Correlation between copy number variation genes (focal events) and molecular subtypes
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 528 patients, 126 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

  • amp_5q35.1 cnv correlated to 'CN_CNMF'.

  • 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',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_xp11.4 cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_1p31.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CNMF'.

  • del_1q43 cnv correlated to 'CN_CNMF'.

  • del_2q37.3 cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.

  • del_3p26.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p22.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p14.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p12.2 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',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  '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', and 'MIRSEQ_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, 126 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 14q31 1 228 (43%) 300 7e-05
(0.0183) 		0.00041
(0.1) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		4e-05
(0.0107) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.0906
(1.00) 		0.952
(1.00)
amp 8q24 22 79 (15%) 449 0.225
(1.00) 		0.105
(1.00) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		3e-05
(0.0081) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.0245
(1.00)
del 3p26 3 455 (86%) 73 1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		3e-05
(0.0081) 		0.032
(1.00) 		1e-05
(0.0036) 		1e-05
(0.0036) 		8e-05
(0.0207) 		2e-05
(0.00562) 		0.00238
(0.521) 		0.0101
(1.00)
del 3p22 2 465 (88%) 63 1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.0698
(1.00) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.0064
(1.00) 		0.0303
(1.00)
del 1p36 23 103 (20%) 425 0.00016
(0.0405) 		0.00097
(0.229) 		1e-05
(0.0036) 		0.0811
(1.00) 		2e-05
(0.00562) 		3e-05
(0.0081) 		0.00017
(0.0427) 		0.0001
(0.0256) 		1e-05
(0.0036) 		0.0041
(0.849) 		0.021
(1.00) 		0.313
(1.00)
del 9p23 152 (29%) 376 0.00397
(0.826) 		0.0357
(1.00) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		2e-05
(0.00562) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.00275
(0.597) 		0.124
(1.00)
del 9p21 3 159 (30%) 369 0.00129
(0.298) 		0.0166
(1.00) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.00127
(0.295) 		0.0121
(1.00)
del 13q14 2 82 (16%) 446 0.0142
(1.00) 		0.0838
(1.00) 		1e-05
(0.0036) 		8e-05
(0.0207) 		1e-05
(0.0036) 		9e-05
(0.0231) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.0971
(1.00) 		0.149
(1.00)
amp 3q26 32 87 (16%) 441 0.0566
(1.00) 		0.12
(1.00) 		1e-05
(0.0036) 		4e-05
(0.0107) 		0.00264
(0.576) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		1e-05
(0.0036) 		0.00095
(0.225) 		0.00541
(1.00) 		0.128
(1.00)
del 6q26 151 (29%) 377 0.0152
(1.00) 		0.0986
(1.00) 		1e-05
(0.0036) 		0.0131
(1.00) 		4e-05
(0.0107) 		1e-05
(0.0036) 		0.00106
(0.249) 		0.00012
(0.0306) 		2e-05
(0.00562) 		0.00018
(0.0448) 		0.03
(1.00) 		0.133
(1.00)
del 6q26 151 (29%) 377 0.0149
(1.00) 		0.0983
(1.00) 		1e-05
(0.0036) 		0.0126
(1.00) 		2e-05
(0.00562) 		1e-05
(0.0036) 		0.00054
(0.131) 		0.00012
(0.0306) 		1e-05
(0.0036) 		0.00017
(0.0427) 		0.0293
(1.00) 		0.133
(1.00)
amp 1q32 1 62 (12%) 466 0.407
(1.00) 		0.9
(1.00) 		1e-05
(0.0036) 		0.0395
(1.00) 		0.0675
(1.00) 		0.0502
(1.00) 		1e-05
(0.0036) 		0.00492
(1.00) 		1e-05
(0.0036) 		0.00071
(0.17) 		0.277
(1.00) 		0.748
(1.00)
del 4q34 3 78 (15%) 450 0.239
(1.00) 		0.493
(1.00) 		1e-05
(0.0036) 		2e-05
(0.00562) 		0.0402
(1.00) 		0.00582
(1.00) 		0.00016
(0.0405) 		1e-05
(0.0036) 		0.15
(1.00) 		0.00861
(1.00) 		0.18
(1.00) 		0.0159
