Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1ZS2V0S
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZS2V0S
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 76 arm-level events and 12 molecular subtypes across 365 patients, 110 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 3p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 3q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 5p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 15q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 18p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 18q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'METHLYATION_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 5q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xq loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 76 arm-level 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, 110 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 Chi-square test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test
1p loss 133 (36%) 232 0.0286
(1.00) 		0.000173
(0.124) 		1.8e-53
(1.46e-50) 		4.24e-72
(3.45e-69) 		0.000311
(0.22) 		0.142
(1.00) 		1.25e-37
(1.01e-34) 		3.35e-44
(2.71e-41) 		3.37e-10
(2.66e-07) 		1.84e-05
(0.0136) 		1.49e-10
(1.18e-07) 		2.06e-09
(1.62e-06)
19q loss 148 (41%) 217 0.0908
(1.00) 		0.0786
(1.00) 		5.43e-51
(4.4e-48) 		6.46e-59
(5.25e-56) 		0.0216
(1.00) 		0.138
(1.00) 		7.28e-32
(5.86e-29) 		3.49e-38
(2.82e-35) 		1.57e-06
(0.00118) 		4.68e-05
(0.0342) 		1.48e-09
(1.16e-06) 		1.06e-07
(8.15e-05)
10p loss 57 (16%) 308 0.271
(1.00) 		0.561
(1.00) 		1.28e-27
(1.03e-24) 		8.28e-39
(6.7e-36) 		2.54e-07
(0.000194) 		0.00232
(1.00) 		6.32e-26
(5.06e-23) 		1.79e-06
(0.00134) 		0.00184
(1.00) 		0.0135
(1.00) 		9.23e-16
(7.37e-13) 		1.45e-06
(0.00109)
10q loss 69 (19%) 296 0.271
(1.00) 		0.561
(1.00) 		7.74e-26
(6.19e-23) 		3.61e-32
(2.91e-29) 		1.32e-06
(0.000999) 		0.000874
(0.599) 		4.32e-25
(3.45e-22) 		5.88e-08
(4.53e-05) 		0.00259
(1.00) 		0.0171
(1.00) 		8.72e-13
(6.93e-10) 		1.46e-06
(0.0011)
7p gain 89 (24%) 276 0.745
(1.00) 		0.648
(1.00) 		1.19e-28
(9.56e-26) 		9.44e-16
(7.52e-13) 		0.000379
(0.266) 		0.0131
(1.00) 		7.16e-12
(5.68e-09) 		2.17e-05
(0.016) 		0.00311
(1.00) 		0.029
(1.00) 		4.02e-05
(0.0295) 		1.53e-06
(0.00115)
20q gain 34 (9%) 331 4.21e-08
(3.25e-05) 		5.45e-11
(4.32e-08) 		0.000898
(0.615) 		0.11
(1.00) 		3.93e-08
(3.04e-05) 		9.62e-05
(0.0698) 		0.0177
(1.00) 		0.0198
(1.00) 		2.56e-05
(0.0188) 		5.89e-05
(0.043)
7q gain 114 (31%) 251 0.764
(1.00) 		0.495
(1.00) 		7.65e-29
(6.15e-26) 		2.51e-14
(2e-11) 		0.00531
(1.00) 		0.0386
(1.00) 		6.37e-08
(4.9e-05) 		1.1e-05
(0.0082) 		0.0114
(1.00) 		0.0878
(1.00) 		0.00132
(0.9) 		6.3e-05
(0.046)
4p loss 54 (15%) 311 1
(1.00) 		0.607
(1.00) 		1.14e-05
(0.00847) 		1.8e-08
(1.4e-05) 		0.415
(1.00) 		0.0353
(1.00) 		2.24e-08
(1.74e-05) 		1.16e-07
(8.88e-05) 		0.0178
(1.00) 		0.0506
(1.00) 		0.000147
(0.106) 		0.125
(1.00)
22q loss 39 (11%) 326 0.815
(1.00) 		0.106
(1.00) 		5.45e-08
(4.21e-05) 		6.42e-06
(0.00479) 		7.58e-05
(0.0552) 		0.0405
(1.00) 		4.95e-07
(0.000376) 		0.000146
(0.105) 		0.177
(1.00) 		0.0971
(1.00) 		0.000868
(0.596) 		0.0672
(1.00)
19q gain 18 (5%) 347 5.64e-08
(4.35e-05) 		2.18e-09
(1.7e-06) 		0.0571
(1.00) 		0.418
(1.00) 		1.13e-06
(0.000853) 		0.0015
(1.00) 		0.0387
(1.00) 		0.258
(1.00) 		3.4e-06
(0.00255) 		0.0182
(1.00)
4q loss 70 (19%) 295 1
(1.00) 		0.196
(1.00) 		0.000727
(0.501) 		5.78e-07
(0.00044) 		0.266
(1.00) 		0.0665
(1.00) 		4.1e-06
(0.00306) 		1.01e-06
(0.000769) 		0.00447
(1.00) 		0.00809
(1.00) 		7.43e-05
(0.0541) 		0.0543
(1.00)
11p loss 46 (13%) 319 1
(1.00) 		0.0138
(1.00) 		1.73e-06
(0.0013) 		2.98e-08
(2.31e-05) 		0.0127
(1.00) 		0.59
(1.00) 		1.73e-08
(1.35e-05) 		8.68e-05
(0.0631) 		0.0315
(1.00) 		0.0172
(1.00) 		0.00144
(0.973) 		0.104
(1.00)
14q loss 56 (15%) 309 0.467
(1.00) 		0.473
(1.00) 		0.000189
(0.136) 		0.00113
