.407) 		0.0127
(0.0516)
10q loss 494 (86%) 83 1e-05
(0.000132) 		1e-05
(0.000132) 		0.00575
(0.0256) 		0.00011
(0.000902) 		1e-05
(0.000132) 		0.00015
(0.00116) 		0.323
(0.53) 		5e-05
(0.000461) 		0.261
(0.453) 		0.0218
(0.0804)
15q loss 106 (18%) 471 4e-05
(0.000381) 		2e-05
(0.000231) 		0.00401
(0.0195) 		0.00358
(0.0175) 		1e-05
(0.000132) 		0.0754
(0.201) 		0.176
(0.35) 		0.0193
(0.0736) 		0.0034
(0.0167) 		0.0226
(0.0821)
20p gain 222 (38%) 355 1e-05
(0.000132) 		1e-05
(0.000132) 		0.00447
(0.0211) 		1e-05
(0.000132) 		4e-05
(0.000381) 		8e-05
(0.000691) 		0.35
(0.557) 		0.00047
(0.00319) 		0.796
(0.906) 		0.12
(0.274)
20q gain 220 (38%) 357 1e-05
(0.000132) 		1e-05
(0.000132) 		0.00283
(0.0144) 		1e-05
(0.000132) 		4e-05
(0.000381) 		1e-05
(0.000132) 		0.262
(0.453) 		0.00041
(0.00287) 		0.797
(0.906) 		0.119
(0.271)
21q gain 64 (11%) 513 0.00116
(0.00665) 		0.00759
(0.0335) 		0.0107
(0.0448) 		0.00412
(0.0198) 		0.00017
(0.00128) 		0.00174
(0.00945) 		0.116
(0.267) 		0.755
(0.88) 		0.0179
(0.0705) 		0.328
(0.537)
17p gain 48 (8%) 529 0.00047
(0.00319) 		0.0204
(0.0767) 		0.0783
(0.206) 		0.0393
(0.124) 		0.0002
(0.00146) 		0.034
(0.111) 		0.0255
(0.091) 		0.203
(0.382) 		0.339
(0.548) 		0.39
(0.596)
19p gain 226 (39%) 351 1e-05
(0.000132) 		1e-05
(0.000132) 		0.0902
(0.227) 		0.00028
(0.00201) 		1e-05
(0.000132) 		1e-05
(0.000132) 		0.206
(0.385) 		4e-05
(0.000381) 		0.189
(0.367) 		0.656
(0.806)
19q gain 199 (34%) 378 1e-05
(0.000132) 		1e-05
(0.000132) 		0.142
(0.305) 		0.00324
(0.016) 		1e-05
(0.000132) 		1e-05
(0.000132) 		0.208
(0.388) 		0.0002
(0.00146) 		0.063
(0.176) 		0.344
(0.551)
5q loss 44 (8%) 533 4e-05
(0.000381) 		2e-05
(0.000231) 		0.00092
(0.00555) 		0.187
(0.366) 		0.00015
(0.00116) 		1e-05
(0.000132) 		0.665
(0.809) 		0.0842
(0.216) 		0.224
(0.41) 		0.0421
(0.13)
11p loss 99 (17%) 478 1e-05
(0.000132) 		1e-05
(0.000132) 		0.831
(0.923) 		0.0142
(0.0572) 		1e-05
(0.000132) 		0.00279
(0.0144) 		0.818
(0.92) 		0.0299
(0.101) 		0.0954
(0.236) 		0.0878
(0.222)
13q loss 186 (32%) 391 6e-05
(0.000541) 		0.00177
(0.00948) 		0.75
(0.877) 		0.589
(0.758) 		1e-05
(0.000132) 		0.0115
(0.0477) 		0.521
(0.708) 		0.0271
(0.0947) 		0.0492
(0.148) 		0.401
(0.606)
20p loss 19 (3%) 558 0.00017
(0.00128) 		2e-05
(0.000231) 		0.036
(0.115) 		0.0928
(0.232) 		2e-05
(0.000231) 		0.309
(0.512) 		0.0778
(0.206) 		0.453
(0.655) 		0.0105
(0.0442) 		0.00215
(0.0113)
xp loss 114 (20%) 463 0.00306
(0.0155) 		0.0122
(0.0502) 		0.0423
(0.13) 		0.166
(0.334) 		1e-05
(0.000132) 		0.00011
(0.000902) 		0.0299
(0.101) 		0.462
(0.66) 		0.391
(0.596) 		0.831
(0.923)
8q gain 59 (10%) 518 3e-05
(0.000324) 		2e-05
(0.000231) 		0.0401
(0.126) 		0.455
(0.655) 		1e-05
(0.000132) 		0.00052
(0.00347) 		0.276
(0.468) 		0.158
(0.323) 		0.123
(0.277) 		0.512
(0.707)
10p gain 13 (2%) 564 0.00111
(0.00647) 		0.00013
(0.00105) 		0.118
(0.27) 		0.0583
(0.17) 		0.00098
(0.00582) 		0.0004
(0.00283) 		0.408
(0.612) 		0.00444
(0.021)
16q gain 37 (6%) 540 0.0183
(0.0714) 		0.0053
(0.0244) 		0.358
(0.568) 		0.0639
(0.178) 		5e-05
(0.000461) 		0.0263
(0.0925) 		0.023
(0.083) 		0.884
(0.963) 		0.42
(0.623) 		0.735
(0.863)
18p gain 58 (10%) 519 1e-05
(0.000132) 		0.00063
(0.00397) 		0.155
(0.32) 		0.364
(0.569) 		1e-05
(0.000132) 		0.00506
(0.0234) 		0.439
(0.639) 		0.395
(0.599) 		0.0192
(0.0736) 		0.0987
(0.241)
18q gain 58 (10%) 519 2e-05
(0.000231) 		0.00062
(0.00394) 		0.155
(0.32) 		0.431
(0.633) 		1e-05
(0.000132) 		0.00571
(0.0256) 		0.366
(0.57) 		0.612
(0.777) 		0.0189
(0.0733) 		0.112
(0.263)
4q loss 56 (10%) 521 0.0008
(0.00493) 		0.00061
(0.00391) 		0.0188
(0.0731) 		0.155
(0.32) 		0.00017
(0.00128) 		0.00097
(0.00581) 		0.764
(0.889) 		0.398
(0.604) 		0.559
(0.737) 		1
(1.00)
5p loss 43 (7%) 534 1e-05
(0.000132) 		2e-05
(0.000231) 		0.00178
(0.00948) 		0.0962
(0.237) 		3e-05
(0.000324) 		1e-05
(0.000132) 		0.8
(0.909) 		0.209
(0.389) 		0.344
(0.551) 		0.0523
(0.156)
14q loss 146 (25%) 431 1e-05
(0.000132) 		0.00011
(0.000902) 		0.509
(0.707) 		0.539
(0.722) 		1e-05
(0.000132) 		0.0241
(0.0866) 		0.188
(0.366) 		0.0293
(0.101) 		0.163
(0.331) 		0.703
(0.838)
19p loss 27 (5%) 550 0.00059
(0.00381) 		0.00132
(0.00746) 		0.0609
(0.175) 		0.436
(0.635) 		0.0136
(0.055) 		6e-05
(0.000541) 		0.0684
(0.187) 		0.036
(0.115) 		0.853
(0.943) 		0.668
(0.809)
20q loss 17 (3%) 560 0.00142
(0.00792) 		0.00011
(0.000902) 		0.364
(0.569) 		0.269
(0.46) 		1e-05
(0.000132) 		0.312
(0.517) 		0.579
(0.749) 		0.454
(0.655) 		0.0402
(0.126) 		0.012
(0.0495)
21q loss 42 (7%) 535 0.0206
(0.077) 		0.00124
(0.00706) 		0.0538
(0.159) 		0.26
(0.452) 		0.00058
(0.0038) 		0.00158
(0.00875) 		0.447
(0.647) 		0.0262
(0.0925) 		0.824
(0.921) 		1
(1.00)
3p gain 58 (10%) 519 0.00044
(0.00303) 		0.0291
(0.1) 		0.671
(0.81) 		0.0263
(0.0925) 		1e-05
(0.000132) 		0.131
(0.289) 		0.988
(1.00) 		0.706
(0.838) 		0.814
