Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K936WQ
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 82 arm-level events and 10 molecular subtypes across 577 patients, 270 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 6p gain cnv correlated to 'MRNA_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 7p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF', and 'CN_CNMF'.

  • 8q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 9p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'MIR_CHIERARCHICAL' and 'MRNASEQ_CNMF'.

  • 14q gain cnv correlated to 'MIR_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • 17p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • 17q gain cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

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

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

  • 19q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 22q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • xq gain cnv correlated to 'MRNASEQ_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 4p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 4q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 5p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

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

  • 8q loss cnv correlated to 'MIR_CNMF'.

  • 9p loss cnv correlated to 'MRNA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 12p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 12q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

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

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF'.

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

  • 17p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 17q loss cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

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

  • 19p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 20p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xp loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • xq loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level 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, 270 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
7p gain 468 (81%) 109 1e-05
(0.000182)
1e-05
(0.000182)
0.00024
(0.00246)
1e-05
(0.000182)
1e-05
(0.000182)
2e-05
(0.000298)
0.0084
(0.0425)
0.00055
(0.00496)
0.00942
(0.0454)
8e-05
(0.000937)
15q loss 104 (18%) 473 6e-05
(0.000745)
1e-05
(0.000182)
0.00182
(0.0128)
0.00205
(0.014)
1e-05
(0.000182)
0.022
(0.0889)
0.175
(0.353)
0.019
(0.0785)
0.00393
(0.0237)
0.0231
(0.0918)
7q gain 475 (82%) 102 2e-05
(0.000298)
1e-05
(0.000182)
0.00208
(0.014)
0.0001
(0.00114)
1e-05
(0.000182)
0.00043
(0.0041)
0.343
(0.549)
0.0112
(0.0504)
0.0661
(0.183)
0.00157
(0.0115)
10p loss 480 (83%) 97 1e-05
(0.000182)
1e-05
(0.000182)
0.0151
(0.0648)
8e-05
(0.000937)
1e-05
(0.000182)
1e-05
(0.000182)
0.273
(0.468)
0.00137
(0.0107)
0.221
(0.405)
0.0126
(0.0553)
10q loss 492 (85%) 85 1e-05
(0.000182)
1e-05
(0.000182)
0.00763
(0.0399)
0.00036
(0.00356)
1e-05
(0.000182)
8e-05
(0.000937)
0.439
(0.643)
0.00073
(0.00617)
0.258
(0.453)
0.021
(0.0854)
19q gain 198 (34%) 379 1e-05
(0.000182)
1e-05
(0.000182)
0.277
(0.474)
0.00471
(0.0266)
1e-05
(0.000182)
1e-05
(0.000182)
0.208
(0.392)
0.00022
(0.00228)
0.0448
(0.141)
0.342
(0.549)
20p gain 222 (38%) 355 1e-05
(0.000182)
1e-05
(0.000182)
0.00352
(0.0215)
2e-05
(0.000298)
1e-05
(0.000182)
0.00016
(0.0017)
0.352
(0.559)
0.00066
(0.0057)
0.664
(0.818)
0.12
(0.275)
20q gain 220 (38%) 357 1e-05
(0.000182)
1e-05
(0.000182)
0.00174
(0.0123)
2e-05
(0.000298)
1e-05
(0.000182)
4e-05
(0.000521)
0.263
(0.458)
0.00039
(0.00381)
0.664
(0.818)
0.121
(0.278)
17p gain 49 (8%) 528 0.00044
(0.00415)
0.0275
(0.101)
0.0505
(0.152)
0.0274
(0.101)
0.0291
(0.105)
0.0245
(0.0958)
0.0247
(0.0959)
0.204
(0.387)
0.218
(0.403)
0.236
(0.422)
19p gain 226 (39%) 351 1e-05
(0.000182)
1e-05
(0.000182)
0.122
(0.278)
0.00025
(0.00253)
1e-05
(0.000182)
1e-05
(0.000182)
0.203
(0.386)
2e-05
(0.000298)
0.146
(0.317)
0.656
(0.814)
21q gain 64 (11%) 513 0.00301
(0.0187)
0.00751
(0.0395)
0.0174
(0.0733)
0.00378
(0.023)
0.06
(0.172)
0.00571
(0.0312)
0.117
(0.273)
0.758
(0.883)
0.0193
(0.079)
0.329
(0.535)
5q loss 45 (8%) 532 3e-05
(0.000424)
1e-05
(0.000182)
0.00103
(0.00862)
0.147
(0.317)
0.0044
(0.0252)
4e-05
(0.000521)
0.669
(0.818)
0.0848
(0.217)
0.0981
(0.24)
0.0428
(0.135)
11p loss 98 (17%) 479 2e-05
(0.000298)
1e-05
(0.000182)
0.898
(0.97)
0.0177
(0.0739)
1e-05
(0.000182)
0.00153
(0.0114)
0.816
(0.913)
0.0322
(0.11)
0.0576
(0.167)
0.0875
(0.22)
20p loss 19 (3%) 558 0.00035
(0.0035)
2e-05
(0.000298)
0.0483
(0.149)
0.093
(0.233)
0.00817
(0.0421)
0.475
(0.674)
0.0756
(0.201)
0.452
(0.653)
0.0105
(0.0481)
0.00202
(0.0139)
3p gain 58 (10%) 519 0.00153
(0.0114)
0.0293
(0.105)
0.376
(0.581)
0.027
(0.1)
0.0169
(0.0719)
0.0245
(0.0958)
0.988
(1.00)
0.705
(0.846)
0.813
(0.911)
0.255
(0.45)
8q gain 59 (10%) 518 1e-05
(0.000182)
3e-05
(0.000424)
0.0396
(0.127)
0.456
(0.656)
0.00137
(0.0107)
0.00942
(0.0454)
0.281
(0.476)
0.159
(0.332)
0.143
(0.312)
0.514
(0.704)
10p gain 13 (2%) 564 0.00136
(0.0107)
0.00016
(0.0017)
0.16
(0.332)
0.0597
(0.172)
0.00136
(0.0107)
0.00475
(0.0267)
0.406
(0.612)