(0.774) 		0.0459
(1.00) 		0.148
(1.00) 		0.000245
(0.174) 		0.0866
(1.00) 		0.000348
(0.246) 		0.00216
(1.00) 		0.00011
(0.0796) 		0.128
(1.00)
10p gain 36 (10%) 329 1
(1.00) 		0.0879
(1.00) 		1.86e-11
(1.47e-08) 		1.75e-09
(1.37e-06) 		0.0233
(1.00) 		0.546
(1.00) 		4.1e-05
(0.03) 		0.000638
(0.443) 		0.315
(1.00) 		0.637
(1.00) 		0.00187
(1.00) 		0.157
(1.00)
19p gain 66 (18%) 299 0.221
(1.00) 		0.836
(1.00) 		4.4e-07
(0.000335) 		2.64e-09
(2.06e-06) 		0.567
(1.00) 		0.361
(1.00) 		0.000315
(0.222) 		0.0232
(1.00) 		0.316
(1.00) 		0.781
(1.00) 		0.182
(1.00) 		0.838
(1.00)
20p gain 34 (9%) 331 1.98e-08
(1.54e-05) 		1.22e-09
(9.65e-07) 		0.00101
(0.691) 		0.158
(1.00) 		4.37e-06
(0.00326) 		0.00139
(0.944) 		0.181
(1.00) 		0.0804
(1.00) 		0.000366
(0.258) 		0.00118
(0.806)
1q gain 14 (4%) 351 0.000264
(0.188) 		0.00413
(1.00) 		0.436
(1.00) 		0.738
(1.00) 		0.00022
(0.157) 		0.11
(1.00) 		0.537
(1.00) 		0.118
(1.00) 		0.11
(1.00) 		0.118
(1.00)
22q gain 12 (3%) 353 0.000567
(0.395) 		0.000169
(0.122) 		1
(1.00) 		0.56
(1.00) 		0.000674
(0.466) 		0.000678
(0.469) 		0.0114
(1.00) 		0.0898
(1.00) 		9.98e-05
(0.0723) 		0.0372
(1.00)
5p loss 28 (8%) 337 0.745
(1.00) 		0.0422
(1.00) 		1.75e-05
(0.0129) 		0.000268
(0.191) 		0.849
(1.00) 		1
(1.00) 		0.105
(1.00) 		0.019
(1.00) 		0.096
(1.00) 		0.19
(1.00) 		0.0335
(1.00) 		0.904
(1.00)
12q loss 35 (10%) 330 1
(1.00) 		0.0879
(1.00) 		9.07e-08
(6.97e-05) 		0.00022
(0.157) 		0.686
(1.00) 		0.69
(1.00) 		0.265
(1.00) 		0.00291
(1.00) 		0.219
(1.00) 		0.637
(1.00) 		0.371
(1.00) 		1
(1.00)
xq loss 49 (13%) 316 0.839
(1.00) 		0.022
(1.00) 		0.0423
(1.00) 		0.000467
(0.327) 		0.0874
(1.00) 		0.0143
(1.00) 		2.03e-05
(0.015) 		2.44e-05
(0.018) 		0.0896
(1.00) 		0.34
(1.00) 		0.113
(1.00) 		0.349
(1.00)
1p gain 9 (2%) 356 0.00188
(1.00) 		0.00738
(1.00) 		0.0241
(1.00) 		1
(1.00) 		3.13e-08
(2.43e-05) 		0.00639
(1.00) 		0.114
(1.00) 		0.00608
(1.00) 		0.00317
(1.00) 		0.0733
(1.00)
3p gain 8 (2%) 357 1
(1.00) 		0.753
(1.00) 		0.691
(1.00) 		0.56
(1.00) 		0.000155
(0.112) 		0.889
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.645
(1.00) 		1
(1.00)
3q gain 7 (2%) 358 0.549
(1.00) 		0.275
(1.00) 		0.056
(1.00) 		0.74
(1.00) 		8.65e-06
(0.00645) 		0.603
(1.00) 		0.338
(1.00) 		0.497
(1.00) 		0.295
(1.00) 		0.766
(1.00)
5p gain 6 (2%) 359 0.0158
(1.00) 		0.0775
(1.00) 		0.0217
(1.00) 		1
(1.00) 		1.25e-07
(9.58e-05) 		0.0477
(1.00) 		0.188
(1.00) 		0.00458
(1.00) 		0.102
(1.00) 		0.166
(1.00)
8q gain 37 (10%) 328 0.0519
(1.00) 		0.303
(1.00) 		0.000272
(0.193) 		0.00358
(1.00) 		0.0129
(1.00) 		0.618
(1.00) 		0.0173
(1.00) 		0.0052
(1.00) 		0.365
(1.00) 		0.0568
(1.00) 		0.0498
(1.00) 		0.0102
(1.00)
15q gain 6 (2%) 359 0.0729
(1.00) 		0.218
(1.00) 		0.114
(1.00) 		0.465
(1.00) 		1.03e-06
(0.000782) 		0.0477
(1.00) 		0.491
(1.00) 		0.0209
(1.00) 		0.724
(1.00) 		0.0407
(1.00)
18p gain 11 (3%) 354 0.00765
(1.00) 		0.0666
(1.00) 		0.0226
(1.00) 		0.205
(1.00) 		1.45e-09
(1.14e-06) 		0.288
(1.00) 		0.674
(1.00) 		0.0537
(1.00) 		0.417
(1.00) 		0.663
(1.00)
18q gain 8 (2%) 357 0.0277
(1.00) 		0.161
(1.00) 		0.0804
(1.00) 		0.142
(1.00) 		3.23e-07
(0.000247) 		0.603
(1.00) 		0.868
(1.00) 		0.0348
(1.00) 		0.297
(1.00) 		1
(1.00)
xq gain 30 (8%) 335 0.00782
(1.00) 		3.04e-05
(0.0223) 		0.182
(1.00) 		0.753
(1.00) 		0.00597
(1.00) 		0.00732
(1.00) 		0.356
(1.00) 		0.511
(1.00) 		0.00323
(1.00) 		0.0841
(1.00)
2p loss 16 (4%) 349 0.203
(1.00) 		0.0638
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.016
(1.00) 		0.0287
(1.00) 		0.515
(1.00) 		0.000245
(0.174) 		0.434
(1.00) 		0.224
(1.00)
3p loss 19 (5%) 346 0.231
(1.00) 		0.693
(1.00) 		0.00652
(1.00) 		0.483
(1.00) 		0.000272
(0.193) 		0.0813
(1.00) 		0.0305
(1.00) 		0.0128
(1.00) 		0.075
(1.00) 		0.0051
(1.00)
5q loss 27 (7%) 338 0.446
(1.00) 		0.0182
(1.00) 		0.00041
(0.288) 		0.000489
(0.342) 		0.0218
(1.00) 		0.508
(1.00) 		2.28e-10
(1.8e-07) 		0.00258
