Correlation between copy number variation genes and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C18G8HQ1
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18G8HQ1
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 32 peak regions and 12 molecular subtypes across 504 patients, 133 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1q24.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 3(3q26.32) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 5(5q35.1) cnvs correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 6(7q36.3) cnvs correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • Amp Peak 7(8q24.22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 1(1p36.23) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 2(1p31.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 3(1q43) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 4(2q37.3) cnvs correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 5(3p25.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 6(3p21.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 7(3p12.3) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 8(3p12.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 9(3q11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(3q21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 11(4q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 12(6q26) cnvs correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 13(6q26) cnvs correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 14(8p23.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 15(9p23) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 16(9p21.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 18(13q13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 19(14q31.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 32 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Del Peak 16(9p21 3) 0 (0%) 350 0.00125
(0.307) 		0.000168
(0.0456) 		7.82e-49
(2.98e-46) 		6.57e-20
(2.44e-17) 		5.23e-08
(1.75e-05) 		0.000469
(0.122) 		2.08e-23
(7.76e-21) 		1.15e-27
(4.31e-25) 		4.52e-16
(1.65e-13) 		2.26e-07
(7.35e-05) 		1.7e-09
(5.83e-07) 		8.33e-07
(0.000267)
Del Peak 1(1p36 23) 0 (0%) 406 0.000181
(0.0488) 		0.000139
(0.0381) 		2.6e-12
(9.14e-10) 		0.0348
(1.00) 		2.28e-05
(0.00678) 		0.000147
(0.0402) 		0.000118
(0.0327) 		0.000449
(0.117) 		6.83e-07
(0.00022) 		6.69e-09
(2.27e-06) 		0.00824
(1.00) 		0.000562
(0.144)
Del Peak 5(3p25 3) 0 (0%) 63 1.55e-07
(5.11e-05) 		1.19e-08
(4.03e-06) 		7.78e-31
(2.93e-28) 		0.000223
(0.0589) 		3.42e-05
(0.01) 		0.0317
(1.00) 		2.88e-12
(1.01e-09) 		7.52e-16
(2.73e-13) 		3.19e-05
(0.00939) 		1.34e-14
(4.8e-12) 		0.0269
(1.00) 		0.00031
(0.0812)
Del Peak 6(3p21 32) 0 (0%) 60 1.55e-07
(5.11e-05) 		1.19e-08
(4.03e-06) 		2.81e-33
(1.06e-30) 		0.00063
(0.159) 		5.46e-05
(0.0157) 		0.0234
(1.00) 		1.15e-13
(4.1e-11) 		3.21e-16
(1.17e-13) 		1.01e-06
(0.000322) 		2.54e-15
(9.15e-13) 		0.00282
(0.662) 		2.11e-05
(0.0063)
Del Peak 15(9p23) 0 (0%) 357 0.00362
(0.823) 		0.000587
(0.15) 		9.66e-51
(3.69e-48) 		1.34e-19
(4.94e-17) 		1.41e-07
(4.67e-05) 		0.002
(0.475) 		3.59e-23
(1.34e-20) 		9.21e-24
(3.46e-21) 		1.07e-15
(3.88e-13) 		3.08e-05
(0.00908) 		1.16e-09
(3.98e-07) 		7.85e-07
(0.000252)
Del Peak 19(14q31 1) 0 (0%) 282 5.92e-05
(0.0169) 		0.000113
(0.0316) 		1.15e-17
(4.22e-15) 		5.98e-07
(0.000194) 		2.35e-14
(8.41e-12) 		1.88e-07
(6.16e-05) 		6.67e-20
(2.47e-17) 		6.4e-15
(2.3e-12) 		5.25e-11
(1.82e-08) 		0.536
(1.00) 		0.000185
(0.0497) 		0.00765
(1.00)
Amp Peak 7(8q24 22) 0 (0%) 429 0.226
(1.00) 		0.325
(1.00) 		3.33e-21
(1.24e-18) 		2.16e-06
(0.000677) 		3.77e-06
(0.00116) 		0.00425
(0.937) 		2.78e-12
(9.77e-10) 		2.89e-11
(1.01e-08) 		3.18e-09
(1.08e-06) 		5.88e-05
(0.0168) 		6.69e-07
(0.000216) 		0.000235
(0.0618)
Del Peak 18(13q13 3) 0 (0%) 428 0.0144
(1.00) 		0.0174
(1.00) 		3.56e-09
(1.21e-06) 		0.000101
(0.0286) 		2e-06
(0.000627) 		0.14
(1.00) 		1.24e-06
(0.000392) 		9.39e-08
(3.12e-05) 		2.38e-06
(0.000743) 		1.59e-06
(5e-04) 		0.0292
(1.00) 		2.14e-05
(0.00639)
Amp Peak 3(3q26 32) 0 (0%) 422 0.0484
(1.00) 		0.0491
(1.00) 		2.14e-12
(7.56e-10) 		1.86e-05
(0.00558) 		0.0035
(0.802) 		1.06e-05
(0.00321) 		1.41e-06
(0.000447) 		9.53e-08
(3.15e-05) 		5.45e-08
(1.81e-05) 		0.000979
(0.245) 		0.0017
(0.409) 		0.171
(1.00)
Del Peak 12(6q26) 0 (0%) 359 0.015
(1.00) 		0.00669
(1.00) 		1.88e-17
(6.9e-15) 		0.0894
(1.00) 		6.38e-05
(0.0181) 		0.004
(0.892) 		0.000478
(0.123) 		0.0191
(1.00) 		4.89e-08
(1.64e-05) 		0.0157
(1.00) 		0.000508
(0.13) 		5.18e-05
(0.015)
Del Peak 13(6q26) 0 (0%) 359 0.015
(1.00) 		0.00669
(1.00) 		1.88e-17
(6.9e-15) 		0.0894
(1.00) 		3.06e-05
(0.00905) 		0.00542
(1.00) 		0.000159
(0.0433) 		0.0191
(1.00) 		1.35e-08
(4.54e-06) 		0.0403