0.00433
(0.025)
16q gain 37 (6%) 540 0.028
(0.102)
0.00534
(0.0296)
0.446
(0.65)
0.0663
(0.183)
0.0264
(0.0992)
0.0287
(0.104)
0.023
(0.0918)
0.886
(0.967)
0.474
(0.673)
0.735
(0.865)
18p gain 58 (10%) 519 1e-05
(0.000182)
0.00053
(0.00483)
0.434
(0.639)
0.367
(0.571)
1e-05
(0.000182)
0.00893
(0.044)
0.441
(0.645)
0.39
(0.596)
0.0276
(0.101)
0.0963
(0.237)
18q gain 58 (10%) 519 1e-05
(0.000182)
0.0006
(0.00535)
0.382
(0.588)
0.433
(0.639)
2e-05
(0.000298)
0.0106
(0.0482)
0.364
(0.571)
0.607
(0.773)
0.0265
(0.0993)
0.114
(0.268)
22q gain 34 (6%) 543 3e-05
(0.000424)
0.00305
(0.0188)
0.455
(0.656)
0.217
(0.403)
0.00407
(0.0242)
0.0452
(0.142)
0.268
(0.463)
0.0296
(0.105)
0.287
(0.483)
0.193
(0.376)
4q loss 55 (10%) 522 0.00217
(0.0145)
0.00146
(0.0112)
0.0248
(0.0961)
0.141
(0.309)
0.00507
(0.0283)
0.00161
(0.0116)
0.763
(0.888)
0.392
(0.596)
0.39
(0.596)
1
(1.00)
5p loss 43 (7%) 534 2e-05
(0.000298)
2e-05
(0.000298)
0.00416
(0.0244)
0.0959
(0.237)
0.00649
(0.035)
0.00153
(0.0114)
0.8
(0.905)
0.212
(0.397)
0.183
(0.363)
0.054
(0.161)
13q loss 185 (32%) 392 6e-05
(0.000745)
0.00243
(0.0157)
0.599
(0.768)
0.62
(0.786)
1e-05
(0.000182)
0.00461
(0.0263)
0.521
(0.711)
0.0266
(0.0993)
0.125
(0.28)
0.488
(0.683)
19p loss 26 (5%) 551 0.00167
(0.0119)
0.00291
(0.0182)
0.0143
(0.062)
0.313
(0.512)
0.178
(0.356)
0.00061
(0.00538)
0.0685
(0.187)
0.0363
(0.12)
0.839
(0.927)
0.804
(0.907)
20q loss 17 (3%) 560 0.00245
(0.0157)
0.0001
(0.00114)
0.474
(0.673)
0.265
(0.459)
0.0389
(0.126)
0.472
(0.673)
0.573
(0.752)
0.452
(0.653)
0.0391
(0.126)
0.0124
(0.055)
21q loss 42 (7%) 535 0.0228
(0.0918)
0.0013
(0.0106)
0.0833
(0.214)
0.262
(0.458)
0.0319
(0.11)
0.0324
(0.11)
0.45
(0.653)
0.0264
(0.0992)
0.907
(0.976)
1
(1.00)
xp loss 116 (20%) 461 0.00408
(0.0242)
0.0105
(0.0481)
0.0729
(0.195)
0.221
(0.405)
4e-05
(0.000521)
0.00021
(0.00221)
0.033
(0.111)
0.515
(0.704)
0.287
(0.483)
0.648
(0.809)
6q gain 23 (4%) 554 0.00784
(0.0407)
0.0368
(0.121)
0.755
(0.882)
0.105
(0.252)
0.00549
(0.0302)
0.00063
(0.0055)
0.682
(0.831)
0.671
(0.82)
0.813
(0.911)
1
(1.00)
8p gain 52 (9%) 525 1e-05
(0.000182)
0.00053
(0.00483)
0.0375
(0.123)
0.557
(0.737)
0.00129
(0.0106)
0.0543
(0.161)
0.278
(0.475)
0.159
(0.332)
0.19
(0.373)
0.677
(0.826)
17q gain 61 (11%) 516 0.00159
(0.0115)
0.0639
(0.18)
0.0495
(0.151)
0.0514
(0.154)
0.0437
(0.138)
0.0104
(0.0481)
0.0586
(0.169)
0.0609
(0.174)
0.692
(0.84)
0.479
(0.679)
4p loss 56 (10%) 521 0.0559
(0.165)
0.00188
(0.0131)
0.0327
(0.111)
0.176
(0.354)
0.00913
(0.0446)
0.00159
(0.0115)
0.769
(0.893)
0.358
(0.567)
0.819
(0.914)
1
(1.00)
7p loss 8 (1%) 569 0.0235
(0.093)
0.034
(0.114)
0.548
(0.728)
0.0414
(0.132)
0.0302
(0.106)
12p loss 59 (10%) 518 0.00975
(0.0462)
0.0368
(0.121)
0.546
(0.728)
0.725
(0.862)
0.00241
(0.0157)
0.0395
(0.127)
0.122
(0.278)
0.171
(0.348)
0.728
(0.863)
0.579
(0.756)
14q loss 147 (25%) 430 1e-05
(0.000182)
0.00011
(0.00124)
0.534
(0.717)
0.481
(0.68)
1e-05
(0.000182)
0.0568
(0.166)
0.189
(0.373)
0.0296
(0.105)
0.147
(0.317)
0.602
(0.769)
17q loss 41 (7%) 536 0.00881
(0.0438)
0.0614
(0.174)
0.122
(0.278)
0.047
(0.145)
4e-05
(0.000521)
0.0255
(0.0968)
0.154
(0.326)
1
(1.00)
0.157
(0.33)
0.107
(0.257)
18p loss 71 (12%) 506 0.0102
(0.0473)
0.0316
(0.109)
0.305
(0.504)
0.218
(0.403)
0.00042
(0.00405)
0.173
(0.351)
0.467
(0.668)
0.0428
(0.135)
0.205
(0.387)
0.598
(0.768)
18q loss 62 (11%) 515 0.034
(0.114)
0.00707
(0.0379)
0.529
(0.715)
0.239
(0.426)
0.00233
(0.0153)
0.607
(0.773)
0.704
(0.846)
0.00272
(0.0172)
0.699
(0.846)
0.119
(0.274)
19q loss 35 (6%) 542 0.00721
(0.0384)
0.00953
(0.0457)
0.262
(0.458)
0.151
(0.321)
0.0321
(0.11)
0.0013
(0.0106)
0.201
(0.384)
0.191
(0.373)
0.78
(0.899)
0.483
(0.68)
xq loss 106 (18%) 471 0.0252
(0.0965)
0.0236
(0.093)
0.179
(0.357)
0.172
(0.349)
4e-05
(0.000521)
0.00874
(0.0438)
0.0569
(0.166)
0.827
(0.918)
0.451
(0.653)
0.961
(1.00)
3q gain 64 (11%) 513 0.00067
(0.00572)
0.0613
(0.174)
0.505
(0.699)
0.0642
(0.18)
0.00879
(0.0438)
0.0346
(0.115)
0.809
(0.909)
1
(1.00)
0.589
(0.763)
0.151
(0.321)
9p gain 47 (8%) 530 0.0107
(0.0487)
0.0308
(0.108)
0.84
(0.927)
0.435
(0.639)
0.0122
(0.0545)
0.369
(0.572)
0.321
(0.523)
0.704
(0.846)
0.206
(0.39)
0.112
(0.264)
16p gain 38 (7%) 539 0.0148
(0.064)
0.0664
(0.183)
0.489
(0.683)
0.273
(0.468)
0.0041
(0.0242)
0.0377
(0.123)
0.193
(0.375)
0.661
(0.818)
1
(1.00)
1
(1.00)
2p loss 32 (6%) 545 0.00138
(0.0107)
0.0276
(0.101)
0.483
(0.68)
0.771
(0.894)
0.011
(0.0497)
0.28
(0.476)
0.115
(0.269)
0.939
(0.997)
0.237
(0.423)
0.226
(0.411)
2q loss 33 (6%) 544 0.00227
(0.015)
0.0138
(0.0604)
0.343
(0.549)
0.665
(0.818)
0.00896
(0.044)
0.269
(0.464)
0.0675
(0.186)
0.871
(0.956)
0.105
(0.253)
0.0731
(0.195)
9p loss 203 (35%) 374 0.00752
(0.0395)
0.124
(0.279)
0.629
(0.79)
0.489
(0.683)
0.601
(0.769)
0.907
(0.976)
0.101
(0.245)
0.0702
(0.19)
0.00968
(0.0461)
0.00839
(0.0425)
11q loss 92 (16%) 485 5e-05
(0.000641)
0.00014
(0.00153)
0.928
(0.991)
0.07
(0.19)
1e-05
(0.000182)
0.227
(0.413)
0.332
(0.539)
0.151
(0.321)
0.14
(0.308)
0.533
(0.717)
12q loss 57 (10%) 520 0.00829
(0.0425)
0.0299
(0.106)
0.569
(0.749)
0.418
(0.624)
7e-05
(0.000857)
0.05
(0.151)
0.0763
(0.201)
0.533
(0.717)
0.729
(0.863)
0.578
(0.755)
6p gain 24 (4%) 553 0.0315
(0.109)
0.118
(0.273)
0.891
(0.967)
0.16
(0.332)
0.0535
(0.16)
0.00576
(0.0313)
