Correlation between copy number variation genes (focal events) and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1BK19R0
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/C1BK19R0
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 40 focal events and 10 molecular subtypes across 560 patients, 79 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p cnv correlated to 'CN_CNMF'.

  • 1q cnv correlated to 'CN_CNMF'.

  • 2p cnv correlated to 'CN_CNMF'.

  • 2q cnv correlated to 'CN_CNMF'.

  • 3p cnv correlated to 'CN_CNMF'.

  • 3q cnv correlated to 'CN_CNMF'.

  • 4p cnv correlated to 'CN_CNMF'.

  • 4q cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 5p cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 5q cnv correlated to 'CN_CNMF'.

  • 6p cnv correlated to 'CN_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

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

  • 7q cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 8p cnv correlated to 'CN_CNMF'.

  • 8q cnv correlated to 'CN_CNMF'.

  • 9q cnv correlated to 'CN_CNMF'.

  • 10p cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 10q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CNMF'.

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

  • 11q cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 12p cnv correlated to 'CN_CNMF'.

  • 12q cnv correlated to 'CN_CNMF'.

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

  • 14q cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 15q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 16p cnv correlated to 'CN_CNMF'.

  • 16q cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 17p cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 17q cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 20p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 20q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 21q cnv correlated to 'CN_CNMF'.

  • 22q cnv correlated to 'CN_CNMF'.

