Correlation between copy number variations of arm-level result and molecular subtypes
Bladder Urothelial Carcinoma (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/C18K78F6
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 408 patients, 280 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'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

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

  • 20p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • xp gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 2p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 20q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • xq loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 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, 280 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
xp gain 65 (16%) 343 0.00617
(0.0308)
0.0002
(0.00208)
0.00021
(0.0021)
0.00879
(0.0396)
1e-05
(0.000155)
0.0381
(0.121)
0.0422
(0.13)
0.0436
(0.132)
0.0153
(0.0593)
0.0382
(0.121)
5p gain 166 (41%) 242 1e-05
(0.000155)
0.0253
(0.0879)
0.00035
(0.00334)
0.00288
(0.0172)
0.00408
(0.0226)
0.00055
(0.00465)
0.0399
(0.124)
0.244
(0.404)
0.0246
(0.0866)
0.00454
(0.0247)
3p loss 51 (12%) 357 0.043
(0.132)
0.0083
(0.0376)
0.0167
(0.063)
0.00661
(0.0323)
1e-05
(0.000155)
1e-05
(0.000155)
0.014
(0.0552)
0.14
(0.284)
6e-05
(0.000703)
0.00968
(0.0416)
9p loss 174 (43%) 234 1e-05
(0.000155)
0.0002
(0.00208)
0.00322
(0.0189)
0.00017
(0.00183)
6e-05
(0.000703)
1e-05
(0.000155)
0.00702
(0.0335)
0.184
(0.338)
4e-05
(0.000521)
0.00043
(0.00392)
9q loss 169 (41%) 239 1e-05
(0.000155)
1e-05
(0.000155)
0.0005
(0.00441)
1e-05
(0.000155)
1e-05
(0.000155)
1e-05
(0.000155)
5e-05
(0.000612)
0.309
(0.47)
1e-05
(0.000155)
2e-05
(0.000278)
11p loss 178 (44%) 230 1e-05
(0.000155)
1e-05
(0.000155)
0.12
(0.261)
0.00012
(0.00137)
0.00021
(0.0021)
1e-05
(0.000155)
2e-05
(0.000278)
0.455
(0.588)
2e-05
(0.000278)
0.00195
(0.0125)
2p gain 111 (27%) 297 1e-05
(0.000155)
6e-05
(0.000703)
0.133
(0.276)
0.604
(0.701)
0.0313
(0.105)
0.0102
(0.043)
0.00653
(0.0323)
0.0179
(0.0665)
0.206
(0.358)
0.00236
(0.0144)
9q gain 56 (14%) 352 2e-05
(0.000278)
0.0805
(0.2)
0.159
(0.306)
0.00612
(0.0308)
0.00203
(0.0128)
0.00043
(0.00392)
0.0399
(0.124)
0.886
(0.921)
2e-05
(0.000278)
0.00121
(0.00848)
21q gain 116 (28%) 292 1e-05
(0.000155)
3e-05
(0.000397)
0.527
(0.639)
0.405
(0.552)
0.0795
(0.199)
0.00074
(0.00578)
0.00167
(0.0112)
0.00037
(0.00349)
0.00424
(0.0233)
0.0112
(0.0464)
8p loss 188 (46%) 220 1e-05
(0.000155)
0.00383
(0.0216)
0.0137
(0.0544)
0.00098
(0.00724)
0.00279
(0.0169)
0.00578
(0.0294)
0.166
(0.316)
0.037
(0.12)
0.0655
(0.174)
0.448
(0.587)
13q loss 85 (21%) 323 1e-05
(0.000155)
0.505
