Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1W66JDG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1W66JDG
Overview
Introduction

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

Summary

Testing the association between copy number variation 30 focal events and 12 molecular subtypes across 514 patients, 135 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q24.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_3q26.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_4q32.1 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5q35.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q36.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • amp_8q24.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_10p14 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.23 cnv 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_1p31.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1q43 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p25.3 cnv 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_3p24.3 cnv 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_3p12.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p11.1 cnv correlated to 'CN_CNMF'.

  • del_3q11.2 cnv correlated to 'CN_CNMF'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF'.

  • del_9p23 cnv 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_9p21.3 cnv 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_10q23.31 cnv correlated to 'CN_CNMF'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_14q31.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 30 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 135 significant findings detected.

Clinical
Features 		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 Chi-square test
del 9p21 3 156 (30%) 358 0.00149
(0.33) 		0.000169
(0.0422) 		1.04e-47
(3.73e-45) 		3.3e-20
(1.15e-17) 		4.2e-08
(1.3e-05) 		0.000428
(0.102) 		1e-24
(3.52e-22) 		1.22e-29
(4.34e-27) 		5.96e-18
(2.06e-15) 		1.07e-06
(0.000314) 		4.94e-12
(1.6e-09) 		0.000672
(0.154)
del 14q31 1 224 (44%) 290 6.06e-05
(0.0161) 		9.68e-05
(0.025) 		2.25e-17
(7.69e-15) 		1.47e-06
(0.000424) 		6.3e-14
(2.09e-11) 		2.09e-07
(6.34e-05) 		4.9e-21
(1.71e-18) 		2.35e-16
(7.95e-14) 		6.5e-11
(2.09e-08) 		0.0777
(1.00) 		5.99e-07
(0.000178) 		7.27e-05
(0.0191)
del 1p36 23 101 (20%) 413 0.000212
(0.052) 		0.000158
(0.0397) 		2.84e-14
(9.47e-12) 		0.0293
(1.00) 		3.6e-05
(0.00978) 		9.32e-05
(0.0241) 		2.52e-05
(0.0069) 		0.000632
(0.146) 		1.38e-06
(0.000398) 		1.43e-08
(4.49e-06) 		0.00175
(0.378) 		0.000476
(0.112)
del 3p25 3 452 (88%) 62 1.67e-07
(5.1e-05) 		1.83e-08
(5.74e-06) 		1.06e-31
(3.78e-29) 		8.74e-06
(0.00247) 		2.46e-05
(0.00678) 		0.0205
(1.00) 		1.93e-13
(6.34e-11) 		1.05e-16
(3.56e-14) 		9.77e-07
(0.000289) 		2.71e-08
(8.44e-06) 		0.00196
(0.418) 		1.01e-14
(3.39e-12)
del 3p24 3 453 (88%) 61 1.67e-07
(5.1e-05) 		1.83e-08
(5.74e-06) 		3.29e-33
(1.17e-30) 		8.74e-06
(0.00247) 		6.84e-05
(0.0181) 		0.0182
(1.00) 		4.73e-14
(1.57e-11) 		2.67e-17
(9.09e-15) 		2.56e-07
(7.77e-05) 		1.27e-08
(3.99e-06) 		0.00196
(0.418) 		1.01e-14
(3.39e-12)
del 9p23 149 (29%) 365 0.00417
(0.818) 		0.000533
(0.125) 		5.94e-50
(2.14e-47) 		4.89e-20
(1.7e-17) 		1.06e-07
(3.27e-05) 		0.00159
(0.348) 		7.67e-25
(2.71e-22) 		3.67e-26
(1.3e-23) 		6.84e-18
(2.36e-15) 		5.02e-05
(0.0134) 		1.75e-12
(5.72e-10) 		0.000424
(0.101)
amp 8q24 22 79 (15%) 435 0.226
(1.00) 		0.325
(1.00) 		5.4e-22
(1.89e-19) 		1.08e-06
(0.000315) 		1.01e-06
(0.000298) 		0.00733
(1.00) 		4.83e-14
(1.6e-11) 		1.16e-12
(3.81e-10) 		8.15e-10
(2.59e-07) 		0.000331
(0.0798) 		1.03e-06
(0.000304) 		0.000958
(0.218)
amp 3q26 32 87 (17%) 427 0.0574
(1.00) 		0.0539
(1.00) 		3.46e-13
(1.13e-10) 		8.3e-05
(0.0216) 		0.0028
(0.579) 		1.09e-05
(0.00305) 		4.71e-07
(0.000141) 		7.97e-09
(2.52e-06) 		3.98e-09
(1.26e-06) 		0.00535
(1.00) 		0.000406
(0.0975) 		0.0986
(1.00)
del 13q14 2 80 (16%) 434 0.0144
(1.00) 		0.0174
(1.00) 		6.6e-10
(2.11e-07) 		0.000544
(0.126) 		1.36e-06
(0.000395) 		0.0187
(1.00) 		1.68e-05
(0.0047) 		3.6e-06
(0.00103) 		4.02e-06
(0.00115) 		0.000542
(0.126) 		0.0268
(1.00) 		0.00704
(1.00)
del 1p31 1 75 (15%) 439 0.00175
(0.378) 		0.00063
(0.146) 		2.72e-11
(8.8e-09) 		0.06
(1.00) 		7.82e-05
(0.0205) 		0.00658
(1.00) 		0.00982
(1.00) 		0.00136
(0.304) 		2.24e-05
(0.00617) 		1.09e-07
(3.35e-05) 		0.036
(1.00) 		0.000462
(0.11)
del 3p12 3 328 (64%) 186 0.00359