(1.00)
del 8p23 2 154 (29%) 374 0.503
(1.00) 		0.246
(1.00) 		1e-05
(0.0036) 		0.0413
(1.00) 		0.00632
(1.00) 		0.0111
(1.00) 		0.00185
(0.414) 		1e-05
(0.0036) 		0.0008
(0.191) 		0.00088
(0.209) 		0.139
(1.00) 		0.338
(1.00)
amp 1q24 1 62 (12%) 466 0.258
(1.00) 		0.785
(1.00) 		1e-05
(0.0036) 		0.147
(1.00) 		0.165
(1.00) 		0.135
(1.00) 		2e-05
(0.00562) 		0.00489
(1.00) 		2e-05
(0.00562) 		0.00725
(1.00) 		0.584
(1.00) 		0.926
(1.00)
amp 7q36 3 176 (33%) 352 0.453
(1.00) 		0.86
(1.00) 		1e-05
(0.0036) 		0.00588
(1.00) 		0.00054
(0.131) 		0.00334
(0.715) 		4e-05
(0.0107) 		0.00362
(0.767) 		0.00682
(1.00) 		0.0147
(1.00) 		0.147
(1.00) 		0.787
(1.00)
del 1p31 1 77 (15%) 451 0.00155
(0.355) 		0.00659
(1.00) 		1e-05
(0.0036) 		0.0948
(1.00) 		0.00024
(0.0595) 		0.00116
(0.27) 		0.0123
(1.00) 		0.00375
(0.784) 		1e-05
(0.0036) 		0.00296
(0.636) 		0.00494
(1.00) 		0.618
(1.00)
del 3p14 1 373 (71%) 155 0.00347
(0.739) 		0.0104
(1.00) 		1e-05
(0.0036) 		0.00558
(1.00) 		0.0931
(1.00) 		0.0554
(1.00) 		1e-05
(0.0036) 		0.00026
(0.064) 		0.0916
(1.00) 		0.00676
(1.00) 		0.335
(1.00) 		0.882
(1.00)
amp 10p14 20 (4%) 508 0.189
(1.00) 		0.774
(1.00) 		2e-05
(0.00562) 		0.18
(1.00) 		0.33
(1.00) 		0.201
(1.00) 		0.00218
(0.482) 		2e-05
(0.00562) 		0.032
(1.00) 		0.036
(1.00) 		0.862
(1.00) 		0.369
(1.00)
amp xp11 4 33 (6%) 495 0.841
(1.00) 		0.798
(1.00) 		0.00171
(0.386) 		0.114
(1.00) 		0.0007
(0.169) 		0.00203
(0.453) 		0.0292
(1.00) 		7e-05
(0.0183) 		0.0484
(1.00) 		0.245
(1.00) 		0.791
(1.00) 		1
(1.00)
del 2q37 3 50 (9%) 478 0.00157
(0.358) 		0.00047
(0.115) 		0.765
(1.00) 		0.621
(1.00) 		0.239
(1.00) 		0.113
(1.00) 		2e-05
(0.00562) 		0.00218
(0.482) 		0.012
(1.00) 		0.0692
(1.00) 		0.252
(1.00) 		0.135
(1.00)
del 10q23 31 96 (18%) 432 0.442
(1.00) 		0.546
(1.00) 		1e-05
(0.0036) 		0.00161
(0.365) 		0.915
(1.00) 		0.00674
(1.00) 		0.0467
(1.00) 		0.00286
(0.618) 		0.0147
(1.00) 		5e-05
(0.0131) 		0.8
(1.00) 		0.438
(1.00)
amp 5q35 1 332 (63%) 196 0.0618
(1.00) 		0.0508
(1.00) 		0.00024
(0.0595) 		0.332
(1.00) 		0.0392
(1.00) 		0.00942
(1.00) 		0.00372
(0.781) 		0.0845
(1.00) 		0.13
(1.00) 		0.405
(1.00) 		0.621
(1.00) 		0.742
(1.00)
del 1q43 42 (8%) 486 0.0114
(1.00) 		0.0111
(1.00) 		4e-05
(0.0107) 		0.358
(1.00) 		0.019
(1.00) 		0.0636
(1.00) 		0.00364
(0.768) 		0.222
(1.00) 		0.0993
(1.00) 		0.0157
(1.00) 		0.292
(1.00) 		0.823
(1.00)
del 3p12 2 305 (58%) 223 0.0398
(1.00) 		0.0636
(1.00) 		1e-05
(0.0036) 		0.0201
(1.00) 		0.35
(1.00) 		0.559
(1.00) 		0.0013
(0.299) 		0.0232
(1.00) 		0.256
(1.00) 		0.0456
(1.00) 		0.524
(1.00) 		0.737
(1.00)
del 3q11 2 161 (30%) 367 0.183
(1.00) 		0.165
(1.00) 		1e-05
(0.0036) 		0.0415
(1.00) 		0.865
(1.00) 		0.471
(1.00) 		0.505
(1.00) 		0.187
(1.00) 		0.538
(1.00) 		0.0632
(1.00) 		0.749
(1.00) 		0.757
(1.00)
amp 4q32 1 16 (3%) 512 0.189
(1.00) 		0.775
(1.00) 		0.236
(1.00) 		0.706
(1.00) 		0.633
(1.00) 		0.219
(1.00) 		0.0131
(1.00) 		0.0194
(1.00) 		0.00175
(0.394) 		0.102
(1.00) 		0.236
(1.00) 		0.493
(1.00)
amp xp22 2 31 (6%) 497 1
(1.00) 		0.524
(1.00) 		0.00809
(1.00) 		0.236
(1.00) 		0.00107
(0.25) 		0.0153
(1.00) 		0.0577
(1.00) 		0.00204
(0.453) 		0.0368
(1.00) 		0.348
(1.00) 		0.942
(1.00) 		0.879
(1.00)
amp xq11 2 29 (5%) 499 0.172
(1.00) 		0.161
(1.00) 		0.165
(1.00) 		0.257
(1.00) 		0.167
(1.00) 		0.0278
(1.00) 		0.173
(1.00) 		0.0767
(1.00) 		0.141
(1.00) 		0.426
(1.00) 		0.393
(1.00) 		0.855
(1.00)
amp xq28 37 (7%) 491 0.491
(1.00) 		0.703
(1.00) 		0.163
(1.00) 		0.637
(1.00) 		0.184
(1.00) 		0.106
(1.00) 		0.0651
(1.00) 		0.0686
(1.00) 		0.108
(1.00) 		0.327
(1.00) 		0.73
(1.00) 		0.486
(1.00)
'amp_1q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 1(1Q24.1) MUTATED 12 3 47
AMP PEAK 1(1Q24.1) WILD-TYPE 226 132 108