0.652
(0.812)
0.889
(0.967)
1
(1.00)
1
(1.00)
12q gain 49 (8%) 528 0.591
(0.764)
0.955
(1.00)
0.403
(0.609)
0.01
(0.0469)
0.299
(0.498)
0.779
(0.899)
0.213
(0.399)
0.527
(0.715)
0.0253
(0.0965)
0.123
(0.278)
15q gain 25 (4%) 552 0.0819
(0.213)
0.0973
(0.238)
0.772
(0.895)
0.0764
(0.201)
0.0462
(0.144)
0.838
(0.927)
0.0684
(0.187)
0.802
(0.906)
0.039
(0.126)
0.387
(0.594)
1p loss 16 (3%) 561 0.756
(0.882)
0.828
(0.919)
0.913
(0.98)
0.196
(0.378)
0.0498
(0.151)
0.73
(0.864)
0.346
(0.55)
0.265
(0.459)
0.101
(0.245)
0.0179
(0.0742)
3p loss 41 (7%) 536 0.932
(0.994)
0.916
(0.98)
0.58
(0.756)
0.0814
(0.212)
0.00208
(0.014)
0.939
(0.997)
0.0169
(0.0719)
0.654
(0.814)
0.435
(0.639)
0.167
(0.341)
3q loss 36 (6%) 541 0.1
(0.244)
0.279
(0.475)
0.5
(0.693)
0.394
(0.597)
0.00051
(0.00475)
0.624
(0.789)
0.0125
(0.055)
0.0948
(0.235)
0.497
(0.691)
0.0664
(0.183)
6q loss 126 (22%) 451 0.947
(1.00)
0.613
(0.779)
0.294
(0.493)
0.98
(1.00)
0.0171
(0.0721)
0.726
(0.862)
0.0484
(0.149)
0.334
(0.54)
0.367
(0.571)
0.295
(0.494)
16q loss 83 (14%) 494 0.025
(0.0962)
0.427
(0.634)
0.364
(0.571)
0.895
(0.97)
0.00998
(0.0469)
0.72
(0.858)
0.228
(0.413)
0.2
(0.384)
0.712
(0.851)
0.597
(0.768)
17p loss 65 (11%) 512 0.0969
(0.238)
0.0205
(0.0838)
0.305
(0.504)
0.582
(0.757)
1e-05
(0.000182)
0.148
(0.317)
0.533
(0.717)
0.21
(0.394)
0.299
(0.498)
0.704
(0.846)
1p gain 82 (14%) 495 0.547
(0.728)
0.131
(0.29)
0.428
(0.634)
0.248
(0.441)
1e-05
(0.000182)
0.794
(0.902)
0.377
(0.581)
0.522
(0.711)
0.232
(0.417)
0.273
(0.468)
1q gain 89 (15%) 488 0.0935
(0.233)
0.0888
(0.223)
0.108
(0.258)
0.627
(0.79)
1e-05
(0.000182)
0.192
(0.375)
0.0867
(0.219)
0.531
(0.717)
0.625
(0.789)
0.505
(0.699)
11q gain 15 (3%) 562 0.148
(0.317)
0.0636
(0.179)
0.524
(0.712)
0.244
(0.434)
0.306
(0.504)
0.00253
(0.0161)
0.705
(0.846)
0.884
(0.967)
1
(1.00)
1
(1.00)
12p gain 60 (10%) 517 0.785
(0.9)
0.793
(0.902)
0.685
(0.834)
0.165
(0.339)
0.0949
(0.235)
1
(1.00)
0.255
(0.45)
0.577
(0.755)
0.00433
(0.025)
0.078
(0.204)
14q gain 22 (4%) 555 0.393
(0.596)
0.782
(0.9)
0.0177
(0.0739)
0.806
(0.908)
0.752
(0.882)
0.915
(0.98)
0.407
(0.612)
0.11
(0.262)
0.363
(0.571)
0.326
(0.531)
xq gain 17 (3%) 560 0.297
(0.496)
0.967
(1.00)
0.985
(1.00)
0.514
(0.704)
0.732
(0.865)
0.584
(0.758)
0.508
(0.702)
1
(1.00)
0.0469
(0.145)
0.259
(0.454)
6p loss 87 (15%) 490 0.559
(0.74)
0.369
(0.572)
0.511
(0.704)
0.778
(0.899)
0.00013
(0.00144)
0.84
(0.927)
0.111
(0.262)
0.0691
(0.188)
0.755
(0.882)
0.596
(0.768)
8q loss 42 (7%) 535 0.341
(0.548)
0.154
(0.325)
0.0494
(0.151)
0.808
(0.909)
0.226
(0.411)
0.597
(0.768)
0.458
(0.657)
1
(1.00)
0.458
(0.657)
0.144
(0.314)
16p loss 63 (11%) 514 0.524
(0.712)
0.851
(0.937)
0.56
(0.74)
0.735
(0.865)
0.0306
(0.107)
0.073
(0.195)
0.719
(0.858)
0.795
(0.902)
0.564
(0.744)
0.646
(0.809)
22q loss 181 (31%) 396 0.582
(0.757)
0.669
(0.818)
0.47
(0.671)
0.888
(0.967)
1e-05
(0.000182)
0.0865
(0.219)
0.423
(0.631)
0.163
(0.337)
0.2
(0.384)
0.156
(0.329)
2p gain 37 (6%) 540 0.602
(0.769)
0.735
(0.865)
0.546
(0.728)
0.223
(0.407)
0.425
(0.633)
0.31
(0.508)
0.796
(0.902)
0.139
(0.307)
0.924
(0.988)
0.537
(0.72)
2q gain 35 (6%) 542 0.794
(0.902)
0.91
(0.978)
0.12
(0.275)
0.201
(0.384)
0.428
(0.634)
0.449
(0.653)
0.883
(0.967)
0.37
(0.572)
0.701
(0.846)
0.177
(0.355)
4p gain 35 (6%) 542 0.19
(0.373)
0.754
(0.882)
0.257
(0.452)
0.482
(0.68)
0.217
(0.403)
0.411
(0.616)
0.491
(0.685)
0.549
(0.728)
0.617
(0.783)
0.792
(0.902)
4q gain 34 (6%) 543 0.225
(0.411)
0.194
(0.376)
0.161
(0.333)
0.656
(0.814)
0.186
(0.367)
0.32
(0.523)
0.392
(0.596)
0.701
(0.846)
0.366
(0.571)
0.661
(0.818)
5p gain 49 (8%) 528 0.124
(0.279)
0.157
(0.33)
0.218
(0.403)
0.345
(0.55)
0.0867
(0.219)
0.115
(0.269)
0.056
(0.165)
0.359
(0.567)
0.14
(0.308)
0.229
(0.414)
5q gain 41 (7%) 536 0.13
(0.288)
0.23
(0.414)
0.165
(0.339)
0.0543
(0.161)
0.302
(0.501)
0.0569
(0.166)
0.0839
(0.215)
0.339
(0.546)
0.202
(0.385)
0.403
(0.609)
9q gain 70 (12%) 507 0.165
(0.339)
0.0779
(0.204)
0.666
(0.818)
0.123
(0.278)
0.061
(0.174)
0.11
(0.261)
0.513
(0.704)
0.365
(0.571)
0.412
(0.616)
0.0786
(0.205)
10q gain 3 (1%) 574 0.789
(0.902)
1
(1.00)
0.0733
(0.195)
0.795
(0.902)
1
(1.00)
0.488
(0.683)
11p gain 18 (3%) 559 0.96
(1.00)
0.9
(0.971)
0.665
(0.818)
0.898
(0.97)
0.642
(0.805)
0.346
(0.55)
0.407
(0.612)
0.886
(0.967)
0.687
(0.835)
1
(1.00)
13q gain 10 (2%) 567 0.0712
(0.192)
0.496
(0.69)
0.22
(0.405)
0.824
(0.917)
0.118
(0.274)
0.936
(0.997)
0.148
(0.317)
0.824
(0.917)
0.866
(0.952)
1
(1.00)
xp gain 15 (3%) 562 0.195
(0.376)
1
(1.00)
0.818
(0.914)
0.185
(0.366)
0.89
(0.967)
0.632
(0.793)
1
(1.00)
0.626
(0.79)
0.0859
(0.219)
0.433
(0.639)
1q loss 15 (3%) 562 0.784
(0.9)
0.978
(1.00)
0.795
(0.902)
0.361
(0.569)
0.254
(0.45)
0.849
(0.935)
0.339
(0.546)
0.288
(0.484)
0.512
(0.704)
0.0827
(0.214)
7q loss 6 (1%) 571 0.0832
(0.214)
0.3
(0.499)
0.895
(0.97)
0.126
(0.281)
0.105
(0.253)
8p loss 58 (10%) 519 0.285
(0.483)
0.446
(0.65)
0.217
(0.403)
0.782
(0.9)
0.308
(0.507)
0.939
(0.997)
0.737
(0.865)
1
(1.00)
0.571
(0.75)
0.392
(0.596)
9q loss 94 (16%) 483 0.305
(0.504)
0.13
(0.288)
0.175
(0.353)
0.175
(0.353)
0.234
(0.42)
0.709
(0.849)
0.147
(0.317)
0.547
(0.728)
0.647
(0.809)
0.179
(0.357)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
1P GAIN MUTATED 35 42 5
1P GAIN WILD-TYPE 220 155 120