  • xq cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 79 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
10q 481 (86%) 79 1.1e-07
(4.02e-05) 		1.82e-06
(0.000652) 		0.00917
(1.00) 		0.000184
(0.0612) 		2.77e-23
(1.1e-20) 		0.0361
(1.00) 		0.0005
(0.162) 		0.0448
(1.00) 		0.175
(1.00) 		0.161
(1.00)
7p 463 (83%) 97 6.76e-05
(0.0228) 		1.6e-05
(0.00555) 		0.00141
(0.452) 		3.25e-07
(0.000118) 		3.85e-09
(1.45e-06) 		0.00731
(1.00) 		0.00223
(0.697) 		0.294
(1.00) 		0.0162
(1.00) 		0.00177
(0.564)
13q 191 (34%) 369 6.34e-06
(0.00222) 		0.000102
(0.0342) 		0.701
(1.00) 		0.147
(1.00) 		1.08e-24
(4.31e-22) 		0.000362
(0.119) 		0.677
(1.00) 		0.06
(1.00) 		0.13
(1.00) 		0.446
(1.00)
15q 123 (22%) 437 1.47e-06
(0.000529) 		1.97e-06
(0.000705) 		0.0512
(1.00) 		0.00969
(1.00) 		7.08e-13
(2.76e-10) 		1.54e-05
(0.00533) 		0.14
(1.00) 		0.0129
(1.00) 		0.061
(1.00) 		0.196
(1.00)
19p 246 (44%) 314 1.35e-07
(4.95e-05) 		0.000385
(0.126) 		0.0173
(1.00) 		0.00538
(1.00) 		2.58e-10
(9.87e-08) 		0.152
(1.00) 		0.00724
(1.00) 		5.61e-05
(0.0191) 		0.397
(1.00) 		0.0519
(1.00)
19q 227 (41%) 333 4.99e-07
(0.000181) 		2.48e-05
(0.00855) 		0.163
(1.00) 		0.0794
(1.00) 		1.89e-09
(7.15e-07) 		0.201
(1.00) 		0.0208
(1.00) 		0.000373
(0.122) 		0.169
(1.00) 		0.0814
(1.00)
20p 235 (42%) 325 2.65e-05
(0.00913) 		2.37e-06
(0.000847) 		0.0698
(1.00) 		0.000216
(0.0716) 		0.000361
(0.119) 		0.113
(1.00) 		0.128
(1.00) 		0.021
(1.00) 		0.917
(1.00) 		0.00509
(1.00)
20q 231 (41%) 329 7.18e-06
(0.00251) 		2.84e-06
(0.00101) 		0.0102
(1.00) 		6.24e-05
(0.0211) 		0.000187
(0.062) 		0.0349
(1.00) 		0.0886
(1.00) 		0.0179
(1.00) 		0.967
(1.00) 		0.00379
(1.00)
10p 479 (86%) 81 3.53e-05
(0.0121) 		0.00212
(0.664) 		0.0744
(1.00) 		0.000129
(0.0431) 		8.14e-18
(3.23e-15) 		0.0745
(1.00) 		0.0148
(1.00) 		0.0738
(1.00) 		0.25
(1.00) 		0.11
(1.00)
11p 114 (20%) 446 8.9e-07
(0.000322) 		5.45e-05
(0.0186) 		0.658
(1.00) 		0.00808
(1.00) 		2.86e-16
(1.13e-13) 		0.159
(1.00) 		0.833
(1.00) 		0.0456
(1.00) 		0.252
(1.00) 		0.33
(1.00)
18p 126 (22%) 434 3.89e-08
(1.44e-05) 		8.39e-06
(0.00293) 		0.0279
(1.00) 		0.243
(1.00) 		2.64e-14
(1.04e-11) 		0.138
(1.00) 		0.059
(1.00) 		0.00521
(1.00) 		0.115
(1.00) 		0.734
(1.00)
18q 118 (21%) 442 2.66e-06
(0.000946) 		8.75e-05
(0.0294) 		0.306
(1.00) 		0.184
(1.00) 		2.63e-12
(1.02e-09) 		0.243
(1.00) 		0.0528
(1.00) 		0.00418
(1.00) 		0.406
(1.00) 		1
(1.00)
4q 87 (16%) 473 0.000628
(0.202) 		0.00269
(0.829) 		0.13
(1.00) 		0.0681
(1.00) 		2.69e-06
(0.000956) 		0.0437
(1.00) 		0.976
(1.00) 		0.48
(1.00) 		0.173
(1.00) 		0.306
(1.00)
5p 90 (16%) 470 0.000242
(0.0797) 		0.139
(1.00) 		0.432
(1.00) 		0.38
(1.00) 		6.07e-09
(2.27e-06) 		0.0492
(1.00) 		0.867
(1.00) 		0.904
(1.00) 		0.0819
(1.00) 		0.572
(1.00)
7q 466 (83%) 94 1.29e-05
(0.0045) 		0.00196
(0.617) 		0.00322
(0.985) 		0.00175
(0.559) 		1.43e-07
(5.22e-05) 		0.0024
(0.747) 		0.11
(1.00) 		0.178
(1.00) 		0.0513
(1.00) 		0.00799
(1.00)
11q 105 (19%) 455 3.08e-06
(0.00109) 		0.000816
(0.262) 		0.875
(1.00) 		0.0702
(1.00) 		8e-15
(3.15e-12) 		0.65
(1.00) 		0.94
(1.00) 		0.13
(1.00) 		0.45
(1.00) 		0.393
(1.00)
14q 163 (29%) 397 6.17e-06
(0.00217) 		0.0019
(0.6) 		0.539
(1.00) 		0.632
(1.00) 		3.84e-28
(1.54e-25) 		0.0128
(1.00) 		0.89
(1.00) 		0.325
(1.00) 		0.218
(1.00) 		0.0066
(1.00)
16q 117 (21%) 443 0.000518
(0.167) 		0.157
(1.00) 		0.867
(1.00) 		0.422
(1.00) 		1.25e-06
(0.00045) 		0.815
(1.00) 		0.0791
(1.00) 		0.356
(1.00) 		0.847
(1.00) 		0.501
(1.00)
17p 108 (19%) 452 0.000463
(0.15) 		0.213
(1.00) 		0.637
(1.00) 		0.126
(1.00) 		3.26e-15
(1.29e-12) 		0.0169
(1.00) 		0.121
(1.00) 		0.0805
(1.00) 		0.87
(1.00) 		0.696
