Correlation between copy number variation genes and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C10R9MB0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Kidney Renal Clear Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10R9MB0
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 30 peak regions and 10 molecular subtypes across 493 patients, 117 significant findings detected with Q value < 0.25.

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

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

  • Del Peak 7(3p12.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 8(3q11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 9(4q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 10(6q26) cnvs correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Del Peak 11(6q26) cnvs correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Del Peak 12(8p23.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 13(9p23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 14(9p21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(10q23.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 16(13q13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 17(14q31.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Del Peak 18(Xq23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 30 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 117 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
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
Del Peak 14(9p21 3) 0 (0%) 341 0.00125
(0.229) 		0.000662
(0.126) 		1.96e-29
(5.78e-27) 		2.24e-21
(6.46e-19) 		5.23e-08
(1.36e-05) 		0.000469
(0.0915) 		2.08e-23
(6.02e-21) 		1.15e-27
(3.37e-25) 		4.52e-16
(1.28e-13) 		2.26e-07
(5.64e-05)
Del Peak 1(1p36 23) 0 (0%) 395 0.000181
(0.0365) 		7.87e-05
(0.0165) 		1.28e-09
(3.42e-07) 		0.0201
(1.00) 		2.28e-05
(0.00509) 		0.000147
(0.03) 		0.000118
(0.0242) 		0.000449
(0.088) 		6.83e-07
(0.00017) 		6.69e-09
(1.77e-06)
Del Peak 5(3p25 3) 0 (0%) 61 1.55e-07
(3.93e-05) 		1.19e-08
(3.15e-06) 		5.54e-30
(1.65e-27) 		0.000657
(0.126) 		3.42e-05
(0.00743) 		0.0317
(1.00) 		2.88e-12
(7.82e-10) 		7.52e-16
(2.12e-13) 		3.19e-05
(0.00696) 		1.34e-14
(3.71e-12)
Del Peak 17(14q31 1) 0 (0%) 275 5.92e-05
(0.0125) 		2.77e-05
(0.00616) 		2.06e-13
(5.64e-11) 		6.79e-08
(1.75e-05) 		2.35e-14
(6.5e-12) 		1.88e-07
(4.73e-05) 		6.67e-20
(1.91e-17) 		6.4e-15
(1.78e-12) 		5.25e-11
(1.42e-08) 		0.536
(1.00)
Del Peak 6(3p21 32) 0 (0%) 58 1.55e-07
(3.93e-05) 		1.19e-08
(3.15e-06) 		1.74e-29
(5.14e-27) 		0.00169
(0.302) 		5.46e-05
(0.0117) 		0.0234
(1.00) 		1.15e-13
(3.18e-11) 		3.21e-16
(9.12e-14) 		1.01e-06
(0.000249) 		2.54e-15
(7.08e-13)
Amp Peak 3(3q26 32) 0 (0%) 413 0.0484
(1.00) 		0.0372
(1.00) 		1.5e-06
(0.000363) 		6.37e-06
(0.00149) 		0.0035
(0.592) 		1.06e-05
(0.0024) 		1.41e-06
(0.000342) 		9.53e-08
(2.44e-05) 		5.45e-08
(1.41e-05) 		0.000979
(0.181)
Amp Peak 7(8q24 22) 0 (0%) 420 0.226
(1.00) 		0.278
(1.00) 		2.35e-15
(6.57e-13) 		1.18e-06
(0.000289) 		3.77e-06
(0.000889) 		0.00425
(0.678) 		2.78e-12
(7.6e-10) 		2.89e-11
(7.83e-09) 		3.18e-09
(8.49e-07) 		5.88e-05
(0.0125)
Del Peak 13(9p23) 0 (0%) 349 0.00362
(0.609) 		0.0023
(0.401) 		3.36e-30
(1e-27) 		3.43e-20
(9.85e-18) 		1.41e-07
(3.59e-05) 		0.002
(0.355) 		3.59e-23
(1.04e-20) 		9.21e-24
(2.68e-21) 		1.07e-15
(3.01e-13) 		3.08e-05
(0.00674)
Del Peak 16(13q13 3) 0 (0%) 417 0.0144
(1.00) 		0.0117
(1.00) 		4.05e-06
(0.000951) 		0.000675
(0.128) 		2e-06
(0.000477) 		0.14
(1.00) 		1.24e-06
(0.000302) 		9.39e-08
(2.41e-05) 		2.38e-06
(0.000566) 		1.59e-06
(0.000381)
Del Peak 2(1p31 1) 0 (0%) 421 0.00167
(0.301) 		0.000542
(0.105) 		2.84e-05
(0.00627) 		0.0474
(1.00) 		4e-05
(0.00859) 		0.00807
(1.00) 		0.0596
(1.00) 		0.00727
(1.00) 		0.000111
(0.023) 		2.92e-06
(0.000691)
Amp Peak 1(1q24 1) 0 (0%) 433 0.259
(1.00) 		0.491