(0.726) 		0.000978
(0.222) 		4.82e-36
(1.73e-33) 		0.0189
(1.00) 		0.485
(1.00) 		0.45
(1.00) 		1.96e-05
(0.00543) 		1.51e-07
(4.64e-05) 		0.0367
(1.00) 		0.0116
(1.00) 		0.0165
(1.00) 		0.000115
(0.0294)
del 6q26 148 (29%) 366 0.0135
(1.00) 		0.00615
(1.00) 		1.57e-17
(5.4e-15) 		0.116
(1.00) 		2.61e-05
(0.00713) 		0.00225
(0.473) 		0.000499
(0.117) 		0.0246
(1.00) 		1.21e-06
(0.000353) 		0.0425
(1.00) 		0.000139
(0.0354) 		0.0413
(1.00)
del 6q26 148 (29%) 366 0.0135
(1.00) 		0.00615
(1.00) 		1.57e-17
(5.4e-15) 		0.116
(1.00) 		1.21e-05
(0.00339) 		0.00319
(0.648) 		0.000186
(0.0463) 		0.0246
(1.00) 		3.79e-07
(0.000114) 		0.0933
(1.00) 		3.86e-05
(0.0104) 		0.0413
(1.00)
amp 1q24 1 62 (12%) 452 0.259
(1.00) 		0.245
(1.00) 		6.87e-14
(2.27e-11) 		0.241
(1.00) 		0.258
(1.00) 		0.382
(1.00) 		4.47e-05
(0.012) 		0.000278
(0.0677) 		4.14e-05
(0.0111) 		0.964
(1.00) 		0.0197
(1.00) 		0.0026
(0.54)
amp 1q32 1 62 (12%) 452 0.41
(1.00) 		0.411
(1.00) 		1.6e-15
(5.41e-13) 		0.0806
(1.00) 		0.166
(1.00) 		0.0858
(1.00) 		6.22e-06
(0.00177) 		6.38e-05
(0.0169) 		1.68e-05
(0.0047) 		0.817
(1.00) 		0.00634
(1.00) 		0.0141
(1.00)
del 4q34 3 78 (15%) 436 0.238
(1.00) 		0.195
(1.00) 		6.44e-11
(2.07e-08) 		0.000141
(0.0358) 		0.004
(0.789) 		0.0622
(1.00) 		0.00029
(0.0702) 		2.73e-06
(0.000785) 		0.361
(1.00) 		0.0493
(1.00) 		0.0119
(1.00) 		0.0218
(1.00)
amp 7q36 3 173 (34%) 341 0.416
(1.00) 		0.577
(1.00) 		9.08e-15
(3.06e-12) 		0.0185
(1.00) 		0.000153
(0.0387) 		0.00718
(1.00) 		3.62e-05
(0.00981) 		0.00314
(0.641) 		0.0087
(1.00) 		0.279
(1.00) 		0.0191
(1.00) 		0.00659
(1.00)
del 1q43 40 (8%) 474 0.0107
(1.00) 		0.0133
(1.00) 		5.19e-07
(0.000155) 		0.39
(1.00) 		0.00651
(1.00) 		0.0165
(1.00) 		0.00449
(0.872) 		0.00517
(0.988) 		0.246
(1.00) 		3.18e-07
(9.61e-05) 		1
(1.00) 		0.000131
(0.0336)
del 2q37 3 50 (10%) 464 0.00156
(0.344) 		0.00299
(0.612) 		0.668
(1.00) 		0.972
(1.00) 		0.154
(1.00) 		0.313
(1.00) 		8.11e-05
(0.0212) 		0.000208
(0.0511) 		0.0101
(1.00) 		0.00027
(0.066) 		0.0335
(1.00) 		0.00372
(0.743)
amp 10p14 20 (4%) 494 0.189
(1.00) 		0.207
(1.00) 		0.000207
(0.051) 		0.126
(1.00) 		0.748
(1.00) 		0.185
(1.00) 		0.00234
(0.489) 		0.0002
(0.0496) 		0.0829
(1.00) 		0.152
(1.00) 		0.619
(1.00) 		0.107
(1.00)
amp 4q32 1 16 (3%) 498 0.189
(1.00) 		0.207
(1.00) 		0.28
(1.00) 		0.707
(1.00) 		0.609
(1.00) 		0.28
(1.00) 		0.0187
(1.00) 		0.271
(1.00) 		0.00146
(0.326) 		0.00554
(1.00) 		0.014
(1.00) 		0.00107
(0.242)
amp 5q35 1 328 (64%) 186 0.0648
(1.00) 		0.0314
(1.00) 		0.00457
(0.881) 		0.725
(1.00) 		0.0102
(1.00) 		0.00385
(0.767) 		0.00169
(0.367) 		0.000145
(0.0366) 		0.139
(1.00) 		0.0135
(1.00) 		0.927
(1.00) 		0.0446
(1.00)
del 3p11 1 234 (46%) 280 0.18
(1.00) 		0.0887
(1.00) 		1.43e-24
(5.02e-22) 		0.631
(1.00) 		0.93
(1.00) 		0.183
(1.00) 		0.0448
(1.00) 		0.00149
(0.33) 		0.511
(1.00) 		0.192
(1.00) 		0.0243
(1.00) 		0.00797
(1.00)
del 3q11 2 158 (31%) 356 0.188
(1.00) 		0.111
(1.00) 		3.03e-12
(9.85e-10) 		0.344
(1.00) 		0.861
(1.00) 		0.135
(1.00) 		0.604
(1.00) 		0.0308
(1.00) 		0.473
(1.00) 		0.187
(1.00) 		0.254
(1.00) 		0.0844
(1.00)
del 8p23 2 153 (30%) 361 0.497
(1.00) 		0.585
(1.00) 		3.78e-07
(0.000114) 		0.0513
(1.00) 		0.00575
(1.00) 		0.131
(1.00) 		0.0012
(0.269) 		0.00501
(0.963) 		0.00193
(0.413) 		0.00426
(0.831) 		0.0253
(1.00) 		0.1
(1.00)
del 10q23 31 94 (18%) 420 0.431
(1.00) 		0.524
(1.00) 		5.17e-10
(1.65e-07) 		0.00162
(0.352) 		0.981
(1.00) 		0.0906
(1.00) 		0.0506
(1.00) 		0.0799
(1.00) 		0.044
(1.00) 		0.19
(1.00) 		0.0933
(1.00) 		0.0178
(1.00)
amp xp22 2 31 (6%) 483 1
(1.00) 		1
(1.00) 		0.00617
(1.00) 		0.242
(1.00) 		0.00362
(0.728) 		0.00806
(1.00) 		0.0555
(1.00) 		0.167
(1.00) 		0.0674
(1.00) 		0.525
(1.00) 		0.326
(1.00) 		0.339
(1.00)
amp xp11 4 33 (6%) 481 0.843
(1.00) 		0.842
(1.00) 		0.00395
(0.782) 		0.108
(1.00) 		0.00283
(0.583) 		0.00196
(0.418) 		0.0299
(1.00) 		0.121
(1.00) 		0.0408
(1.00) 		0.489
(1.00) 		0.172
(1.00) 		0.193
(1.00)
amp xq11 2 29 (6%) 485 0.172
(1.00) 		0.182
(1.00) 		0.165
(1.00) 		0.396
(1.00) 		0.0864
(1.00) 		0.0429
(1.00) 		0.187
(1.00) 		0.517
(1.00) 		0.142
(1.00) 		0.401
(1.00) 		0.241
(1.00) 		0.337
(1.00)
amp xq28 36 (7%) 478 0.49
(1.00) 		0.591
(1.00) 		0.121
(1.00) 		0.858
(1.00) 		0.0523
(1.00) 		0.0508
(1.00) 		0.102
(1.00) 		0.0225
(1.00) 		0.0998
(1.00) 		0.151
(1.00) 		0.0712
(1.00) 		0.149
(1.00)
'amp_1q24.1' versus 'CN_CNMF'