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
1Q GAIN MUTATED 38 47 4
1Q GAIN WILD-TYPE 217 150 121

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

'3p gain' versus 'MRNA_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.011

Table S3.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
3P GAIN MUTATED 16 18 5 15
3P GAIN WILD-TYPE 142 78 132 102

Figure S3.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
3P GAIN MUTATED 13 18 5 18
3P GAIN WILD-TYPE 135 84 95 140

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
3P GAIN MUTATED 35 5 15
3P GAIN WILD-TYPE 258 119 114

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.072

Table S6.  Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
3P GAIN MUTATED 33 20 5
3P GAIN WILD-TYPE 222 177 120

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.096

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
3P GAIN MUTATED 6 0 7 13
3P GAIN WILD-TYPE 64 42 74 69

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0057

Table S8.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
3Q GAIN MUTATED 18 21 6 15
3Q GAIN WILD-TYPE 140 75 131 102

Figure S8.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.044

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
3Q GAIN MUTATED 35 24 5
3Q GAIN WILD-TYPE 220 173 120

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
3Q GAIN MUTATED 5 1 9 15
3Q GAIN WILD-TYPE 65 41 72 67

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.11

Table S11.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
6P GAIN MUTATED 5 9 2 4
6P GAIN WILD-TYPE 153 87 135 113

Figure S11.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.031

Table S12.  Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
6P GAIN MUTATED 0 1 1 8
6P GAIN WILD-TYPE 70 41 80 74

Figure S12.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q gain' versus 'MRNA_CNMF'

P value = 0.00784 (Fisher's exact test), Q value = 0.041

Table S13.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
6Q GAIN MUTATED 4 10 2 4
6Q GAIN WILD-TYPE 154 86 135 113

Figure S13.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
6Q GAIN MUTATED 5 7 0 8
6Q GAIN WILD-TYPE 143 95 100 150

Figure S14.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00549 (Fisher's exact test), Q value = 0.03

Table S15.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
6Q GAIN MUTATED 16 7 0
6Q GAIN WILD-TYPE 239 190 125

Figure S15.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0055

Table S16.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
6Q GAIN MUTATED 0 0 1 9
6Q GAIN WILD-TYPE 70 42 80 73

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S17.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
7P GAIN MUTATED 146 65 115 84
7P GAIN WILD-TYPE 12 31 22 33

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7P GAIN MUTATED 132 55 85 138
7P GAIN WILD-TYPE 16 47 15 20

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0025

Table S19.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
7P GAIN MUTATED 128 142 64 110
7P GAIN WILD-TYPE 15 45 26 16

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7P GAIN MUTATED 214 113 117
7P GAIN WILD-TYPE 79 11 12

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
7P GAIN MUTATED 180 183 105
7P GAIN WILD-TYPE 75 14 20

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S22.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
7P GAIN MUTATED 65 36 70 50
7P GAIN WILD-TYPE 5 6 11 32

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.043

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
7P GAIN MUTATED 42 47 29 26 37
7P GAIN WILD-TYPE 2 10 15 4 8

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.005

Table S24.  Gene #13: '7p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
7P GAIN MUTATED 81 47 53
7P GAIN WILD-TYPE 9 23 7

Figure S24.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.045

Table S25.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
7P GAIN MUTATED 31 62 27
7P GAIN WILD-TYPE 14 6 7

Figure S25.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00094

Table S26.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
7P GAIN MUTATED 16 84 20
7P GAIN WILD-TYPE 14 8 5

Figure S26.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S27.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
7Q GAIN MUTATED 145 64 116 89
7Q GAIN WILD-TYPE 13 32 21 28

Figure S27.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S28.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7Q GAIN MUTATED 130 61 85 138
7Q GAIN WILD-TYPE 18 41 15 20

Figure S28.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'MIR_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.014

Table S29.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
7Q GAIN MUTATED 129 142 69 108
7Q GAIN WILD-TYPE 14 45 21 18

Figure S29.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S30.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7Q GAIN MUTATED 221 112 115
7Q GAIN WILD-TYPE 72 12 14

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S31.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
7Q GAIN MUTATED 185 184 106
7Q GAIN WILD-TYPE 70 13 19

Figure S31.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0041

Table S32.  Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
7Q GAIN MUTATED 64 37 68 54
7Q GAIN WILD-TYPE 6 5 13 28

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.05

Table S33.  Gene #14: '7q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
7Q GAIN MUTATED 80 51 54
7Q GAIN WILD-TYPE 10 19 6

Figure S33.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.012

Table S34.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
7Q GAIN MUTATED 19 84 21
7Q GAIN WILD-TYPE 11 8 4

Figure S34.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S35.  Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
8P GAIN MUTATED 7 19 5 17
8P GAIN WILD-TYPE 151 77 132 100

Figure S35.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0048

Table S36.  Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8P GAIN MUTATED 10 21 4 13
8P GAIN WILD-TYPE 138 81 96 145

Figure S36.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'MIR_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.12

Table S37.  Gene #15: '8p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
8P GAIN MUTATED 7 21 13 8
8P GAIN WILD-TYPE 136 166 77 118

Figure S37.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.011

Table S38.  Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
8P GAIN MUTATED 27 23 2
8P GAIN WILD-TYPE 228 174 123

Figure S38.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S39.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
8Q GAIN MUTATED 7 20 6 21
8Q GAIN WILD-TYPE 151 76 131 96

Figure S39.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S40.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8Q GAIN MUTATED 9 26 4 15
8Q GAIN WILD-TYPE 139 76 96 143

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'MIR_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.13

Table S41.  Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
8Q GAIN MUTATED 9 26 12 8
8Q GAIN WILD-TYPE 134 161 78 118

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.011

Table S42.  Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
8Q GAIN MUTATED 32 24 3
8Q GAIN WILD-TYPE 223 173 122

Figure S42.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.045

Table S43.  Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
8Q GAIN MUTATED 4 2 10 18
8Q GAIN WILD-TYPE 66 40 71 64

Figure S43.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p gain' versus 'MRNA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.049

Table S44.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
9P GAIN MUTATED 16 15 5 8
9P GAIN WILD-TYPE 142 81 132 109

Figure S44.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.11

Table S45.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
9P GAIN MUTATED 15 12 2 15
9P GAIN WILD-TYPE 133 90 98 143

Figure S45.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.054

Table S46.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
9P GAIN MUTATED 27 17 3
9P GAIN WILD-TYPE 228 180 122

Figure S46.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.011

Table S47.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
10P GAIN MUTATED 1 6 0 5
10P GAIN WILD-TYPE 157 90 137 112

Figure S47.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0017

Table S48.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P GAIN MUTATED 2 9 0 1
10P GAIN WILD-TYPE 146 93 100 157

Figure S48.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.011

Table S49.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
10P GAIN MUTATED 12 1 0
10P GAIN WILD-TYPE 243 196 125

Figure S49.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.027

Table S50.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
10P GAIN MUTATED 1 0 0 7
10P GAIN WILD-TYPE 69 42 81 75

Figure S50.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.025

Table S51.  Gene #19: '10p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
10P GAIN MUTATED 0 5 0
10P GAIN WILD-TYPE 90 65 60

Figure S51.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.016

Table S52.  Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
11Q GAIN MUTATED 2 0 0 8
11Q GAIN WILD-TYPE 68 42 81 74

Figure S52.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.025

Table S53.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
12P GAIN MUTATED 0 12 3
12P GAIN WILD-TYPE 45 56 31

Figure S53.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.047

Table S54.  Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
12Q GAIN MUTATED 16 15 17
12Q GAIN WILD-TYPE 277 109 112

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.097

Table S55.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
12Q GAIN MUTATED 0 9 3
12Q GAIN WILD-TYPE 45 59 31

Figure S55.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'14q gain' versus 'MIR_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.074

Table S56.  Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
14Q GAIN MUTATED 9 5 7 1
14Q GAIN WILD-TYPE 134 182 83 125

Figure S56.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.14

Table S57.  Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
15Q GAIN MUTATED 12 12 1
15Q GAIN WILD-TYPE 243 185 124