(1.00) 		0.000126
(0.0348) 		5.18e-05
(0.015)
Del Peak 2(1p31 1) 0 (0%) 432 0.00167
(0.404) 		0.000606
(0.153) 		2.11e-09
(7.2e-07) 		0.0318
(1.00) 		4e-05
(0.0116) 		0.00807
(1.00) 		0.0596
(1.00) 		0.00727
(1.00) 		0.000111
(0.0312) 		2.92e-06
(0.000904) 		0.0894
(1.00) 		0.00374
(0.843)
Amp Peak 2(1q32 1) 0 (0%) 444 0.41
(1.00) 		0.411
(1.00) 		3.01e-15
(1.08e-12) 		0.164
(1.00) 		0.265
(1.00) 		0.123
(1.00) 		7.94e-06
(0.00243) 		0.000588
(0.15) 		8.39e-06
(0.00256) 		0.175
(1.00) 		0.0253
(1.00) 		0.0468
(1.00)
Del Peak 7(3p12 3) 0 (0%) 184 0.0035
(0.802) 		0.00103
(0.257) 		6.2e-37
(2.36e-34) 		0.0459
(1.00) 		0.485
(1.00) 		0.446
(1.00) 		8.39e-05
(0.0238) 		2.57e-06
(8e-04) 		0.0595
(1.00) 		0.000183
(0.0491) 		0.0192
(1.00) 		0.0409
(1.00)
Del Peak 11(4q34 3) 0 (0%) 428 0.314
(1.00) 		0.27
(1.00) 		3.4e-12
(1.19e-09) 		0.000139
(0.0382) 		0.00312
(0.721) 		0.134
(1.00) 		0.000344
(0.0898) 		1.18e-05
(0.00355) 		0.246
(1.00) 		0.0168
(1.00) 		0.00944
(1.00) 		0.0467
(1.00)
Amp Peak 1(1q24 1) 0 (0%) 443 0.259
(1.00) 		0.245
(1.00) 		6.12e-13
(2.17e-10) 		0.342
(1.00) 		0.258
(1.00) 		0.388
(1.00) 		3.88e-05
(0.0113) 		0.00128
(0.314) 		9.74e-06
(0.00295) 		0.417
(1.00) 		0.0509
(1.00) 		0.0928
(1.00)
Amp Peak 6(7q36 3) 0 (0%) 338 0.667
(1.00) 		0.753
(1.00) 		9.1e-14
(3.24e-11) 		0.0325
(1.00) 		0.000192
(0.051) 		0.0175
(1.00) 		0.00013
(0.0358) 		0.00373
(0.843) 		0.0275
(1.00) 		0.12
(1.00) 		0.00581
(1.00) 		0.0228
(1.00)
Del Peak 4(2q37 3) 0 (0%) 454 0.00156
(0.379) 		0.00299
(0.696) 		0.86
(1.00) 		0.825
(1.00) 		0.199
(1.00) 		0.413
(1.00) 		0.000109
(0.0306) 		0.00019
(0.0507) 		0.0445
(1.00) 		8.72e-06
(0.00265) 		0.479
(1.00) 		0.00179
(0.429)
Amp Peak 5(5q35 1) 0 (0%) 188 0.0174
(1.00) 		0.00717
(1.00) 		0.00541
(1.00) 		0.928
(1.00) 		0.0151
(1.00) 		0.00332
(0.764) 		0.0134
(1.00) 		0.000701
(0.176) 		0.411
(1.00) 		6.65e-06
(0.00205) 		0.948
(1.00) 		0.287
(1.00)
Del Peak 3(1q43) 0 (0%) 466 0.0107
(1.00) 		0.0133
(1.00) 		7.08e-06
(0.00217) 		0.64
(1.00) 		0.00409
(0.908) 		0.0108
(1.00) 		0.00846
(1.00) 		0.00476
(1.00) 		0.409
(1.00) 		9.26e-07
(0.000295) 		0.685
(1.00) 		0.657
(1.00)
Del Peak 8(3p12 2) 0 (0%) 212 0.0404
(1.00) 		0.0199
(1.00) 		2.6e-32
(9.81e-30) 		0.439
(1.00) 		0.422
(1.00) 		0.358
(1.00) 		0.00398
(0.892) 		0.000211
(0.0559) 		0.335
(1.00) 		0.00742
(1.00) 		0.0116
(1.00) 		0.0323
(1.00)
Del Peak 9(3q11 2) 0 (0%) 350 0.183
(1.00) 		0.121
(1.00) 		1.15e-09
(3.97e-07) 		0.578
(1.00) 		0.861
(1.00) 		0.135
(1.00) 		0.523
(1.00) 		0.106
(1.00) 		0.701
(1.00) 		0.0601
(1.00) 		0.169
(1.00) 		0.0251
(1.00)
Del Peak 10(3q21 3) 0 (0%) 399 0.538
(1.00) 		0.462
(1.00) 		3.67e-05
(0.0107) 		0.67
(1.00) 		0.471
(1.00) 		0.0773
(1.00) 		0.342
(1.00) 		0.0962
(1.00) 		0.968
(1.00) 		0.14
(1.00) 		0.253
(1.00) 		0.132
(1.00)
Del Peak 14(8p23 2) 0 (0%) 356 0.502
(1.00) 		0.626
(1.00) 		2.67e-07
(8.67e-05) 		0.0539
(1.00) 		0.00424
(0.937) 		0.156
(1.00) 		0.00256
(0.604) 		0.00869
(1.00) 		0.00111
(0.274) 		0.0143
(1.00) 		0.0104
(1.00) 		0.0248
(1.00)
Del Peak 17(10q23 31) 0 (0%) 414 0.441
(1.00) 		0.554
(1.00) 		6.49e-10
(2.24e-07) 		0.00103
(0.257) 		0.911
(1.00) 		0.0717
(1.00) 		0.0578
(1.00) 		0.0344
(1.00) 		0.0231
(1.00) 		0.0238
(1.00) 		0.201
(1.00) 		0.0354
(1.00)
Amp Peak 4(4q32 1) 0 (0%) 490 0.476
(1.00) 		0.337
(1.00) 		0.693
(1.00) 		0.516
(1.00) 		0.0813
(1.00) 		0.466
(1.00) 		0.0071
(1.00) 		0.055
(1.00) 		0.0532
(1.00) 		1
(1.00)
Amp Peak 8(10p14) 0 (0%) 488 0.189
(1.00) 		0.207
(1.00) 		0.00126
(0.309) 		0.171
(1.00) 		0.548
(1.00) 		0.054
(1.00) 		0.0321
(1.00) 		0.00295
(0.691) 		0.134
(1.00) 		0.118
(1.00) 		0.873
(1.00) 		0.881
(1.00)
Amp Peak 9(17q24 3) 0 (0%) 467 0.0692
(1.00) 		0.0988
(1.00) 		0.00197
(0.469) 		0.212
(1.00) 		0.243
(1.00) 		0.0371
(1.00) 		0.197
(1.00) 		0.0204
(1.00) 		0.128
(1.00) 		0.0476
(1.00) 		0.00642
(1.00) 		0.0234
(1.00)
Amp Peak 10(Xp22 2) 0 (0%) 468 1
(1.00) 		1
(1.00) 		0.00311
(0.721) 		0.09
(1.00) 		0.00598
(1.00) 		0.0129
(1.00) 		0.1
(1.00) 		0.166
(1.00) 		0.0221
(1.00) 		0.618
(1.00) 		0.0784
(1.00) 		0.439
(1.00)
Amp Peak 11(Xp11 4) 0 (0%) 467 0.843
(1.00) 		0.842
(1.00) 		0.00177
(0.426) 		0.0298
(1.00) 		0.00732
(1.00) 		0.00446
(0.976) 		0.0321
(1.00) 		0.0469
(1.00) 		0.0221
(1.00) 		0.373
(1.00) 		0.0784
(1.00) 		0.439
(1.00)
Amp Peak 12(Xq11 2) 0 (0%) 471 0.172
(1.00) 		0.182
(1.00) 		0.0473
(1.00) 		0.154
(1.00) 		0.105
(1.00) 		0.0545
(1.00) 		0.104
(1.00) 		0.391
(1.00) 		0.0745
(1.00) 		0.166
(1.00) 		0.156
(1.00) 		0.412
(1.00)
Amp Peak 13(Xq28) 0 (0%) 465 0.49
(1.00) 		0.591
(1.00) 		0.18
(1.00) 		0.648
(1.00) 		0.0552
(1.00) 		0.0292
(1.00) 		0.0807
(1.00) 		0.119
(1.00) 		0.258
(1.00) 		0.153
(1.00) 		0.034
(1.00) 		0.0442
(1.00)
'Amp Peak 1(1q24.1)' versus 'CN_CNMF'