P value = 6.87e-14 (Fisher's exact test), Q value = 2.3e-11

Table S1.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
AMP PEAK 1(1Q24.1) MUTATED 47 12 3
AMP PEAK 1(1Q24.1) WILD-TYPE 115 211 126

Figure S1.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CNMF'

P value = 4.47e-05 (Fisher's exact test), Q value = 0.012

Table S2.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
AMP PEAK 1(1Q24.1) MUTATED 19 4 37
AMP PEAK 1(1Q24.1) WILD-TYPE 196 104 150

Figure S2.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000278 (Fisher's exact test), Q value = 0.068

Table S3.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
AMP PEAK 1(1Q24.1) MUTATED 21 37 2
AMP PEAK 1(1Q24.1) WILD-TYPE 205 168 77

Figure S3.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q24.1' versus 'MIRSEQ_CNMF'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.011

Table S4.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
AMP PEAK 1(1Q24.1) MUTATED 4 20 36
AMP PEAK 1(1Q24.1) WILD-TYPE 106 189 141

Figure S4.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1.6e-15 (Fisher's exact test), Q value = 5.4e-13

Table S5.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
AMP PEAK 2(1Q32.1) MUTATED 49 9 4
AMP PEAK 2(1Q32.1) WILD-TYPE 113 214 125

Figure S5.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0018

Table S6.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
AMP PEAK 2(1Q32.1) MUTATED 19 3 38
AMP PEAK 2(1Q32.1) WILD-TYPE 196 105 149

Figure S6.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.38e-05 (Fisher's exact test), Q value = 0.017

Table S7.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
AMP PEAK 2(1Q32.1) MUTATED 22 37 1
AMP PEAK 2(1Q32.1) WILD-TYPE 204 168 78

Figure S7.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0047

Table S8.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
AMP PEAK 2(1Q32.1) MUTATED 4 19 37
AMP PEAK 2(1Q32.1) WILD-TYPE 106 190 140

Figure S8.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'CN_CNMF'

P value = 3.46e-13 (Fisher's exact test), Q value = 1.1e-10

Table S9.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
AMP PEAK 3(3Q26.32) MUTATED 55 11 21
AMP PEAK 3(3Q26.32) WILD-TYPE 107 212 108

Figure S9.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 8.3e-05 (Fisher's exact test), Q value = 0.022

Table S10.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
AMP PEAK 3(3Q26.32) MUTATED 27 7 16
AMP PEAK 3(3Q26.32) WILD-TYPE 73 107 60

Figure S10.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.003

Table S11.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
AMP PEAK 3(3Q26.32) MUTATED 18 25 35
AMP PEAK 3(3Q26.32) WILD-TYPE 168 127 74

Figure S11.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 4.71e-07 (Fisher's exact test), Q value = 0.00014

Table S12.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
AMP PEAK 3(3Q26.32) MUTATED 19 14 54
AMP PEAK 3(3Q26.32) WILD-TYPE 196 94 133

Figure S12.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.97e-09 (Fisher's exact test), Q value = 2.5e-06

Table S13.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
AMP PEAK 3(3Q26.32) MUTATED 17 60 10
AMP PEAK 3(3Q26.32) WILD-TYPE 209 145 69

Figure S13.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 3.98e-09 (Fisher's exact test), Q value = 1.3e-06

Table S14.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
AMP PEAK 3(3Q26.32) MUTATED 13 16 55
AMP PEAK 3(3Q26.32) WILD-TYPE 97 193 122

Figure S14.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000406 (Fisher's exact test), Q value = 0.097

Table S15.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
AMP PEAK 3(3Q26.32) MUTATED 5 10 27
AMP PEAK 3(3Q26.32) WILD-TYPE 45 89 60

Figure S15.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Chi-square test), Q value = 0.24

Table S16.  Gene #4: 'amp_4q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
AMP PEAK 4(4Q32.1) MUTATED 2 1 1 1 0
AMP PEAK 4(4Q32.1) WILD-TYPE 9 53 78 10 81