Figure S57.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.13

Table S58.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
15Q GAIN MUTATED 0 7 1
15Q GAIN WILD-TYPE 45 61 33

Figure S58.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.064

Table S59.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
16P GAIN MUTATED 11 10 3 13
16P GAIN WILD-TYPE 147 86 134 104

Figure S59.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.024

Table S60.  Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
16P GAIN MUTATED 20 17 1
16P GAIN WILD-TYPE 235 180 124

Figure S60.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.12

Table S61.  Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
16P GAIN MUTATED 5 1 4 13
16P GAIN WILD-TYPE 65 41 77 69

Figure S61.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q gain' versus 'MRNA_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.1

Table S62.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
16Q GAIN MUTATED 9 11 4 12
16Q GAIN WILD-TYPE 149 85 133 105

Figure S62.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00534 (Fisher's exact test), Q value = 0.03

Table S63.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
16Q GAIN MUTATED 10 15 2 9
16Q GAIN WILD-TYPE 138 87 98 149

Figure S63.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.099

Table S64.  Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
16Q GAIN MUTATED 19 16 2
16Q GAIN WILD-TYPE 236 181 123

Figure S64.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.1

Table S65.  Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
16Q GAIN MUTATED 4 1 4 13
16Q GAIN WILD-TYPE 66 41 77 69

Figure S65.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.092

Table S66.  Gene #29: '16q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
16Q GAIN MUTATED 1 8 4 1 0
16Q GAIN WILD-TYPE 43 49 40 29 45

Figure S66.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0041

Table S67.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
17P GAIN MUTATED 9 16 4 15
17P GAIN WILD-TYPE 149 80 133 102

Figure S67.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.1

Table S68.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17P GAIN MUTATED 10 16 4 14
17P GAIN WILD-TYPE 138 86 96 144

Figure S68.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.1

Table S69.  Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17P GAIN MUTATED 33 8 5
17P GAIN WILD-TYPE 260 116 124

Figure S69.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.1

Table S70.  Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
17P GAIN MUTATED 23 22 4
17P GAIN WILD-TYPE 232 175 121

Figure S70.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.096

Table S71.  Gene #30: '17p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
17P GAIN MUTATED 4 2 5 15
17P GAIN WILD-TYPE 66 40 76 67

Figure S71.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.096

Table S72.  Gene #30: '17p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
17P GAIN MUTATED 4 4 1 5 0
17P GAIN WILD-TYPE 40 53 43 25 45

Figure S72.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.012

Table S73.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
17Q GAIN MUTATED 13 18 6 17
17Q GAIN WILD-TYPE 145 78 131 100

Figure S73.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MIR_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.15

Table S74.  Gene #31: '17q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
17Q GAIN MUTATED 7 25 10 16
17Q GAIN WILD-TYPE 136 162 80 110

Figure S74.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.14

Table S75.  Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
17Q GAIN MUTATED 30 25 6
17Q GAIN WILD-TYPE 225 172 119

Figure S75.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.048

Table S76.  Gene #31: '17q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
17Q GAIN MUTATED 5 2 7 18
17Q GAIN WILD-TYPE 65 40 74 64

Figure S76.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S77.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18P GAIN MUTATED 12 23 4 16
18P GAIN WILD-TYPE 146 73 133 101

Figure S77.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0048

Table S78.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18P GAIN MUTATED 11 22 4 18
18P GAIN WILD-TYPE 137 80 96 140

Figure S78.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S79.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
18P GAIN MUTATED 36 21 1
18P GAIN WILD-TYPE 219 176 124

Figure S79.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00893 (Fisher's exact test), Q value = 0.044

Table S80.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
18P GAIN MUTATED 6 1 9 18
18P GAIN WILD-TYPE 64 41 72 64

Figure S80.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.1

Table S81.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
18P GAIN MUTATED 6 11 0
18P GAIN WILD-TYPE 39 57 34

Figure S81.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S82.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18Q GAIN MUTATED 11 22 5 17
18Q GAIN WILD-TYPE 147 74 132 100

Figure S82.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0053

Table S83.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18Q GAIN MUTATED 10 23 6 16
18Q GAIN WILD-TYPE 138 79 94 142

Figure S83.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S84.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
18Q GAIN MUTATED 35 22 1
18Q GAIN WILD-TYPE 220 175 124

Figure S84.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.048

Table S85.  Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
18Q GAIN MUTATED 7 1 8 18
18Q GAIN WILD-TYPE 63 41 73 64

Figure S85.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.099

Table S86.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
18Q GAIN MUTATED 6 11 0
18Q GAIN WILD-TYPE 39 57 34

Figure S86.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S87.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19P GAIN MUTATED 58 33 85 22
19P GAIN WILD-TYPE 100 63 52 95

Figure S87.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S88.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P GAIN MUTATED 62 25 58 53
19P GAIN WILD-TYPE 86 77 42 105

Figure S88.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0025

Table S89.  Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19P GAIN MUTATED 94 50 68
19P GAIN WILD-TYPE 199 74 61

Figure S89.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S90.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
19P GAIN MUTATED 66 56 104
19P GAIN WILD-TYPE 189 141 21

Figure S90.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S91.  Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
19P GAIN MUTATED 25 17 53 13
19P GAIN WILD-TYPE 45 25 28 69

Figure S91.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S92.  Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
19P GAIN MUTATED 31 16 37
19P GAIN WILD-TYPE 59 54 23

Figure S92.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S93.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19Q GAIN MUTATED 51 29 78 15
19Q GAIN WILD-TYPE 107 67 59 102

Figure S93.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S94.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q GAIN MUTATED 55 18 55 45
19Q GAIN WILD-TYPE 93 84 45 113

Figure S94.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.027

Table S95.  Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19Q GAIN MUTATED 82 47 56
19Q GAIN WILD-TYPE 211 77 73

Figure S95.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S96.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
19Q GAIN MUTATED 53 47 98
19Q GAIN WILD-TYPE 202 150 27

Figure S96.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S97.  Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
19Q GAIN MUTATED 21 17 47 7
19Q GAIN WILD-TYPE 49 25 34 75

Figure S97.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0023

Table S98.  Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
19Q GAIN MUTATED 25 13 31
19Q GAIN WILD-TYPE 65 57 29

Figure S98.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.14

Table S99.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
19Q GAIN MUTATED 8 27 11
19Q GAIN WILD-TYPE 37 41 23

Figure S99.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S100.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20P GAIN MUTATED 53 29 80 30
20P GAIN WILD-TYPE 105 67 57 87

Figure S100.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S101.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P GAIN MUTATED 55 21 64 52
20P GAIN WILD-TYPE 93 81 36 106

Figure S101.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.022

Table S102.  Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
20P GAIN MUTATED 60 76 20 56
20P GAIN WILD-TYPE 83 111 70 70

Figure S102.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S103.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20P GAIN MUTATED 85 58 69
20P GAIN WILD-TYPE 208 66 60

Figure S103.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S104.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
20P GAIN MUTATED 68 71 83
20P GAIN WILD-TYPE 187 126 42

Figure S104.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0017

Table S105.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
20P GAIN MUTATED 29 22 41 17
20P GAIN WILD-TYPE 41 20 40 65

Figure S105.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0057

Table S106.  Gene #36: '20p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
20P GAIN MUTATED 27 17 33
20P GAIN WILD-TYPE 63 53 27

Figure S106.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S107.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20Q GAIN MUTATED 53 30 80 28
20Q GAIN WILD-TYPE 105 66 57 89

Figure S107.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S108.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q GAIN MUTATED 58 22 62 49
20Q GAIN WILD-TYPE 90 80 38 109

Figure S108.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.012

Table S109.  Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
20Q GAIN MUTATED 61 75 19 55
20Q GAIN WILD-TYPE 82 112 71 71

Figure S109.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S110.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20Q GAIN MUTATED 85 57 68
20Q GAIN WILD-TYPE 208 67 61

Figure S110.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S111.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
20Q GAIN MUTATED 67 70 83
20Q GAIN WILD-TYPE 188 127 42

Figure S111.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00052

Table S112.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
20Q GAIN MUTATED 28 22 41 16
20Q GAIN WILD-TYPE 42 20 40 66