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 = 2e-05 (Fisher's exact test), Q value = 0.0056

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
AMP PEAK 1(1Q24.1) MUTATED 3 19 38
AMP PEAK 1(1Q24.1) WILD-TYPE 103 203 157

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

'amp_1q24.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S3.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 1(1Q24.1) MUTATED 4 19 37
AMP PEAK 1(1Q24.1) WILD-TYPE 120 185 145

Figure S3.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S4.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 2(1Q32.1) MUTATED 9 3 50
AMP PEAK 2(1Q32.1) WILD-TYPE 229 132 105

Figure S4.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S5.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
AMP PEAK 2(1Q32.1) MUTATED 2 19 39
AMP PEAK 2(1Q32.1) WILD-TYPE 104 203 156

Figure S5.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S6.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 2(1Q32.1) MUTATED 4 18 38
AMP PEAK 2(1Q32.1) WILD-TYPE 120 186 144

Figure S6.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.17

Table S7.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 2(1Q32.1) MUTATED 12 20 16 12
AMP PEAK 2(1Q32.1) WILD-TYPE 132 114 179 25

Figure S7.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S8.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 3(3Q26.32) MUTATED 14 19 54
AMP PEAK 3(3Q26.32) WILD-TYPE 224 116 101

Figure S8.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S9.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
AMP PEAK 3(3Q26.32) MUTATED 7 14 30
AMP PEAK 3(3Q26.32) WILD-TYPE 121 62 80