(0.917) 		0.258
(0.451)
6q gain 23 (4%) 554 0.0017
(0.00929) 		0.0356
(0.115) 		0.786
(0.906) 		0.104
(0.25) 		0.0247
(0.0886) 		0.0056
(0.0254) 		0.68
(0.818) 		0.669
(0.809) 		0.814
(0.917) 		1
(1.00)
8p gain 52 (9%) 525 3e-05
(0.000324) 		0.00072
(0.00447) 		0.0624
(0.176) 		0.558
(0.737) 		1e-05
(0.000132) 		0.00416
(0.0198) 		0.278
(0.469) 		0.157
(0.32) 		0.138
(0.299) 		0.676
(0.814)
17q gain 60 (10%) 517 0.00112
(0.00647) 		0.0466
(0.142) 		0.128
(0.283) 		0.0691
(0.188) 		1e-05
(0.000132) 		0.0373
(0.119) 		0.0582
(0.17) 		0.0609
(0.175) 		0.944
(1.00) 		0.617
(0.778)
22q gain 34 (6%) 543 1e-05
(0.000132) 		0.00319
(0.0159) 		0.469
(0.666) 		0.218
(0.401) 		0.00011
(0.000902) 		0.144
(0.307) 		0.267
(0.457) 		0.0287
(0.0997) 		0.244
(0.433) 		0.193
(0.371)
4p loss 55 (10%) 522 0.0809
(0.211) 		0.00317
(0.0158) 		0.0331
(0.109) 		0.227
(0.411) 		0.00217
(0.0113) 		0.00183
(0.00968) 		0.855
(0.943) 		0.336
(0.546) 		0.747
(0.875) 		1
(1.00)
7p loss 8 (1%) 569 0.0222
(0.0812) 		0.0339
(0.111) 		0.455
(0.655) 		0.0409
(0.127) 		0.0157
(0.0627)
17q loss 41 (7%) 536 0.00491
(0.0229) 		0.0618
(0.175) 		0.211
(0.391) 		0.0465
(0.142) 		1e-05
(0.000132) 		0.0367
(0.117) 		0.151
(0.316) 		1
(1.00) 		0.145
(0.309) 		0.108
(0.257)
18p loss 71 (12%) 506 0.0472
(0.143) 		0.0321
(0.107) 		0.363
(0.569) 		0.218
(0.401) 		3e-05
(0.000324) 		0.504
(0.702) 		0.465
(0.662) 		0.0407
(0.127) 		0.134
(0.292) 		0.598
(0.765)
19q loss 35 (6%) 542 0.00059
(0.00381) 		0.00472
(0.0221) 		0.413
(0.618) 		0.154
(0.319) 		0.00112
(0.00647) 		0.00083
(0.00504) 		0.203
(0.382) 		0.191
(0.369) 		0.929
(0.997) 		0.518
(0.708)
xq loss 106 (18%) 471 0.0192
(0.0736) 		0.0159
(0.0631) 		0.112
(0.263) 		0.106
(0.254) 		1e-05
(0.000132) 		0.00532
(0.0244) 		0.115
(0.267) 		0.755
(0.88) 		0.413
(0.618) 		0.961
(1.00)
9p gain 47 (8%) 530 0.00317
(0.0158) 		0.0297
(0.101) 		0.704
(0.838) 		0.433
(0.635) 		3e-05
(0.000324) 		0.545
(0.728) 		0.32
(0.527) 		0.706
(0.838) 		0.43
(0.633) 		0.113
(0.265)
12q gain 49 (8%) 528 0.521
(0.708) 		0.954
(1.00) 		0.537
(0.721) 		0.0104
(0.0442) 		0.0014
(0.00786) 		0.592
(0.76) 		0.21
(0.391) 		0.525
(0.712) 		0.0224
(0.0818) 		0.122
(0.275)
16p gain 38 (7%) 539 0.00785
(0.0344) 		0.0661
(0.182) 		0.415
(0.619) 		0.272
(0.463) 		1e-05
(0.000132) 		0.0317
(0.106) 		0.191
(0.369) 		0.662
(0.808) 		1
(1.00) 		1
(1.00)
2p loss 32 (6%) 545 0.0309
(0.104) 		0.0271
(0.0947) 		0.265
(0.456) 		0.769
(0.891) 		1e-05
(0.000132) 		0.617
(0.778) 		0.114
(0.265) 		0.938
(1.00) 		0.242
(0.432) 		0.227
(0.411)
2q loss 32 (6%) 545 0.0296
(0.101) 		0.0288
(0.0997) 		0.263
(0.453) 		0.767
(0.891) 		1e-05
(0.000132) 		0.614
(0.777) 		0.0661
(0.182) 		0.87
(0.956) 		0.0848
(0.217) 		0.0719
(0.194)
3q loss 34 (6%) 543 0.23
(0.415) 		0.127
(0.282) 		0.513
(0.707) 		0.675
(0.814) 		2e-05
(0.000231) 		0.0348
(0.113) 		0.0337
(0.111) 		0.176
(0.35) 		0.889
(0.965) 		0.183
(0.36)
9p loss 202 (35%) 375 0.00789
(0.0344) 		0.111
(0.262) 		0.55
(0.731) 		0.485
(0.684) 		0.597
(0.765) 		0.475
(0.672) 		0.138
(0.299) 		0.0992
(0.241) 		0.0221
(0.0812) 		0.00893
(0.0385)
11q loss 93 (16%) 484 4e-05
(0.000381) 		0.0002
(0.00146) 		0.932
(0.999) 		0.0616
(0.175) 		1e-05
(0.000132) 		0.417
(0.621) 		0.335
(0.545) 		0.152
(0.318) 		0.346
(0.551) 		0.533
(0.719)
17p loss 65 (11%) 512 0.0201
(0.0762) 		0.0202
(0.0762) 		0.652
(0.804) 		0.583
(0.752) 		1e-05
(0.000132) 		0.132
(0.291) 		0.53
(0.715) 		0.211
(0.391) 		0.304
(0.505) 		0.703
(0.838)
18q loss 62 (11%) 515 0.146
(0.309) 		0.00738
(0.0327) 		0.62
(0.778) 		0.241
(0.43) 		0.00015
(0.00116) 		0.476
(0.672) 		0.705
(0.838) 		0.00282
(0.0144) 		0.418
(0.622) 		0.121
(0.274)
3q gain 64 (11%) 513 0.0005
(0.00336) 		0.0626
(0.176) 		0.899
(0.971) 		0.0625
(0.176) 		1e-05
(0.000132) 		0.0644
(0.178) 		0.813
(0.917) 		1
(1.00) 		0.518
(0.708) 		0.151
(0.316)
12p gain 60 (10%) 517 0.668
(0.809) 		0.792
(0.906) 		0.646
(0.804) 		0.164
(0.331) 		4e-05
(0.000381) 		0.9
(0.971) 		0.254
(0.444) 		0.575
(0.747) 		0.00411
(0.0198) 		0.0784
(0.206)
15q gain 24 (4%) 553 0.0613
(0.175) 		0.111
(0.262) 		0.569
(0.744) 		0.133
(0.291) 		4e-05
(0.000381) 		0.282
(0.474) 		0.0683
(0.187) 		0.802
(0.909) 		0.0341
(0.111) 		0.385
(0.594)
1p loss 16 (3%) 561 0.635
(0.793) 		0.828
(0.923) 		0.94
(1.00) 		0.194
(0.371) 		0.0211
(0.0788) 		0.587
(0.757) 		0.346
(0.551) 		0.266
(0.456) 		0.11
(0.262) 		0.0181
(0.0712)
3p loss 40 (7%) 537 0.91
(0.98) 		0.79
(0.906) 		0.716
(0.847) 		0.148
(0.313) 		7e-05
(0.000611) 		0.202
(0.381) 		0.0423
(0.13) 		0.82
(0.921) 		0.638
(0.797) 		0.231
(0.415)
6q loss 125 (22%) 452 0.94
(1.00) 		0.579
(0.749) 		0.565
(0.74) 		0.941
(1.00) 		1e-05
(0.000132) 		0.653
(0.804) 		0.0487
(0.147) 		0.334
(0.545) 		0.499
(0.696) 		0.295
(0.492)
1p gain 82 (14%) 495 0.605
(0.77) 		0.129
(0.286) 		0.487
(0.684) 		0.25