(1.00) 		0.00246
(1.00) 		0.00409
(1.00) 		0.00258
(1.00) 		0.112
(1.00)
6q loss 49 (13%) 316 0.000104
(0.0751) 		0.00275
(1.00) 		0.254
(1.00) 		0.398
(1.00) 		0.188
(1.00) 		0.0377
(1.00) 		0.000628
(0.436) 		0.231
(1.00) 		0.527
(1.00) 		0.0311
(1.00)
8p loss 12 (3%) 353 0.615
(1.00) 		0.00137
(0.929) 		0.00387
(1.00) 		0.00352
(1.00) 		0.0185
(1.00) 		0.628
(1.00) 		2.49e-05
(0.0183) 		0.0439
(1.00) 		0.101
(1.00) 		0.255
(1.00) 		0.00299
(1.00) 		0.0282
(1.00)
8q loss 8 (2%) 357 0.00167
(1.00) 		0.000186
(0.133) 		0.0806
(1.00) 		0.74
(1.00) 		0.000379
(0.266) 		0.12
(1.00) 		0.0379
(1.00) 		0.131
(1.00) 		0.00174
(1.00) 		0.0163
(1.00)
11q loss 17 (5%) 348 0.00211
(1.00) 		0.00202
(1.00) 		0.0179
(1.00) 		1
(1.00) 		2.64e-08
(2.05e-05) 		0.0324
(1.00) 		0.525
(1.00) 		0.0025
(1.00) 		0.0412
(1.00) 		0.0684
(1.00)
2p gain 6 (2%) 359 0.0585
(1.00) 		0.115
(1.00) 		0.311
(1.00) 		0.43
(1.00) 		0.061
(1.00) 		0.394
(1.00) 		0.165
(1.00) 		0.265
(1.00) 		0.223
(1.00) 		0.0309
(1.00)
2q gain 5 (1%) 360 0.256
(1.00) 		0.0977
(1.00) 		0.311
(1.00) 		0.43
(1.00) 		0.043
(1.00) 		0.717
(1.00) 		0.188
(1.00) 		0.41
(1.00) 		0.48
(1.00) 		0.0407
(1.00)
4p gain 8 (2%) 357 0.0233
(1.00) 		0.0975
(1.00) 		0.0925
(1.00) 		1
(1.00) 		0.129
(1.00) 		0.357
(1.00) 		0.486
(1.00) 		0.0485
(1.00) 		0.0743
(1.00) 		0.246
(1.00)
4q gain 3 (1%) 362 0.186
(1.00) 		0.575
(1.00) 		0.337
(1.00) 		1
(1.00) 		0.00402
(1.00) 		1
(1.00) 		0.912
(1.00) 		0.0197
(1.00) 		0.438
(1.00) 		1
(1.00)
5q gain 4 (1%) 361 0.043
(1.00) 		0.0277
(1.00) 		0.0248
(1.00) 		0.172
(1.00) 		0.0638
(1.00) 		0.273
(1.00) 		0.0997
(1.00) 		0.336
(1.00)
6p gain 5 (1%) 360 1
(1.00) 		0.153
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.484
(1.00) 		0.491
(1.00) 		0.41
(1.00) 		0.0242
(1.00) 		0.0407
(1.00)
8p gain 30 (8%) 335 0.00682
(1.00) 		0.0321
(1.00) 		0.0858
(1.00) 		0.63
(1.00) 		0.349
(1.00) 		0.0379
(1.00) 		0.561
(1.00) 		0.0654
(1.00) 		0.0462
(1.00) 		0.0383
(1.00)
9p gain 13 (4%) 352 0.0427
(1.00) 		0.0766
(1.00) 		0.294
(1.00) 		0.82
(1.00) 		0.0868
(1.00) 		0.379
(1.00) 		0.286
(1.00) 		0.0493
(1.00) 		0.056
(1.00) 		0.273
(1.00)
9q gain 17 (5%) 348 0.0231
(1.00) 		0.259
(1.00) 		0.258
(1.00) 		0.661
(1.00) 		0.00679
(1.00) 		0.186
(1.00) 		0.191
(1.00) 		0.00151
(1.00) 		0.0718
(1.00) 		0.26
(1.00)
10q gain 5 (1%) 360 0.0199
(1.00) 		0.153
(1.00) 		0.573
(1.00) 		0.668
(1.00) 		0.0232
(1.00) 		0.585
(1.00) 		0.0836
(1.00) 		0.0614
(1.00) 		0.508
(1.00) 		0.401
(1.00)
11p gain 25 (7%) 340 0.0636
(1.00) 		0.00244
(1.00) 		0.027
(1.00) 		0.496
(1.00) 		0.0144
(1.00) 		0.0388
(1.00) 		0.15
(1.00) 		0.745
(1.00) 		0.0258
(1.00) 		0.437
(1.00)
11q gain 42 (12%) 323 0.615
(1.00) 		0.117
(1.00) 		0.233
(1.00) 		0.0342
(1.00) 		0.0837
(1.00) 		0.141
(1.00) 		0.168
(1.00) 		0.172
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.229
(1.00) 		1
(1.00)
12p gain 24 (7%) 341 0.754
(1.00) 		0.0879
(1.00) 		0.046
(1.00) 		0.283
(1.00) 		0.261
(1.00) 		0.875
(1.00) 		0.209
(1.00) 		0.0803
(1.00) 		0.104
(1.00) 		0.0141
(1.00) 		0.0535
(1.00) 		0.071
(1.00)
12q gain 11 (3%) 354 0.0572
(1.00) 		0.247
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.0372
(1.00) 		0.0703
(1.00) 		0.185
(1.00) 		0.0621
(1.00) 		0.0123
(1.00) 		0.078
(1.00)
13q gain 4 (1%) 361 0.234
(1.00) 		0.325
(1.00) 		0.523
(1.00) 		0.663
(1.00) 		0.414
(1.00) 		0.273
(1.00) 		0.369
(1.00) 		0.336
(1.00)
14q gain 3 (1%) 362 0.354
(1.00) 		1
(1.00) 		0.887
(1.00) 		0.406
(1.00) 		0.196
(1.00) 		0.592
(1.00) 		0.000493
(0.344) 		0.0961
(1.00)
16p gain 12 (3%) 353 0.61
(1.00) 		0.729
(1.00) 		0.561
(1.00) 		0.658
(1.00) 		0.00665
(1.00) 		0.236
(1.00) 		0.136
(1.00) 		0.00937
(1.00) 		0.168
(1.00) 		0.0157
(1.00)
16q gain 13 (4%) 352 0.434
(1.00) 		0.633
(1.00) 		0.469
(1.00) 		0.738
(1.00) 		0.0115
(1.00) 		0.163
(1.00) 		0.423
(1.00) 		0.00593
(1.00) 		0.206
(1.00) 		0.0134
(1.00)
17p gain 11 (3%) 354 0.281
(1.00) 		0.853