P value = 6.12e-13 (Fisher's exact test), Q value = 2.2e-10

Table S1.  Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
AMP PEAK 1(1Q24.1) CNV 46 12 3
AMP PEAK 1(1Q24.1) WILD-TYPE 118 204 121

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 1(1q24.1)' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.011

Table S2.  Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
AMP PEAK 1(1Q24.1) CNV 18 36 3
AMP PEAK 1(1Q24.1) WILD-TYPE 179 143 94

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1q24.1)' versus 'MIRSEQ_CNMF'

P value = 9.74e-06 (Fisher's exact test), Q value = 0.003

Table S3.  Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
AMP PEAK 1(1Q24.1) CNV 4 18 36
AMP PEAK 1(1Q24.1) WILD-TYPE 111 173 133

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 2(1q32.1)' versus 'CN_CNMF'

P value = 3.01e-15 (Fisher's exact test), Q value = 1.1e-12

Table S4.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
AMP PEAK 2(1Q32.1) CNV 48 9 3
AMP PEAK 2(1Q32.1) WILD-TYPE 116 207 121

Figure S4.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'MRNASEQ_CNMF'

P value = 7.94e-06 (Fisher's exact test), Q value = 0.0024

Table S5.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
AMP PEAK 2(1Q32.1) CNV 18 36 2
AMP PEAK 2(1Q32.1) WILD-TYPE 179 143 95

Figure S5.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(1q32.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000588 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
AMP PEAK 2(1Q32.1) CNV 1 22 33
AMP PEAK 2(1Q32.1) WILD-TYPE 68 192 157

Figure S6.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1q32.1)' versus 'MIRSEQ_CNMF'

P value = 8.39e-06 (Fisher's exact test), Q value = 0.0026

Table S7.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
AMP PEAK 2(1Q32.1) CNV 4 17 36
AMP PEAK 2(1Q32.1) WILD-TYPE 111 174 133

Figure S7.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(3q26.32)' versus 'CN_CNMF'

P value = 2.14e-12 (Fisher's exact test), Q value = 7.6e-10

Table S8.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
AMP PEAK 3(3Q26.32) CNV 54 11 17
AMP PEAK 3(3Q26.32) WILD-TYPE 110 205 107

Figure S8.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(3q26.32)' versus 'METHLYATION_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.0056

Table S9.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
AMP PEAK 3(3Q26.32) CNV 26 6 15
AMP PEAK 3(3Q26.32) WILD-TYPE 73 113 56

Figure S9.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(3q26.32)' versus 'RPPA_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0032

Table S10.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
AMP PEAK 3(3Q26.32) CNV 17 24 34
AMP PEAK 3(3Q26.32) WILD-TYPE 169 128 75

Figure S10.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 3(3q26.32)' versus 'MRNASEQ_CNMF'

P value = 1.41e-06 (Fisher's exact test), Q value = 0.00045

Table S11.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
AMP PEAK 3(3Q26.32) CNV 18 51 11
AMP PEAK 3(3Q26.32) WILD-TYPE 179 128 86

Figure S11.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(3q26.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.53e-08 (Fisher's exact test), Q value = 3.2e-05

Table S12.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
AMP PEAK 3(3Q26.32) CNV 7 18 55
AMP PEAK 3(3Q26.32) WILD-TYPE 62 196 135

Figure S12.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(3q26.32)' versus 'MIRSEQ_CNMF'