(1.00) 		1.06e-07
(2.71e-05) 		0.359
(1.00) 		0.258
(1.00) 		0.388
(1.00) 		3.88e-05
(0.00838) 		0.00128
(0.234) 		9.74e-06
(0.00221) 		0.417
(1.00)
Amp Peak 2(1q32 1) 0 (0%) 434 0.41
(1.00) 		0.724
(1.00) 		7.5e-10
(2.02e-07) 		0.172
(1.00) 		0.265
(1.00) 		0.123
(1.00) 		7.94e-06
(0.00183) 		0.000588
(0.113) 		8.39e-06
(0.00193) 		0.175
(1.00)
Del Peak 9(4q34 3) 0 (0%) 417 0.314
(1.00) 		0.292
(1.00) 		5.47e-09
(1.46e-06) 		0.000408
(0.0805) 		0.00312
(0.533) 		0.134
(1.00) 		0.000344
(0.0681) 		1.18e-05
(0.00265) 		0.246
(1.00) 		0.0168
(1.00)
Del Peak 10(6q26) 0 (0%) 351 0.015
(1.00) 		0.00364
(0.609) 		1.84e-25
(5.4e-23) 		0.0171
(1.00) 		6.38e-05
(0.0134) 		0.004
(0.649) 		0.000478
(0.0927) 		0.0191
(1.00) 		4.89e-08
(1.28e-05) 		0.0157
(1.00)
Del Peak 11(6q26) 0 (0%) 351 0.015
(1.00) 		0.00364
(0.609) 		1.84e-25
(5.4e-23) 		0.0171
(1.00) 		3.06e-05
(0.00673) 		0.00542
(0.839) 		0.000159
(0.0323) 		0.0191
(1.00) 		1.35e-08
(3.54e-06) 		0.0403
(1.00)
Amp Peak 5(5q35 1) 0 (0%) 182 0.0174
(1.00) 		0.00729
(1.00) 		5.53e-05
(0.0118) 		0.888
(1.00) 		0.0151
(1.00) 		0.00332
(0.565) 		0.0134
(1.00) 		0.000701
(0.132) 		0.411
(1.00) 		6.65e-06
(0.00154)
Amp Peak 6(7q36 3) 0 (0%) 330 0.667
(1.00) 		0.639
(1.00) 		1.25e-06
(0.000303) 		0.0283
(1.00) 		0.000192
(0.0383) 		0.0175
(1.00) 		0.00013
(0.0266) 		0.00373
(0.612) 		0.0275
(1.00) 		0.12
(1.00)
Del Peak 4(2q37 3) 0 (0%) 445 0.00156
(0.283) 		0.00222
(0.388) 		0.396
(1.00) 		0.757
(1.00) 		0.199
(1.00) 		0.413
(1.00) 		0.000109
(0.0226) 		0.00019
(0.0381) 		0.0445
(1.00) 		8.72e-06
(0.002)
Del Peak 18(Xq23) 0 (0%) 438 0.109
(1.00) 		0.0776
(1.00) 		6.53e-06
(0.00152) 		0.000715
(0.134) 		0.033
(1.00) 		0.00371
(0.612) 		0.208
(1.00) 		0.0183
(1.00) 		0.00194
(0.346) 		1.58e-05
(0.00353)
Del Peak 7(3p12 2) 0 (0%) 210 0.0404
(1.00) 		0.0145
(1.00) 		2.28e-17
(6.51e-15) 		0.349
(1.00) 		0.422
(1.00) 		0.358
(1.00) 		0.00398
(0.649) 		0.000211
(0.042) 		0.335
(1.00) 		0.00742
(1.00)
Del Peak 12(8p23 2) 0 (0%) 347 0.502
(1.00) 		0.475
(1.00) 		9.42e-06
(0.00215) 		0.0223
(1.00) 		0.00424
(0.678) 		0.156
(1.00) 		0.00256
(0.443) 		0.00869
(1.00) 		0.00111
(0.204) 		0.0143
(1.00)
Del Peak 3(1q43) 0 (0%) 455 0.0107
(1.00) 		0.0123
(1.00) 		0.00529
(0.825) 		0.697
(1.00) 		0.00409
(0.658) 		0.0108
(1.00) 		0.00846
(1.00) 		0.00476
(0.747) 		0.409
(1.00) 		9.26e-07
(0.00023)
Del Peak 8(3q11 2) 0 (0%) 343 0.183
(1.00) 		0.0989
(1.00) 		0.000919
(0.171) 		0.687
(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)
Del Peak 15(10q23 31) 0 (0%) 403 0.441
(1.00) 		0.643
(1.00) 		9.29e-07
(0.00023) 		0.00202
(0.355) 		0.911
(1.00) 		0.0717
(1.00) 		0.0578
(1.00) 		0.0344
(1.00) 		0.0231
(1.00) 		0.0238
(1.00)
Amp Peak 4(4q32 1) 0 (0%) 479 0.698
(1.00) 		1
(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)
Amp Peak 8(10p14) 0 (0%) 477 0.189
(1.00) 		0.197
(1.00) 		0.00753
(1.00) 		0.342
(1.00) 		0.548
(1.00) 		0.054
(1.00) 		0.0321
(1.00) 		0.00295
(0.508) 		0.134
(1.00) 		0.118
(1.00)
Amp Peak 9(17q24 3) 0 (0%) 456 0.0692
(1.00) 		0.0971
(1.00) 		0.00541
(0.839) 		0.163
(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)
Amp Peak 10(Xp22 2) 0 (0%) 458 1
(1.00) 		1
(1.00) 		0.00655
(0.996) 		0.137
(1.00) 		0.00598
(0.915) 		0.0129
(1.00) 		0.1
(1.00) 		0.166
(1.00) 		0.0221
(1.00) 		0.618
(1.00)
Amp Peak 11(Xp11 4) 0 (0%) 457 0.843
(1.00) 		0.845
(1.00) 		0.0113
(1.00) 		0.0575
(1.00) 		0.00732
(1.00) 		0.00446
(0.704) 		0.0321
(1.00) 		0.0469
(1.00) 		0.0221
(1.00) 		0.373
(1.00)
Amp Peak 12(Xq11 2) 0 (0%) 461 0.172
(1.00) 		0.182
(1.00) 		0.253
(1.00) 		0.233
(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)
'Amp Peak 1(1q24.1)' versus 'CN_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 2.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
AMP PEAK 1(1Q24.1) CNV 35 11 14
AMP PEAK 1(1Q24.1) WILD-TYPE 97 186 150