(1.00) 		0.637
(1.00) 		0.531
(1.00) 		0.000721
(0.497) 		0.134
(1.00) 		0.0674
(1.00) 		0.0262
(1.00) 		0.0179
(1.00) 		0.0737
(1.00)
17q gain 12 (3%) 353 0.348
(1.00) 		0.694
(1.00) 		0.637
(1.00) 		0.531
(1.00) 		0.000832
(0.572) 		0.111
(1.00) 		0.0227
(1.00) 		0.0176
(1.00) 		0.00728
(1.00) 		0.0368
(1.00)
21q gain 19 (5%) 346 0.0328
(1.00) 		0.0288
(1.00) 		0.11
(1.00) 		0.531
(1.00) 		0.0135
(1.00) 		0.466
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.206
(1.00) 		0.419
(1.00)
1q loss 19 (5%) 346 0.344
(1.00) 		0.144
(1.00) 		0.448
(1.00) 		0.398
(1.00) 		0.552
(1.00) 		0.54
(1.00) 		0.112
(1.00) 		0.428
(1.00) 		0.233
(1.00) 		0.118
(1.00) 		0.277
(1.00) 		0.8
(1.00)
2q loss 15 (4%) 350 0.0779
(1.00) 		0.00961
(1.00) 		0.0692
(1.00) 		0.628
(1.00) 		0.00832
(1.00) 		0.0445
(1.00) 		0.162
(1.00) 		0.0277
(1.00) 		0.268
(1.00) 		0.124
(1.00)
3q loss 22 (6%) 343 0.175
(1.00) 		0.561
(1.00) 		0.205
(1.00) 		0.368
(1.00) 		0.258
(1.00) 		0.191
(1.00) 		0.00265
(1.00) 		0.18
(1.00) 		0.243
(1.00) 		0.0723
(1.00) 		0.241
(1.00) 		0.0439
(1.00)
6p loss 24 (7%) 341 0.0684
(1.00) 		0.0706
(1.00) 		0.186
(1.00) 		0.708
(1.00) 		0.331
(1.00) 		0.418
(1.00) 		0.0604
(1.00) 		0.752
(1.00) 		0.714
(1.00) 		0.00905
(1.00)
9p loss 82 (22%) 283 0.384
(1.00) 		0.27
(1.00) 		0.0225
(1.00) 		0.0191
(1.00) 		0.0318
(1.00) 		0.0664
(1.00) 		0.00371
(1.00) 		0.473
(1.00) 		0.982
(1.00) 		0.53
(1.00) 		0.408
(1.00) 		0.14
(1.00)
9q loss 34 (9%) 331 0.503
(1.00) 		0.91
(1.00) 		0.607
(1.00) 		0.506
(1.00) 		0.0297
(1.00) 		0.483
(1.00) 		0.927
(1.00) 		0.578
(1.00) 		0.42
(1.00) 		0.622
(1.00)
12p loss 18 (5%) 347 0.0484
(1.00) 		0.131
(1.00) 		0.434
(1.00) 		0.36
(1.00) 		0.535
(1.00) 		0.081
(1.00) 		0.531
(1.00) 		0.258
(1.00) 		0.623
(1.00) 		0.419
(1.00)
13q loss 85 (23%) 280 0.18
(1.00) 		0.000618
(0.43) 		0.117
(1.00) 		0.0337
(1.00) 		0.0291
(1.00) 		0.566
(1.00) 		0.0362
(1.00) 		0.316
(1.00) 		0.287
(1.00) 		0.0701
(1.00) 		0.0406
(1.00) 		0.274
(1.00)
15q loss 34 (9%) 331 1
(1.00) 		0.892
(1.00) 		0.0141
(1.00) 		0.00153
(1.00) 		0.277
(1.00) 		0.0476
(1.00) 		0.000783
(0.539) 		0.0154
(1.00) 		0.139
(1.00) 		0.338
(1.00) 		0.508
(1.00) 		0.286
(1.00)
16p loss 10 (3%) 355 0.0551
(1.00) 		0.477
(1.00) 		0.865
(1.00) 		0.447
(1.00) 		0.00196
(1.00) 		0.916
(1.00) 		0.104
(1.00) 		0.0296
(1.00) 		0.669
(1.00) 		0.0147
(1.00)
16q loss 16 (4%) 349 0.0445
(1.00) 		0.0174
(1.00) 		0.374
(1.00) 		0.219
(1.00) 		0.276
(1.00) 		0.248
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.0194
(1.00)
17p loss 13 (4%) 352 0.0982
(1.00) 		0.0612
(1.00) 		0.916
(1.00) 		0.531
(1.00) 		0.000648
(0.449) 		0.0821
(1.00) 		0.06
(1.00) 		0.00957
(1.00) 		0.0203
(1.00) 		0.102
(1.00)
17q loss 9 (2%) 356 0.198
(1.00) 		0.282
(1.00) 		0.967
(1.00) 		0.383
(1.00) 		0.215
(1.00) 		0.438
(1.00) 		0.0985
(1.00) 		0.348
(1.00) 		0.0855
(1.00) 		0.0733
(1.00)
18p loss 48 (13%) 317 0.321
(1.00) 		0.316
(1.00) 		0.347
(1.00) 		0.0134
(1.00) 		0.573
(1.00) 		0.0801
(1.00) 		0.333
(1.00) 		0.457
(1.00) 		0.7
(1.00) 		0.192
(1.00) 		0.744
(1.00) 		0.84
(1.00)
18q loss 43 (12%) 322 0.344
(1.00) 		0.212
(1.00) 		0.0517
(1.00) 		0.00314
(1.00) 		0.285
(1.00) 		0.202
(1.00) 		0.044
(1.00) 		0.122
(1.00) 		0.641
(1.00) 		0.218
(1.00) 		0.673
(1.00) 		0.89
(1.00)
19p loss 16 (4%) 349 0.574
(1.00) 		0.178
(1.00) 		0.848
(1.00) 		0.953
(1.00) 		0.376
(1.00) 		0.182
(1.00) 		0.41
(1.00) 		0.493
(1.00) 		0.643
(1.00) 		0.471
(1.00) 		0.664
(1.00) 		0.26
(1.00)
20p loss 3 (1%) 362 0.354
(1.00) 		0.483
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.00485
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.592
(1.00) 		0.758
(1.00) 		1
(1.00)
21q loss 27 (7%) 338 0.615
(1.00) 		0.407
(1.00) 		0.0614
(1.00) 		0.0227
(1.00) 		0.461
(1.00) 		0.834
(1.00) 		0.128
(1.00) 		0.0634
(1.00) 		0.0828
(1.00) 		0.0257
(1.00) 		0.324
(1.00) 		0.365
(1.00)
'1p gain' versus 'MRNASEQ_CNMF'