(0.441) 		1e-05
(0.000132) 		0.829
(0.923) 		0.379
(0.586) 		0.52
(0.708) 		0.34
(0.548) 		0.271
(0.463)
1q gain 89 (15%) 488 0.0765
(0.204) 		0.089
(0.225) 		0.13
(0.287) 		0.627
(0.785) 		1e-05
(0.000132) 		0.526
(0.713) 		0.0863
(0.22) 		0.53
(0.715) 		0.823
(0.921) 		0.508
(0.706)
2p gain 37 (6%) 540 0.469
(0.666) 		0.735
(0.863) 		0.252
(0.443) 		0.226
(0.411) 		0.00269
(0.014) 		0.391
(0.596) 		0.795
(0.906) 		0.136
(0.296) 		1
(1.00) 		0.538
(0.722)
2q gain 36 (6%) 541 0.648
(0.804) 		0.913
(0.982) 		0.0957
(0.236) 		0.278
(0.469) 		0.00177
(0.00948) 		0.391
(0.596) 		0.884
(0.963) 		0.369
(0.571) 		0.769
(0.891) 		0.177
(0.35)
4p gain 36 (6%) 541 0.243
(0.432) 		0.613
(0.777) 		0.487
(0.684) 		0.518
(0.708) 		0.00081
(0.00496) 		0.46
(0.659) 		0.512
(0.707) 		0.536
(0.721) 		0.613
(0.777) 		0.791
(0.906)
4q gain 33 (6%) 544 0.313
(0.517) 		0.317
(0.523) 		0.496
(0.694) 		0.54
(0.722) 		0.00542
(0.0247) 		0.266
(0.456) 		0.392
(0.597) 		0.701
(0.838) 		0.364
(0.569) 		0.66
(0.808)
5p gain 49 (8%) 528 0.114
(0.266) 		0.154
(0.32) 		0.177
(0.35) 		0.346
(0.551) 		5e-05
(0.000461) 		0.231
(0.415) 		0.0553
(0.163) 		0.36
(0.569) 		0.126
(0.282) 		0.231
(0.415)
5q gain 41 (7%) 536 0.141
(0.304) 		0.236
(0.422) 		0.116
(0.267) 		0.0531
(0.158) 		0.00012
(0.000974) 		0.117
(0.268) 		0.0832
(0.215) 		0.34
(0.548) 		0.17
(0.34) 		0.406
(0.611)
6p gain 24 (4%) 553 0.0118
(0.0488) 		0.119
(0.271) 		0.877
(0.961) 		0.162
(0.33) 		0.157
(0.32) 		0.0838
(0.216) 		0.653
(0.804) 		0.889
(0.965) 		1
(1.00) 		1
(1.00)
9q gain 71 (12%) 506 0.0795
(0.208) 		0.0708
(0.192) 		0.579
(0.749) 		0.164
(0.331) 		7e-05
(0.000611) 		0.197
(0.375) 		0.514
(0.708) 		0.368
(0.571) 		0.668
(0.809) 		0.0782
(0.206)
11q gain 14 (2%) 563 0.188
(0.366) 		0.0631
(0.176) 		0.219
(0.402) 		0.361
(0.569) 		0.149
(0.313) 		0.00042
(0.00292) 		0.708
(0.839) 		0.883
(0.963) 		1
(1.00) 		1
(1.00)
14q gain 22 (4%) 555 0.432
(0.634) 		0.78
(0.9) 		0.0101
(0.0433) 		0.805
(0.912) 		0.387
(0.595) 		0.51
(0.707) 		0.406
(0.611) 		0.111
(0.262) 		0.426
(0.63) 		0.325
(0.534)
xq gain 16 (3%) 561 0.253
(0.444) 		0.948
(1.00) 		0.985
(1.00) 		0.362
(0.569) 		0.95
(1.00) 		0.717
(0.847) 		0.507
(0.706) 		1
(1.00) 		0.038
(0.12) 		0.26
(0.452)
6p loss 86 (15%) 491 0.565
(0.74) 		0.334
(0.545) 		0.771
(0.892) 		0.706
(0.838) 		1e-05
(0.000132) 		0.571
(0.745) 		0.111
(0.262) 		0.0697
(0.189) 		0.869
(0.956) 		0.595
(0.763)
8q loss 42 (7%) 535 0.618
(0.778) 		0.153
(0.319) 		0.0213
(0.0791) 		0.807
(0.913) 		0.105
(0.253) 		0.139
(0.301) 		0.459
(0.659) 		1
(1.00) 		0.461
(0.659) 		0.145
(0.309)
12p loss 58 (10%) 519 0.0951
(0.236) 		0.0941
(0.234) 		0.56
(0.737) 		0.833
(0.923) 		0.00564
(0.0254) 		0.599
(0.765) 		0.123
(0.277) 		0.171
(0.342) 		1
(1.00) 		0.661
(0.808)
12q loss 57 (10%) 520 0.142
(0.304) 		0.0998
(0.242) 		0.44
(0.639) 		0.653
(0.804) 		0.00026
(0.00189) 		0.551
(0.731) 		0.0807
(0.211) 		0.472
(0.669) 		1
(1.00) 		0.662
(0.808)
16p loss 63 (11%) 514 0.285
(0.479) 		0.852
(0.943) 		0.663
(0.808) 		0.732
(0.862) 		0.0331
(0.109) 		0.0585
(0.17) 		0.717
(0.847) 		0.791
(0.906) 		0.564
(0.74) 		0.646
(0.804)
16q loss 83 (14%) 494 0.0605
(0.175) 		0.429
(0.633) 		0.465
(0.662) 		0.896
(0.97) 		0.0139
(0.0561) 		0.368
(0.571) 		0.227
(0.411) 		0.199
(0.378) 		0.662
(0.808) 		0.6
(0.765)
22q loss 181 (31%) 396 0.651
(0.804) 		0.56
(0.737) 		0.194
(0.371) 		0.876
(0.961) 		1e-05
(0.000132) 		0.0722
(0.194) 		0.426
(0.63) 		0.164
(0.331) 		0.201
(0.379) 		0.0927
(0.232)
10q gain 3 (1%) 574 0.557
(0.737) 		1
(1.00) 		0.0512
(0.154) 		0.796
(0.906) 		0.195
(0.372) 		0.194
(0.371)
11p gain 17 (3%) 560 0.904
(0.974) 		0.88
(0.963) 		0.246
(0.435) 		0.944
(1.00) 		0.198
(0.375) 		0.0842
(0.216) 		0.403
(0.609) 		0.885
(0.963) 		0.695
(0.835) 		1
(1.00)
13q gain 10 (2%) 567 0.0523
(0.156) 		0.496
(0.694) 		0.179
(0.353) 		0.826
(0.923) 		0.0568
(0.166) 		1
(1.00) 		0.149
(0.313) 		0.823
(0.921) 		0.428
(0.633) 		1
(1.00)
xp gain 15 (3%) 562 0.282
(0.474) 		1
(1.00) 		0.795
(0.906) 		0.184
(0.361) 		0.897
(0.97) 		0.889
(0.965) 		1
(1.00) 		0.622
(0.78) 		0.0867
(0.22) 		0.435
(0.635)
1q loss 15 (3%) 562 0.831
(0.923) 		0.978
(1.00) 		0.856
(0.944) 		0.364
(0.569) 		0.133
(0.291) 		1
(1.00) 		0.339
(0.548) 		0.288
(0.481) 		0.517
(0.708) 		0.0821
(0.213)
7q loss 6 (1%) 571 0.101
(0.243) 		0.302
(0.504) 		0.942
(1.00) 		0.125
(0.28) 		0.0981
(0.24)
8p loss 58 (10%) 519 0.546
(0.729) 		0.442
(0.642) 		0.179
(0.353) 		0.778
(0.899) 		0.258
(0.451) 		0.649
(0.804) 		0.736
(0.863) 		1
(1.00) 		0.574
(0.747) 		0.39
(0.596)
9q loss 94 (16%) 483 0.368
(0.571) 		0.0966
(0.237) 		0.0732
(0.196) 		0.276
(0.468) 		0.548
(0.729) 		0.573
(0.747) 		0.246
(0.435) 		0.619
(0.778) 		0.754
(0.88) 		0.181
(0.356)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
1P GAIN MUTATED 50 15 17
1P GAIN WILD-TYPE 112 203 180