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 = 0.0084

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 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.23

Table S3.  Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
AMP PEAK 1(1Q24.1) CNV 2 21 34
AMP PEAK 1(1Q24.1) WILD-TYPE 67 193 156

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.74e-06 (Fisher's exact test), Q value = 0.0022

Table S4.  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 S4.  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 = 7.5e-10 (Fisher's exact test), Q value = 2e-07

Table S5.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
AMP PEAK 2(1Q32.1) CNV 37 8 14
AMP PEAK 2(1Q32.1) WILD-TYPE 95 189 150

Figure S5.  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 = 0.0018

Table S6.  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 S6.  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 = 0.11

Table S7.  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 S7.  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 = 0.0019

Table S8.  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 S8.  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 = 1.5e-06 (Fisher's exact test), Q value = 0.00036

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
AMP PEAK 3(3Q26.32) CNV 35 13 32
AMP PEAK 3(3Q26.32) WILD-TYPE 97 184 132

Figure S9.  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 = 6.37e-06 (Fisher's exact test), Q value = 0.0015

Table S10.  Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
AMP PEAK 3(3Q26.32) CNV 28 6 11
AMP PEAK 3(3Q26.32) WILD-TYPE 68 112 53

Figure S10.  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 = 0.0024

Table S11.  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 S11.  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 = 0.00034

Table S12.  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 S12.  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 = 2.4e-05

Table S13.  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 S13.  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 = 1.4e-05

Table S14.  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 S14.  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 = 0.18

Table S15.  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 S15.  Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.53e-05 (Fisher's exact test), Q value = 0.012

Table S16.  Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
AMP PEAK 5(5Q35.1) CNV 94 136 81
AMP PEAK 5(5Q35.1) WILD-TYPE 38 61 83

Figure S16.  Get High-res Image Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000701 (Fisher's exact test), Q value = 0.13

Table S17.  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 S17.  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 = 0.0015