(1.00)
1p 98 (18%) 462 0.405
(1.00) 		0.336
(1.00) 		0.465
(1.00) 		0.138
(1.00) 		1.14e-10
(4.36e-08) 		0.387
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.665
(1.00) 		0.825
(1.00)
1q 103 (18%) 457 0.117
(1.00) 		0.368
(1.00) 		0.279
(1.00) 		0.238
(1.00) 		1.11e-13
(4.35e-11) 		0.247
(1.00) 		0.682
(1.00) 		0.866
(1.00) 		1
(1.00) 		0.86
(1.00)
2p 66 (12%) 494 0.0336
(1.00) 		0.155
(1.00) 		0.309
(1.00) 		0.937
(1.00) 		2.35e-09
(8.88e-07) 		0.00246
(0.761) 		0.884
(1.00) 		0.76
(1.00) 		0.592
(1.00) 		0.734
(1.00)
2q 65 (12%) 495 0.0563
(1.00) 		0.232
(1.00) 		0.25
(1.00) 		0.929
(1.00) 		5.86e-09
(2.2e-06) 		0.00246
(0.761) 		0.984
(1.00) 		0.904
(1.00) 		0.592
(1.00) 		0.734
(1.00)
3p 96 (17%) 464 0.027
(1.00) 		0.113
(1.00) 		0.961
(1.00) 		0.297
(1.00) 		2.06e-12
(8.01e-10) 		0.0235
(1.00) 		0.232
(1.00) 		0.3
(1.00) 		0.582
(1.00) 		0.337
(1.00)
3q 96 (17%) 464 0.00909
(1.00) 		0.079
(1.00) 		0.809
(1.00) 		0.0582
(1.00) 		7.83e-13
(3.05e-10) 		0.0219
(1.00) 		0.484
(1.00) 		0.3
(1.00) 		0.479
(1.00) 		0.365
(1.00)
4p 88 (16%) 472 0.0231
(1.00) 		0.0326
(1.00) 		0.202
(1.00) 		0.172
(1.00) 		3e-05
(0.0103) 		0.862
(1.00) 		0.702
(1.00) 		0.547
(1.00) 		0.638
(1.00) 		0.408
(1.00)
5q 83 (15%) 477 0.00187
(0.594) 		0.157
(1.00) 		0.392
(1.00) 		0.713
(1.00) 		2.62e-08
(9.68e-06) 		0.0216
(1.00) 		0.858
(1.00) 		0.591
(1.00) 		0.035
(1.00) 		0.765
(1.00)
6p 107 (19%) 453 0.121
(1.00) 		0.0904
(1.00) 		0.917
(1.00) 		0.987
(1.00) 		7.34e-14
(2.88e-11) 		0.333
(1.00) 		0.849
(1.00) 		0.0704
(1.00) 		0.847
(1.00) 		0.269
(1.00)
6q 143 (26%) 417 0.177
(1.00) 		0.273
(1.00) 		0.776
(1.00) 		0.534
(1.00) 		3.71e-12
(1.43e-09) 		0.877
(1.00) 		0.903
(1.00) 		0.128
(1.00) 		0.677
(1.00) 		0.592
(1.00)
8p 109 (19%) 451 0.0232
(1.00) 		0.0247
(1.00) 		0.543
(1.00) 		0.0274
(1.00) 		3.06e-10
(1.17e-07) 		0.0946
(1.00) 		0.642
(1.00) 		0.298
(1.00) 		0.669
(1.00) 		0.958
(1.00)
8q 100 (18%) 460 0.00209
(0.656) 		0.00797
(1.00) 		0.241
(1.00) 		0.0318
(1.00) 		4.66e-10
(1.77e-07) 		0.0305
(1.00) 		0.71
(1.00) 		0.181
(1.00) 		0.669
(1.00) 		0.958
(1.00)
9q 158 (28%) 402 0.974
(1.00) 		0.738
(1.00) 		0.0947
(1.00) 		0.879
(1.00) 		6.62e-05
(0.0224) 		0.0583
(1.00) 		0.99
(1.00) 		0.324
(1.00) 		0.48
(1.00) 		0.197
(1.00)
12p 117 (21%) 443 0.0294
(1.00) 		0.185
(1.00) 		0.457
(1.00) 		0.684
(1.00) 		7.4e-09
(2.74e-06) 		0.28
(1.00) 		0.0843
(1.00) 		0.111
(1.00) 		0.0813
(1.00) 		0.327
(1.00)
12q 105 (19%) 455 0.167
(1.00) 		0.358
(1.00) 		0.292
(1.00) 		0.52
(1.00) 		5.8e-09
(2.18e-06) 		0.219
(1.00) 		0.124
(1.00) 		0.244
(1.00) 		0.254
(1.00) 		0.495
(1.00)
16p 99 (18%) 461 0.0029
(0.89) 		0.0745
(1.00) 		0.63
(1.00) 		0.647
(1.00) 		6.01e-08
(2.21e-05) 		0.421
(1.00) 		0.199
(1.00) 		0.327
(1.00) 		0.645
(1.00) 		0.598
(1.00)
17q 98 (18%) 462 0.00683
(1.00) 		0.865
(1.00) 		0.655
(1.00) 		0.643
(1.00) 		7.25e-12
(2.79e-09) 		0.0492
(1.00) 		0.468
(1.00) 		0.455
(1.00) 		0.475
(1.00) 		0.508
(1.00)
21q 102 (18%) 458 0.0557
(1.00) 		0.119
(1.00) 		0.67
(1.00) 		0.198
(1.00) 		6.55e-09
(2.44e-06) 		0.357
(1.00) 		0.54
(1.00) 		0.728
(1.00) 		0.0295
(1.00) 		0.178
(1.00)
22q 207 (37%) 353 0.0351
(1.00) 		0.485
(1.00) 		0.265
(1.00) 		0.376
(1.00) 		3.76e-10
(1.43e-07) 		0.238
(1.00) 		0.71
(1.00) 		0.183
(1.00) 		0.475
(1.00) 		0.276
(1.00)
xq 118 (21%) 442 0.00511
(1.00) 		0.256
(1.00) 		0.283
(1.00) 		0.37
(1.00) 		6.05e-09
(2.26e-06) 		0.169
(1.00) 		0.961
(1.00) 		0.733
(1.00) 		0.612
(1.00) 		0.8
(1.00)
9p 241 (43%) 319 0.619
(1.00) 		0.602
(1.00) 		0.487
(1.00) 		0.331
(1.00) 		0.218
(1.00) 		0.853
(1.00) 		0.76
(1.00) 		0.205
(1.00) 		0.105
(1.00) 		0.216
(1.00)
'1p' versus 'CN_CNMF'