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
1Q GAIN MUTATED 57 13 19
1Q GAIN WILD-TYPE 105 205 178

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.014

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
2P GAIN MUTATED 20 9 8
2P GAIN WILD-TYPE 142 209 189

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0095

Table S4.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
2Q GAIN MUTATED 20 9 7
2Q GAIN WILD-TYPE 142 209 190

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.003

Table S5.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
3P GAIN MUTATED 16 18 5 15
3P GAIN WILD-TYPE 131 78 147 98

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
3P GAIN MUTATED 13 18 5 18
3P GAIN WILD-TYPE 135 84 95 140

Figure S6.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.092

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
3P GAIN MUTATED 35 5 15
3P GAIN WILD-TYPE 258 119 114

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3P GAIN MUTATED 37 5 16
3P GAIN WILD-TYPE 125 213 181

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

'3q gain' versus 'MRNA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0034

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
3Q GAIN MUTATED 17 21 7 15
3Q GAIN WILD-TYPE 130 75 145 98

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3Q GAIN MUTATED 38 7 19
3Q GAIN WILD-TYPE 124 211 178

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.005

Table S11.  Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
4P GAIN MUTATED 19 5 12
4P GAIN WILD-TYPE 143 213 185

Figure S11.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.025

Table S12.  Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
4Q GAIN MUTATED 16 5 12
4Q GAIN WILD-TYPE 146 213 185

Figure S12.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5P GAIN MUTATED 27 7 15
5P GAIN WILD-TYPE 135 211 182

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00097

Table S14.  Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5Q GAIN MUTATED 23 6 12
5Q GAIN WILD-TYPE 139 212 185

Figure S14.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.049

Table S15.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
6P GAIN MUTATED 4 10 3 3
6P GAIN WILD-TYPE 143 86 149 110

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0093

Table S16.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
6Q GAIN MUTATED 4 11 2 3
6Q GAIN WILD-TYPE 143 85 150 110

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.11

Table S17.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
6Q GAIN MUTATED 5 7 0 8
6Q GAIN WILD-TYPE 143 95 100 150

Figure S17.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.089

Table S18.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
6Q GAIN MUTATED 10 3 10
6Q GAIN WILD-TYPE 152 215 187

Figure S18.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.025

Table S19.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
6Q GAIN MUTATED 0 3 7
6Q GAIN WILD-TYPE 89 105 71

Figure S19.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7P GAIN MUTATED 135 65 128 82
7P GAIN WILD-TYPE 12 31 24 31

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7P GAIN MUTATED 132 55 85 138
7P GAIN WILD-TYPE 16 47 15 20

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0021

Table S22.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
7P GAIN MUTATED 139 136 64 105
7P GAIN WILD-TYPE 17 47 23 15

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7P GAIN MUTATED 214 113 117
7P GAIN WILD-TYPE 79 11 12

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S24.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
7P GAIN MUTATED 145 196 127
7P GAIN WILD-TYPE 17 22 70

Figure S24.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S25.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
7P GAIN MUTATED 82 93 46
7P GAIN WILD-TYPE 7 15 32

Figure S25.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0083 (Fisher's exact test), Q value = 0.036

Table S26.  Gene #13: '7p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
7P GAIN MUTATED 42 47 29 26 37
7P GAIN WILD-TYPE 2 10 15 4 8

Figure S26.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0041

Table S27.  Gene #13: '7p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
7P GAIN MUTATED 81 47 53
7P GAIN WILD-TYPE 9 23 7

Figure S27.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.062

Table S28.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
7P GAIN MUTATED 31 61 28
7P GAIN WILD-TYPE 13 6 8

Figure S28.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S29.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
7P GAIN MUTATED 16 84 20
7P GAIN WILD-TYPE 14 8 5

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S30.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7Q GAIN MUTATED 135 62 129 87
7Q GAIN WILD-TYPE 12 34 23 26

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S31.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7Q GAIN MUTATED 130 61 84 138
7Q GAIN WILD-TYPE 18 41 16 20

Figure S31.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'MIR_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0064

Table S32.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
7Q GAIN MUTATED 140 136 68 103
7Q GAIN WILD-TYPE 16 47 19 17

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S33.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7Q GAIN MUTATED 221 112 114
7Q GAIN WILD-TYPE 72 12 15

Figure S33.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S34.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
7Q GAIN MUTATED 141 199 134
7Q GAIN WILD-TYPE 21 19 63

Figure S34.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S35.  Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
7Q GAIN MUTATED 81 91 50
7Q GAIN WILD-TYPE 8 17 28

Figure S35.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.046

Table S36.  Gene #14: '7q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
7Q GAIN MUTATED 80 51 54
7Q GAIN WILD-TYPE 10 19 6

Figure S36.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0089

Table S37.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
7Q GAIN MUTATED 19 84 21
7Q GAIN WILD-TYPE 11 8 4

Figure S37.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S38.  Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
8P GAIN MUTATED 7 18 6 17
8P GAIN WILD-TYPE 140 78 146 96

Figure S38.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0045

Table S39.  Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8P GAIN MUTATED 10 21 4 13
8P GAIN WILD-TYPE 138 81 96 145

Figure S39.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S40.  Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
8P GAIN MUTATED 35 4 13
8P GAIN WILD-TYPE 127 214 184

Figure S40.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.02

Table S41.  Gene #15: '8p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
8P GAIN MUTATED 4 10 16
8P GAIN WILD-TYPE 85 98 62

Figure S41.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S42.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
8Q GAIN MUTATED 7 20 7 20
8Q GAIN WILD-TYPE 140 76 145 93

Figure S42.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S43.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8Q GAIN MUTATED 9 26 4 15
8Q GAIN WILD-TYPE 139 76 96 143

Figure S43.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'MIR_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.13

Table S44.  Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
8Q GAIN MUTATED 10 27 10 8
8Q GAIN WILD-TYPE 146 156 77 112

Figure S44.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S45.  Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
8Q GAIN MUTATED 34 6 19
8Q GAIN WILD-TYPE 128 212 178

Figure S45.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0035

Table S46.  Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
8Q GAIN MUTATED 4 11 19
8Q GAIN WILD-TYPE 85 97 59

Figure S46.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p gain' versus 'MRNA_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.016

Table S47.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
9P GAIN MUTATED 14 17 7 6
9P GAIN WILD-TYPE 133 79 145 107

Figure S47.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.1

Table S48.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
9P GAIN MUTATED 15 12 2 15
9P GAIN WILD-TYPE 133 90 98 143

Figure S48.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S49.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
9P GAIN MUTATED 27 7 13
9P GAIN WILD-TYPE 135 211 184

Figure S49.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00061

Table S50.  Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
9Q GAIN MUTATED 36 14 21
9Q GAIN WILD-TYPE 126 204 176

Figure S50.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0065

Table S51.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10P GAIN MUTATED 1 6 0 5
10P GAIN WILD-TYPE 146 90 152 108

Figure S51.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.001

Table S52.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P GAIN MUTATED 2 9 0 1
10P GAIN WILD-TYPE 146 93 100 157

Figure S52.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0058

Table S53.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
10P GAIN MUTATED 3 0 10
10P GAIN WILD-TYPE 159 218 187

Figure S53.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0028

Table S54.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
10P GAIN MUTATED 1 0 7
10P GAIN WILD-TYPE 88 108 71

Figure S54.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.021

Table S55.  Gene #19: '10p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
10P GAIN MUTATED 0 5 0
10P GAIN WILD-TYPE 90 65 60