Figure S16.  Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000145 (Fisher's exact test), Q value = 0.037

Table S17.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
AMP PEAK 5(5Q35.1) MUTATED 157 135 34
AMP PEAK 5(5Q35.1) WILD-TYPE 69 70 45

Figure S17.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q36.3' versus 'CN_CNMF'

P value = 9.08e-15 (Fisher's exact test), Q value = 3.1e-12

Table S18.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
AMP PEAK 6(7Q36.3) MUTATED 86 35 52
AMP PEAK 6(7Q36.3) WILD-TYPE 76 188 77

Figure S18.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q36.3' versus 'RPPA_CNMF'

P value = 0.000153 (Chi-square test), Q value = 0.039

Table S19.  Gene #6: 'amp_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) MUTATED 22 23 34 33 10 30
AMP PEAK 6(7Q36.3) WILD-TYPE 78 65 50 42 33 27

Figure S19.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q36.3' versus 'MRNASEQ_CNMF'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.0098

Table S20.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
AMP PEAK 6(7Q36.3) MUTATED 52 34 85
AMP PEAK 6(7Q36.3) WILD-TYPE 163 74 102

Figure S20.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'CN_CNMF'

P value = 5.4e-22 (Fisher's exact test), Q value = 1.9e-19

Table S21.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
AMP PEAK 7(8Q24.22) MUTATED 58 2 19
AMP PEAK 7(8Q24.22) WILD-TYPE 104 221 110

Figure S21.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 1.08e-06 (Fisher's exact test), Q value = 0.00032

Table S22.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
AMP PEAK 7(8Q24.22) MUTATED 32 6 14
AMP PEAK 7(8Q24.22) WILD-TYPE 68 108 62

Figure S22.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 1.01e-06 (Chi-square test), Q value = 3e-04

Table S23.  Gene #7: 'amp_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) MUTATED 6 14 16 12 1 22
AMP PEAK 7(8Q24.22) WILD-TYPE 94 74 68 63 42 35

Figure S23.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 4.83e-14 (Fisher's exact test), Q value = 1.6e-11

Table S24.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
AMP PEAK 7(8Q24.22) MUTATED 9 10 59
AMP PEAK 7(8Q24.22) WILD-TYPE 206 98 128

Figure S24.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-12 (Fisher's exact test), Q value = 3.8e-10

Table S25.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
AMP PEAK 7(8Q24.22) MUTATED 13 61 4
AMP PEAK 7(8Q24.22) WILD-TYPE 213 144 75

Figure S25.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 8.15e-10 (Fisher's exact test), Q value = 2.6e-07

Table S26.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
AMP PEAK 7(8Q24.22) MUTATED 13 12 52
AMP PEAK 7(8Q24.22) WILD-TYPE 97 197 125

Figure S26.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000331 (Fisher's exact test), Q value = 0.08

Table S27.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
AMP PEAK 7(8Q24.22) MUTATED 10 26 41
AMP PEAK 7(8Q24.22) WILD-TYPE 33 243 143

Figure S27.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 3e-04

Table S28.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
AMP PEAK 7(8Q24.22) MUTATED 3 5 27
AMP PEAK 7(8Q24.22) WILD-TYPE 47 94 60

Figure S28.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000958 (Chi-square test), Q value = 0.22

Table S29.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
AMP PEAK 7(8Q24.22) MUTATED 1 11 20 1 2
AMP PEAK 7(8Q24.22) WILD-TYPE 10 43 59 10 79

Figure S29.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.051

Table S30.  Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
AMP PEAK 8(10P14) MUTATED 13 1 6
AMP PEAK 8(10P14) WILD-TYPE 149 222 123

Figure S30.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.05

Table S31.  Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
AMP PEAK 8(10P14) MUTATED 2 17 1
AMP PEAK 8(10P14) WILD-TYPE 224 188 78

Figure S31.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MRNA_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.052

Table S32.  Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S32.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.23' versus 'MRNA_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.04

Table S33.  Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S33.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 2.84e-14 (Fisher's exact test), Q value = 9.5e-12

Table S34.  Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 1(1P36.23) MUTATED 54 11 36
DEL PEAK 1(1P36.23) WILD-TYPE 108 212 93

Figure S34.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.23' versus 'RPPA_CNMF'

P value = 3.6e-05 (Chi-square test), Q value = 0.0098

Table S35.  Gene #13: 'del_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) MUTATED 9 10 23 24 5 18
DEL PEAK 1(1P36.23) WILD-TYPE 91 78 61 51 38 39

Figure S35.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.23' versus 'RPPA_CHIERARCHICAL'

P value = 9.32e-05 (Fisher's exact test), Q value = 0.024

Table S36.  Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 1(1P36.23) MUTATED 20 37 32
DEL PEAK 1(1P36.23) WILD-TYPE 166 115 77

Figure S36.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.0069

Table S37.  Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 1(1P36.23) MUTATED 25 20 56
DEL PEAK 1(1P36.23) WILD-TYPE 190 88 131

Figure S37.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000632 (Fisher's exact test), Q value = 0.15

Table S38.  Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 1(1P36.23) MUTATED 28 54 19
DEL PEAK 1(1P36.23) WILD-TYPE 198 151 60

Figure S38.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 4e-04

Table S39.  Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 1(1P36.23) MUTATED 19 24 58
DEL PEAK 1(1P36.23) WILD-TYPE 91 185 119

Figure S39.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.43e-08 (Fisher's exact test), Q value = 4.5e-06

Table S40.  Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 1(1P36.23) MUTATED 23 34 44
DEL PEAK 1(1P36.23) WILD-TYPE 20 235 140

Figure S40.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000476 (Chi-square test), Q value = 0.11

Table S41.  Gene #13: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 1(1P36.23) MUTATED 6 14 21 1 6
DEL PEAK 1(1P36.23) WILD-TYPE 5 40 58 10 75