Figure S9.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S10.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 3(3Q26.32) MUTATED 14 22 42
AMP PEAK 3(3Q26.32) WILD-TYPE 107 174 88

Figure S10.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S11.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
AMP PEAK 3(3Q26.32) MUTATED 14 18 55
AMP PEAK 3(3Q26.32) WILD-TYPE 92 204 140

Figure S11.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S12.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
AMP PEAK 3(3Q26.32) MUTATED 24 21 42
AMP PEAK 3(3Q26.32) WILD-TYPE 137 216 83

Figure S12.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S13.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 3(3Q26.32) MUTATED 13 16 55
AMP PEAK 3(3Q26.32) WILD-TYPE 111 188 127

Figure S13.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.23

Table S14.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 3(3Q26.32) MUTATED 29 32 17 6
AMP PEAK 3(3Q26.32) WILD-TYPE 115 102 178 31

Figure S14.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.06

Table S15.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 5(5Q35.1) MUTATED 162 65 105
AMP PEAK 5(5Q35.1) WILD-TYPE 76 70 50

Figure S15.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S16.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 6(7Q36.3) MUTATED 39 48 89
AMP PEAK 6(7Q36.3) WILD-TYPE 199 87 66

Figure S16.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q36.3' versus 'RPPA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.13

Table S17.  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 108 62 75 80 79 43
AMP PEAK 6(7Q36.3) MUTATED 23 30 31 35 23 10
AMP PEAK 6(7Q36.3) WILD-TYPE 85 32 44 45 56 33

Figure S17.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q36.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S18.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
AMP PEAK 6(7Q36.3) MUTATED 33 53 88
AMP PEAK 6(7Q36.3) WILD-TYPE 73 169 107

Figure S18.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S19.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 7(8Q24.22) MUTATED 6 17 56
AMP PEAK 7(8Q24.22) WILD-TYPE 232 118 99

Figure S19.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S20.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
AMP PEAK 7(8Q24.22) MUTATED 6 14 33
AMP PEAK 7(8Q24.22) WILD-TYPE 122 62 77

Figure S20.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S21.  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 108 62 75 80 79 43
AMP PEAK 7(8Q24.22) MUTATED 5 24 15 15 10 2
AMP PEAK 7(8Q24.22) WILD-TYPE 103 38 60 65 69 41

Figure S21.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0081

Table S22.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 7(8Q24.22) MUTATED 15 18 38
AMP PEAK 7(8Q24.22) WILD-TYPE 106 178 92

Figure S22.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S23.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
AMP PEAK 7(8Q24.22) MUTATED 8 9 61
AMP PEAK 7(8Q24.22) WILD-TYPE 98 213 134

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

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S24.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
AMP PEAK 7(8Q24.22) MUTATED 12 15 51
AMP PEAK 7(8Q24.22) WILD-TYPE 149 222 74

Figure S24.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S25.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 7(8Q24.22) MUTATED 13 11 53
AMP PEAK 7(8Q24.22) WILD-TYPE 111 193 129

Figure S25.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S26.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 7(8Q24.22) MUTATED 29 24 11 13
AMP PEAK 7(8Q24.22) WILD-TYPE 115 110 184 24

Figure S26.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S27.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
AMP PEAK 7(8Q24.22) MUTATED 3 1 1 14
AMP PEAK 7(8Q24.22) WILD-TYPE 35 20 47 21

Figure S27.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p14' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S28.  Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 8(10P14) MUTATED 1 5 14
AMP PEAK 8(10P14) WILD-TYPE 237 130 141

Figure S28.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S29.  Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
AMP PEAK 8(10P14) MUTATED 5 2 13
AMP PEAK 8(10P14) WILD-TYPE 156 235 112

Figure S29.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'RPPA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.17

Table S30.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 10(XP11.4) MUTATED 0 5 5 10 5 0
AMP PEAK 10(XP11.4) WILD-TYPE 108 57 70 70 74 43

Figure S30.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.018

Table S31.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
AMP PEAK 10(XP11.4) MUTATED 6 8 19
AMP PEAK 10(XP11.4) WILD-TYPE 155 229 106

Figure S31.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.04

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 = 0.00097 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 1(1P36.23) MUTATED 0 2 2 5 1 1 7
DEL PEAK 1(1P36.23) WILD-TYPE 11 10 2 6 12 8 3