P value = 1.14e-10 (Fisher's exact test), Q value = 4.4e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
1P MUTATED 53 17 28
1P WILD-TYPE 97 203 162

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

'1q' versus 'CN_CNMF'

P value = 1.11e-13 (Fisher's exact test), Q value = 4.4e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
1Q MUTATED 59 16 28
1Q WILD-TYPE 91 204 162

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

'2p' versus 'CN_CNMF'

P value = 2.35e-09 (Fisher's exact test), Q value = 8.9e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
2P MUTATED 39 9 18
2P WILD-TYPE 111 211 172

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

'2q' versus 'CN_CNMF'

P value = 5.86e-09 (Fisher's exact test), Q value = 2.2e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
2Q MUTATED 38 9 18
2Q WILD-TYPE 112 211 172

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

'3p' versus 'CN_CNMF'

P value = 2.06e-12 (Fisher's exact test), Q value = 8e-10

Table S5.  Gene #5: '3p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
3P MUTATED 52 12 32
3P WILD-TYPE 98 208 158

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

'3q' versus 'CN_CNMF'

P value = 7.83e-13 (Fisher's exact test), Q value = 3e-10

Table S6.  Gene #6: '3q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
3Q MUTATED 53 12 31
3Q WILD-TYPE 97 208 159

Figure S6.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #5: 'CN_CNMF'

'4p' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.01

Table S7.  Gene #7: '4p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
4P MUTATED 41 21 26
4P WILD-TYPE 109 199 164

Figure S7.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #5: 'CN_CNMF'

'4q' versus 'MRNA_CNMF'

P value = 0.000628 (Fisher's exact test), Q value = 0.2

Table S8.  Gene #8: '4q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
4Q MUTATED 17 29 17 18
4Q WILD-TYPE 130 67 135 95

Figure S8.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q' versus 'CN_CNMF'

P value = 2.69e-06 (Fisher's exact test), Q value = 0.00096

Table S9.  Gene #8: '4q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
4Q MUTATED 41 17 29
4Q WILD-TYPE 109 203 161

Figure S9.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #5: 'CN_CNMF'

'5p' versus 'MRNA_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.08

Table S10.  Gene #9: '5p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
5P MUTATED 23 29 13 19
5P WILD-TYPE 124 67 139 94