Figure S41.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.15

Table S42.  Gene #14: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S42.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 2.72e-11 (Fisher's exact test), Q value = 8.8e-09

Table S43.  Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 2(1P31.1) MUTATED 40 7 28
DEL PEAK 2(1P31.1) WILD-TYPE 122 216 101

Figure S43.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CNMF'

P value = 7.82e-05 (Chi-square test), Q value = 0.02

Table S44.  Gene #14: 'del_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) MUTATED 10 4 13 21 4 15
DEL PEAK 2(1P31.1) WILD-TYPE 90 84 71 54 39 42

Figure S44.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0062

Table S45.  Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 2(1P31.1) MUTATED 10 20 45
DEL PEAK 2(1P31.1) WILD-TYPE 100 189 132

Figure S45.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.09e-07 (Fisher's exact test), Q value = 3.4e-05

Table S46.  Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 2(1P31.1) MUTATED 21 30 24
DEL PEAK 2(1P31.1) WILD-TYPE 22 239 160

Figure S46.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000462 (Chi-square test), Q value = 0.11

Table S47.  Gene #14: 'del_1p31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 2(1P31.1) MUTATED 5 7 17 1 3
DEL PEAK 2(1P31.1) WILD-TYPE 6 47 62 10 78

Figure S47.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 5.19e-07 (Fisher's exact test), Q value = 0.00015

Table S48.  Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 3(1Q43) MUTATED 11 5 24
DEL PEAK 3(1Q43) WILD-TYPE 151 218 105

Figure S48.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.18e-07 (Fisher's exact test), Q value = 9.6e-05

Table S49.  Gene #15: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 3(1Q43) MUTATED 15 15 10
DEL PEAK 3(1Q43) WILD-TYPE 28 254 174

Figure S49.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000131 (Chi-square test), Q value = 0.034

Table S50.  Gene #15: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 3(1Q43) MUTATED 5 5 4 1 4
DEL PEAK 3(1Q43) WILD-TYPE 6 49 75 10 77

Figure S50.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 8.11e-05 (Fisher's exact test), Q value = 0.021

Table S51.  Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 4(2Q37.3) MUTATED 9 21 19
DEL PEAK 4(2Q37.3) WILD-TYPE 206 87 168

Figure S51.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000208 (Fisher's exact test), Q value = 0.051

Table S52.  Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 4(2Q37.3) MUTATED 9 27 13
DEL PEAK 4(2Q37.3) WILD-TYPE 217 178 66

Figure S52.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.066

Table S53.  Gene #16: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 4(2Q37.3) MUTATED 12 17 19
DEL PEAK 4(2Q37.3) WILD-TYPE 31 252 165

Figure S53.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MRNA_CNMF'

P value = 1.67e-07 (Fisher's exact test), Q value = 5.1e-05

Table S54.  Gene #17: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S54.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p25.3' versus 'MRNA_CHIERARCHICAL'

P value = 1.83e-08 (Fisher's exact test), Q value = 5.7e-06

Table S55.  Gene #17: 'del_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S55.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p25.3' versus 'CN_CNMF'

P value = 1.06e-31 (Fisher's exact test), Q value = 3.8e-29

Table S56.  Gene #17: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 5(3P25.3) MUTATED 157 222 73
DEL PEAK 5(3P25.3) WILD-TYPE 5 1 56

Figure S56.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p25.3' versus 'METHLYATION_CNMF'

P value = 8.74e-06 (Fisher's exact test), Q value = 0.0025

Table S57.  Gene #17: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 5(3P25.3) MUTATED 96 107 56
DEL PEAK 5(3P25.3) WILD-TYPE 4 7 20

Figure S57.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p25.3' versus 'RPPA_CNMF'

P value = 2.46e-05 (Chi-square test), Q value = 0.0068

Table S58.  Gene #17: 'del_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) MUTATED 99 74 76 56 40 52
DEL PEAK 5(3P25.3) WILD-TYPE 1 14 8 19 3 5

Figure S58.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p25.3' versus 'MRNASEQ_CNMF'

P value = 1.93e-13 (Fisher's exact test), Q value = 6.3e-11

Table S59.  Gene #17: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 5(3P25.3) MUTATED 208 71 169
DEL PEAK 5(3P25.3) WILD-TYPE 7 37 18

Figure S59.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-16 (Fisher's exact test), Q value = 3.6e-14

Table S60.  Gene #17: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 5(3P25.3) MUTATED 218 186 44
DEL PEAK 5(3P25.3) WILD-TYPE 8 19 35

Figure S60.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_CNMF'

P value = 9.77e-07 (Fisher's exact test), Q value = 0.00029

Table S61.  Gene #17: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 5(3P25.3) MUTATED 92 201 142
DEL PEAK 5(3P25.3) WILD-TYPE 18 8 35

Figure S61.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.71e-08 (Fisher's exact test), Q value = 8.4e-06

Table S62.  Gene #17: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 5(3P25.3) MUTATED 26 253 156
DEL PEAK 5(3P25.3) WILD-TYPE 17 16 28

Figure S62.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.01e-14 (Chi-square test), Q value = 3.4e-12

Table S63.  Gene #17: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 5(3P25.3) MUTATED 1 41 74 10 78
DEL PEAK 5(3P25.3) WILD-TYPE 10 13 5 1 3

Figure S63.  Get High-res Image Gene #17: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.3' versus 'MRNA_CNMF'

P value = 1.67e-07 (Fisher's exact test), Q value = 5.1e-05

Table S64.  Gene #18: 'del_3p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 6(3P24.3) MUTATED 32 22 3
DEL PEAK 6(3P24.3) WILD-TYPE 1 2 10

Figure S64.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1.83e-08 (Fisher's exact test), Q value = 5.7e-06