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 = 1e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 1(1P36.23) MUTATED 13 37 53
DEL PEAK 1(1P36.23) WILD-TYPE 225 98 102

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 = 2e-05 (Fisher's exact test), Q value = 0.0056

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 108 62 75 80 79 43
DEL PEAK 1(1P36.23) MUTATED 10 20 20 26 7 6
DEL PEAK 1(1P36.23) WILD-TYPE 98 42 55 54 72 37

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 = 3e-05 (Fisher's exact test), Q value = 0.0081

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 1(1P36.23) MUTATED 26 22 41
DEL PEAK 1(1P36.23) WILD-TYPE 95 174 89

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 = 0.00017 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 1(1P36.23) MUTATED 20 27 56
DEL PEAK 1(1P36.23) WILD-TYPE 86 195 139

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 = 1e-04 (Fisher's exact test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 1(1P36.23) MUTATED 38 28 37
DEL PEAK 1(1P36.23) WILD-TYPE 123 209 88

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 = 1e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 1(1P36.23) MUTATED 19 23 61
DEL PEAK 1(1P36.23) WILD-TYPE 105 181 121

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

'del_1p31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S40.  Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 2(1P31.1) MUTATED 8 29 40
DEL PEAK 2(1P31.1) WILD-TYPE 230 106 115

Figure S40.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.06

Table S41.  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 108 62 75 80 79 43
DEL PEAK 2(1P31.1) MUTATED 9 16 12 21 4 5
DEL PEAK 2(1P31.1) WILD-TYPE 99 46 63 59 75 38

Figure S41.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S42.  Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 2(1P31.1) MUTATED 10 20 47
DEL PEAK 2(1P31.1) WILD-TYPE 114 184 135

Figure S42.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1q43' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S43.  Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 3(1Q43) MUTATED 7 22 13
DEL PEAK 3(1Q43) WILD-TYPE 231 113 142

Figure S43.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.11

Table S44.  Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 4(2Q37.3) MUTATED 0 4 0 0 1 0 6
DEL PEAK 4(2Q37.3) WILD-TYPE 11 8 4 11 12 9 4

Figure S44.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S45.  Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 4(2Q37.3) MUTATED 21 8 20
DEL PEAK 4(2Q37.3) WILD-TYPE 85 214 175

Figure S45.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S46.  Gene #17: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 5(3P26.3) MUTATED 32 22 3
DEL PEAK 5(3P26.3) WILD-TYPE 1 2 10

Figure S46.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S47.  Gene #17: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 5(3P26.3) MUTATED 11 11 1 11 12 9 2
DEL PEAK 5(3P26.3) WILD-TYPE 0 1 3 0 1 0 8

Figure S47.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S48.  Gene #17: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 5(3P26.3) MUTATED 236 69 150
DEL PEAK 5(3P26.3) WILD-TYPE 2 66 5

Figure S48.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S49.  Gene #17: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 5(3P26.3) MUTATED 118 50 103
DEL PEAK 5(3P26.3) WILD-TYPE 10 26 7

Figure S49.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0081

Table S50.  Gene #17: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 5(3P26.3) MUTATED 106 54 67 60 64 39
DEL PEAK 5(3P26.3) WILD-TYPE 2 8 8 20 15 4

Figure S50.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S51.  Gene #17: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 5(3P26.3) MUTATED 67 212 172
DEL PEAK 5(3P26.3) WILD-TYPE 39 10 23

Figure S51.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S52.  Gene #17: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 5(3P26.3) MUTATED 115 228 108
DEL PEAK 5(3P26.3) WILD-TYPE 46 9 17

Figure S52.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.021

Table S53.  Gene #17: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 5(3P26.3) MUTATED 103 191 144
DEL PEAK 5(3P26.3) WILD-TYPE 21 13 38

Figure S53.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S54.  Gene #17: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 5(3P26.3) MUTATED 112 108 184 34
DEL PEAK 5(3P26.3) WILD-TYPE 32 26 11 3

Figure S54.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S55.  Gene #18: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 6(3P22.2) MUTATED 32 22 3
DEL PEAK 6(3P22.2) WILD-TYPE 1 2 10