P value = 3.13e-08 (Chi-square test), Q value = 2.4e-05

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
1P GAIN MUTATED 0 7 0 0 2 0
1P GAIN WILD-TYPE 94 63 65 109 5 18

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.19

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
1Q GAIN MUTATED 3 10 1
1Q GAIN WILD-TYPE 135 77 139

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Chi-square test), Q value = 0.16

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
1Q GAIN MUTATED 1 7 0 4 2 0
1Q GAIN WILD-TYPE 93 63 65 105 5 18

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.000155 (Chi-square test), Q value = 0.11

Table S4.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
3P GAIN MUTATED 1 2 2 1 2 0
3P GAIN WILD-TYPE 93 68 63 108 5 18

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 8.65e-06 (Chi-square test), Q value = 0.0064

Table S5.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
3Q GAIN MUTATED 0 3 1 1 2 0
3Q GAIN WILD-TYPE 94 67 64 108 5 18

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1.25e-07 (Chi-square test), Q value = 9.6e-05

Table S6.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
5P GAIN MUTATED 0 3 0 0 2 1
5P GAIN WILD-TYPE 94 67 65 109 5 17

Figure S6.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.19e-28 (Fisher's exact test), Q value = 9.6e-26

Table S7.  Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
7P GAIN MUTATED 19 62 8
7P GAIN WILD-TYPE 119 25 132

Figure S7.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 9.44e-16 (Fisher's exact test), Q value = 7.5e-13

Table S8.  Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
7P GAIN MUTATED 29 40 13 5
7P GAIN WILD-TYPE 132 15 95 31

Figure S8.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 7.16e-12 (Chi-square test), Q value = 5.7e-09

Table S9.  Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
7P GAIN MUTATED 16 40 7 19 4 1
7P GAIN WILD-TYPE 78 30 58 90 3 17

Figure S9.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.016

Table S10.  Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
7P GAIN MUTATED 6 60 21
7P GAIN WILD-TYPE 55 114 107

Figure S10.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.02e-05 (Chi-square test), Q value = 0.029

Table S11.  Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
7P GAIN MUTATED 9 24 12 11 4 13 1 1
7P GAIN WILD-TYPE 40 23 32 70 24 21 3 15

Figure S11.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.53e-06 (Fisher's exact test), Q value = 0.0012

Table S12.  Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
7P GAIN MUTATED 8 51 16
7P GAIN WILD-TYPE 2 118 108

Figure S12.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 7.65e-29 (Fisher's exact test), Q value = 6.1e-26

Table S13.  Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
7Q GAIN MUTATED 29 70 15
7Q GAIN WILD-TYPE 109 17 125

Figure S13.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.51e-14 (Fisher's exact test), Q value = 2e-11

Table S14.  Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
7Q GAIN MUTATED 44 43 19 6
7Q GAIN WILD-TYPE 117 12 89 30

Figure S14.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6.37e-08 (Chi-square test), Q value = 4.9e-05

Table S15.  Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
7Q GAIN MUTATED 27 42 10 26 4 3
7Q GAIN WILD-TYPE 67 28 55 83 3 15

Figure S15.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0082

Table S16.  Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
7Q GAIN MUTATED 9 74 29
7Q GAIN WILD-TYPE 52 100 99

Figure S16.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.3e-05 (Fisher's exact test), Q value = 0.046

Table S17.  Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
7Q GAIN MUTATED 8 62 26
7Q GAIN WILD-TYPE 2 107 98

Figure S17.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.000272 (Fisher's exact test), Q value = 0.19

Table S18.  Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
8Q GAIN MUTATED 23 10 4
8Q GAIN WILD-TYPE 115 77 136

Figure S18.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1.86e-11 (Fisher's exact test), Q value = 1.5e-08

Table S19.  Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
10P GAIN MUTATED 33 1 2
10P GAIN WILD-TYPE 105 86 138

Figure S19.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 1.4e-06

Table S20.  Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
10P GAIN MUTATED 34 1 0 1
10P GAIN WILD-TYPE 127 54 108 35

Figure S20.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 4.1e-05 (Chi-square test), Q value = 0.03

Table S21.  Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
10P GAIN MUTATED 18 4 0 8 3 3
10P GAIN WILD-TYPE 76 66 65 101 4 15

Figure S21.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1.03e-06 (Chi-square test), Q value = 0.00078

Table S22.  Gene #26: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
15Q GAIN MUTATED 3 1 0 0 2 0
15Q GAIN WILD-TYPE 91 69 65 109 5 18

Figure S22.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1.45e-09 (Chi-square test), Q value = 1.1e-06

Table S23.  Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
18P GAIN MUTATED 1 2 0 2 3 2
18P GAIN WILD-TYPE 93 68 65 107 4 16

Figure S23.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 3.23e-07 (Chi-square test), Q value = 0.00025

Table S24.  Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
18Q GAIN MUTATED 0 2 0 1 2 2
18Q GAIN WILD-TYPE 94 68 65 108 5 16

Figure S24.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 4.4e-07 (Fisher's exact test), Q value = 0.00034