Table S18.  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 S18.  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 = 1.25e-06 (Fisher's exact test), Q value = 3e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
AMP PEAK 6(7Q36.3) CNV 63 41 59
AMP PEAK 6(7Q36.3) WILD-TYPE 69 156 105

Figure S19.  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 = 0.038

Table S20.  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 S20.  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 = 0.027

Table S21.  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 S21.  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 = 2.35e-15 (Fisher's exact test), Q value = 6.6e-13

Table S22.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
AMP PEAK 7(8Q24.22) CNV 42 3 28
AMP PEAK 7(8Q24.22) WILD-TYPE 90 194 136

Figure S22.  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 = 1.18e-06 (Fisher's exact test), Q value = 0.00029

Table S23.  Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
AMP PEAK 7(8Q24.22) CNV 30 6 11
AMP PEAK 7(8Q24.22) WILD-TYPE 66 112 53

Figure S23.  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 = 0.00089

Table S24.  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 S24.  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 = 7.6e-10

Table S25.  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 S25.  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 = 7.8e-09

Table S26.  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 S26.  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 = 8.5e-07

Table S27.  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 S27.  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 = 0.012

Table S28.  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 S28.  Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000181 (Fisher's exact test), Q value = 0.036

Table S29.  Gene #13: '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 #13: 'Del Peak 1(1p36.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 7.87e-05 (Fisher's exact test), Q value = 0.016

Table S30.  Gene #13: 'Del Peak 1(1p36.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
DEL PEAK 1(1P36.23) CNV 9 7 2
DEL PEAK 1(1P36.23) WILD-TYPE 5 16 31

Figure S30.  Get High-res Image Gene #13: 'Del Peak 1(1p36.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.28e-09 (Fisher's exact test), Q value = 3.4e-07

Table S31.  Gene #13: 'Del Peak 1(1p36.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 1(1P36.23) CNV 36 13 49
DEL PEAK 1(1P36.23) WILD-TYPE 96 184 115

Figure S31.  Get High-res Image Gene #13: '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 = 0.0051

Table S32.  Gene #13: '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 #13: '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 = 0.03

Table S33.  Gene #13: '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 #13: '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 = 0.024

Table S34.  Gene #13: '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 #13: '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 = 0.088

Table S35.  Gene #13: '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 #13: '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 = 0.00017

Table S36.  Gene #13: '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 #13: '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 = 1.8e-06

Table S37.  Gene #13: '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 #13: 'Del Peak 1(1p36.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000542 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #14: 'Del Peak 2(1p31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
DEL PEAK 2(1P31.1) CNV 8 4 2
DEL PEAK 2(1P31.1) WILD-TYPE 6 19 31

Figure S38.  Get High-res Image Gene #14: 'Del Peak 2(1p31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 2.84e-05 (Fisher's exact test), Q value = 0.0063

Table S39.  Gene #14: 'Del Peak 2(1p31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 2(1P31.1) CNV 27 12 33
DEL PEAK 2(1P31.1) WILD-TYPE 105 185 131

Figure S39.  Get High-res Image Gene #14: '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 = 0.0086

Table S40.  Gene #14: '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 S40.  Get High-res Image Gene #14: '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 = 0.023

Table S41.  Gene #14: '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 S41.  Get High-res Image Gene #14: '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 = 0.00069

Table S42.  Gene #14: '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 S42.  Get High-res Image Gene #14: 'Del Peak 2(1p31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.26e-07 (Fisher's exact test), Q value = 0.00023

Table S43.  Gene #15: '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 S43.  Get High-res Image Gene #15: '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 = 0.023

Table S44.  Gene #16: '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 S44.  Get High-res Image Gene #16: '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 = 0.038

Table S45.  Gene #16: '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 S45.  Get High-res Image Gene #16: '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 = 0.002

Table S46.  Gene #16: '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 S46.  Get High-res Image Gene #16: '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 = 3.9e-05

Table S47.  Gene #17: '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 S47.  Get High-res Image Gene #17: '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 = 3.1e-06

Table S48.  Gene #17: 'Del Peak 5(3p25.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
DEL PEAK 5(3P25.3) CNV 3 22 32
DEL PEAK 5(3P25.3) WILD-TYPE 11 1 1

Figure S48.  Get High-res Image Gene #17: 'Del Peak 5(3p25.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.54e-30 (Fisher's exact test), Q value = 1.6e-27

Table S49.  Gene #17: 'Del Peak 5(3p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 5(3P25.3) CNV 130 197 105
DEL PEAK 5(3P25.3) WILD-TYPE 2 0 59