Figure S112.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0038

Table S113.  Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
20Q GAIN MUTATED 28 17 34
20Q GAIN WILD-TYPE 62 53 26

Figure S113.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 0.00301 (Fisher's exact test), Q value = 0.019

Table S114.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
21Q GAIN MUTATED 29 10 8 8
21Q GAIN WILD-TYPE 129 86 129 109

Figure S114.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.04

Table S115.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
21Q GAIN MUTATED 25 6 5 19
21Q GAIN WILD-TYPE 123 96 95 139

Figure S115.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'MIR_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.073

Table S116.  Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
21Q GAIN MUTATED 23 15 5 19
21Q GAIN WILD-TYPE 120 172 85 107

Figure S116.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'21q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00378 (Fisher's exact test), Q value = 0.023

Table S117.  Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
21Q GAIN MUTATED 26 25 11
21Q GAIN WILD-TYPE 267 99 118

Figure S117.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.031

Table S118.  Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
21Q GAIN MUTATED 17 3 5 8
21Q GAIN WILD-TYPE 53 39 76 74

Figure S118.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.079

Table S119.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
21Q GAIN MUTATED 2 16 5
21Q GAIN WILD-TYPE 43 52 29

Figure S119.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S120.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
22Q GAIN MUTATED 6 13 0 12
22Q GAIN WILD-TYPE 152 83 137 105

Figure S120.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00305 (Fisher's exact test), Q value = 0.019

Table S121.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
22Q GAIN MUTATED 11 11 0 9
22Q GAIN WILD-TYPE 137 91 100 149

Figure S121.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.024

Table S122.  Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
22Q GAIN MUTATED 22 11 1
22Q GAIN WILD-TYPE 233 186 124

Figure S122.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.14

Table S123.  Gene #39: '22q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
22Q GAIN MUTATED 4 0 6 11
22Q GAIN WILD-TYPE 66 42 75 71

Figure S123.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.11

Table S124.  Gene #39: '22q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
22Q GAIN MUTATED 5 7 0
22Q GAIN WILD-TYPE 85 63 60

Figure S124.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.15

Table S125.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
XQ GAIN MUTATED 0 6 0
XQ GAIN WILD-TYPE 45 62 34

Figure S125.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.15

Table S126.  Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
1P LOSS MUTATED 12 3 1
1P LOSS WILD-TYPE 243 194 124

Figure S126.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.074

Table S127.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
1P LOSS MUTATED 2 0 2
1P LOSS WILD-TYPE 28 92 23

Figure S127.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.011

Table S128.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
2P LOSS MUTATED 7 14 3 5
2P LOSS WILD-TYPE 151 82 134 112

Figure S128.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.1

Table S129.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
2P LOSS MUTATED 8 12 2 7
2P LOSS WILD-TYPE 140 90 98 151

Figure S129.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.05

Table S130.  Gene #44: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
2P LOSS MUTATED 16 15 1
2P LOSS WILD-TYPE 239 182 124

Figure S130.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.015

Table S131.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
2Q LOSS MUTATED 7 14 3 6
2Q LOSS WILD-TYPE 151 82 134 111

Figure S131.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.06

Table S132.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
2Q LOSS MUTATED 8 13 2 7
2Q LOSS WILD-TYPE 140 89 98 151

Figure S132.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00896 (Fisher's exact test), Q value = 0.044

Table S133.  Gene #45: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
2Q LOSS MUTATED 17 15 1
2Q LOSS WILD-TYPE 238 182 124

Figure S133.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.014

Table S134.  Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
3P LOSS MUTATED 22 18 1
3P LOSS WILD-TYPE 233 179 124

Figure S134.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.072

Table S135.  Gene #46: '3p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
3P LOSS MUTATED 2 4 1 2 10
3P LOSS WILD-TYPE 42 53 43 28 35

Figure S135.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0048

Table S136.  Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
3Q LOSS MUTATED 21 15 0
3Q LOSS WILD-TYPE 234 182 125

Figure S136.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.055

Table S137.  Gene #47: '3q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
3Q LOSS MUTATED 1 4 1 1 9
3Q LOSS WILD-TYPE 43 53 43 29 36

Figure S137.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.013

Table S138.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
4P LOSS MUTATED 10 20 4 17
4P LOSS WILD-TYPE 138 82 96 141

Figure S138.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'MIR_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.11

Table S139.  Gene #48: '4p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
4P LOSS MUTATED 6 25 10 12
4P LOSS WILD-TYPE 137 162 80 114

Figure S139.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 0.00913 (Fisher's exact test), Q value = 0.045

Table S140.  Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
4P LOSS MUTATED 21 29 6
4P LOSS WILD-TYPE 234 168 119

Figure S140.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.012

Table S141.  Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
4P LOSS MUTATED 2 1 10 16
4P LOSS WILD-TYPE 68 41 71 66

Figure S141.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.014

Table S142.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
4Q LOSS MUTATED 12 17 5 14
4Q LOSS WILD-TYPE 146 79 132 103

Figure S142.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.011

Table S143.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
4Q LOSS MUTATED 10 19 3 16
4Q LOSS WILD-TYPE 138 83 97 142

Figure S143.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'MIR_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.096

Table S144.  Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
4Q LOSS MUTATED 5 23 10 13
4Q LOSS WILD-TYPE 138 164 80 113

Figure S144.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.028

Table S145.  Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
4Q LOSS MUTATED 24 27 4
4Q LOSS WILD-TYPE 231 170 121

Figure S145.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.012

Table S146.  Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
4Q LOSS MUTATED 2 1 10 16
4Q LOSS WILD-TYPE 68 41 71 66

Figure S146.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S147.  Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
5P LOSS MUTATED 5 21 5 9
5P LOSS WILD-TYPE 153 75 132 108

Figure S147.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S148.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5P LOSS MUTATED 6 22 5 7
5P LOSS WILD-TYPE 142 80 95 151

Figure S148.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'MIR_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.024

Table S149.  Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
5P LOSS MUTATED 4 24 6 6
5P LOSS WILD-TYPE 139 163 84 120

Figure S149.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.035

Table S150.  Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
5P LOSS MUTATED 25 16 2
5P LOSS WILD-TYPE 230 181 123

Figure S150.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.011

Table S151.  Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
5P LOSS MUTATED 1 1 5 14
5P LOSS WILD-TYPE 69 41 76 68

Figure S151.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S152.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
5Q LOSS MUTATED 6 20 5 11
5Q LOSS WILD-TYPE 152 76 132 106

Figure S152.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S153.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5Q LOSS MUTATED 9 22 4 7
5Q LOSS WILD-TYPE 139 80 96 151

Figure S153.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'MIR_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0086

Table S154.  Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
5Q LOSS MUTATED 4 26 6 6
5Q LOSS WILD-TYPE 139 161 84 120

Figure S154.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.025

Table S155.  Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
5Q LOSS MUTATED 26 17 2
5Q LOSS WILD-TYPE 229 180 123

Figure S155.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00052

Table S156.  Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
5Q LOSS MUTATED 0 1 5 16
5Q LOSS WILD-TYPE 70 41 76 66

Figure S156.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.14

Table S157.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
5Q LOSS MUTATED 6 10 0
5Q LOSS WILD-TYPE 24 82 25

Figure S157.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S158.  Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
6P LOSS MUTATED 45 37 5
6P LOSS WILD-TYPE 210 160 120

Figure S158.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.072

Table S159.  Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
6Q LOSS MUTATED 62 48 16
6Q LOSS WILD-TYPE 193 149 109

Figure S159.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.15

Table S160.  Gene #53: '6q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
6Q LOSS MUTATED 11 10 3 9 12
6Q LOSS WILD-TYPE 33 47 41 21 33

Figure S160.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.093

Table S161.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
7P LOSS MUTATED 0 4 1 3
7P LOSS WILD-TYPE 158 92 136 114

Figure S161.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.11

Table S162.  Gene #54: '7p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7P LOSS MUTATED 1 5 0 2
7P LOSS WILD-TYPE 147 97 100 156

Figure S162.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.13

Table S163.  Gene #54: '7p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7P LOSS MUTATED 8 0 0
7P LOSS WILD-TYPE 285 124 129

Figure S163.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.11

Table S164.  Gene #54: '7p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
7P LOSS MUTATED 7 0 1
7P LOSS WILD-TYPE 248 197 124