Figure S55.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p22.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S56.  Gene #18: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 6(3P22.2) MUTATED 11 11 1 11 12 9 2
DEL PEAK 6(3P22.2) WILD-TYPE 0 1 3 0 1 0 8

Figure S56.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S57.  Gene #18: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 6(3P22.2) MUTATED 238 75 152
DEL PEAK 6(3P22.2) WILD-TYPE 0 60 3

Figure S57.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S58.  Gene #18: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 6(3P22.2) MUTATED 119 52 106
DEL PEAK 6(3P22.2) WILD-TYPE 9 24 4

Figure S58.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p22.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S59.  Gene #18: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 6(3P22.2) MUTATED 107 59 66 63 65 40
DEL PEAK 6(3P22.2) WILD-TYPE 1 3 9 17 14 3

Figure S59.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S60.  Gene #18: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 6(3P22.2) MUTATED 67 217 177
DEL PEAK 6(3P22.2) WILD-TYPE 39 5 18

Figure S60.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S61.  Gene #18: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 6(3P22.2) MUTATED 117 234 110
DEL PEAK 6(3P22.2) WILD-TYPE 44 3 15

Figure S61.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S62.  Gene #18: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 6(3P22.2) MUTATED 103 197 148
DEL PEAK 6(3P22.2) WILD-TYPE 21 7 34

Figure S62.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S63.  Gene #18: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 6(3P22.2) MUTATED 114 111 187 36
DEL PEAK 6(3P22.2) WILD-TYPE 30 23 8 1

Figure S63.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S64.  Gene #19: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 7(3P14.1) MUTATED 199 32 142
DEL PEAK 7(3P14.1) WILD-TYPE 39 103 13

Figure S64.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S65.  Gene #19: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 7(3P14.1) MUTATED 47 175 148
DEL PEAK 7(3P14.1) WILD-TYPE 59 47 47

Figure S65.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.064

Table S66.  Gene #19: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 7(3P14.1) MUTATED 94 182 94
DEL PEAK 7(3P14.1) WILD-TYPE 67 55 31

Figure S66.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S67.  Gene #20: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 8(3P12.2) MUTATED 160 22 123
DEL PEAK 8(3P12.2) WILD-TYPE 78 113 32

Figure S67.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S68.  Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 9(3Q11.2) MUTATED 83 13 65
DEL PEAK 9(3Q11.2) WILD-TYPE 155 122 90

Figure S68.  Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S69.  Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 10(4Q34.3) MUTATED 10 17 51
DEL PEAK 10(4Q34.3) WILD-TYPE 228 118 104

Figure S69.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S70.  Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 10(4Q34.3) MUTATED 10 9 34
DEL PEAK 10(4Q34.3) WILD-TYPE 118 67 76

Figure S70.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.04

Table S71.  Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 10(4Q34.3) MUTATED 7 26 45
DEL PEAK 10(4Q34.3) WILD-TYPE 99 196 150

Figure S71.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S72.  Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 10(4Q34.3) MUTATED 11 30 37
DEL PEAK 10(4Q34.3) WILD-TYPE 150 207 88

Figure S72.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S73.  Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 11(6Q26) MUTATED 37 26 88
DEL PEAK 11(6Q26) WILD-TYPE 201 109 67

Figure S73.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S74.  Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 11(6Q26) MUTATED 35 30 25 23 9 8
DEL PEAK 11(6Q26) WILD-TYPE 73 32 50 57 70 35

Figure S74.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S75.  Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 11(6Q26) MUTATED 39 36 55
DEL PEAK 11(6Q26) WILD-TYPE 82 160 75

Figure S75.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.25

Table S76.  Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 11(6Q26) MUTATED 21 54 73
DEL PEAK 11(6Q26) WILD-TYPE 85 168 122

Figure S76.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.031

Table S77.  Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 11(6Q26) MUTATED 41 53 54
DEL PEAK 11(6Q26) WILD-TYPE 120 184 71

Figure S77.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S78.  Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 11(6Q26) MUTATED 25 43 79
DEL PEAK 11(6Q26) WILD-TYPE 99 161 103