Figure S49.  Get High-res Image Gene #17: 'Del Peak 5(3p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000657 (Fisher's exact test), Q value = 0.13

Table S50.  Gene #17: 'Del Peak 5(3p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 5(3P25.3) CNV 91 108 48
DEL PEAK 5(3P25.3) WILD-TYPE 5 10 16

Figure S50.  Get High-res Image Gene #17: '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 = 0.0074

Table S51.  Gene #17: '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 S51.  Get High-res Image Gene #17: '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 = 7.8e-10

Table S52.  Gene #17: '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 S52.  Get High-res Image Gene #17: '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 = 2.1e-13

Table S53.  Gene #17: '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 S53.  Get High-res Image Gene #17: '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 = 0.007

Table S54.  Gene #17: '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 S54.  Get High-res Image Gene #17: '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 = 3.7e-12

Table S55.  Gene #17: '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 S55.  Get High-res Image Gene #17: 'Del Peak 5(3p25.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.55e-07 (Fisher's exact test), Q value = 3.9e-05

Table S56.  Gene #18: '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 S56.  Get High-res Image Gene #18: '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 = 3.1e-06

Table S57.  Gene #18: 'Del Peak 6(3p21.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
DEL PEAK 6(3P21.32) CNV 3 22 32
DEL PEAK 6(3P21.32) WILD-TYPE 11 1 1

Figure S57.  Get High-res Image Gene #18: 'Del Peak 6(3p21.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.74e-29 (Fisher's exact test), Q value = 5.1e-27

Table S58.  Gene #18: 'Del Peak 6(3p21.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 6(3P21.32) CNV 132 196 107
DEL PEAK 6(3P21.32) WILD-TYPE 0 1 57

Figure S58.  Get High-res Image Gene #18: 'Del Peak 6(3p21.32)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.46e-05 (Chi-square test), Q value = 0.012

Table S59.  Gene #18: '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 S59.  Get High-res Image Gene #18: '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 = 3.2e-11

Table S60.  Gene #18: '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 S60.  Get High-res Image Gene #18: '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 = 9.1e-14

Table S61.  Gene #18: '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 S61.  Get High-res Image Gene #18: '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 = 0.00025

Table S62.  Gene #18: '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 S62.  Get High-res Image Gene #18: '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 = 7.1e-13

Table S63.  Gene #18: '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 S63.  Get High-res Image Gene #18: 'Del Peak 6(3p21.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(3p12.2)' versus 'CN_CNMF'

P value = 2.28e-17 (Fisher's exact test), Q value = 6.5e-15

Table S64.  Gene #19: 'Del Peak 7(3p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 7(3P12.2) CNV 115 102 66
DEL PEAK 7(3P12.2) WILD-TYPE 17 95 98

Figure S64.  Get High-res Image Gene #19: 'Del Peak 7(3p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000211 (Fisher's exact test), Q value = 0.042

Table S65.  Gene #19: 'Del Peak 7(3p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 7(3P12.2) CNV 24 125 120
DEL PEAK 7(3P12.2) WILD-TYPE 45 89 70

Figure S65.  Get High-res Image Gene #19: 'Del Peak 7(3p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(3q11.2)' versus 'CN_CNMF'

P value = 0.000919 (Fisher's exact test), Q value = 0.17

Table S66.  Gene #20: 'Del Peak 8(3q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 8(3Q11.2) CNV 57 54 39
DEL PEAK 8(3Q11.2) WILD-TYPE 75 143 125

Figure S66.  Get High-res Image Gene #20: 'Del Peak 8(3q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4q34.3)' versus 'CN_CNMF'

P value = 5.47e-09 (Fisher's exact test), Q value = 1.5e-06

Table S67.  Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 9(4Q34.3) CNV 37 9 30
DEL PEAK 9(4Q34.3) WILD-TYPE 95 188 134

Figure S67.  Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4q34.3)' versus 'METHLYATION_CNMF'

P value = 0.000408 (Fisher's exact test), Q value = 0.08

Table S68.  Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 9(4Q34.3) CNV 30 12 10
DEL PEAK 9(4Q34.3) WILD-TYPE 66 106 54

Figure S68.  Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.068

Table S69.  Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 9(4Q34.3) CNV 24 41 6
DEL PEAK 9(4Q34.3) WILD-TYPE 173 138 91

Figure S69.  Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0027

Table S70.  Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 9(4Q34.3) CNV 2 24 45
DEL PEAK 9(4Q34.3) WILD-TYPE 67 190 145