Figure S55.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0029

Table S56.  Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
11Q GAIN MUTATED 2 0 8
11Q GAIN WILD-TYPE 87 108 70

Figure S56.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S57.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
12P GAIN MUTATED 31 11 18
12P GAIN WILD-TYPE 131 207 179

Figure S57.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.02

Table S58.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
12P GAIN MUTATED 0 12 3
12P GAIN WILD-TYPE 44 55 33

Figure S58.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.044

Table S59.  Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
12Q GAIN MUTATED 16 15 17
12Q GAIN WILD-TYPE 277 109 112

Figure S59.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0079

Table S60.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
12Q GAIN MUTATED 25 11 13
12Q GAIN WILD-TYPE 137 207 184

Figure S60.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.082

Table S61.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
12Q GAIN MUTATED 0 9 3
12Q GAIN WILD-TYPE 44 58 33

Figure S61.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'14q gain' versus 'MIR_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.043

Table S62.  Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
14Q GAIN MUTATED 10 4 7 1
14Q GAIN WILD-TYPE 146 179 80 119

Figure S62.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S63.  Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
15Q GAIN MUTATED 15 1 8
15Q GAIN WILD-TYPE 147 217 189

Figure S63.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
15Q GAIN MUTATED 0 7 1
15Q GAIN WILD-TYPE 44 60 35

Figure S64.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00785 (Fisher's exact test), Q value = 0.034

Table S65.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
16P GAIN MUTATED 12 11 3 11
16P GAIN WILD-TYPE 135 85 149 102

Figure S65.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S66.  Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
16P GAIN MUTATED 25 4 9
16P GAIN WILD-TYPE 137 214 188

Figure S66.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.11

Table S67.  Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
16P GAIN MUTATED 6 5 12
16P GAIN WILD-TYPE 83 103 66

Figure S67.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q gain' versus 'MRNA_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.071

Table S68.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
16Q GAIN MUTATED 10 12 4 10
16Q GAIN WILD-TYPE 137 84 148 103

Figure S68.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.024

Table S69.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
16Q GAIN MUTATED 10 15 2 9
16Q GAIN WILD-TYPE 138 87 98 149

Figure S69.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S70.  Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
16Q GAIN MUTATED 22 5 10
16Q GAIN WILD-TYPE 140 213 187

Figure S70.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.092

Table S71.  Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
16Q GAIN MUTATED 5 5 12
16Q GAIN WILD-TYPE 84 103 66

Figure S71.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.083

Table S72.  Gene #29: '16q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
16Q GAIN MUTATED 1 8 4 1 0
16Q GAIN WILD-TYPE 43 49 40 29 45

Figure S72.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0032

Table S73.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
17P GAIN MUTATED 9 14 4 16
17P GAIN WILD-TYPE 138 82 148 97

Figure S73.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.077

Table S74.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17P GAIN MUTATED 9 16 4 14
17P GAIN WILD-TYPE 139 86 96 144

Figure S74.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.12

Table S75.  Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17P GAIN MUTATED 32 8 5
17P GAIN WILD-TYPE 261 116 124

Figure S75.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0015

Table S76.  Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17P GAIN MUTATED 27 9 12
17P GAIN WILD-TYPE 135 209 185

Figure S76.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.11

Table S77.  Gene #30: '17p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
17P GAIN MUTATED 5 7 13
17P GAIN WILD-TYPE 84 101 65

Figure S77.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.091

Table S78.  Gene #30: '17p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
17P GAIN MUTATED 4 4 1 5 0
17P GAIN WILD-TYPE 40 53 43 25 45

Figure S78.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0065

Table S79.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
17Q GAIN MUTATED 13 17 6 17
17Q GAIN WILD-TYPE 134 79 146 96

Figure S79.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.14

Table S80.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17Q GAIN MUTATED 11 17 6 19
17Q GAIN WILD-TYPE 137 85 94 139

Figure S80.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S81.  Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17Q GAIN MUTATED 34 12 14
17Q GAIN WILD-TYPE 128 206 183

Figure S81.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.12

Table S82.  Gene #31: '17q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
17Q GAIN MUTATED 6 10 15
17Q GAIN WILD-TYPE 83 98 63

Figure S82.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S83.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18P GAIN MUTATED 10 25 5 15
18P GAIN WILD-TYPE 137 71 147 98

Figure S83.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S84.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18P GAIN MUTATED 11 22 4 18
18P GAIN WILD-TYPE 137 80 96 140

Figure S84.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S85.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18P GAIN MUTATED 34 3 21
18P GAIN WILD-TYPE 128 215 176

Figure S85.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00506 (Fisher's exact test), Q value = 0.023

Table S86.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
18P GAIN MUTATED 6 10 18
18P GAIN WILD-TYPE 83 98 60

Figure S86.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.074

Table S87.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
18P GAIN MUTATED 6 11 0
18P GAIN WILD-TYPE 38 56 36

Figure S87.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S88.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18Q GAIN MUTATED 9 24 6 16
18Q GAIN WILD-TYPE 138 72 146 97

Figure S88.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0039

Table S89.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18Q GAIN MUTATED 10 23 6 16
18Q GAIN WILD-TYPE 138 79 94 142

Figure S89.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S90.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18Q GAIN MUTATED 37 4 17
18Q GAIN WILD-TYPE 125 214 180

Figure S90.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.026

Table S91.  Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
18Q GAIN MUTATED 7 9 18
18Q GAIN WILD-TYPE 82 99 60

Figure S91.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.073

Table S92.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
18Q GAIN MUTATED 6 11 0
18Q GAIN WILD-TYPE 38 56 36

Figure S92.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S93.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19P GAIN MUTATED 52 34 91 21
19P GAIN WILD-TYPE 95 62 61 92

Figure S93.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S94.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P GAIN MUTATED 62 25 58 53
19P GAIN WILD-TYPE 86 77 42 105

Figure S94.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.002

Table S95.  Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19P GAIN MUTATED 94 50 68
19P GAIN WILD-TYPE 199 74 61

Figure S95.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S96.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
19P GAIN MUTATED 45 137 44
19P GAIN WILD-TYPE 117 81 153

Figure S96.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S97.  Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19P GAIN MUTATED 28 68 12
19P GAIN WILD-TYPE 61 40 66

Figure S97.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S98.  Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
19P GAIN MUTATED 31 16 37
19P GAIN WILD-TYPE 59 54 23

Figure S98.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S99.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19Q GAIN MUTATED 46 28 85 15
19Q GAIN WILD-TYPE 101 68 67 98

Figure S99.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S100.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q GAIN MUTATED 55 18 55 46
19Q GAIN WILD-TYPE 93 84 45 112

Figure S100.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.016

Table S101.  Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19Q GAIN MUTATED 82 47 57
19Q GAIN WILD-TYPE 211 77 72

Figure S101.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S102.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
19Q GAIN MUTATED 39 127 33
19Q GAIN WILD-TYPE 123 91 164

Figure S102.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S103.  Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19Q GAIN MUTATED 25 62 6
19Q GAIN WILD-TYPE 64 46 72

Figure S103.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0015

Table S104.  Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
19Q GAIN MUTATED 25 13 31
19Q GAIN WILD-TYPE 65 57 29

Figure S104.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S105.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20P GAIN MUTATED 51 26 86 29
20P GAIN WILD-TYPE 96 70 66 84

Figure S105.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S106.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P GAIN MUTATED 55 21 64 52
20P GAIN WILD-TYPE 93 81 36 106

Figure S106.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.021

Table S107.  Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
20P GAIN MUTATED 61 75 20 56
20P GAIN WILD-TYPE 95 108 67 64

Figure S107.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S108.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20P GAIN MUTATED 85 58 69
20P GAIN WILD-TYPE 208 66 60

Figure S108.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S109.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20P GAIN MUTATED 61 108 53
20P GAIN WILD-TYPE 101 110 144

Figure S109.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S110.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
20P GAIN MUTATED 35 57 17
20P GAIN WILD-TYPE 54 51 61

Figure S110.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0032

Table S111.  Gene #36: '20p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
20P GAIN MUTATED 27 17 33
20P GAIN WILD-TYPE 63 53 27