P value = 5.45e-08 (Fisher's exact test), Q value = 1.8e-05

Table S13.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
AMP PEAK 3(3Q26.32) CNV 12 15 50
AMP PEAK 3(3Q26.32) WILD-TYPE 103 176 119

Figure S13.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(3q26.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000979 (Fisher's exact test), Q value = 0.24

Table S14.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
AMP PEAK 3(3Q26.32) CNV 9 37 31
AMP PEAK 3(3Q26.32) WILD-TYPE 26 123 249

Figure S14.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(5q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000701 (Fisher's exact test), Q value = 0.18

Table S15.  Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
AMP PEAK 5(5Q35.1) CNV 30 148 122
AMP PEAK 5(5Q35.1) WILD-TYPE 39 66 68

Figure S15.  Get High-res Image Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(5q35.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.65e-06 (Fisher's exact test), Q value = 0.002

Table S16.  Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
AMP PEAK 5(5Q35.1) CNV 9 101 192
AMP PEAK 5(5Q35.1) WILD-TYPE 26 59 88

Figure S16.  Get High-res Image Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(7q36.3)' versus 'CN_CNMF'

P value = 9.1e-14 (Fisher's exact test), Q value = 3.2e-11

Table S17.  Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
AMP PEAK 6(7Q36.3) CNV 86 34 46
AMP PEAK 6(7Q36.3) WILD-TYPE 78 182 78

Figure S17.  Get High-res Image Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7q36.3)' versus 'RPPA_CNMF'

P value = 0.000192 (Chi-square test), Q value = 0.051

Table S18.  Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
AMP PEAK 6(7Q36.3) CNV 21 23 32 32 10 30
AMP PEAK 6(7Q36.3) WILD-TYPE 79 65 52 43 33 27

Figure S18.  Get High-res Image Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 6(7q36.3)' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.036

Table S19.  Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
AMP PEAK 6(7Q36.3) CNV 48 80 29
AMP PEAK 6(7Q36.3) WILD-TYPE 149 99 68

Figure S19.  Get High-res Image Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(8q24.22)' versus 'CN_CNMF'

P value = 3.33e-21 (Fisher's exact test), Q value = 1.2e-18

Table S20.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
AMP PEAK 7(8Q24.22) CNV 57 2 16
AMP PEAK 7(8Q24.22) WILD-TYPE 107 214 108

Figure S20.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q24.22)' versus 'METHLYATION_CNMF'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.00068

Table S21.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
AMP PEAK 7(8Q24.22) CNV 30 6 13
AMP PEAK 7(8Q24.22) WILD-TYPE 69 113 58

Figure S21.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(8q24.22)' versus 'RPPA_CNMF'

P value = 3.77e-06 (Chi-square test), Q value = 0.0012

Table S22.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
AMP PEAK 7(8Q24.22) CNV 6 14 14 12 1 21
AMP PEAK 7(8Q24.22) WILD-TYPE 94 74 70 63 42 36

Figure S22.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 7(8q24.22)' versus 'MRNASEQ_CNMF'

P value = 2.78e-12 (Fisher's exact test), Q value = 9.8e-10

Table S23.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
AMP PEAK 7(8Q24.22) CNV 8 53 8
AMP PEAK 7(8Q24.22) WILD-TYPE 189 126 89

Figure S23.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(8q24.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-11 (Fisher's exact test), Q value = 1e-08

Table S24.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
AMP PEAK 7(8Q24.22) CNV 3 12 54
AMP PEAK 7(8Q24.22) WILD-TYPE 66 202 136

Figure S24.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_CNMF'

P value = 3.18e-09 (Fisher's exact test), Q value = 1.1e-06

Table S25.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
AMP PEAK 7(8Q24.22) CNV 13 10 48
AMP PEAK 7(8Q24.22) WILD-TYPE 102 181 121

Figure S25.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.017

Table S26.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
AMP PEAK 7(8Q24.22) CNV 5 40 26
AMP PEAK 7(8Q24.22) WILD-TYPE 30 120 254

Figure S26.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00022

Table S27.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
AMP PEAK 7(8Q24.22) CNV 2 4 23
AMP PEAK 7(8Q24.22) WILD-TYPE 48 85 51

Figure S27.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000235 (Fisher's exact test), Q value = 0.062

Table S28.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
AMP PEAK 7(8Q24.22) CNV 16 4 9
AMP PEAK 7(8Q24.22) WILD-TYPE 41 88 55

Figure S28.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MRNA_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.049

Table S29.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 1(1P36.23) CNV 2 8 8
DEL PEAK 1(1P36.23) WILD-TYPE 31 16 5

Figure S29.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.23)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.038

Table S30.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 1(1P36.23) CNV 9 2 7
DEL PEAK 1(1P36.23) WILD-TYPE 5 30 17

Figure S30.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'CN_CNMF'

P value = 2.6e-12 (Fisher's exact test), Q value = 9.1e-10

Table S31.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 1(1P36.23) CNV 52 12 34
DEL PEAK 1(1P36.23) WILD-TYPE 112 204 90

Figure S31.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.23)' versus 'RPPA_CNMF'

P value = 2.28e-05 (Chi-square test), Q value = 0.0068

Table S32.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 1(1P36.23) CNV 8 10 22 24 5 18
DEL PEAK 1(1P36.23) WILD-TYPE 92 78 62 51 38 39

Figure S32.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 1(1p36.23)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000147 (Fisher's exact test), Q value = 0.04

Table S33.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 1(1P36.23) CNV 20 35 32
DEL PEAK 1(1P36.23) WILD-TYPE 166 117 77

Figure S33.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MRNASEQ_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.033

Table S34.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 1(1P36.23) CNV 24 53 17
DEL PEAK 1(1P36.23) WILD-TYPE 173 126 80

Figure S34.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000449 (Fisher's exact test), Q value = 0.12

Table S35.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 1(1P36.23) CNV 18 26 50
DEL PEAK 1(1P36.23) WILD-TYPE 51 188 140

Figure S35.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MIRSEQ_CNMF'