Figure S70.  Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q26)' versus 'CN_CNMF'

P value = 1.84e-25 (Fisher's exact test), Q value = 5.4e-23

Table S71.  Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 10(6Q26) CNV 84 19 39
DEL PEAK 10(6Q26) WILD-TYPE 48 178 125

Figure S71.  Get High-res Image Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(6q26)' versus 'RPPA_CNMF'

P value = 6.38e-05 (Chi-square test), Q value = 0.013

Table S72.  Gene #22: 'Del Peak 10(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 10(6Q26) CNV 32 10 29 22 8 27
DEL PEAK 10(6Q26) WILD-TYPE 68 78 55 53 35 30

Figure S72.  Get High-res Image Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 10(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.093

Table S73.  Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 10(6Q26) CNV 48 68 17
DEL PEAK 10(6Q26) WILD-TYPE 149 111 80

Figure S73.  Get High-res Image Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q26)' versus 'MIRSEQ_CNMF'

P value = 4.89e-08 (Fisher's exact test), Q value = 1.3e-05

Table S74.  Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 10(6Q26) CNV 22 39 77
DEL PEAK 10(6Q26) WILD-TYPE 93 152 92

Figure S74.  Get High-res Image Gene #22: 'Del Peak 10(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 11(6q26)' versus 'CN_CNMF'

P value = 1.84e-25 (Fisher's exact test), Q value = 5.4e-23

Table S75.  Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 11(6Q26) CNV 84 19 39
DEL PEAK 11(6Q26) WILD-TYPE 48 178 125

Figure S75.  Get High-res Image Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q26)' versus 'RPPA_CNMF'

P value = 3.06e-05 (Chi-square test), Q value = 0.0067

Table S76.  Gene #23: 'Del Peak 11(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 11(6Q26) CNV 31 10 29 22 8 28
DEL PEAK 11(6Q26) WILD-TYPE 69 78 55 53 35 29

Figure S76.  Get High-res Image Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 11(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.032

Table S77.  Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 11(6Q26) CNV 48 69 16
DEL PEAK 11(6Q26) WILD-TYPE 149 110 81

Figure S77.  Get High-res Image Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(6q26)' versus 'MIRSEQ_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 3.5e-06

Table S78.  Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 11(6Q26) CNV 21 39 78
DEL PEAK 11(6Q26) WILD-TYPE 94 152 91

Figure S78.  Get High-res Image Gene #23: 'Del Peak 11(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(8p23.2)' versus 'CN_CNMF'

P value = 9.42e-06 (Fisher's exact test), Q value = 0.0021

Table S79.  Gene #24: 'Del Peak 12(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 12(8P23.2) CNV 51 35 60
DEL PEAK 12(8P23.2) WILD-TYPE 81 162 104

Figure S79.  Get High-res Image Gene #24: 'Del Peak 12(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.2

Table S80.  Gene #24: 'Del Peak 12(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 12(8P23.2) CNV 32 43 68
DEL PEAK 12(8P23.2) WILD-TYPE 83 148 101

Figure S80.  Get High-res Image Gene #24: 'Del Peak 12(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(9p23)' versus 'CN_CNMF'

P value = 3.36e-30 (Fisher's exact test), Q value = 1e-27

Table S81.  Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 13(9P23) CNV 80 9 55
DEL PEAK 13(9P23) WILD-TYPE 52 188 109

Figure S81.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(9p23)' versus 'METHLYATION_CNMF'

P value = 3.43e-20 (Fisher's exact test), Q value = 9.9e-18

Table S82.  Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 13(9P23) CNV 60 6 21
DEL PEAK 13(9P23) WILD-TYPE 36 112 43

Figure S82.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(9p23)' versus 'RPPA_CNMF'

P value = 1.41e-07 (Chi-square test), Q value = 3.6e-05

Table S83.  Gene #25: 'Del Peak 13(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 13(9P23) CNV 17 23 32 18 10 35
DEL PEAK 13(9P23) WILD-TYPE 83 65 52 57 33 22

Figure S83.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 13(9p23)' versus 'MRNASEQ_CNMF'

P value = 3.59e-23 (Fisher's exact test), Q value = 1e-20

Table S84.  Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S84.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(9p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.21e-24 (Fisher's exact test), Q value = 2.7e-21

Table S85.  Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 13(9P23) CNV 9 24 105
DEL PEAK 13(9P23) WILD-TYPE 60 190 85

Figure S85.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(9p23)' versus 'MIRSEQ_CNMF'