Figure S111.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S112.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20Q GAIN MUTATED 50 28 86 27
20Q GAIN WILD-TYPE 97 68 66 86

Figure S112.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S113.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q GAIN MUTATED 58 22 62 49
20Q GAIN WILD-TYPE 90 80 38 109

Figure S113.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CNMF'

P value = 0.00283 (Fisher's exact test), Q value = 0.014

Table S114.  Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
20Q GAIN MUTATED 62 74 19 55
20Q GAIN WILD-TYPE 94 109 68 65

Figure S114.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S115.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20Q GAIN MUTATED 85 57 68
20Q GAIN WILD-TYPE 208 67 61

Figure S115.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S116.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20Q GAIN MUTATED 59 107 54
20Q GAIN WILD-TYPE 103 111 143

Figure S116.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S117.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
20Q GAIN MUTATED 34 57 16
20Q GAIN WILD-TYPE 55 51 62

Figure S117.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0029

Table S118.  Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
20Q GAIN MUTATED 28 17 34
20Q GAIN WILD-TYPE 62 53 26

Figure S118.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0067

Table S119.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
21Q GAIN MUTATED 28 11 9 7
21Q GAIN WILD-TYPE 119 85 143 106

Figure S119.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00759 (Fisher's exact test), Q value = 0.033

Table S120.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
21Q GAIN MUTATED 25 6 5 19
21Q GAIN WILD-TYPE 123 96 95 139

Figure S120.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'MIR_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.045

Table S121.  Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
21Q GAIN MUTATED 24 15 4 19
21Q GAIN WILD-TYPE 132 168 83 101

Figure S121.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'21q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.02

Table S122.  Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
21Q GAIN MUTATED 26 25 11
21Q GAIN WILD-TYPE 267 99 118

Figure S122.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0013

Table S123.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
21Q GAIN MUTATED 30 11 23
21Q GAIN WILD-TYPE 132 207 174

Figure S123.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0094

Table S124.  Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
21Q GAIN MUTATED 20 7 6
21Q GAIN WILD-TYPE 69 101 72

Figure S124.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.071

Table S125.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
21Q GAIN MUTATED 2 16 5
21Q GAIN WILD-TYPE 42 51 31

Figure S125.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S126.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
22Q GAIN MUTATED 6 14 0 11
22Q GAIN WILD-TYPE 141 82 152 102

Figure S126.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.016

Table S127.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
22Q GAIN MUTATED 11 11 0 9
22Q GAIN WILD-TYPE 137 91 100 149

Figure S127.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 9e-04

Table S128.  Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
22Q GAIN MUTATED 19 3 12
22Q GAIN WILD-TYPE 143 215 185

Figure S128.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.1

Table S129.  Gene #39: '22q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
22Q GAIN MUTATED 5 7 0
22Q GAIN WILD-TYPE 85 63 60

Figure S129.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.12

Table S130.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
XQ GAIN MUTATED 0 6 0
XQ GAIN WILD-TYPE 44 61 36

Figure S130.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.079

Table S131.  Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
1P LOSS MUTATED 2 3 11
1P LOSS WILD-TYPE 160 215 186

Figure S131.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.071

Table S132.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
1P LOSS MUTATED 2 0 2
1P LOSS WILD-TYPE 28 92 23

Figure S132.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.1

Table S133.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
2P LOSS MUTATED 7 12 5 5
2P LOSS WILD-TYPE 140 84 147 108

Figure S133.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.095

Table S134.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
2P LOSS MUTATED 8 12 2 7
2P LOSS WILD-TYPE 140 90 98 151

Figure S134.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S135.  Gene #44: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
2P LOSS MUTATED 21 2 9
2P LOSS WILD-TYPE 141 216 188

Figure S135.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

'2q loss' versus 'MRNA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.1

Table S136.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
2Q LOSS MUTATED 7 12 5 5
2Q LOSS WILD-TYPE 140 84 147 108

Figure S136.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.1

Table S137.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
2Q LOSS MUTATED 8 12 2 7
2Q LOSS WILD-TYPE 140 90 98 151

Figure S137.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S138.  Gene #45: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
2Q LOSS MUTATED 21 2 9
2Q LOSS WILD-TYPE 141 216 188

Figure S138.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00061

Table S139.  Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3P LOSS MUTATED 21 4 15
3P LOSS WILD-TYPE 141 214 182

Figure S139.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.13

Table S140.  Gene #46: '3p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
3P LOSS MUTATED 2 4 1 2 9
3P LOSS WILD-TYPE 42 53 43 28 36

Figure S140.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S141.  Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3Q LOSS MUTATED 20 2 12
3Q LOSS WILD-TYPE 142 216 185

Figure S141.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.11

Table S142.  Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
3Q LOSS MUTATED 7 2 8
3Q LOSS WILD-TYPE 82 106 70

Figure S142.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

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

Table S143.  Gene #47: '3q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
3Q LOSS MUTATED 1 4 1 1 8
3Q LOSS WILD-TYPE 43 53 43 29 37

Figure S143.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.016

Table S144.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
4P LOSS MUTATED 10 19 4 17
4P LOSS WILD-TYPE 138 83 96 141

Figure S144.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'MIR_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.11

Table S145.  Gene #48: '4p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
4P LOSS MUTATED 7 25 8 12
4P LOSS WILD-TYPE 149 158 79 108

Figure S145.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.011

Table S146.  Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
4P LOSS MUTATED 27 15 13
4P LOSS WILD-TYPE 135 203 184

Figure S146.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0097

Table S147.  Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
4P LOSS MUTATED 2 12 14
4P LOSS WILD-TYPE 87 96 64

Figure S147.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q loss' versus 'MRNA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0049

Table S148.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
4Q LOSS MUTATED 10 19 7 13
4Q LOSS WILD-TYPE 137 77 145 100

Figure S148.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0039

Table S149.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
4Q LOSS MUTATED 10 20 3 16
4Q LOSS WILD-TYPE 138 82 97 142

Figure S149.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'MIR_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.073

Table S150.  Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
4Q LOSS MUTATED 6 24 9 13
4Q LOSS WILD-TYPE 150 159 78 107

Figure S150.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0013

Table S151.  Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
4Q LOSS MUTATED 29 11 16
4Q LOSS WILD-TYPE 133 207 181

Figure S151.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0058

Table S152.  Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
4Q LOSS MUTATED 2 12 15
4Q LOSS WILD-TYPE 87 96 63

Figure S152.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S153.  Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
5P LOSS MUTATED 5 20 6 9
5P LOSS WILD-TYPE 142 76 146 104

Figure S153.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S154.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5P LOSS MUTATED 6 22 5 7
5P LOSS WILD-TYPE 142 80 95 151

Figure S154.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'MIR_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0095

Table S155.  Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
5P LOSS MUTATED 4 24 6 6
5P LOSS WILD-TYPE 152 159 81 114

Figure S155.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S156.  Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5P LOSS MUTATED 21 4 18
5P LOSS WILD-TYPE 141 214 179

Figure S156.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S157.  Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
5P LOSS MUTATED 1 5 15
5P LOSS WILD-TYPE 88 103 63

Figure S157.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S158.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
5Q LOSS MUTATED 6 19 5 11
5Q LOSS WILD-TYPE 141 77 147 102

Figure S158.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S159.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5Q LOSS MUTATED 9 21 4 7
5Q LOSS WILD-TYPE 139 81 96 151

Figure S159.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'MIR_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0055

Table S160.  Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
5Q LOSS MUTATED 4 25 6 6
5Q LOSS WILD-TYPE 152 158 81 114

Figure S160.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S161.  Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5Q LOSS MUTATED 21 5 18
5Q LOSS WILD-TYPE 141 213 179

Figure S161.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S162.  Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
5Q LOSS MUTATED 0 5 17
5Q LOSS WILD-TYPE 89 103 61

Figure S162.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.13

Table S163.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
5Q LOSS MUTATED 6 10 0
5Q LOSS WILD-TYPE 24 82 25

Figure S163.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S164.  Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
6P LOSS MUTATED 51 13 22
6P LOSS WILD-TYPE 111 205 175

Figure S164.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S165.  Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
6Q LOSS MUTATED 62 30 33
6Q LOSS WILD-TYPE 100 188 164