Table S25.  Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
19P GAIN MUTATED 7 24 35
19P GAIN WILD-TYPE 131 63 105

Figure S25.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 2.64e-09 (Fisher's exact test), Q value = 2.1e-06

Table S26.  Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
19P GAIN MUTATED 9 19 33 3
19P GAIN WILD-TYPE 152 36 75 33

Figure S26.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.000315 (Chi-square test), Q value = 0.22

Table S27.  Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
19P GAIN MUTATED 5 19 20 20 1 1
19P GAIN WILD-TYPE 89 51 45 89 6 17

Figure S27.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 5.64e-08 (Fisher's exact test), Q value = 4.3e-05

Table S28.  Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
19Q GAIN MUTATED 3 15 0
19Q GAIN WILD-TYPE 135 72 140

Figure S28.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2.18e-09 (Fisher's exact test), Q value = 1.7e-06

Table S29.  Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
19Q GAIN MUTATED 2 14 0 1
19Q GAIN WILD-TYPE 159 41 108 35

Figure S29.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1.13e-06 (Chi-square test), Q value = 0.00085

Table S30.  Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
19Q GAIN MUTATED 1 13 0 4 0 0
19Q GAIN WILD-TYPE 93 57 65 105 7 18

Figure S30.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.4e-06 (Chi-square test), Q value = 0.0025

Table S31.  Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
19Q GAIN MUTATED 0 10 0 3 0 1 1 0
19Q GAIN WILD-TYPE 49 37 44 78 28 33 3 16

Figure S31.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.98e-08 (Fisher's exact test), Q value = 1.5e-05

Table S32.  Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
20P GAIN MUTATED 8 23 3
20P GAIN WILD-TYPE 130 64 137

Figure S32.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 9.6e-07

Table S33.  Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
20P GAIN MUTATED 8 21 4 1
20P GAIN WILD-TYPE 153 34 104 35

Figure S33.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 4.37e-06 (Chi-square test), Q value = 0.0033

Table S34.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
20P GAIN MUTATED 4 18 3 7 2 0
20P GAIN WILD-TYPE 90 52 62 102 5 18

Figure S34.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 4.21e-08 (Fisher's exact test), Q value = 3.3e-05

Table S35.  Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
20Q GAIN MUTATED 7 23 4
20Q GAIN WILD-TYPE 131 64 136

Figure S35.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.45e-11 (Fisher's exact test), Q value = 4.3e-08

Table S36.  Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
20Q GAIN MUTATED 8 22 4 0
20Q GAIN WILD-TYPE 153 33 104 36

Figure S36.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 3.93e-08 (Chi-square test), Q value = 3e-05

Table S37.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
20Q GAIN MUTATED 4 20 3 5 2 0
20Q GAIN WILD-TYPE 90 50 62 104 5 18

Figure S37.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.62e-05 (Fisher's exact test), Q value = 0.07

Table S38.  Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
20Q GAIN MUTATED 1 28 5
20Q GAIN WILD-TYPE 60 146 123

Figure S38.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.56e-05 (Chi-square test), Q value = 0.019

Table S39.  Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
20Q GAIN MUTATED 1 12 3 1 2 8 1 1
20Q GAIN WILD-TYPE 48 35 41 80 26 26 3 15

Figure S39.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.89e-05 (Fisher's exact test), Q value = 0.043

Table S40.  Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
20Q GAIN MUTATED 4 22 3
20Q GAIN WILD-TYPE 6 147 121

Figure S40.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
22Q GAIN MUTATED 1 0 11 0
22Q GAIN WILD-TYPE 160 55 97 36

Figure S41.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.98e-05 (Chi-square test), Q value = 0.072

Table S42.  Gene #38: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
22Q GAIN MUTATED 0 0 0 0 3 3 1 0
22Q GAIN WILD-TYPE 49 47 44 81 25 31 3 16

Figure S42.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 3.04e-05 (Fisher's exact test), Q value = 0.022

Table S43.  Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
XQ GAIN MUTATED 24 4 0 2
XQ GAIN WILD-TYPE 137 51 108 34

Figure S43.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.12

Table S44.  Gene #40: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
1P LOSS MUTATED 7 2 1 0
1P LOSS WILD-TYPE 0 4 9 4

Figure S44.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.8e-53 (Fisher's exact test), Q value = 1.5e-50

Table S45.  Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
1P LOSS MUTATED 5 11 117
1P LOSS WILD-TYPE 133 76 23

Figure S45.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.24e-72 (Fisher's exact test), Q value = 3.5e-69

Table S46.  Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
1P LOSS MUTATED 5 4 107 14
1P LOSS WILD-TYPE 156 51 1 22

Figure S46.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.22

Table S47.  Gene #40: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
1P LOSS MUTATED 8 15 26 36
1P LOSS WILD-TYPE 44 47 42 38

Figure S47.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.25e-37 (Chi-square test), Q value = 1e-34

Table S48.  Gene #40: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
1P LOSS MUTATED 3 6 64 50 1 9
1P LOSS WILD-TYPE 91 64 1 59 6 9

Figure S48.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-44 (Fisher's exact test), Q value = 2.7e-41

Table S49.  Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
1P LOSS MUTATED 60 12 61
1P LOSS WILD-TYPE 1 162 67

Figure S49.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 3.37e-10 (Chi-square test), Q value = 2.7e-07

Table S50.  Gene #40: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 61 100 16 49
1P LOSS MUTATED 16 7 49 14 18
1P LOSS WILD-TYPE 61 54 51 2 31

Figure S50.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.014

Table S51.  Gene #40: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
1P LOSS MUTATED 1 40 63
1P LOSS WILD-TYPE 1 129 69

Figure S51.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.49e-10 (Chi-square test), Q value = 1.2e-07

Table S52.  Gene #40: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
1P LOSS MUTATED 2 8 15 38 22 11 0 8
1P LOSS WILD-TYPE 47 39 29 43 6 23 4 8

Figure S52.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.06e-09 (Fisher's exact test), Q value = 1.6e-06

Table S53.  Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
1P LOSS MUTATED 0 37 67
1P LOSS WILD-TYPE 10 132 57

Figure S53.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000245 (Fisher's exact test), Q value = 0.17

Table S54.  Gene #42: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
2P LOSS MUTATED 2 10 2
2P LOSS WILD-TYPE 0 159 130