Figure S78.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.045

Table S79.  Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 11(6Q26) MUTATED 38 50 40 19
DEL PEAK 11(6Q26) WILD-TYPE 106 84 155 18

Figure S79.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S80.  Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 12(6Q26) MUTATED 37 26 88
DEL PEAK 12(6Q26) WILD-TYPE 201 109 67

Figure S80.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S81.  Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 12(6Q26) MUTATED 34 31 25 23 9 8
DEL PEAK 12(6Q26) WILD-TYPE 74 31 50 57 70 35

Figure S81.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S82.  Gene #24: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 12(6Q26) MUTATED 39 36 55
DEL PEAK 12(6Q26) WILD-TYPE 82 160 75

Figure S82.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.13

Table S83.  Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 12(6Q26) MUTATED 20 54 74
DEL PEAK 12(6Q26) WILD-TYPE 86 168 121

Figure S83.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.031

Table S84.  Gene #24: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 12(6Q26) MUTATED 40 53 55
DEL PEAK 12(6Q26) WILD-TYPE 121 184 70

Figure S84.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S85.  Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 12(6Q26) MUTATED 24 43 80
DEL PEAK 12(6Q26) WILD-TYPE 100 161 102

Figure S85.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.043

Table S86.  Gene #24: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 12(6Q26) MUTATED 38 50 40 19
DEL PEAK 12(6Q26) WILD-TYPE 106 84 155 18

Figure S86.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S87.  Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 13(8P23.2) MUTATED 43 37 74
DEL PEAK 13(8P23.2) WILD-TYPE 195 98 81

Figure S87.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S88.  Gene #25: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 13(8P23.2) MUTATED 39 56 57
DEL PEAK 13(8P23.2) WILD-TYPE 122 181 68

Figure S88.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.19

Table S89.  Gene #25: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 13(8P23.2) MUTATED 36 44 71
DEL PEAK 13(8P23.2) WILD-TYPE 88 160 111

Figure S89.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.21

Table S90.  Gene #25: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 13(8P23.2) MUTATED 51 39 42 19
DEL PEAK 13(8P23.2) WILD-TYPE 93 95 153 18

Figure S90.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S91.  Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 14(9P23) MUTATED 9 34 109
DEL PEAK 14(9P23) WILD-TYPE 229 101 46

Figure S91.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S92.  Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 14(9P23) MUTATED 6 21 68
DEL PEAK 14(9P23) WILD-TYPE 122 55 42

Figure S92.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S93.  Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 14(9P23) MUTATED 17 38 31 21 19 10
DEL PEAK 14(9P23) WILD-TYPE 91 24 44 59 60 33

Figure S93.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0056

Table S94.  Gene #26: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 14(9P23) MUTATED 34 42 60
DEL PEAK 14(9P23) WILD-TYPE 87 154 70

Figure S94.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S95.  Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 14(9P23) MUTATED 14 25 111
DEL PEAK 14(9P23) WILD-TYPE 92 197 84

Figure S95.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S96.  Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 14(9P23) MUTATED 37 35 78
DEL PEAK 14(9P23) WILD-TYPE 124 202 47

Figure S96.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S97.  Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 14(9P23) MUTATED 26 25 96
DEL PEAK 14(9P23) WILD-TYPE 98 179 86

Figure S97.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S98.  Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 14(9P23) MUTATED 44 56 23 24
DEL PEAK 14(9P23) WILD-TYPE 100 78 172 13

Figure S98.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S99.  Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 15(9P21.3) MUTATED 12 35 112
DEL PEAK 15(9P21.3) WILD-TYPE 226 100 43

Figure S99.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S100.  Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 15(9P21.3) MUTATED 6 24 68
DEL PEAK 15(9P21.3) WILD-TYPE 122 52 42

Figure S100.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S101.  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 108 62 75 80 79 43
DEL PEAK 15(9P21.3) MUTATED 18 40 31 22 22 10
DEL PEAK 15(9P21.3) WILD-TYPE 90 22 44 58 57 33

Figure S101.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S102.  Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 15(9P21.3) MUTATED 34 45 64
DEL PEAK 15(9P21.3) WILD-TYPE 87 151 66

Figure S102.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S103.  Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 15(9P21.3) MUTATED 16 27 114
DEL PEAK 15(9P21.3) WILD-TYPE 90 195 81