Figure S10.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p' versus 'CN_CNMF'

P value = 6.07e-09 (Fisher's exact test), Q value = 2.3e-06

Table S11.  Gene #9: '5p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
5P MUTATED 44 13 33
5P WILD-TYPE 106 207 157

Figure S11.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #5: 'CN_CNMF'

'5q' versus 'CN_CNMF'

P value = 2.62e-08 (Fisher's exact test), Q value = 9.7e-06

Table S12.  Gene #10: '5q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
5Q MUTATED 41 12 30
5Q WILD-TYPE 109 208 160

Figure S12.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #5: 'CN_CNMF'

'6p' versus 'CN_CNMF'

P value = 7.34e-14 (Fisher's exact test), Q value = 2.9e-11

Table S13.  Gene #11: '6p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
6P MUTATED 60 16 31
6P WILD-TYPE 90 204 159

Figure S13.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #5: 'CN_CNMF'

'6q' versus 'CN_CNMF'

P value = 3.71e-12 (Fisher's exact test), Q value = 1.4e-09

Table S14.  Gene #12: '6q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
6Q MUTATED 71 30 42
6Q WILD-TYPE 79 190 148

Figure S14.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #5: 'CN_CNMF'

'7p' versus 'MRNA_CNMF'

P value = 6.76e-05 (Fisher's exact test), Q value = 0.023

Table S15.  Gene #13: '7p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7P MUTATED 135 69 130 85
7P WILD-TYPE 12 27 22 28

Figure S15.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0056

Table S16.  Gene #13: '7p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
7P MUTATED 100 122 197
7P WILD-TYPE 17 49 23

Figure S16.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p' versus 'MIR_CHIERARCHICAL'

P value = 3.25e-07 (Fisher's exact test), Q value = 0.00012

Table S17.  Gene #13: '7p' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
7P MUTATED 162 130 161
7P WILD-TYPE 15 54 24

Figure S17.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p' versus 'CN_CNMF'

P value = 3.85e-09 (Fisher's exact test), Q value = 1.5e-06

Table S18.  Gene #13: '7p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
7P MUTATED 137 196 130
7P WILD-TYPE 13 24 60

Figure S18.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'CN_CNMF'

'7q' versus 'MRNA_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0045

Table S19.  Gene #14: '7q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7Q MUTATED 135 65 131 89
7Q WILD-TYPE 12 31 21 24

Figure S19.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q' versus 'CN_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 5.2e-05

Table S20.  Gene #14: '7q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
7Q MUTATED 133 199 134
7Q WILD-TYPE 17 21 56

Figure S20.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #5: 'CN_CNMF'

'8p' versus 'CN_CNMF'

P value = 3.06e-10 (Fisher's exact test), Q value = 1.2e-07

Table S21.  Gene #15: '8p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
8P MUTATED 55 19 35
8P WILD-TYPE 95 201 155

Figure S21.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #5: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 4.66e-10 (Fisher's exact test), Q value = 1.8e-07

Table S22.  Gene #16: '8q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
8Q MUTATED 51 16 33
8Q WILD-TYPE 99 204 157

Figure S22.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'CN_CNMF'

'9q' versus 'CN_CNMF'

P value = 6.62e-05 (Fisher's exact test), Q value = 0.022

Table S23.  Gene #18: '9q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
9Q MUTATED 63 47 48
9Q WILD-TYPE 87 173 142

Figure S23.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #5: 'CN_CNMF'

'10p' versus 'MRNA_CNMF'

P value = 3.53e-05 (Fisher's exact test), Q value = 0.012

Table S24.  Gene #19: '10p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10P MUTATED 133 70 140 89
10P WILD-TYPE 14 26 12 24

Figure S24.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p' versus 'MIR_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.043

Table S25.  Gene #19: '10p' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
10P MUTATED 158 141 169
10P WILD-TYPE 19 43 16

Figure S25.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 8.14e-18 (Fisher's exact test), Q value = 3.2e-15

Table S26.  Gene #19: '10p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
10P MUTATED 140 212 127
10P WILD-TYPE 10 8 63

Figure S26.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'CN_CNMF'

'10q' versus 'MRNA_CNMF'