P value = 6.83e-07 (Fisher's exact test), Q value = 0.00022

Table S36.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 1(1P36.23) CNV 22 20 56
DEL PEAK 1(1P36.23) WILD-TYPE 93 171 113

Figure S36.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.69e-09 (Fisher's exact test), Q value = 2.3e-06

Table S37.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 1(1P36.23) CNV 20 42 36
DEL PEAK 1(1P36.23) WILD-TYPE 15 118 244

Figure S37.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000562 (Fisher's exact test), Q value = 0.14

Table S38.  Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 1(1P36.23) CNV 20 9 16
DEL PEAK 1(1P36.23) WILD-TYPE 37 83 48

Figure S38.  Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p31.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000606 (Fisher's exact test), Q value = 0.15

Table S39.  Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 2(1P31.1) CNV 8 2 4
DEL PEAK 2(1P31.1) WILD-TYPE 6 30 20

Figure S39.  Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p31.1)' versus 'CN_CNMF'

P value = 2.11e-09 (Fisher's exact test), Q value = 7.2e-07

Table S40.  Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 2(1P31.1) CNV 38 8 26
DEL PEAK 2(1P31.1) WILD-TYPE 126 208 98

Figure S40.  Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p31.1)' versus 'RPPA_CNMF'

P value = 4e-05 (Chi-square test), Q value = 0.012

Table S41.  Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 2(1P31.1) CNV 9 4 12 21 4 15
DEL PEAK 2(1P31.1) WILD-TYPE 91 84 72 54 39 42

Figure S41.  Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 2(1p31.1)' versus 'MIRSEQ_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.031

Table S42.  Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 2(1P31.1) CNV 12 18 42
DEL PEAK 2(1P31.1) WILD-TYPE 103 173 127

Figure S42.  Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p31.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 9e-04

Table S43.  Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 2(1P31.1) CNV 17 22 33
DEL PEAK 2(1P31.1) WILD-TYPE 18 138 247

Figure S43.  Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(1q43)' versus 'CN_CNMF'

P value = 7.08e-06 (Fisher's exact test), Q value = 0.0022

Table S44.  Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 3(1Q43) CNV 12 5 21
DEL PEAK 3(1Q43) WILD-TYPE 152 211 103

Figure S44.  Get High-res Image Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1q43)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.26e-07 (Fisher's exact test), Q value = 3e-04

Table S45.  Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 3(1Q43) CNV 13 9 16
DEL PEAK 3(1Q43) WILD-TYPE 22 151 264

Figure S45.  Get High-res Image Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.031

Table S46.  Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 4(2Q37.3) CNV 7 19 18
DEL PEAK 4(2Q37.3) WILD-TYPE 190 160 79

Figure S46.  Get High-res Image Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.051

Table S47.  Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 4(2Q37.3) CNV 12 8 24
DEL PEAK 4(2Q37.3) WILD-TYPE 57 206 166

Figure S47.  Get High-res Image Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.72e-06 (Fisher's exact test), Q value = 0.0027

Table S48.  Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 4(2Q37.3) CNV 12 18 16
DEL PEAK 4(2Q37.3) WILD-TYPE 23 142 264

Figure S48.  Get High-res Image Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'MRNA_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 5.1e-05

Table S49.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 5(3P25.3) CNV 32 22 3
DEL PEAK 5(3P25.3) WILD-TYPE 1 2 10

Figure S49.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(3p25.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 4e-06

Table S50.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 5(3P25.3) CNV 3 31 23
DEL PEAK 5(3P25.3) WILD-TYPE 11 1 1

Figure S50.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'CN_CNMF'

P value = 7.78e-31 (Fisher's exact test), Q value = 2.9e-28

Table S51.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 5(3P25.3) CNV 158 214 69
DEL PEAK 5(3P25.3) WILD-TYPE 6 2 55

Figure S51.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(3p25.3)' versus 'METHLYATION_CNMF'

P value = 0.000223 (Fisher's exact test), Q value = 0.059

Table S52.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 5(3P25.3) CNV 94 109 53
DEL PEAK 5(3P25.3) WILD-TYPE 5 10 18

Figure S52.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(3p25.3)' versus 'RPPA_CNMF'

P value = 3.42e-05 (Chi-square test), Q value = 0.01

Table S53.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 5(3P25.3) CNV 99 74 75 56 40 52
DEL PEAK 5(3P25.3) WILD-TYPE 1 14 9 19 3 5

Figure S53.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 5(3p25.3)' versus 'MRNASEQ_CNMF'

P value = 2.88e-12 (Fisher's exact test), Q value = 1e-09

Table S54.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 5(3P25.3) CNV 190 160 63
DEL PEAK 5(3P25.3) WILD-TYPE 7 19 34

Figure S54.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(3p25.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.52e-16 (Fisher's exact test), Q value = 2.7e-13

Table S55.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 5(3P25.3) CNV 37 206 170
DEL PEAK 5(3P25.3) WILD-TYPE 32 8 20

Figure S55.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'MIRSEQ_CNMF'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.0094

Table S56.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 5(3P25.3) CNV 96 182 137
DEL PEAK 5(3P25.3) WILD-TYPE 19 9 32

Figure S56.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(3p25.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-14 (Fisher's exact test), Q value = 4.8e-12

Table S57.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 5(3P25.3) CNV 15 133 267
DEL PEAK 5(3P25.3) WILD-TYPE 20 27 13

Figure S57.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.081

Table S58.  Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 5(3P25.3) CNV 49 88 47
DEL PEAK 5(3P25.3) WILD-TYPE 8 4 17

Figure S58.  Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'MRNA_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 5.1e-05

Table S59.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 6(3P21.32) CNV 32 22 3
DEL PEAK 6(3P21.32) WILD-TYPE 1 2 10

Figure S59.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 6(3p21.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 4e-06

Table S60.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 6(3P21.32) CNV 3 31 23
DEL PEAK 6(3P21.32) WILD-TYPE 11 1 1

Figure S60.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'CN_CNMF'

P value = 2.81e-33 (Fisher's exact test), Q value = 1.1e-30

Table S61.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 6(3P21.32) CNV 160 215 69
DEL PEAK 6(3P21.32) WILD-TYPE 4 1 55