Table S65.  Gene #18: 'del_3p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 6(3P24.3) MUTATED 3 31 23
DEL PEAK 6(3P24.3) WILD-TYPE 11 1 1

Figure S65.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p24.3' versus 'CN_CNMF'

P value = 3.29e-33 (Fisher's exact test), Q value = 1.2e-30

Table S66.  Gene #18: 'del_3p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 6(3P24.3) MUTATED 157 223 73
DEL PEAK 6(3P24.3) WILD-TYPE 5 0 56

Figure S66.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p24.3' versus 'METHLYATION_CNMF'

P value = 8.74e-06 (Fisher's exact test), Q value = 0.0025

Table S67.  Gene #18: 'del_3p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 6(3P24.3) MUTATED 96 107 56
DEL PEAK 6(3P24.3) WILD-TYPE 4 7 20

Figure S67.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p24.3' versus 'RPPA_CNMF'

P value = 6.84e-05 (Chi-square test), Q value = 0.018

Table S68.  Gene #18: 'del_3p24.3' 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 6(3P24.3) MUTATED 99 74 76 57 40 52
DEL PEAK 6(3P24.3) WILD-TYPE 1 14 8 18 3 5

Figure S68.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p24.3' versus 'MRNASEQ_CNMF'

P value = 4.73e-14 (Fisher's exact test), Q value = 1.6e-11

Table S69.  Gene #18: 'del_3p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 6(3P24.3) MUTATED 209 71 169
DEL PEAK 6(3P24.3) WILD-TYPE 6 37 18

Figure S69.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-17 (Fisher's exact test), Q value = 9.1e-15

Table S70.  Gene #18: 'del_3p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 6(3P24.3) MUTATED 219 186 44
DEL PEAK 6(3P24.3) WILD-TYPE 7 19 35

Figure S70.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.3' versus 'MIRSEQ_CNMF'

P value = 2.56e-07 (Fisher's exact test), Q value = 7.8e-05

Table S71.  Gene #18: 'del_3p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 6(3P24.3) MUTATED 92 202 142
DEL PEAK 6(3P24.3) WILD-TYPE 18 7 35

Figure S71.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.27e-08 (Fisher's exact test), Q value = 4e-06

Table S72.  Gene #18: 'del_3p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 6(3P24.3) MUTATED 26 254 156
DEL PEAK 6(3P24.3) WILD-TYPE 17 15 28

Figure S72.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.01e-14 (Chi-square test), Q value = 3.4e-12

Table S73.  Gene #18: 'del_3p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 6(3P24.3) MUTATED 1 41 74 10 78
DEL PEAK 6(3P24.3) WILD-TYPE 10 13 5 1 3

Figure S73.  Get High-res Image Gene #18: 'del_3p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.000978 (Fisher's exact test), Q value = 0.22

Table S74.  Gene #19: 'del_3p12.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 7(3P12.3) MUTATED 2 19 18
DEL PEAK 7(3P12.3) WILD-TYPE 12 13 6

Figure S74.  Get High-res Image Gene #19: 'del_3p12.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 4.82e-36 (Fisher's exact test), Q value = 1.7e-33

Table S75.  Gene #19: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 7(3P12.3) MUTATED 145 157 26
DEL PEAK 7(3P12.3) WILD-TYPE 17 66 103

Figure S75.  Get High-res Image Gene #19: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0054

Table S76.  Gene #19: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 7(3P12.3) MUTATED 149 48 129
DEL PEAK 7(3P12.3) WILD-TYPE 66 60 58

Figure S76.  Get High-res Image Gene #19: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.51e-07 (Fisher's exact test), Q value = 4.6e-05

Table S77.  Gene #19: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 7(3P12.3) MUTATED 157 141 28
DEL PEAK 7(3P12.3) WILD-TYPE 69 64 51

Figure S77.  Get High-res Image Gene #19: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000115 (Chi-square test), Q value = 0.029

Table S78.  Gene #19: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 7(3P12.3) MUTATED 1 29 61 7 54
DEL PEAK 7(3P12.3) WILD-TYPE 10 25 18 4 27

Figure S78.  Get High-res Image Gene #19: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p11.1' versus 'CN_CNMF'

P value = 1.43e-24 (Fisher's exact test), Q value = 5e-22

Table S79.  Gene #20: 'del_3p11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 8(3P11.1) MUTATED 112 108 14
DEL PEAK 8(3P11.1) WILD-TYPE 50 115 115

Figure S79.  Get High-res Image Gene #20: 'del_3p11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.2' versus 'CN_CNMF'

P value = 3.03e-12 (Fisher's exact test), Q value = 9.9e-10

Table S80.  Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 9(3Q11.2) MUTATED 74 73 11
DEL PEAK 9(3Q11.2) WILD-TYPE 88 150 118

Figure S80.  Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 6.44e-11 (Fisher's exact test), Q value = 2.1e-08

Table S81.  Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 10(4Q34.3) MUTATED 49 11 18
DEL PEAK 10(4Q34.3) WILD-TYPE 113 212 111

Figure S81.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.036

Table S82.  Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 10(4Q34.3) MUTATED 31 10 12
DEL PEAK 10(4Q34.3) WILD-TYPE 69 104 64

Figure S82.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.07

Table S83.  Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 10(4Q34.3) MUTATED 26 8 44
DEL PEAK 10(4Q34.3) WILD-TYPE 189 100 143

Figure S83.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-06 (Fisher's exact test), Q value = 0.00078

Table S84.  Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 10(4Q34.3) MUTATED 27 49 2
DEL PEAK 10(4Q34.3) WILD-TYPE 199 156 77

Figure S84.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1.57e-17 (Fisher's exact test), Q value = 5.4e-15

Table S85.  Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 11(6Q26) MUTATED 88 30 30
DEL PEAK 11(6Q26) WILD-TYPE 74 193 99

Figure S85.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 2.61e-05 (Chi-square test), Q value = 0.0071