Figure S165.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.15

Table S166.  Gene #53: '6q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
6Q LOSS MUTATED 11 10 3 9 12
6Q LOSS WILD-TYPE 33 47 41 21 33

Figure S166.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.081

Table S167.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7P LOSS MUTATED 0 4 1 3
7P LOSS WILD-TYPE 147 92 151 110

Figure S167.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.11

Table S168.  Gene #54: '7p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7P LOSS MUTATED 1 5 0 2
7P LOSS WILD-TYPE 147 97 100 156

Figure S168.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.13

Table S169.  Gene #54: '7p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7P LOSS MUTATED 8 0 0
7P LOSS WILD-TYPE 285 124 129

Figure S169.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.063

Table S170.  Gene #54: '7p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
7P LOSS MUTATED 2 0 6
7P LOSS WILD-TYPE 160 218 191

Figure S170.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'CN_CNMF'

'8q loss' versus 'MIR_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.079

Table S171.  Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
8Q LOSS MUTATED 21 9 6 6
8Q LOSS WILD-TYPE 135 174 81 114

Figure S171.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.034

Table S172.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
9P LOSS MUTATED 50 20 62 44
9P LOSS WILD-TYPE 97 76 90 69

Figure S172.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.081

Table S173.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
9P LOSS MUTATED 8 23 17
9P LOSS WILD-TYPE 36 44 19

Figure S173.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00893 (Fisher's exact test), Q value = 0.039

Table S174.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
9P LOSS MUTATED 4 31 13
9P LOSS WILD-TYPE 26 61 12

Figure S174.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S175.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10P LOSS MUTATED 132 64 140 84
10P LOSS WILD-TYPE 15 32 12 29

Figure S175.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S176.  Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P LOSS MUTATED 127 63 93 137
10P LOSS WILD-TYPE 21 39 7 21

Figure S176.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CNMF'

P value = 0.00999 (Fisher's exact test), Q value = 0.043

Table S177.  Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
10P LOSS MUTATED 141 145 67 103
10P LOSS WILD-TYPE 15 38 20 17

Figure S177.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00061

Table S178.  Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10P LOSS MUTATED 227 109 120
10P LOSS WILD-TYPE 66 15 9

Figure S178.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S179.  Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
10P LOSS MUTATED 150 212 121
10P LOSS WILD-TYPE 12 6 76

Figure S179.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S180.  Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
10P LOSS MUTATED 79 99 46
10P LOSS WILD-TYPE 10 9 32

Figure S180.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0036

Table S181.  Gene #60: '10p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
10P LOSS MUTATED 83 53 58
10P LOSS WILD-TYPE 7 17 2

Figure S181.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.052

Table S182.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
10P LOSS MUTATED 22 85 24
10P LOSS WILD-TYPE 8 7 1

Figure S182.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S183.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10Q LOSS MUTATED 132 68 146 87
10Q LOSS WILD-TYPE 15 28 6 26

Figure S183.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S184.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10Q LOSS MUTATED 128 69 97 139
10Q LOSS WILD-TYPE 20 33 3 19

Figure S184.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.026

Table S185.  Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
10Q LOSS MUTATED 144 152 67 105
10Q LOSS WILD-TYPE 12 31 20 15

Figure S185.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 9e-04

Table S186.  Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10Q LOSS MUTATED 236 109 123
10Q LOSS WILD-TYPE 57 15 6

Figure S186.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S187.  Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
10Q LOSS MUTATED 150 214 130
10Q LOSS WILD-TYPE 12 4 67

Figure S187.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S188.  Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
10Q LOSS MUTATED 78 102 56
10Q LOSS WILD-TYPE 11 6 22

Figure S188.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S189.  Gene #61: '10q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
10Q LOSS MUTATED 83 52 59
10Q LOSS WILD-TYPE 7 18 1

Figure S189.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.08

Table S190.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
10Q LOSS MUTATED 23 86 24
10Q LOSS WILD-TYPE 7 6 1

Figure S190.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S191.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11P LOSS MUTATED 27 32 9 22
11P LOSS WILD-TYPE 120 64 143 91

Figure S191.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S192.  Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11P LOSS MUTATED 26 36 4 24
11P LOSS WILD-TYPE 122 66 96 134

Figure S192.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.057

Table S193.  Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
11P LOSS MUTATED 63 20 13
11P LOSS WILD-TYPE 230 104 116

Figure S193.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S194.  Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
11P LOSS MUTATED 59 8 32
11P LOSS WILD-TYPE 103 210 165

Figure S194.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.014

Table S195.  Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
11P LOSS MUTATED 14 16 27
11P LOSS WILD-TYPE 75 92 51

Figure S195.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.1

Table S196.  Gene #62: '11p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
11P LOSS MUTATED 11 17 5
11P LOSS WILD-TYPE 79 53 55

Figure S196.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S197.  Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11Q LOSS MUTATED 31 28 10 18
11Q LOSS WILD-TYPE 116 68 142 95

Figure S197.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0015

Table S198.  Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11Q LOSS MUTATED 28 28 5 26
11Q LOSS WILD-TYPE 120 74 95 132

Figure S198.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S199.  Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
11Q LOSS MUTATED 58 10 25
11Q LOSS WILD-TYPE 104 208 172

Figure S199.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.025

Table S200.  Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
12P LOSS MUTATED 26 13 19
12P LOSS WILD-TYPE 136 205 178

Figure S200.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0019

Table S201.  Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
12Q LOSS MUTATED 28 10 19
12Q LOSS WILD-TYPE 134 208 178

Figure S201.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00054

Table S202.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
13Q LOSS MUTATED 57 35 26 45
13Q LOSS WILD-TYPE 90 61 126 68

Figure S202.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0095

Table S203.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
13Q LOSS MUTATED 50 41 17 55
13Q LOSS WILD-TYPE 98 61 83 103

Figure S203.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S204.  Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
13Q LOSS MUTATED 112 20 54
13Q LOSS WILD-TYPE 50 198 143

Figure S204.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.048

Table S205.  Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
13Q LOSS MUTATED 30 27 36
13Q LOSS WILD-TYPE 59 81 42

Figure S205.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.095

Table S206.  Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
13Q LOSS MUTATED 27 28 11
13Q LOSS WILD-TYPE 63 42 49

Figure S206.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.15

Table S207.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
13Q LOSS MUTATED 20 18 8
13Q LOSS WILD-TYPE 24 49 28

Figure S207.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S208.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
14Q LOSS MUTATED 46 33 17 39
14Q LOSS WILD-TYPE 101 63 135 74

Figure S208.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 9e-04

Table S209.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
14Q LOSS MUTATED 43 35 10 47
14Q LOSS WILD-TYPE 105 67 90 111

Figure S209.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S210.  Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
14Q LOSS MUTATED 82 12 52
14Q LOSS WILD-TYPE 80 206 145

Figure S210.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.087

Table S211.  Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
14Q LOSS MUTATED 25 19 27
14Q LOSS WILD-TYPE 64 89 51

Figure S211.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.1

Table S212.  Gene #67: '14q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
14Q LOSS MUTATED 28 21 8
14Q LOSS WILD-TYPE 62 49 52

Figure S212.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S213.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
15Q LOSS MUTATED 26 26 12 31
15Q LOSS WILD-TYPE 121 70 140 82

Figure S213.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S214.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
15Q LOSS MUTATED 22 37 7 29
15Q LOSS WILD-TYPE 126 65 93 129

Figure S214.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.019

Table S215.  Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
15Q LOSS MUTATED 21 48 15 14
15Q LOSS WILD-TYPE 135 135 72 106

Figure S215.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.017

Table S216.  Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
15Q LOSS MUTATED 65 11 22
15Q LOSS WILD-TYPE 228 113 107

Figure S216.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S217.  Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
15Q LOSS MUTATED 58 20 28
15Q LOSS WILD-TYPE 104 198 169

Figure S217.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.074

Table S218.  Gene #68: '15q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
15Q LOSS MUTATED 16 19 5
15Q LOSS WILD-TYPE 74 51 55

Figure S218.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.0034 (Fisher's exact test), Q value = 0.017

Table S219.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
15Q LOSS MUTATED 16 8 4
15Q LOSS WILD-TYPE 28 59 32