P value = 1.1e-07 (Fisher's exact test), Q value = 4e-05

Table S27.  Gene #20: '10q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10Q MUTATED 133 69 145 88
10Q WILD-TYPE 14 27 7 25

Figure S27.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q' versus 'MRNA_CHIERARCHICAL'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.00065

Table S28.  Gene #20: '10q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
10Q MUTATED 113 130 192
10Q WILD-TYPE 4 41 28

Figure S28.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q' versus 'MIR_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.061

Table S29.  Gene #20: '10q' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
10Q MUTATED 160 142 168
10Q WILD-TYPE 17 42 17

Figure S29.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 2.77e-23 (Fisher's exact test), Q value = 1.1e-20

Table S30.  Gene #20: '10q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
10Q MUTATED 140 217 124
10Q WILD-TYPE 10 3 66

Figure S30.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'CN_CNMF'

'10q' versus 'RPPA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.16

Table S31.  Gene #20: '10q' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
10Q MUTATED 49 43 44 41
10Q WILD-TYPE 5 15 0 4

Figure S31.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'RPPA_CNMF'

'11p' versus 'MRNA_CNMF'

P value = 8.9e-07 (Fisher's exact test), Q value = 0.00032

Table S32.  Gene #21: '11p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11P MUTATED 32 36 13 25
11P WILD-TYPE 115 60 139 88

Figure S32.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p' versus 'MRNA_CHIERARCHICAL'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.019

Table S33.  Gene #21: '11p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
11P MUTATED 11 52 43
11P WILD-TYPE 106 119 177

Figure S33.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 2.86e-16 (Fisher's exact test), Q value = 1.1e-13

Table S34.  Gene #21: '11p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
11P MUTATED 61 12 41
11P WILD-TYPE 89 208 149

Figure S34.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #5: 'CN_CNMF'

'11q' versus 'MRNA_CNMF'

P value = 3.08e-06 (Fisher's exact test), Q value = 0.0011

Table S35.  Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11Q MUTATED 33 33 12 21
11Q WILD-TYPE 114 63 140 92

Figure S35.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q' versus 'CN_CNMF'

P value = 8e-15 (Fisher's exact test), Q value = 3.2e-12

Table S36.  Gene #22: '11q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
11Q MUTATED 59 13 33
11Q WILD-TYPE 91 207 157

Figure S36.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #5: 'CN_CNMF'

'12p' versus 'CN_CNMF'

P value = 7.4e-09 (Fisher's exact test), Q value = 2.7e-06

Table S37.  Gene #23: '12p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
12P MUTATED 57 25 35
12P WILD-TYPE 93 195 155

Figure S37.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'CN_CNMF'

'12q' versus 'CN_CNMF'

P value = 5.8e-09 (Fisher's exact test), Q value = 2.2e-06

Table S38.  Gene #24: '12q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
12Q MUTATED 53 21 31
12Q WILD-TYPE 97 199 159

Figure S38.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #5: 'CN_CNMF'

'13q' versus 'MRNA_CNMF'

P value = 6.34e-06 (Fisher's exact test), Q value = 0.0022

Table S39.  Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
13Q MUTATED 61 39 27 45
13Q WILD-TYPE 86 57 125 68

Figure S39.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.034

Table S40.  Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
13Q MUTATED 21 67 84
13Q WILD-TYPE 96 104 136

Figure S40.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 1.08e-24 (Fisher's exact test), Q value = 4.3e-22

Table S41.  Gene #25: '13q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
13Q MUTATED 97 28 66
13Q WILD-TYPE 53 192 124

Figure S41.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #5: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000362 (Fisher's exact test), Q value = 0.12

Table S42.  Gene #25: '13q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 41 33
13Q MUTATED 7 7 19
13Q WILD-TYPE 28 34 14

Figure S42.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q' versus 'MRNA_CNMF'

P value = 6.17e-06 (Fisher's exact test), Q value = 0.0022

Table S43.  Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
14Q MUTATED 52 39 23 41
14Q WILD-TYPE 95 57 129 72

Figure S43.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q' versus 'CN_CNMF'

P value = 3.84e-28 (Fisher's exact test), Q value = 1.5e-25

Table S44.  Gene #26: '14q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
14Q MUTATED 90 16 57
14Q WILD-TYPE 60 204 133