Figure S54.  Get High-res Image Gene #42: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.000272 (Chi-square test), Q value = 0.19

Table S55.  Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
3P LOSS MUTATED 3 6 2 4 3 1
3P LOSS WILD-TYPE 91 64 63 105 4 17

Figure S55.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0085

Table S56.  Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
4P LOSS MUTATED 8 10 36
4P LOSS WILD-TYPE 130 77 104

Figure S56.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.8e-08 (Fisher's exact test), Q value = 1.4e-05

Table S57.  Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
4P LOSS MUTATED 15 2 36 1
4P LOSS WILD-TYPE 146 53 72 35

Figure S57.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2.24e-08 (Chi-square test), Q value = 1.7e-05

Table S58.  Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
4P LOSS MUTATED 8 2 24 16 3 0
4P LOSS WILD-TYPE 86 68 41 93 4 18

Figure S58.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-07 (Fisher's exact test), Q value = 8.9e-05

Table S59.  Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
4P LOSS MUTATED 23 11 19
4P LOSS WILD-TYPE 38 163 109

Figure S59.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000147 (Chi-square test), Q value = 0.11

Table S60.  Gene #46: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
4P LOSS MUTATED 1 2 12 13 10 6 1 0
4P LOSS WILD-TYPE 48 45 32 68 18 28 3 16

Figure S60.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 5.78e-07 (Fisher's exact test), Q value = 0.00044

Table S61.  Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
4Q LOSS MUTATED 26 2 39 3
4Q LOSS WILD-TYPE 135 53 69 33

Figure S61.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 4.1e-06 (Chi-square test), Q value = 0.0031

Table S62.  Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
4Q LOSS MUTATED 14 3 26 21 3 2
4Q LOSS WILD-TYPE 80 67 39 88 4 16

Figure S62.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00077

Table S63.  Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
4Q LOSS MUTATED 25 17 27
4Q LOSS WILD-TYPE 36 157 101

Figure S63.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.43e-05 (Chi-square test), Q value = 0.054

Table S64.  Gene #47: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
4Q LOSS MUTATED 2 2 15 16 11 8 1 1
4Q LOSS WILD-TYPE 47 45 29 65 17 26 3 15

Figure S64.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.013

Table S65.  Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
5P LOSS MUTATED 20 7 1
5P LOSS WILD-TYPE 118 80 139

Figure S65.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.000268 (Fisher's exact test), Q value = 0.19

Table S66.  Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
5P LOSS MUTATED 23 3 1 1
5P LOSS WILD-TYPE 138 52 107 35

Figure S66.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 2.28e-10 (Chi-square test), Q value = 1.8e-07

Table S67.  Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
5Q LOSS MUTATED 8 8 1 2 5 2
5Q LOSS WILD-TYPE 86 62 64 107 2 16

Figure S67.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.075

Table S68.  Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
6Q LOSS MUTATED 21 21 7
6Q LOSS WILD-TYPE 117 66 133

Figure S68.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.49e-05 (Chi-square test), Q value = 0.018

Table S69.  Gene #52: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
8P LOSS MUTATED 1 7 0 2 2 0
8P LOSS WILD-TYPE 93 63 65 107 5 18

Figure S69.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.13

Table S70.  Gene #53: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
8Q LOSS MUTATED 1 6 0 1
8Q LOSS WILD-TYPE 160 49 108 35

Figure S70.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1.28e-27 (Fisher's exact test), Q value = 1e-24

Table S71.  Gene #56: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
10P LOSS MUTATED 3 49 5
10P LOSS WILD-TYPE 135 38 135

Figure S71.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 8.28e-39 (Fisher's exact test), Q value = 6.7e-36

Table S72.  Gene #56: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
10P LOSS MUTATED 1 46 6 3
10P LOSS WILD-TYPE 160 9 102 33

Figure S72.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 2.54e-07 (Fisher's exact test), Q value = 0.00019

Table S73.  Gene #56: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10P LOSS MUTATED 4 24 3 6
10P LOSS WILD-TYPE 48 38 65 68

Figure S73.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 6.32e-26 (Chi-square test), Q value = 5.1e-23

Table S74.  Gene #56: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
10P LOSS MUTATED 1 41 2 11 1 0
10P LOSS WILD-TYPE 93 29 63 98 6 18

Figure S74.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.0013

Table S75.  Gene #56: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
10P LOSS MUTATED 2 44 10
10P LOSS WILD-TYPE 59 130 118

Figure S75.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.23e-16 (Chi-square test), Q value = 7.4e-13

Table S76.  Gene #56: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
10P LOSS MUTATED 1 28 2 7 1 9 0 2
10P LOSS WILD-TYPE 48 19 42 74 27 25 4 14

Figure S76.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.45e-06 (Fisher's exact test), Q value = 0.0011

Table S77.  Gene #56: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
10P LOSS MUTATED 6 37 7
10P LOSS WILD-TYPE 4 132 117

Figure S77.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 7.74e-26 (Fisher's exact test), Q value = 6.2e-23

Table S78.  Gene #57: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
10Q LOSS MUTATED 10 53 6
10Q LOSS WILD-TYPE 128 34 134

Figure S78.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 3.61e-32 (Fisher's exact test), Q value = 2.9e-29

Table S79.  Gene #57: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
10Q LOSS MUTATED 12 47 6 3
10Q LOSS WILD-TYPE 149 8 102 33

Figure S79.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.001

Table S80.  Gene #57: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10Q LOSS MUTATED 6 27 7 7
10Q LOSS WILD-TYPE 46 35 61 67

Figure S80.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 4.32e-25 (Chi-square test), Q value = 3.4e-22

Table S81.  Gene #57: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
10Q LOSS MUTATED 5 45 2 14 2 0
10Q LOSS WILD-TYPE 89 25 63 95 5 18

Figure S81.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.88e-08 (Fisher's exact test), Q value = 4.5e-05

Table S82.  Gene #57: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
10Q LOSS MUTATED 2 53 13
10Q LOSS WILD-TYPE 59 121 115

Figure S82.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.72e-13 (Chi-square test), Q value = 6.9e-10

Table S83.  Gene #57: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
10Q LOSS MUTATED 3 29 3 10 2 11 1 2
10Q LOSS WILD-TYPE 46 18 41 71 26 23 3 14