Figure S164.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'CN_CNMF'

'8q loss' versus 'MIR_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.15

Table S165.  Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
8Q LOSS MUTATED 19 10 6 7
8Q LOSS WILD-TYPE 124 177 84 119

Figure S165.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.04

Table S166.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
9P LOSS MUTATED 53 21 59 44
9P LOSS WILD-TYPE 105 75 78 73

Figure S166.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00968 (Fisher's exact test), Q value = 0.046

Table S167.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
9P LOSS MUTATED 8 24 17
9P LOSS WILD-TYPE 37 44 17

Figure S167.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.043

Table S168.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
9P LOSS MUTATED 4 32 13
9P LOSS WILD-TYPE 26 60 12

Figure S168.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S169.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
10P LOSS MUTATED 141 63 128 87
10P LOSS WILD-TYPE 17 33 9 30

Figure S169.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S170.  Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P LOSS MUTATED 127 62 93 137
10P LOSS WILD-TYPE 21 40 7 21

Figure S170.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.065

Table S171.  Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
10P LOSS MUTATED 129 150 68 107
10P LOSS WILD-TYPE 14 37 22 19

Figure S171.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00094

Table S172.  Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10P LOSS MUTATED 226 108 120
10P LOSS WILD-TYPE 67 16 9

Figure S172.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S173.  Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
10P LOSS MUTATED 175 191 114
10P LOSS WILD-TYPE 80 6 11

Figure S173.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S174.  Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
10P LOSS MUTATED 62 39 74 48
10P LOSS WILD-TYPE 8 3 7 34

Figure S174.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.011

Table S175.  Gene #60: '10p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
10P LOSS MUTATED 83 52 56
10P LOSS WILD-TYPE 7 18 4

Figure S175.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.055

Table S176.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
10P LOSS MUTATED 22 85 24
10P LOSS WILD-TYPE 8 7 1

Figure S176.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S177.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
10Q LOSS MUTATED 141 69 131 91
10Q LOSS WILD-TYPE 17 27 6 26

Figure S177.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S178.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10Q LOSS MUTATED 127 69 97 139
10Q LOSS WILD-TYPE 21 33 3 19

Figure S178.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.04

Table S179.  Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
10Q LOSS MUTATED 131 157 68 110
10Q LOSS WILD-TYPE 12 30 22 16

Figure S179.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0036

Table S180.  Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10Q LOSS MUTATED 236 108 122
10Q LOSS WILD-TYPE 57 16 7

Figure S180.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S181.  Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
10Q LOSS MUTATED 183 192 117
10Q LOSS WILD-TYPE 72 5 8

Figure S181.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00094

Table S182.  Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
10Q LOSS MUTATED 60 41 76 59
10Q LOSS WILD-TYPE 10 1 5 23

Figure S182.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0062

Table S183.  Gene #61: '10q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
10Q LOSS MUTATED 83 52 57
10Q LOSS WILD-TYPE 7 18 3

Figure S183.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.085

Table S184.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
10Q LOSS MUTATED 23 86 24
10Q LOSS WILD-TYPE 7 6 1

Figure S184.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S185.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
11P LOSS MUTATED 27 32 8 22
11P LOSS WILD-TYPE 131 64 129 95

Figure S185.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S186.  Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11P LOSS MUTATED 26 36 4 23
11P LOSS WILD-TYPE 122 66 96 135

Figure S186.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.074

Table S187.  Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
11P LOSS MUTATED 62 20 13
11P LOSS WILD-TYPE 231 104 116

Figure S187.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S188.  Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
11P LOSS MUTATED 56 40 2
11P LOSS WILD-TYPE 199 157 123

Figure S188.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.011

Table S189.  Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
11P LOSS MUTATED 12 4 12 29
11P LOSS WILD-TYPE 58 38 69 53

Figure S189.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.11

Table S190.  Gene #62: '11p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
11P LOSS MUTATED 11 17 5
11P LOSS WILD-TYPE 79 53 55

Figure S190.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00064

Table S191.  Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
11Q LOSS MUTATED 31 28 9 18
11Q LOSS WILD-TYPE 127 68 128 99

Figure S191.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S192.  Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11Q LOSS MUTATED 28 28 5 25
11Q LOSS WILD-TYPE 120 74 95 133

Figure S192.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S193.  Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
11Q LOSS MUTATED 47 43 2
11Q LOSS WILD-TYPE 208 154 123

Figure S193.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'MRNA_CNMF'

P value = 0.00975 (Fisher's exact test), Q value = 0.046

Table S194.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
12P LOSS MUTATED 16 18 7 15
12P LOSS WILD-TYPE 142 78 130 102

Figure S194.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.12

Table S195.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
12P LOSS MUTATED 15 18 5 18
12P LOSS WILD-TYPE 133 84 95 140

Figure S195.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.016

Table S196.  Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
12P LOSS MUTATED 26 29 4
12P LOSS WILD-TYPE 229 168 121

Figure S196.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.13

Table S197.  Gene #64: '12p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
12P LOSS MUTATED 8 0 10 12
12P LOSS WILD-TYPE 62 42 71 70

Figure S197.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q loss' versus 'MRNA_CNMF'

P value = 0.00829 (Fisher's exact test), Q value = 0.042

Table S198.  Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
12Q LOSS MUTATED 13 17 7 16
12Q LOSS WILD-TYPE 145 79 130 101

Figure S198.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.11

Table S199.  Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
12Q LOSS MUTATED 13 18 5 17
12Q LOSS WILD-TYPE 135 84 95 141

Figure S199.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00086

Table S200.  Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
12Q LOSS MUTATED 25 30 2
12Q LOSS WILD-TYPE 230 167 123

Figure S200.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00075

Table S201.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
13Q LOSS MUTATED 58 35 22 47
13Q LOSS WILD-TYPE 100 61 115 70

Figure S201.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.016

Table S202.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
13Q LOSS MUTATED 50 40 17 55
13Q LOSS WILD-TYPE 98 62 83 103

Figure S202.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S203.  Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
13Q LOSS MUTATED 92 83 10
13Q LOSS WILD-TYPE 163 114 115

Figure S203.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.026

Table S204.  Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
13Q LOSS MUTATED 27 7 22 37
13Q LOSS WILD-TYPE 43 35 59 45

Figure S204.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.099

Table S205.  Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
13Q LOSS MUTATED 27 28 11
13Q LOSS WILD-TYPE 63 42 49

Figure S205.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S206.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
14Q LOSS MUTATED 48 34 13 41
14Q LOSS WILD-TYPE 110 62 124 76

Figure S206.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0012

Table S207.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
14Q LOSS MUTATED 43 36 10 47
14Q LOSS WILD-TYPE 105 66 90 111

Figure S207.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S208.  Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
14Q LOSS MUTATED 86 58 3
14Q LOSS WILD-TYPE 169 139 122

Figure S208.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.11

Table S209.  Gene #67: '14q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
14Q LOSS MUTATED 28 21 8
14Q LOSS WILD-TYPE 62 49 52

Figure S209.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00075

Table S210.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
15Q LOSS MUTATED 25 24 11 33
15Q LOSS WILD-TYPE 133 72 126 84

Figure S210.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S211.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
15Q LOSS MUTATED 20 37 7 29
15Q LOSS WILD-TYPE 128 65 93 129

Figure S211.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.013

Table S212.  Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
15Q LOSS MUTATED 16 48 17 15
15Q LOSS WILD-TYPE 127 139 73 111

Figure S212.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.014

Table S213.  Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
15Q LOSS MUTATED 64 10 22
15Q LOSS WILD-TYPE 229 114 107

Figure S213.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S214.  Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
15Q LOSS MUTATED 54 47 3
15Q LOSS WILD-TYPE 201 150 122

Figure S214.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.089

Table S215.  Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
15Q LOSS MUTATED 11 3 16 24
15Q LOSS WILD-TYPE 59 39 65 58

Figure S215.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.078

Table S216.  Gene #68: '15q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
15Q LOSS MUTATED 16 19 5
15Q LOSS WILD-TYPE 74 51 55

Figure S216.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.024

Table S217.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
15Q LOSS MUTATED 16 9 3
15Q LOSS WILD-TYPE 29 59 31

Figure S217.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.092

Table S218.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
15Q LOSS MUTATED 11 15 2
15Q LOSS WILD-TYPE 19 77 23