Figure S44.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'CN_CNMF'

'15q' versus 'MRNA_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00053

Table S45.  Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
15Q MUTATED 35 33 14 35
15Q WILD-TYPE 112 63 138 78

Figure S45.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q' versus 'MRNA_CHIERARCHICAL'

P value = 1.97e-06 (Fisher's exact test), Q value = 7e-04

Table S46.  Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
15Q MUTATED 11 59 47
15Q WILD-TYPE 106 112 173

Figure S46.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 7.08e-13 (Fisher's exact test), Q value = 2.8e-10

Table S47.  Gene #27: '15q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
15Q MUTATED 64 21 38
15Q WILD-TYPE 86 199 152

Figure S47.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0053

Table S48.  Gene #27: '15q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 41 33
15Q MUTATED 2 1 13
15Q WILD-TYPE 33 40 20

Figure S48.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16p' versus 'CN_CNMF'

P value = 6.01e-08 (Fisher's exact test), Q value = 2.2e-05

Table S49.  Gene #28: '16p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
16P MUTATED 46 17 36
16P WILD-TYPE 104 203 154

Figure S49.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #5: 'CN_CNMF'

'16q' versus 'MRNA_CNMF'

P value = 0.000518 (Fisher's exact test), Q value = 0.17

Table S50.  Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
16Q MUTATED 34 31 17 27
16Q WILD-TYPE 113 65 135 86

Figure S50.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q' versus 'CN_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00045

Table S51.  Gene #29: '16q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
16Q MUTATED 49 24 44
16Q WILD-TYPE 101 196 146

Figure S51.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #5: 'CN_CNMF'

'17p' versus 'MRNA_CNMF'

P value = 0.000463 (Fisher's exact test), Q value = 0.15

Table S52.  Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
17P MUTATED 34 27 14 25
17P WILD-TYPE 113 69 138 88

Figure S52.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'CN_CNMF'

P value = 3.26e-15 (Fisher's exact test), Q value = 1.3e-12

Table S53.  Gene #30: '17p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
17P MUTATED 60 13 35
17P WILD-TYPE 90 207 155

Figure S53.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'CN_CNMF'

'17q' versus 'CN_CNMF'

P value = 7.25e-12 (Fisher's exact test), Q value = 2.8e-09

Table S54.  Gene #31: '17q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
17Q MUTATED 54 15 29
17Q WILD-TYPE 96 205 161

Figure S54.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #5: 'CN_CNMF'

'18p' versus 'MRNA_CNMF'

P value = 3.89e-08 (Fisher's exact test), Q value = 1.4e-05

Table S55.  Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18P MUTATED 30 40 14 30
18P WILD-TYPE 117 56 138 83

Figure S55.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p' versus 'MRNA_CHIERARCHICAL'

P value = 8.39e-06 (Fisher's exact test), Q value = 0.0029

Table S56.  Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
18P MUTATED 9 51 54
18P WILD-TYPE 108 120 166

Figure S56.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 2.64e-14 (Fisher's exact test), Q value = 1e-11

Table S57.  Gene #32: '18p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
18P MUTATED 61 16 49
18P WILD-TYPE 89 204 141

Figure S57.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #5: 'CN_CNMF'

'18q' versus 'MRNA_CNMF'

P value = 2.66e-06 (Fisher's exact test), Q value = 0.00095

Table S58.  Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18Q MUTATED 27 35 15 31
18Q WILD-TYPE 120 61 137 82

Figure S58.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q' versus 'MRNA_CHIERARCHICAL'

P value = 8.75e-05 (Fisher's exact test), Q value = 0.029

Table S59.  Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
18Q MUTATED 10 49 49
18Q WILD-TYPE 107 122 171

Figure S59.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 2.63e-12 (Fisher's exact test), Q value = 1e-09

Table S60.  Gene #33: '18q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
18Q MUTATED 58 17 43
18Q WILD-TYPE 92 203 147

Figure S60.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #5: 'CN_CNMF'

'19p' versus 'MRNA_CNMF'

P value = 1.35e-07 (Fisher's exact test), Q value = 4.9e-05

Table S61.  Gene #34: '19p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19P MUTATED 56 44 93 30
19P WILD-TYPE 91 52 59 83

Figure S61.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p' versus 'MRNA_CHIERARCHICAL'