Figure S61.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3p21.32)' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.16

Table S62.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 6(3P21.32) CNV 94 109 54
DEL PEAK 6(3P21.32) WILD-TYPE 5 10 17

Figure S62.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(3p21.32)' versus 'RPPA_CNMF'

P value = 5.46e-05 (Chi-square test), Q value = 0.016

Table S63.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 6(3P21.32) CNV 99 73 75 58 40 54
DEL PEAK 6(3P21.32) WILD-TYPE 1 15 9 17 3 3

Figure S63.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 6(3p21.32)' versus 'MRNASEQ_CNMF'

P value = 1.15e-13 (Fisher's exact test), Q value = 4.1e-11

Table S64.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 6(3P21.32) CNV 192 161 63
DEL PEAK 6(3P21.32) WILD-TYPE 5 18 34

Figure S64.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(3p21.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.21e-16 (Fisher's exact test), Q value = 1.2e-13

Table S65.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 6(3P21.32) CNV 38 208 170
DEL PEAK 6(3P21.32) WILD-TYPE 31 6 20

Figure S65.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'MIRSEQ_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00032

Table S66.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 6(3P21.32) CNV 94 185 139
DEL PEAK 6(3P21.32) WILD-TYPE 21 6 30

Figure S66.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(3p21.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.54e-15 (Fisher's exact test), Q value = 9.2e-13

Table S67.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 6(3P21.32) CNV 16 132 270
DEL PEAK 6(3P21.32) WILD-TYPE 19 28 10

Figure S67.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0063

Table S68.  Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 6(3P21.32) CNV 51 89 46
DEL PEAK 6(3P21.32) WILD-TYPE 6 3 18

Figure S68.  Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p12.3)' versus 'CN_CNMF'

P value = 6.2e-37 (Fisher's exact test), Q value = 2.4e-34

Table S69.  Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 7(3P12.3) CNV 145 153 22
DEL PEAK 7(3P12.3) WILD-TYPE 19 63 102

Figure S69.  Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p12.3)' versus 'MRNASEQ_CNMF'

P value = 8.39e-05 (Fisher's exact test), Q value = 0.024

Table S70.  Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 7(3P12.3) CNV 133 121 42
DEL PEAK 7(3P12.3) WILD-TYPE 64 58 55

Figure S70.  Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(3p12.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-06 (Fisher's exact test), Q value = 8e-04

Table S71.  Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 7(3P12.3) CNV 24 143 129
DEL PEAK 7(3P12.3) WILD-TYPE 45 71 61

Figure S71.  Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(3p12.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.049

Table S72.  Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 7(3P12.3) CNV 12 95 193
DEL PEAK 7(3P12.3) WILD-TYPE 23 65 87

Figure S72.  Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(3p12.2)' versus 'CN_CNMF'

P value = 2.6e-32 (Fisher's exact test), Q value = 9.8e-30

Table S73.  Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 8(3P12.2) CNV 136 137 19
DEL PEAK 8(3P12.2) WILD-TYPE 28 79 105

Figure S73.  Get High-res Image Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(3p12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000211 (Fisher's exact test), Q value = 0.056

Table S74.  Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 8(3P12.2) CNV 24 125 120
DEL PEAK 8(3P12.2) WILD-TYPE 45 89 70

Figure S74.  Get High-res Image Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(3q11.2)' versus 'CN_CNMF'

P value = 1.15e-09 (Fisher's exact test), Q value = 4e-07

Table S75.  Gene #22: 'Del Peak 9(3q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 9(3Q11.2) CNV 72 69 13
DEL PEAK 9(3Q11.2) WILD-TYPE 92 147 111

Figure S75.  Get High-res Image Gene #22: 'Del Peak 9(3q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(3q21.3)' versus 'CN_CNMF'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.011

Table S76.  Gene #23: 'Del Peak 10(3q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 10(3Q21.3) CNV 52 40 13
DEL PEAK 10(3Q21.3) WILD-TYPE 112 176 111

Figure S76.  Get High-res Image Gene #23: 'Del Peak 10(3q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q34.3)' versus 'CN_CNMF'

P value = 3.4e-12 (Fisher's exact test), Q value = 1.2e-09

Table S77.  Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 11(4Q34.3) CNV 49 8 19
DEL PEAK 11(4Q34.3) WILD-TYPE 115 208 105

Figure S77.  Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q34.3)' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.038

Table S78.  Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 11(4Q34.3) CNV 30 10 12
DEL PEAK 11(4Q34.3) WILD-TYPE 69 109 59

Figure S78.  Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.09

Table S79.  Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 11(4Q34.3) CNV 24 41 6
DEL PEAK 11(4Q34.3) WILD-TYPE 173 138 91

Figure S79.  Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0035

Table S80.  Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 11(4Q34.3) CNV 2 24 45
DEL PEAK 11(4Q34.3) WILD-TYPE 67 190 145

Figure S80.  Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(6q26)' versus 'CN_CNMF'

P value = 1.88e-17 (Fisher's exact test), Q value = 6.9e-15

Table S81.  Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 12(6Q26) CNV 89 30 26
DEL PEAK 12(6Q26) WILD-TYPE 75 186 98

Figure S81.  Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(6q26)' versus 'RPPA_CNMF'

P value = 6.38e-05 (Chi-square test), Q value = 0.018

Table S82.  Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 12(6Q26) CNV 32 10 29 22 8 27
DEL PEAK 12(6Q26) WILD-TYPE 68 78 55 53 35 30

Figure S82.  Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 12(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.12

Table S83.  Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 12(6Q26) CNV 48 68 17
DEL PEAK 12(6Q26) WILD-TYPE 149 111 80

Figure S83.  Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_CNMF'

P value = 4.89e-08 (Fisher's exact test), Q value = 1.6e-05

Table S84.  Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 12(6Q26) CNV 22 39 77
DEL PEAK 12(6Q26) WILD-TYPE 93 152 92

Figure S84.  Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
DEL PEAK 12(6Q26) CNV 9 19 34
DEL PEAK 12(6Q26) WILD-TYPE 41 70 40