Figure S218.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.11

Table S219.  Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
16P LOSS MUTATED 31 26 6
16P LOSS WILD-TYPE 224 171 119

Figure S219.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.096

Table S220.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
16Q LOSS MUTATED 26 19 10 18
16Q LOSS WILD-TYPE 132 77 127 99

Figure S220.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.047

Table S221.  Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
16Q LOSS MUTATED 43 32 8
16Q LOSS WILD-TYPE 212 165 117

Figure S221.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.084

Table S222.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17P LOSS MUTATED 23 16 8 10
17P LOSS WILD-TYPE 125 86 92 148

Figure S222.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S223.  Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
17P LOSS MUTATED 36 29 0
17P LOSS WILD-TYPE 219 168 125

Figure S223.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00881 (Fisher's exact test), Q value = 0.044

Table S224.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
17Q LOSS MUTATED 19 7 9 2
17Q LOSS WILD-TYPE 139 89 128 115

Figure S224.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.15

Table S225.  Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17Q LOSS MUTATED 15 15 10
17Q LOSS WILD-TYPE 278 109 119

Figure S225.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00052

Table S226.  Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
17Q LOSS MUTATED 18 23 0
17Q LOSS WILD-TYPE 237 174 125

Figure S226.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.097

Table S227.  Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
17Q LOSS MUTATED 9 3 2 2
17Q LOSS WILD-TYPE 61 39 79 80

Figure S227.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.047

Table S228.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18P LOSS MUTATED 22 15 6 16
18P LOSS WILD-TYPE 136 81 131 101

Figure S228.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.11

Table S229.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18P LOSS MUTATED 19 16 4 20
18P LOSS WILD-TYPE 129 86 96 138

Figure S229.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0041

Table S230.  Gene #73: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
18P LOSS MUTATED 35 32 4
18P LOSS WILD-TYPE 220 165 121

Figure S230.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.14

Table S231.  Gene #73: '18p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
18P LOSS MUTATED 15 13 3
18P LOSS WILD-TYPE 75 57 57

Figure S231.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.11

Table S232.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18Q LOSS MUTATED 20 11 6 16
18Q LOSS WILD-TYPE 138 85 131 101

Figure S232.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.038

Table S233.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18Q LOSS MUTATED 18 13 2 20
18Q LOSS WILD-TYPE 130 89 98 138

Figure S233.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.015

Table S234.  Gene #74: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
18Q LOSS MUTATED 29 29 4
18Q LOSS WILD-TYPE 226 168 121

Figure S234.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.017

Table S235.  Gene #74: '18q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
18Q LOSS MUTATED 11 14 1
18Q LOSS WILD-TYPE 79 56 59

Figure S235.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.012

Table S236.  Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19P LOSS MUTATED 3 10 2 9
19P LOSS WILD-TYPE 155 86 135 108

Figure S236.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.018

Table S237.  Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P LOSS MUTATED 4 12 1 7
19P LOSS WILD-TYPE 144 90 99 151

Figure S237.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'MIR_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.062

Table S238.  Gene #75: '19p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
19P LOSS MUTATED 3 17 2 4
19P LOSS WILD-TYPE 140 170 88 122

Figure S238.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0054

Table S239.  Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
19P LOSS MUTATED 3 0 0 10
19P LOSS WILD-TYPE 67 42 81 72

Figure S239.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.12

Table S240.  Gene #75: '19p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
19P LOSS MUTATED 1 7 3
19P LOSS WILD-TYPE 89 63 57

Figure S240.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.038

Table S241.  Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19Q LOSS MUTATED 6 10 3 12
19Q LOSS WILD-TYPE 152 86 134 105

Figure S241.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00953 (Fisher's exact test), Q value = 0.046

Table S242.  Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q LOSS MUTATED 7 12 1 11
19Q LOSS WILD-TYPE 141 90 99 147

Figure S242.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.11

Table S243.  Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
19Q LOSS MUTATED 20 13 2
19Q LOSS WILD-TYPE 235 184 123

Figure S243.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.011

Table S244.  Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
19Q LOSS MUTATED 7 0 1 11
19Q LOSS WILD-TYPE 63 42 80 71

Figure S244.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0035

Table S245.  Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20P LOSS MUTATED 4 10 0 3
20P LOSS WILD-TYPE 154 86 137 114

Figure S245.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S246.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P LOSS MUTATED 5 11 0 1
20P LOSS WILD-TYPE 143 91 100 157

Figure S246.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'MIR_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.15

Table S247.  Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
20P LOSS MUTATED 2 7 7 2
20P LOSS WILD-TYPE 141 180 83 124

Figure S247.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.042

Table S248.  Gene #77: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
20P LOSS MUTATED 14 5 0
20P LOSS WILD-TYPE 241 192 125

Figure S248.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.048

Table S249.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
20P LOSS MUTATED 4 0 0
20P LOSS WILD-TYPE 41 68 34

Figure S249.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.014

Table S250.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
20P LOSS MUTATED 4 0 0
20P LOSS WILD-TYPE 26 92 25

Figure S250.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MRNA_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.016

Table S251.  Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20Q LOSS MUTATED 4 8 0 3
20Q LOSS WILD-TYPE 154 88 137 114

Figure S251.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S252.  Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q LOSS MUTATED 4 10 0 1
20Q LOSS WILD-TYPE 144 92 100 157

Figure S252.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.13

Table S253.  Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
20Q LOSS MUTATED 11 6 0
20Q LOSS WILD-TYPE 244 191 125

Figure S253.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.13

Table S254.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 68 34
20Q LOSS MUTATED 3 0 0
20Q LOSS WILD-TYPE 42 68 34

Figure S254.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.055

Table S255.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
20Q LOSS MUTATED 3 0 0
20Q LOSS WILD-TYPE 27 92 25

Figure S255.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.092

Table S256.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
21Q LOSS MUTATED 5 12 8 11
21Q LOSS WILD-TYPE 153 84 129 106

Figure S256.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.011

Table S257.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
21Q LOSS MUTATED 5 17 6 8
21Q LOSS WILD-TYPE 143 85 94 150

Figure S257.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.11

Table S258.  Gene #79: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
21Q LOSS MUTATED 20 19 3
21Q LOSS WILD-TYPE 235 178 122

Figure S258.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.11

Table S259.  Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
21Q LOSS MUTATED 1 2 6 11
21Q LOSS WILD-TYPE 69 40 75 71

Figure S259.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.099

Table S260.  Gene #79: '21q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 70 60
21Q LOSS MUTATED 1 7 4
21Q LOSS WILD-TYPE 89 63 56

Figure S260.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S261.  Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
22Q LOSS MUTATED 79 83 19
22Q LOSS WILD-TYPE 176 114 106

Figure S261.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.024

Table S262.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
XP LOSS MUTATED 23 32 24 25
XP LOSS WILD-TYPE 135 64 113 92

Figure S262.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.048

Table S263.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
XP LOSS MUTATED 22 33 19 30
XP LOSS WILD-TYPE 126 69 81 128

Figure S263.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00052

Table S264.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
XP LOSS MUTATED 43 59 14
XP LOSS WILD-TYPE 212 138 111

Figure S264.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0022

Table S265.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
XP LOSS MUTATED 5 5 18 28
XP LOSS WILD-TYPE 65 37 63 54

Figure S265.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.11

Table S266.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 57 44 30 45
XP LOSS MUTATED 7 14 6 13 13
XP LOSS WILD-TYPE 37 43 38 17 32

Figure S266.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.096

Table S267.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
XQ LOSS MUTATED 22 28 22 22
XQ LOSS WILD-TYPE 136 68 115 95

Figure S267.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.093

Table S268.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
XQ LOSS MUTATED 19 29 18 28
XQ LOSS WILD-TYPE 129 73 82 130

Figure S268.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00052

Table S269.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 255 197 125
XQ LOSS MUTATED 37 56 13
XQ LOSS WILD-TYPE 218 141 112

Figure S269.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.044

Table S270.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 42 81 82
XQ LOSS MUTATED 5 5 18 21
XQ LOSS WILD-TYPE 65 37 63 61

Figure S270.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/22538152/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/22555065/GBM-TP.transferedmergedcluster.txt

  • Number of patients = 577

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • 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

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)