Table S86.  Gene #23: 'del_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) MUTATED 33 10 29 22 8 28
DEL PEAK 11(6Q26) WILD-TYPE 67 78 55 53 35 29

Figure S86.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.000499 (Fisher's exact test), Q value = 0.12

Table S87.  Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 11(6Q26) MUTATED 52 21 72
DEL PEAK 11(6Q26) WILD-TYPE 163 87 115

Figure S87.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00035

Table S88.  Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 11(6Q26) MUTATED 22 45 77
DEL PEAK 11(6Q26) WILD-TYPE 88 164 100

Figure S88.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.035

Table S89.  Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
DEL PEAK 11(6Q26) MUTATED 10 18 39
DEL PEAK 11(6Q26) WILD-TYPE 40 81 48

Figure S89.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1.57e-17 (Fisher's exact test), Q value = 5.4e-15

Table S90.  Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 12(6Q26) MUTATED 88 30 30
DEL PEAK 12(6Q26) WILD-TYPE 74 193 99

Figure S90.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 1.21e-05 (Chi-square test), Q value = 0.0034

Table S91.  Gene #24: 'del_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) MUTATED 32 10 29 22 8 29
DEL PEAK 12(6Q26) WILD-TYPE 68 78 55 53 35 28

Figure S91.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.046

Table S92.  Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 12(6Q26) MUTATED 52 20 73
DEL PEAK 12(6Q26) WILD-TYPE 163 88 114

Figure S92.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 3.79e-07 (Fisher's exact test), Q value = 0.00011

Table S93.  Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 12(6Q26) MUTATED 21 45 78
DEL PEAK 12(6Q26) WILD-TYPE 89 164 99

Figure S93.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.86e-05 (Fisher's exact test), Q value = 0.01

Table S94.  Gene #24: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
DEL PEAK 12(6Q26) MUTATED 9 18 40
DEL PEAK 12(6Q26) WILD-TYPE 41 81 47

Figure S94.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 3.78e-07 (Fisher's exact test), Q value = 0.00011

Table S95.  Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 13(8P23.2) MUTATED 73 43 37
DEL PEAK 13(8P23.2) WILD-TYPE 89 180 92

Figure S95.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.000533 (Fisher's exact test), Q value = 0.12

Table S96.  Gene #26: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S96.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 5.94e-50 (Fisher's exact test), Q value = 2.1e-47

Table S97.  Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 14(9P23) MUTATED 111 4 34
DEL PEAK 14(9P23) WILD-TYPE 51 219 95

Figure S97.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 4.89e-20 (Fisher's exact test), Q value = 1.7e-17

Table S98.  Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 14(9P23) MUTATED 61 5 25
DEL PEAK 14(9P23) WILD-TYPE 39 109 51

Figure S98.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 1.06e-07 (Chi-square test), Q value = 3.3e-05

Table S99.  Gene #26: 'del_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 14(9P23) MUTATED 17 23 33 18 10 35
DEL PEAK 14(9P23) WILD-TYPE 83 65 51 57 33 22

Figure S99.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 7.67e-25 (Fisher's exact test), Q value = 2.7e-22

Table S100.  Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 14(9P23) MUTATED 25 16 106
DEL PEAK 14(9P23) WILD-TYPE 190 92 81

Figure S100.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.67e-26 (Fisher's exact test), Q value = 1.3e-23

Table S101.  Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 14(9P23) MUTATED 24 113 10
DEL PEAK 14(9P23) WILD-TYPE 202 92 69

Figure S101.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 6.84e-18 (Fisher's exact test), Q value = 2.4e-15

Table S102.  Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 14(9P23) MUTATED 26 25 93
DEL PEAK 14(9P23) WILD-TYPE 84 184 84

Figure S102.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.013

Table S103.  Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 14(9P23) MUTATED 15 56 73
DEL PEAK 14(9P23) WILD-TYPE 28 213 111

Figure S103.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.75e-12 (Fisher's exact test), Q value = 5.7e-10

Table S104.  Gene #26: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
DEL PEAK 14(9P23) MUTATED 14 8 49
DEL PEAK 14(9P23) WILD-TYPE 36 91 38

Figure S104.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000424 (Chi-square test), Q value = 0.1

Table S105.  Gene #26: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 14(9P23) MUTATED 3 18 36 0 14
DEL PEAK 14(9P23) WILD-TYPE 8 36 43 11 67

Figure S105.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.042

Table S106.  Gene #27: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 15(9P21.3) MUTATED 1 4 14
DEL PEAK 15(9P21.3) WILD-TYPE 13 28 10

Figure S106.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1.04e-47 (Fisher's exact test), Q value = 3.7e-45

Table S107.  Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 15(9P21.3) MUTATED 113 7 36
DEL PEAK 15(9P21.3) WILD-TYPE 49 216 93

Figure S107.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 3.3e-20 (Fisher's exact test), Q value = 1.1e-17

Table S108.  Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 15(9P21.3) MUTATED 61 5 28
DEL PEAK 15(9P21.3) WILD-TYPE 39 109 48

Figure S108.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 4.2e-08 (Chi-square test), Q value = 1.3e-05

Table S109.  Gene #27: 'del_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 15(9P21.3) MUTATED 18 26 33 19 10 37
DEL PEAK 15(9P21.3) WILD-TYPE 82 62 51 56 33 20

Figure S109.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.000428 (Fisher's exact test), Q value = 0.1

Table S110.  Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 15(9P21.3) MUTATED 42 53 48
DEL PEAK 15(9P21.3) WILD-TYPE 144 99 61

Figure S110.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-24 (Fisher's exact test), Q value = 3.5e-22

Table S111.  Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 15(9P21.3) MUTATED 27 18 109
DEL PEAK 15(9P21.3) WILD-TYPE 188 90 78

Figure S111.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-29 (Fisher's exact test), Q value = 4.3e-27