P value = 1.07e-15 (Fisher's exact test), Q value = 3e-13

Table S86.  Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 13(9P23) CNV 26 25 88
DEL PEAK 13(9P23) WILD-TYPE 89 166 81

Figure S86.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.0067

Table S87.  Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 13(9P23) CNV 10 68 61
DEL PEAK 13(9P23) WILD-TYPE 25 92 219

Figure S87.  Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(9p21.3)' versus 'MRNA_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.23

Table S88.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 14(9P21.3) CNV 5 13 1
DEL PEAK 14(9P21.3) WILD-TYPE 28 11 12

Figure S88.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 14(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000662 (Fisher's exact test), Q value = 0.13

Table S89.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
DEL PEAK 14(9P21.3) CNV 1 13 5
DEL PEAK 14(9P21.3) WILD-TYPE 13 10 28

Figure S89.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(9p21.3)' versus 'CN_CNMF'

P value = 1.96e-29 (Fisher's exact test), Q value = 5.8e-27

Table S90.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 14(9P21.3) CNV 81 11 60
DEL PEAK 14(9P21.3) WILD-TYPE 51 186 104

Figure S90.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.24e-21 (Fisher's exact test), Q value = 6.5e-19

Table S91.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 14(9P21.3) CNV 62 6 23
DEL PEAK 14(9P21.3) WILD-TYPE 34 112 41

Figure S91.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(9p21.3)' versus 'RPPA_CNMF'

P value = 5.23e-08 (Chi-square test), Q value = 1.4e-05

Table S92.  Gene #26: 'Del Peak 14(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 14(9P21.3) CNV 18 26 32 19 10 37
DEL PEAK 14(9P21.3) WILD-TYPE 82 62 52 56 33 20

Figure S92.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 14(9p21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000469 (Fisher's exact test), Q value = 0.091

Table S93.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 14(9P21.3) CNV 42 52 48
DEL PEAK 14(9P21.3) WILD-TYPE 144 100 61

Figure S93.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 14(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 2.08e-23 (Fisher's exact test), Q value = 6e-21

Table S94.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 14(9P21.3) CNV 26 105 15
DEL PEAK 14(9P21.3) WILD-TYPE 171 74 82

Figure S94.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-27 (Fisher's exact test), Q value = 3.4e-25

Table S95.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 14(9P21.3) CNV 8 25 113
DEL PEAK 14(9P21.3) WILD-TYPE 61 189 77

Figure S95.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 4.52e-16 (Fisher's exact test), Q value = 1.3e-13

Table S96.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 14(9P21.3) CNV 29 26 91
DEL PEAK 14(9P21.3) WILD-TYPE 86 165 78

Figure S96.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.26e-07 (Fisher's exact test), Q value = 5.6e-05

Table S97.  Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 14(9P21.3) CNV 11 75 60
DEL PEAK 14(9P21.3) WILD-TYPE 24 85 220

Figure S97.  Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(10q23.31)' versus 'CN_CNMF'

P value = 9.29e-07 (Fisher's exact test), Q value = 0.00023

Table S98.  Gene #27: 'Del Peak 15(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 15(10Q23.31) CNV 36 15 39
DEL PEAK 15(10Q23.31) WILD-TYPE 96 182 125

Figure S98.  Get High-res Image Gene #27: 'Del Peak 15(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(13q13.3)' versus 'CN_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.00095

Table S99.  Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 16(13Q13.3) CNV 31 12 33
DEL PEAK 16(13Q13.3) WILD-TYPE 101 185 131

Figure S99.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(13q13.3)' versus 'METHLYATION_CNMF'

P value = 0.000675 (Fisher's exact test), Q value = 0.13

Table S100.  Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 16(13Q13.3) CNV 21 8 16
DEL PEAK 16(13Q13.3) WILD-TYPE 75 110 48

Figure S100.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(13q13.3)' versus 'RPPA_CNMF'

P value = 2e-06 (Chi-square test), Q value = 0.00048

Table S101.  Gene #28: 'Del Peak 16(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 16(13Q13.3) CNV 2 12 14 13 7 21
DEL PEAK 16(13Q13.3) WILD-TYPE 98 76 70 62 36 36

Figure S101.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 16(13q13.3)' versus 'MRNASEQ_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 3e-04

Table S102.  Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
DEL PEAK 16(13Q13.3) CNV 15 48 11
DEL PEAK 16(13Q13.3) WILD-TYPE 182 131 86