Figure S219.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.082

Table S220.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
15Q LOSS MUTATED 11 15 2
15Q LOSS WILD-TYPE 19 77 23

Figure S220.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.11

Table S221.  Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
16P LOSS MUTATED 24 15 24
16P LOSS WILD-TYPE 138 203 173

Figure S221.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.056

Table S222.  Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
16Q LOSS MUTATED 31 20 32
16Q LOSS WILD-TYPE 131 198 165

Figure S222.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.076

Table S223.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
17P LOSS MUTATED 25 13 10 9
17P LOSS WILD-TYPE 122 83 142 104

Figure S223.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.076

Table S224.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17P LOSS MUTATED 23 16 8 10
17P LOSS WILD-TYPE 125 86 92 148

Figure S224.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S225.  Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17P LOSS MUTATED 37 5 23
17P LOSS WILD-TYPE 125 213 174

Figure S225.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00491 (Fisher's exact test), Q value = 0.023

Table S226.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
17Q LOSS MUTATED 19 7 9 2
17Q LOSS WILD-TYPE 128 89 143 111

Figure S226.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.14

Table S227.  Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17Q LOSS MUTATED 15 15 10
17Q LOSS WILD-TYPE 278 109 119

Figure S227.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S228.  Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17Q LOSS MUTATED 24 4 13
17Q LOSS WILD-TYPE 138 214 184

Figure S228.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.12

Table S229.  Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
17Q LOSS MUTATED 10 3 3
17Q LOSS WILD-TYPE 79 105 75

Figure S229.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.14

Table S230.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18P LOSS MUTATED 20 15 9 15
18P LOSS WILD-TYPE 127 81 143 98

Figure S230.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.11

Table S231.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18P LOSS MUTATED 19 16 4 20
18P LOSS WILD-TYPE 129 86 96 138

Figure S231.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S232.  Gene #73: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18P LOSS MUTATED 34 12 25
18P LOSS WILD-TYPE 128 206 172

Figure S232.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.13

Table S233.  Gene #73: '18p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
18P LOSS MUTATED 15 13 3
18P LOSS WILD-TYPE 75 57 57

Figure S233.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.033

Table S234.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18Q LOSS MUTATED 18 13 2 20
18Q LOSS WILD-TYPE 130 89 98 138

Figure S234.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S235.  Gene #74: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18Q LOSS MUTATED 29 10 23
18Q LOSS WILD-TYPE 133 208 174

Figure S235.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.014

Table S236.  Gene #74: '18q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
18Q LOSS MUTATED 11 14 1
18Q LOSS WILD-TYPE 79 56 59

Figure S236.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0038

Table S237.  Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19P LOSS MUTATED 3 10 2 10
19P LOSS WILD-TYPE 144 86 150 103

Figure S237.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0075

Table S238.  Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P LOSS MUTATED 4 13 1 7
19P LOSS WILD-TYPE 144 89 99 151

Figure S238.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S239.  Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
19P LOSS MUTATED 13 4 10
19P LOSS WILD-TYPE 149 214 187

Figure S239.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00054

Table S240.  Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19P LOSS MUTATED 3 0 10
19P LOSS WILD-TYPE 86 108 68

Figure S240.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.12

Table S241.  Gene #75: '19p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
19P LOSS MUTATED 1 7 3
19P LOSS WILD-TYPE 89 63 57

Figure S241.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0038

Table S242.  Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19Q LOSS MUTATED 6 10 2 13
19Q LOSS WILD-TYPE 141 86 150 100

Figure S242.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.022

Table S243.  Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q LOSS MUTATED 7 13 1 10
19Q LOSS WILD-TYPE 141 89 99 148

Figure S243.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0065

Table S244.  Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
19Q LOSS MUTATED 16 4 15
19Q LOSS WILD-TYPE 146 214 182

Figure S244.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.005

Table S245.  Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19Q LOSS MUTATED 6 1 11
19Q LOSS WILD-TYPE 83 107 67

Figure S245.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0013

Table S246.  Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20P LOSS MUTATED 4 10 0 3
20P LOSS WILD-TYPE 143 86 152 110

Figure S246.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S247.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P LOSS MUTATED 5 11 0 1
20P LOSS WILD-TYPE 143 91 100 157

Figure S247.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'MIR_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.12

Table S248.  Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
20P LOSS MUTATED 2 7 7 2
20P LOSS WILD-TYPE 154 176 80 118

Figure S248.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S249.  Gene #77: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20P LOSS MUTATED 14 0 5
20P LOSS WILD-TYPE 148 218 192

Figure S249.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.044

Table S250.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
20P LOSS MUTATED 4 0 0
20P LOSS WILD-TYPE 40 67 36

Figure S250.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.011

Table S251.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
20P LOSS MUTATED 4 0 0
20P LOSS WILD-TYPE 26 92 25

Figure S251.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MRNA_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0079

Table S252.  Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20Q LOSS MUTATED 4 8 0 3
20Q LOSS WILD-TYPE 143 88 152 110

Figure S252.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 9e-04

Table S253.  Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q LOSS MUTATED 4 10 0 1
20Q LOSS WILD-TYPE 144 92 100 157

Figure S253.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S254.  Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20Q LOSS MUTATED 14 1 2
20Q LOSS WILD-TYPE 148 217 195

Figure S254.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.13

Table S255.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
20Q LOSS MUTATED 3 0 0
20Q LOSS WILD-TYPE 41 67 36

Figure S255.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.05

Table S256.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
20Q LOSS MUTATED 3 0 0
20Q LOSS WILD-TYPE 27 92 25

Figure S256.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.077

Table S257.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
21Q LOSS MUTATED 4 12 10 10
21Q LOSS WILD-TYPE 143 84 142 103

Figure S257.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0071

Table S258.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
21Q LOSS MUTATED 5 17 6 8
21Q LOSS WILD-TYPE 143 85 94 150

Figure S258.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0038

Table S259.  Gene #79: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
21Q LOSS MUTATED 22 7 13
21Q LOSS WILD-TYPE 140 211 184

Figure S259.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0088

Table S260.  Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
21Q LOSS MUTATED 1 7 12
21Q LOSS WILD-TYPE 88 101 66

Figure S260.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.092

Table S261.  Gene #79: '21q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
21Q LOSS MUTATED 1 7 4
21Q LOSS WILD-TYPE 89 63 56

Figure S261.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S262.  Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
22Q LOSS MUTATED 79 47 55
22Q LOSS WILD-TYPE 83 171 142

Figure S262.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.015

Table S263.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
XP LOSS MUTATED 20 32 28 22
XP LOSS WILD-TYPE 127 64 124 91

Figure S263.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.05

Table S264.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
XP LOSS MUTATED 21 32 19 30
XP LOSS WILD-TYPE 127 70 81 128

Figure S264.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'MIR_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.13

Table S265.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
XP LOSS MUTATED 24 48 17 18
XP LOSS WILD-TYPE 132 135 70 102

Figure S265.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'MIR_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S266.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
XP LOSS MUTATED 59 27 28
XP LOSS WILD-TYPE 103 191 169

Figure S266.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 9e-04

Table S267.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
XP LOSS MUTATED 9 19 28
XP LOSS WILD-TYPE 80 89 50

Figure S267.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.1

Table S268.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
XP LOSS MUTATED 7 12 6 13 13
XP LOSS WILD-TYPE 37 45 38 17 32

Figure S268.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.074

Table S269.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
XQ LOSS MUTATED 19 28 26 21
XQ LOSS WILD-TYPE 128 68 126 92

Figure S269.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.063

Table S270.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
XQ LOSS MUTATED 18 29 18 29
XQ LOSS WILD-TYPE 130 73 82 129

Figure S270.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S271.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
XQ LOSS MUTATED 56 25 25
XQ LOSS WILD-TYPE 106 193 172

Figure S271.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.024

Table S272.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
XQ LOSS MUTATED 9 19 23
XQ LOSS WILD-TYPE 80 89 55

Figure S272.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/20146438/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/20125497/GBM-TP.transferedmergedcluster.txt

  • Number of patients = 577

  • Number of significantly arm-level cnvs = 82

  • 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.

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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