Figure S85.  Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.18e-05 (Fisher's exact test), Q value = 0.015

Table S86.  Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 12(6Q26) CNV 30 18 14
DEL PEAK 12(6Q26) WILD-TYPE 27 74 50

Figure S86.  Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(6q26)' versus 'CN_CNMF'

P value = 1.88e-17 (Fisher's exact test), Q value = 6.9e-15

Table S87.  Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 13(6Q26) CNV 89 30 26
DEL PEAK 13(6Q26) WILD-TYPE 75 186 98

Figure S87.  Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(6q26)' versus 'RPPA_CNMF'

P value = 3.06e-05 (Chi-square test), Q value = 0.009

Table S88.  Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 13(6Q26) CNV 31 10 29 22 8 28
DEL PEAK 13(6Q26) WILD-TYPE 69 78 55 53 35 29

Figure S88.  Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 13(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.043

Table S89.  Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 13(6Q26) CNV 48 69 16
DEL PEAK 13(6Q26) WILD-TYPE 149 110 81

Figure S89.  Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(6q26)' versus 'MIRSEQ_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 4.5e-06

Table S90.  Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 13(6Q26) CNV 21 39 78
DEL PEAK 13(6Q26) WILD-TYPE 94 152 91

Figure S90.  Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(6q26)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.035

Table S91.  Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
DEL PEAK 13(6Q26) CNV 8 19 35
DEL PEAK 13(6Q26) WILD-TYPE 42 70 39

Figure S91.  Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(6q26)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.18e-05 (Fisher's exact test), Q value = 0.015

Table S92.  Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 13(6Q26) CNV 30 18 14
DEL PEAK 13(6Q26) WILD-TYPE 27 74 50

Figure S92.  Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'CN_CNMF'

P value = 2.67e-07 (Fisher's exact test), Q value = 8.7e-05

Table S93.  Gene #27: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 14(8P23.2) CNV 73 40 35
DEL PEAK 14(8P23.2) WILD-TYPE 91 176 89

Figure S93.  Get High-res Image Gene #27: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(9p23)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.15

Table S94.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 15(9P23) CNV 1 4 13
DEL PEAK 15(9P23) WILD-TYPE 13 28 11

Figure S94.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 15(9p23)' versus 'CN_CNMF'

P value = 9.66e-51 (Fisher's exact test), Q value = 3.7e-48

Table S95.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 15(9P23) CNV 112 3 32
DEL PEAK 15(9P23) WILD-TYPE 52 213 92

Figure S95.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(9p23)' versus 'METHLYATION_CNMF'

P value = 1.34e-19 (Fisher's exact test), Q value = 4.9e-17

Table S96.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 15(9P23) CNV 60 6 24
DEL PEAK 15(9P23) WILD-TYPE 39 113 47

Figure S96.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(9p23)' versus 'RPPA_CNMF'

P value = 1.41e-07 (Chi-square test), Q value = 4.7e-05

Table S97.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 15(9P23) CNV 17 23 32 18 10 35
DEL PEAK 15(9P23) WILD-TYPE 83 65 52 57 33 22

Figure S97.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 15(9p23)' versus 'MRNASEQ_CNMF'

P value = 3.59e-23 (Fisher's exact test), Q value = 1.3e-20

Table S98.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 15(9P23) CNV 24 101 13
DEL PEAK 15(9P23) WILD-TYPE 173 78 84

Figure S98.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(9p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.21e-24 (Fisher's exact test), Q value = 3.5e-21

Table S99.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 15(9P23) CNV 9 24 105
DEL PEAK 15(9P23) WILD-TYPE 60 190 85

Figure S99.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(9p23)' versus 'MIRSEQ_CNMF'

P value = 1.07e-15 (Fisher's exact test), Q value = 3.9e-13

Table S100.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 15(9P23) CNV 26 25 88
DEL PEAK 15(9P23) WILD-TYPE 89 166 81

Figure S100.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 15(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.0091

Table S101.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 15(9P23) CNV 10 68 61
DEL PEAK 15(9P23) WILD-TYPE 25 92 219

Figure S101.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(9p23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.16e-09 (Fisher's exact test), Q value = 4e-07

Table S102.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
DEL PEAK 15(9P23) CNV 12 11 43
DEL PEAK 15(9P23) WILD-TYPE 38 78 31

Figure S102.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 15(9p23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.85e-07 (Fisher's exact test), Q value = 0.00025

Table S103.  Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 15(9P23) CNV 33 15 18
DEL PEAK 15(9P23) WILD-TYPE 24 77 46

Figure S103.  Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.046

Table S104.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 16(9P21.3) CNV 1 4 14
DEL PEAK 16(9P21.3) WILD-TYPE 13 28 10

Figure S104.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'CN_CNMF'

P value = 7.82e-49 (Fisher's exact test), Q value = 3e-46

Table S105.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 16(9P21.3) CNV 115 6 33
DEL PEAK 16(9P21.3) WILD-TYPE 49 210 91

Figure S105.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(9p21.3)' versus 'METHLYATION_CNMF'

P value = 6.57e-20 (Fisher's exact test), Q value = 2.4e-17

Table S106.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 16(9P21.3) CNV 60 6 27
DEL PEAK 16(9P21.3) WILD-TYPE 39 113 44

Figure S106.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3)' versus 'RPPA_CNMF'

P value = 5.23e-08 (Chi-square test), Q value = 1.7e-05

Table S107.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 16(9P21.3) CNV 18 26 32 19 10 37
DEL PEAK 16(9P21.3) WILD-TYPE 82 62 52 56 33 20

Figure S107.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 16(9p21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000469 (Fisher's exact test), Q value = 0.12

Table S108.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 16(9P21.3) CNV 42 52 48
DEL PEAK 16(9P21.3) WILD-TYPE 144 100 61

Figure S108.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 2.08e-23 (Fisher's exact test), Q value = 7.8e-21

Table S109.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 16(9P21.3) CNV 26 105 15
DEL PEAK 16(9P21.3) WILD-TYPE 171 74 82

Figure S109.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-27 (Fisher's exact test), Q value = 4.3e-25