P value = 0.000385 (Fisher's exact test), Q value = 0.13

Table S62.  Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
19P MUTATED 68 59 96
19P WILD-TYPE 49 112 124

Figure S62.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 2.58e-10 (Fisher's exact test), Q value = 9.9e-08

Table S63.  Gene #34: '19p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
19P MUTATED 55 134 57
19P WILD-TYPE 95 86 133

Figure S63.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #5: 'CN_CNMF'

'19p' versus 'RPPA_CHIERARCHICAL'

P value = 5.61e-05 (Fisher's exact test), Q value = 0.019

Table S64.  Gene #34: '19p' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
19P MUTATED 42 9 36
19P WILD-TYPE 22 24 68

Figure S64.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q' versus 'MRNA_CNMF'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00018

Table S65.  Gene #35: '19q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19Q MUTATED 53 38 87 27
19Q WILD-TYPE 94 58 65 86

Figure S65.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q' versus 'MRNA_CHIERARCHICAL'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.0086

Table S66.  Gene #35: '19q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
19Q MUTATED 64 48 93
19Q WILD-TYPE 53 123 127

Figure S66.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 1.89e-09 (Fisher's exact test), Q value = 7.2e-07

Table S67.  Gene #35: '19q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
19Q MUTATED 48 125 54
19Q WILD-TYPE 102 95 136

Figure S67.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #5: 'CN_CNMF'

'19q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000373 (Fisher's exact test), Q value = 0.12

Table S68.  Gene #35: '19q' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
19Q MUTATED 36 7 31
19Q WILD-TYPE 28 26 73

Figure S68.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p' versus 'MRNA_CNMF'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.0091

Table S69.  Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20P MUTATED 55 36 86 32
20P WILD-TYPE 92 60 66 81

Figure S69.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p' versus 'MRNA_CHIERARCHICAL'

P value = 2.37e-06 (Fisher's exact test), Q value = 0.00085

Table S70.  Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
20P MUTATED 70 51 88
20P WILD-TYPE 47 120 132

Figure S70.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p' versus 'MIR_CHIERARCHICAL'

P value = 0.000216 (Fisher's exact test), Q value = 0.072

Table S71.  Gene #36: '20p' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
20P MUTATED 90 56 84
20P WILD-TYPE 87 128 101

Figure S71.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 0.000361 (Fisher's exact test), Q value = 0.12

Table S72.  Gene #36: '20p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
20P MUTATED 70 107 58
20P WILD-TYPE 80 113 132

Figure S72.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'CN_CNMF'

'20q' versus 'MRNA_CNMF'

P value = 7.18e-06 (Fisher's exact test), Q value = 0.0025

Table S73.  Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20Q MUTATED 54 36 86 30
20Q WILD-TYPE 93 60 66 83

Figure S73.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q' versus 'MRNA_CHIERARCHICAL'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.001

Table S74.  Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
20Q MUTATED 69 50 87
20Q WILD-TYPE 48 121 133

Figure S74.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q' versus 'MIR_CHIERARCHICAL'

P value = 6.24e-05 (Fisher's exact test), Q value = 0.021

Table S75.  Gene #37: '20q' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
20Q MUTATED 89 53 84
20Q WILD-TYPE 88 131 101

Figure S75.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.062

Table S76.  Gene #37: '20q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
20Q MUTATED 68 107 56
20Q WILD-TYPE 82 113 134

Figure S76.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #5: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 6.55e-09 (Fisher's exact test), Q value = 2.4e-06

Table S77.  Gene #38: '21q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
21Q MUTATED 49 17 36
21Q WILD-TYPE 101 203 154

Figure S77.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #5: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 3.76e-10 (Fisher's exact test), Q value = 1.4e-07

Table S78.  Gene #39: '22q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
22Q MUTATED 86 52 69
22Q WILD-TYPE 64 168 121

Figure S78.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #5: 'CN_CNMF'

'xq' versus 'CN_CNMF'

P value = 6.05e-09 (Fisher's exact test), Q value = 2.3e-06

Table S79.  Gene #40: 'xq' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
XQ MUTATED 59 33 26
XQ WILD-TYPE 91 187 164

Figure S79.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 560

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 10

  • 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.

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] 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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