Figure S102.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(13q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.39e-08 (Fisher's exact test), Q value = 2.4e-05

Table S103.  Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 16(13Q13.3) CNV 9 14 51
DEL PEAK 16(13Q13.3) WILD-TYPE 60 200 139

Figure S103.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(13q13.3)' versus 'MIRSEQ_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.00057

Table S104.  Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 16(13Q13.3) CNV 15 14 45
DEL PEAK 16(13Q13.3) WILD-TYPE 100 177 124

Figure S104.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(13q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.00038

Table S105.  Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 16(13Q13.3) CNV 13 36 25
DEL PEAK 16(13Q13.3) WILD-TYPE 22 124 255

Figure S105.  Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(14q31.1)' versus 'MRNA_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.012

Table S106.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 17(14Q31.1) CNV 10 19 2
DEL PEAK 17(14Q31.1) WILD-TYPE 23 5 11

Figure S106.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 17(14q31.1)' versus 'MRNA_CHIERARCHICAL'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.0062

Table S107.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
DEL PEAK 17(14Q31.1) CNV 3 19 9
DEL PEAK 17(14Q31.1) WILD-TYPE 11 4 24

Figure S107.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(14q31.1)' versus 'CN_CNMF'

P value = 2.06e-13 (Fisher's exact test), Q value = 5.6e-11

Table S108.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 17(14Q31.1) CNV 92 54 72
DEL PEAK 17(14Q31.1) WILD-TYPE 40 143 92

Figure S108.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(14q31.1)' versus 'METHLYATION_CNMF'

P value = 6.79e-08 (Fisher's exact test), Q value = 1.8e-05

Table S109.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 17(14Q31.1) CNV 61 30 32
DEL PEAK 17(14Q31.1) WILD-TYPE 35 88 32

Figure S109.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(14q31.1)' versus 'RPPA_CNMF'

P value = 2.35e-14 (Chi-square test), Q value = 6.5e-12

Table S110.  Gene #29: 'Del Peak 17(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 17(14Q31.1) CNV 30 30 64 23 13 41
DEL PEAK 17(14Q31.1) WILD-TYPE 70 58 20 52 30 16

Figure S110.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 17(14q31.1)' versus 'RPPA_CHIERARCHICAL'

P value = 1.88e-07 (Fisher's exact test), Q value = 4.7e-05

Table S111.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 17(14Q31.1) CNV 57 92 52
DEL PEAK 17(14Q31.1) WILD-TYPE 129 60 57

Figure S111.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 17(14q31.1)' versus 'MRNASEQ_CNMF'

P value = 6.67e-20 (Fisher's exact test), Q value = 1.9e-17

Table S112.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S112.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(14q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-15 (Fisher's exact test), Q value = 1.8e-12

Table S113.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
DEL PEAK 17(14Q31.1) CNV 11 76 124
DEL PEAK 17(14Q31.1) WILD-TYPE 58 138 66

Figure S113.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(14q31.1)' versus 'MIRSEQ_CNMF'

P value = 5.25e-11 (Fisher's exact test), Q value = 1.4e-08

Table S114.  Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
DEL PEAK 17(14Q31.1) CNV 37 64 111
DEL PEAK 17(14Q31.1) WILD-TYPE 78 127 58

Figure S114.  Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(Xq23)' versus 'CN_CNMF'

P value = 6.53e-06 (Fisher's exact test), Q value = 0.0015

Table S115.  Gene #30: 'Del Peak 18(Xq23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
DEL PEAK 18(XQ23) CNV 28 8 19
DEL PEAK 18(XQ23) WILD-TYPE 104 189 145

Figure S115.  Get High-res Image Gene #30: 'Del Peak 18(Xq23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(Xq23)' versus 'METHLYATION_CNMF'

P value = 0.000715 (Fisher's exact test), Q value = 0.13

Table S116.  Gene #30: 'Del Peak 18(Xq23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
DEL PEAK 18(XQ23) CNV 18 5 3
DEL PEAK 18(XQ23) WILD-TYPE 78 113 61

Figure S116.  Get High-res Image Gene #30: 'Del Peak 18(Xq23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(Xq23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0035

Table S117.  Gene #30: 'Del Peak 18(Xq23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
DEL PEAK 18(XQ23) CNV 14 14 26
DEL PEAK 18(XQ23) WILD-TYPE 21 146 254

Figure S117.  Get High-res Image Gene #30: 'Del Peak 18(Xq23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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 = 493

  • Number of copy number variation regions = 30

  • Number of molecular subtypes = 10

  • 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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