Table S110.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 16(9P21.3) CNV 8 25 113
DEL PEAK 16(9P21.3) WILD-TYPE 61 189 77

Figure S110.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 4.52e-16 (Fisher's exact test), Q value = 1.6e-13

Table S111.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 16(9P21.3) CNV 29 26 91
DEL PEAK 16(9P21.3) WILD-TYPE 86 165 78

Figure S111.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.26e-07 (Fisher's exact test), Q value = 7.4e-05

Table S112.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 16(9P21.3) CNV 11 75 60
DEL PEAK 16(9P21.3) WILD-TYPE 24 85 220

Figure S112.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.7e-09 (Fisher's exact test), Q value = 5.8e-07

Table S113.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
DEL PEAK 16(9P21.3) CNV 13 11 43
DEL PEAK 16(9P21.3) WILD-TYPE 37 78 31

Figure S113.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.33e-07 (Fisher's exact test), Q value = 0.00027

Table S114.  Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 16(9P21.3) CNV 33 15 19
DEL PEAK 16(9P21.3) WILD-TYPE 24 77 45

Figure S114.  Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 17(10q23.31)' versus 'CN_CNMF'

P value = 6.49e-10 (Fisher's exact test), Q value = 2.2e-07

Table S115.  Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 17(10Q23.31) CNV 49 13 28
DEL PEAK 17(10Q23.31) WILD-TYPE 115 203 96

Figure S115.  Get High-res Image Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q13.3)' versus 'CN_CNMF'

P value = 3.56e-09 (Fisher's exact test), Q value = 1.2e-06

Table S116.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 18(13Q13.3) CNV 43 10 23
DEL PEAK 18(13Q13.3) WILD-TYPE 121 206 101

Figure S116.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q13.3)' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.029

Table S117.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 18(13Q13.3) CNV 18 7 20
DEL PEAK 18(13Q13.3) WILD-TYPE 81 112 51

Figure S117.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(13q13.3)' versus 'RPPA_CNMF'

P value = 2e-06 (Chi-square test), Q value = 0.00063

Table S118.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 18(13Q13.3) CNV 2 12 14 13 7 21
DEL PEAK 18(13Q13.3) WILD-TYPE 98 76 70 62 36 36

Figure S118.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 18(13q13.3)' versus 'MRNASEQ_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00039

Table S119.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 18(13Q13.3) CNV 15 48 11
DEL PEAK 18(13Q13.3) WILD-TYPE 182 131 86

Figure S119.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(13q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.39e-08 (Fisher's exact test), Q value = 3.1e-05

Table S120.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 18(13Q13.3) CNV 9 14 51
DEL PEAK 18(13Q13.3) WILD-TYPE 60 200 139

Figure S120.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(13q13.3)' versus 'MIRSEQ_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.00074

Table S121.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 18(13Q13.3) CNV 15 14 45
DEL PEAK 18(13Q13.3) WILD-TYPE 100 177 124

Figure S121.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(13q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 5e-04

Table S122.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 18(13Q13.3) CNV 13 36 25
DEL PEAK 18(13Q13.3) WILD-TYPE 22 124 255

Figure S122.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(13q13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0064

Table S123.  Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
DEL PEAK 18(13Q13.3) CNV 21 6 10
DEL PEAK 18(13Q13.3) WILD-TYPE 36 86 54

Figure S123.  Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'MRNA_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.017

Table S124.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 19(14Q31.1) CNV 10 19 2
DEL PEAK 19(14Q31.1) WILD-TYPE 23 5 11

Figure S124.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(14q31.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.032

Table S125.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 19(14Q31.1) CNV 3 9 19
DEL PEAK 19(14Q31.1) WILD-TYPE 11 23 5

Figure S125.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'CN_CNMF'

P value = 1.15e-17 (Fisher's exact test), Q value = 4.2e-15

Table S126.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
DEL PEAK 19(14Q31.1) CNV 117 59 46
DEL PEAK 19(14Q31.1) WILD-TYPE 47 157 78

Figure S126.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(14q31.1)' versus 'METHLYATION_CNMF'

P value = 5.98e-07 (Fisher's exact test), Q value = 0.00019

Table S127.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
DEL PEAK 19(14Q31.1) CNV 60 31 36
DEL PEAK 19(14Q31.1) WILD-TYPE 39 88 35

Figure S127.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(14q31.1)' versus 'RPPA_CNMF'

P value = 2.35e-14 (Chi-square test), Q value = 8.4e-12

Table S128.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
DEL PEAK 19(14Q31.1) CNV 30 30 64 23 13 41
DEL PEAK 19(14Q31.1) WILD-TYPE 70 58 20 52 30 16

Figure S128.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 19(14q31.1)' versus 'RPPA_CHIERARCHICAL'

P value = 1.88e-07 (Fisher's exact test), Q value = 6.2e-05

Table S129.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 19(14Q31.1) CNV 57 92 52
DEL PEAK 19(14Q31.1) WILD-TYPE 129 60 57

Figure S129.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'MRNASEQ_CNMF'

P value = 6.67e-20 (Fisher's exact test), Q value = 2.5e-17

Table S130.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 19(14Q31.1) CNV 68 126 17
DEL PEAK 19(14Q31.1) WILD-TYPE 129 53 80

Figure S130.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(14q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-15 (Fisher's exact test), Q value = 2.3e-12

Table S131.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 19(14Q31.1) CNV 11 76 124
DEL PEAK 19(14Q31.1) WILD-TYPE 58 138 66

Figure S131.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'MIRSEQ_CNMF'

P value = 5.25e-11 (Fisher's exact test), Q value = 1.8e-08

Table S132.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 19(14Q31.1) CNV 37 64 111
DEL PEAK 19(14Q31.1) WILD-TYPE 78 127 58

Figure S132.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(14q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.05

Table S133.  Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
DEL PEAK 19(14Q31.1) CNV 18 31 48
DEL PEAK 19(14Q31.1) WILD-TYPE 32 58 26

Figure S133.  Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Molecular subtype file = KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 504

  • Number of copy number variation regions = 32

  • Number of molecular subtypes = 12

  • Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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