Table S112.  Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 15(9P21.3) MUTATED 24 120 10
DEL PEAK 15(9P21.3) WILD-TYPE 202 85 69

Figure S112.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 5.96e-18 (Fisher's exact test), Q value = 2.1e-15

Table S113.  Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 15(9P21.3) MUTATED 29 26 95
DEL PEAK 15(9P21.3) WILD-TYPE 81 183 82

Figure S113.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00031

Table S114.  Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 15(9P21.3) MUTATED 16 55 79
DEL PEAK 15(9P21.3) WILD-TYPE 27 214 105

Figure S114.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.94e-12 (Fisher's exact test), Q value = 1.6e-09

Table S115.  Gene #27: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
DEL PEAK 15(9P21.3) MUTATED 15 8 48
DEL PEAK 15(9P21.3) WILD-TYPE 35 91 39

Figure S115.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000672 (Chi-square test), Q value = 0.15

Table S116.  Gene #27: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 15(9P21.3) MUTATED 3 19 35 0 14
DEL PEAK 15(9P21.3) WILD-TYPE 8 35 44 11 67

Figure S116.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 5.17e-10 (Fisher's exact test), Q value = 1.7e-07

Table S117.  Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 16(10Q23.31) MUTATED 48 14 32
DEL PEAK 16(10Q23.31) WILD-TYPE 114 209 97

Figure S117.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 6.6e-10 (Fisher's exact test), Q value = 2.1e-07

Table S118.  Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 17(13Q14.2) MUTATED 42 10 28
DEL PEAK 17(13Q14.2) WILD-TYPE 120 213 101

Figure S118.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.000544 (Fisher's exact test), Q value = 0.13

Table S119.  Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 17(13Q14.2) MUTATED 21 8 20
DEL PEAK 17(13Q14.2) WILD-TYPE 79 106 56

Figure S119.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 1.36e-06 (Chi-square test), Q value = 4e-04

Table S120.  Gene #29: 'del_13q14.2' 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(13Q14.2) MUTATED 3 12 16 13 6 22
DEL PEAK 17(13Q14.2) WILD-TYPE 97 76 68 62 37 35

Figure S120.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0047

Table S121.  Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 17(13Q14.2) MUTATED 19 13 48
DEL PEAK 17(13Q14.2) WILD-TYPE 196 95 139

Figure S121.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.6e-06 (Fisher's exact test), Q value = 0.001

Table S122.  Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 17(13Q14.2) MUTATED 18 52 10
DEL PEAK 17(13Q14.2) WILD-TYPE 208 153 69

Figure S122.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0011

Table S123.  Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 17(13Q14.2) MUTATED 14 17 47
DEL PEAK 17(13Q14.2) WILD-TYPE 96 192 130

Figure S123.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000542 (Fisher's exact test), Q value = 0.13

Table S124.  Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
DEL PEAK 17(13Q14.2) MUTATED 14 29 35
DEL PEAK 17(13Q14.2) WILD-TYPE 29 240 149

Figure S124.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.016

Table S125.  Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 18(14Q31.1) MUTATED 10 19 2
DEL PEAK 18(14Q31.1) WILD-TYPE 23 5 11

Figure S125.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 9.68e-05 (Fisher's exact test), Q value = 0.025

Table S126.  Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
DEL PEAK 18(14Q31.1) MUTATED 3 9 19
DEL PEAK 18(14Q31.1) WILD-TYPE 11 23 5

Figure S126.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 2.25e-17 (Fisher's exact test), Q value = 7.7e-15

Table S127.  Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
DEL PEAK 18(14Q31.1) MUTATED 115 61 48
DEL PEAK 18(14Q31.1) WILD-TYPE 47 162 81

Figure S127.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00042

Table S128.  Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
DEL PEAK 18(14Q31.1) MUTATED 59 29 38
DEL PEAK 18(14Q31.1) WILD-TYPE 41 85 38

Figure S128.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 6.3e-14 (Chi-square test), Q value = 2.1e-11

Table S129.  Gene #30: 'del_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 18(14Q31.1) MUTATED 30 30 64 23 13 40
DEL PEAK 18(14Q31.1) WILD-TYPE 70 58 20 52 30 17

Figure S129.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 2.09e-07 (Fisher's exact test), Q value = 6.3e-05

Table S130.  Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
DEL PEAK 18(14Q31.1) MUTATED 57 92 51
DEL PEAK 18(14Q31.1) WILD-TYPE 129 60 58

Figure S130.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 4.9e-21 (Fisher's exact test), Q value = 1.7e-18

Table S131.  Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
DEL PEAK 18(14Q31.1) MUTATED 71 19 130
DEL PEAK 18(14Q31.1) WILD-TYPE 144 89 57

Figure S131.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.35e-16 (Fisher's exact test), Q value = 7.9e-14

Table S132.  Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
DEL PEAK 18(14Q31.1) MUTATED 75 132 13
DEL PEAK 18(14Q31.1) WILD-TYPE 151 73 66

Figure S132.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 6.5e-11 (Fisher's exact test), Q value = 2.1e-08

Table S133.  Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
DEL PEAK 18(14Q31.1) MUTATED 37 67 114
DEL PEAK 18(14Q31.1) WILD-TYPE 73 142 63

Figure S133.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.99e-07 (Fisher's exact test), Q value = 0.00018

Table S134.  Gene #30: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
DEL PEAK 18(14Q31.1) MUTATED 16 30 58
DEL PEAK 18(14Q31.1) WILD-TYPE 34 69 29

Figure S134.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.27e-05 (Chi-square test), Q value = 0.019

Table S135.  Gene #30: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
DEL PEAK 18(14Q31.1) MUTATED 1 22 51 3 27
DEL PEAK 18(14Q31.1) WILD-TYPE 10 32 28 8 54

Figure S135.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 514

  • Number of significantly focal cnvs = 30

  • Number of molecular subtypes = 12

  • Exclude genes 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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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