Figure S83.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.0011

Table S84.  Gene #57: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
10Q LOSS MUTATED 7 43 11
10Q LOSS WILD-TYPE 3 126 113

Figure S84.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1.73e-06 (Fisher's exact test), Q value = 0.0013

Table S85.  Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
11P LOSS MUTATED 31 11 4
11P LOSS WILD-TYPE 107 76 136

Figure S85.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 2.98e-08 (Fisher's exact test), Q value = 2.3e-05

Table S86.  Gene #58: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
11P LOSS MUTATED 36 7 0 3
11P LOSS WILD-TYPE 125 48 108 33

Figure S86.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1.73e-08 (Chi-square test), Q value = 1.4e-05

Table S87.  Gene #58: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
11P LOSS MUTATED 10 16 0 9 5 5
11P LOSS WILD-TYPE 84 54 65 100 2 13

Figure S87.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.063

Table S88.  Gene #58: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
11P LOSS MUTATED 0 32 13
11P LOSS WILD-TYPE 61 142 115

Figure S88.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 2.64e-08 (Chi-square test), Q value = 2.1e-05

Table S89.  Gene #59: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
11Q LOSS MUTATED 0 9 0 3 3 2
11Q LOSS WILD-TYPE 94 61 65 106 4 16

Figure S89.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 9.07e-08 (Fisher's exact test), Q value = 7e-05

Table S90.  Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
12Q LOSS MUTATED 29 2 4
12Q LOSS WILD-TYPE 109 85 136

Figure S90.  Get High-res Image Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.16

Table S91.  Gene #61: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
12Q LOSS MUTATED 28 1 4 2
12Q LOSS WILD-TYPE 133 54 104 34

Figure S91.  Get High-res Image Gene #61: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.14

Table S92.  Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
14Q LOSS MUTATED 13 26 17
14Q LOSS WILD-TYPE 125 61 123

Figure S92.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.000245 (Chi-square test), Q value = 0.17

Table S93.  Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
14Q LOSS MUTATED 8 23 6 14 2 2
14Q LOSS WILD-TYPE 86 47 59 95 5 16

Figure S93.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.000348 (Chi-square test), Q value = 0.25

Table S94.  Gene #63: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 61 100 16 49
14Q LOSS MUTATED 25 8 10 2 4
14Q LOSS WILD-TYPE 52 53 90 14 45

Figure S94.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Chi-square test), Q value = 0.08

Table S95.  Gene #63: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
14Q LOSS MUTATED 5 20 5 9 3 4 0 3
14Q LOSS WILD-TYPE 44 27 39 72 25 30 4 13

Figure S95.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 5.43e-51 (Fisher's exact test), Q value = 4.4e-48

Table S96.  Gene #72: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
19Q LOSS MUTATED 14 11 123
19Q LOSS WILD-TYPE 124 76 17

Figure S96.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 6.46e-59 (Fisher's exact test), Q value = 5.2e-56

Table S97.  Gene #72: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
19Q LOSS MUTATED 20 4 107 14
19Q LOSS WILD-TYPE 141 51 1 22

Figure S97.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 7.28e-32 (Chi-square test), Q value = 5.9e-29

Table S98.  Gene #72: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
19Q LOSS MUTATED 11 7 64 52 2 11
19Q LOSS WILD-TYPE 83 63 1 57 5 7

Figure S98.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.49e-38 (Fisher's exact test), Q value = 2.8e-35

Table S99.  Gene #72: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
19Q LOSS MUTATED 60 21 66
19Q LOSS WILD-TYPE 1 153 62

Figure S99.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1.57e-06 (Chi-square test), Q value = 0.0012

Table S100.  Gene #72: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 61 100 16 49
19Q LOSS MUTATED 18 15 52 13 20
19Q LOSS WILD-TYPE 59 46 48 3 29

Figure S100.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.68e-05 (Fisher's exact test), Q value = 0.034

Table S101.  Gene #72: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
19Q LOSS MUTATED 0 49 69
19Q LOSS WILD-TYPE 2 120 63

Figure S101.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.48e-09 (Chi-square test), Q value = 1.2e-06

Table S102.  Gene #72: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
19Q LOSS MUTATED 4 8 22 39 22 13 1 9
19Q LOSS WILD-TYPE 45 39 22 42 6 21 3 7

Figure S102.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-07 (Fisher's exact test), Q value = 8.2e-05

Table S103.  Gene #72: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
19Q LOSS MUTATED 1 46 71
19Q LOSS WILD-TYPE 9 123 53

Figure S103.  Get High-res Image Gene #72: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 5.45e-08 (Fisher's exact test), Q value = 4.2e-05

Table S104.  Gene #75: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
22Q LOSS MUTATED 15 22 2
22Q LOSS WILD-TYPE 123 65 138

Figure S104.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 6.42e-06 (Fisher's exact test), Q value = 0.0048

Table S105.  Gene #75: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
22Q LOSS MUTATED 17 16 2 4
22Q LOSS WILD-TYPE 144 39 106 32

Figure S105.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 7.58e-05 (Fisher's exact test), Q value = 0.055

Table S106.  Gene #75: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
22Q LOSS MUTATED 2 18 5 4
22Q LOSS WILD-TYPE 50 44 63 70

Figure S106.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 4.95e-07 (Chi-square test), Q value = 0.00038

Table S107.  Gene #75: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
22Q LOSS MUTATED 7 19 1 7 3 1
22Q LOSS WILD-TYPE 87 51 64 102 4 17

Figure S107.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000146 (Fisher's exact test), Q value = 0.11

Table S108.  Gene #75: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
22Q LOSS MUTATED 1 30 7
22Q LOSS WILD-TYPE 60 144 121

Figure S108.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 2.03e-05 (Chi-square test), Q value = 0.015

Table S109.  Gene #76: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
XQ LOSS MUTATED 7 9 20 10 3 0
XQ LOSS WILD-TYPE 87 61 45 99 4 18

Figure S109.  Get High-res Image Gene #76: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.018

Table S110.  Gene #76: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
XQ LOSS MUTATED 20 20 9
XQ LOSS WILD-TYPE 41 154 119

Figure S110.  Get High-res Image Gene #76: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

  • Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 365

  • Number of significantly arm-level cnvs = 76

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

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

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