Figure S103.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S104.  Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 15(9P21.3) MUTATED 38 35 84
DEL PEAK 15(9P21.3) WILD-TYPE 123 202 41

Figure S104.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S105.  Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 15(9P21.3) MUTATED 29 26 98
DEL PEAK 15(9P21.3) WILD-TYPE 95 178 84

Figure S105.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S106.  Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 15(9P21.3) MUTATED 48 55 24 26
DEL PEAK 15(9P21.3) WILD-TYPE 96 79 171 11

Figure S106.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S107.  Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 16(10Q23.31) MUTATED 17 29 50
DEL PEAK 16(10Q23.31) WILD-TYPE 221 106 105

Figure S107.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S108.  Gene #28: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 16(10Q23.31) MUTATED 21 35 23 15
DEL PEAK 16(10Q23.31) WILD-TYPE 123 99 172 22

Figure S108.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S109.  Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 17(13Q14.2) MUTATED 11 23 48
DEL PEAK 17(13Q14.2) WILD-TYPE 227 112 107

Figure S109.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.021

Table S110.  Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 17(13Q14.2) MUTATED 8 16 27
DEL PEAK 17(13Q14.2) WILD-TYPE 120 60 83

Figure S110.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S111.  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 108 62 75 80 79 43
DEL PEAK 17(13Q14.2) MUTATED 3 22 15 14 11 7
DEL PEAK 17(13Q14.2) WILD-TYPE 105 40 60 66 68 36

Figure S111.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.023

Table S112.  Gene #29: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 17(13Q14.2) MUTATED 15 20 37
DEL PEAK 17(13Q14.2) WILD-TYPE 106 176 93

Figure S112.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S113.  Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 17(13Q14.2) MUTATED 13 19 50
DEL PEAK 17(13Q14.2) WILD-TYPE 93 203 145

Figure S113.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S114.  Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 17(13Q14.2) MUTATED 23 16 43
DEL PEAK 17(13Q14.2) WILD-TYPE 138 221 82

Figure S114.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S115.  Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 17(13Q14.2) MUTATED 14 16 50
DEL PEAK 17(13Q14.2) WILD-TYPE 110 188 132

Figure S115.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S116.  Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 17(13Q14.2) MUTATED 20 33 14 13
DEL PEAK 17(13Q14.2) WILD-TYPE 124 101 181 24

Figure S116.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.018

Table S117.  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 S117.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.1

Table S118.  Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 18(14Q31.1) MUTATED 4 7 1 11 5 1 2
DEL PEAK 18(14Q31.1) WILD-TYPE 7 5 3 0 8 8 8

Figure S118.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S119.  Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 18(14Q31.1) MUTATED 70 47 111
DEL PEAK 18(14Q31.1) WILD-TYPE 168 88 44

Figure S119.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S120.  Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 18(14Q31.1) MUTATED 32 36 65
DEL PEAK 18(14Q31.1) WILD-TYPE 96 40 45

Figure S120.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S121.  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 108 62 75 80 79 43
DEL PEAK 18(14Q31.1) MUTATED 37 41 56 27 26 13
DEL PEAK 18(14Q31.1) WILD-TYPE 71 21 19 53 53 30

Figure S121.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S122.  Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 18(14Q31.1) MUTATED 69 64 67
DEL PEAK 18(14Q31.1) WILD-TYPE 52 132 63

Figure S122.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S123.  Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 222 195
DEL PEAK 18(14Q31.1) MUTATED 19 73 132
DEL PEAK 18(14Q31.1) WILD-TYPE 87 149 63

Figure S123.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S124.  Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 237 125
DEL PEAK 18(14Q31.1) MUTATED 71 78 75
DEL PEAK 18(14Q31.1) WILD-TYPE 90 159 50

Figure S124.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S125.  Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 18(14Q31.1) MUTATED 38 66 118
DEL PEAK 18(14Q31.1) WILD-TYPE 86 138 64

Figure S125.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S126.  Gene #30: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 18(14Q31.1) MUTATED 52 84 62 24
DEL PEAK 18(14Q31.1) WILD-TYPE 92 50 133 13

Figure S126.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 528

  • 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

Q value calculation

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

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