(0.624)
0.00016
(0.00175)
0.527
(0.639)
0.00057
(0.00477)
0.189
(0.341)
5e-05
(0.000612)
0.012
(0.0486)
0.00939
(0.041)
0.00119
(0.00841)
14q loss 121 (30%) 287 1e-05
(0.000155)
5e-05
(0.000612)
0.808
(0.857)
0.417
(0.563)
0.055
(0.155)
0.00019
(0.00202)
0.00075
(0.0058)
0.00119
(0.00841)
0.0036
(0.0205)
0.00115
(0.00827)
15q loss 144 (35%) 264 1e-05
(0.000155)
1e-05
(0.000155)
0.11
(0.247)
0.0677
(0.177)
0.00543
(0.028)
0.288
(0.453)
0.023
(0.0825)
0.00929
(0.0407)
0.0102
(0.043)
0.0233
(0.0829)
21q loss 79 (19%) 329 0.0175
(0.0656)
0.0656
(0.174)
0.0136
(0.0544)
0.0265
(0.0912)
0.0584
(0.161)
0.00657
(0.0323)
0.003
(0.0177)
0.0906
(0.216)
0.0112
(0.0464)
0.0083
(0.0376)
3p gain 143 (35%) 265 1e-05
(0.000155)
0.184
(0.338)
0.887
(0.921)
0.529
(0.64)
0.0156
(0.06)
0.0129
(0.052)
0.0486
(0.142)
0.00828
(0.0376)
0.116
(0.255)
0.0199
(0.0729)
4p gain 38 (9%) 370 0.00053
(0.00457)
0.00908
(0.0401)
0.00488
(0.0258)
0.0437
(0.132)
0.27
(0.434)
0.00974
(0.0416)
0.0142
(0.0556)
0.447
(0.587)
0.158
(0.305)
0.121
(0.261)
11p gain 29 (7%) 379 0.00828
(0.0376)
0.242
(0.402)
0.06
(0.165)
0.00898
(0.04)
0.0018
(0.0118)
0.0122
(0.0494)
0.062
(0.167)
0.625
(0.716)
0.00139
(0.00942)
0.00479
(0.0258)
18p gain 116 (28%) 292 1e-05
(0.000155)
0.00762
(0.0357)
0.636
(0.723)
0.431
(0.574)
1e-05
(0.000155)
0.0293
(0.0992)
0.00031
(0.00303)
0.614
(0.709)
0.29
(0.453)
0.0385
(0.122)
4q loss 136 (33%) 272 1e-05
(0.000155)
0.0519
(0.149)
0.109
(0.245)
0.0114
(0.0466)
0.00514
(0.0268)
0.00054
(0.00461)
0.00555
(0.0284)
0.926
(0.948)
0.0101
(0.043)
0.0717
(0.185)
22q loss 160 (39%) 248 1e-05
(0.000155)
0.0106
(0.0441)
0.143
(0.287)
0.00058
(0.0048)
0.00437
(0.0239)
0.00064
(0.00515)
0.0548
(0.154)
0.75
(0.813)
0.0373
(0.12)
0.0675
(0.177)
9p gain 69 (17%) 339 1e-05
(0.000155)
0.359
(0.515)
0.175
(0.327)
0.0166
(0.0628)
0.122
(0.261)
0.178
(0.331)
0.00971
(0.0416)
0.558
(0.66)
0.00014
(0.00157)
2e-05
(0.000278)
2q loss 92 (23%) 316 0.00064
(0.00515)
0.00585
(0.0296)
0.404
(0.551)
0.337
(0.494)
0.0106
(0.0441)
0.0266
(0.0912)
0.429
(0.573)
0.953
(0.964)
0.0364
(0.118)
0.553
(0.659)
4p loss 144 (35%) 264 1e-05
(0.000155)
0.12
(0.261)
0.165
(0.316)
0.00332
(0.019)
0.00526
(0.0273)
5e-05
(0.000612)
0.00042
(0.00391)
0.426
(0.57)
0.058
(0.16)
0.186
(0.339)
3q gain 179 (44%) 229 1e-05
(0.000155)
0.42
(0.565)
0.124
(0.264)
0.666
(0.748)
0.216
(0.371)
0.065
(0.173)
0.00816
(0.0376)
0.0079
(0.0368)
0.0559
(0.157)
0.00964
(0.0416)
7p gain 171 (42%) 237 1e-05
(0.000155)
0.0341
(0.113)
0.00327
(0.019)
0.198
(0.351)
0.0976
(0.229)
0.17
(0.32)
0.0565
(0.158)
0.608
(0.703)
0.121
(0.261)
0.0435
(0.132)
10p gain 117 (29%) 291 1e-05
(0.000155)
0.00051
(0.00445)
0.278
(0.442)
0.325
(0.484)
0.0272
(0.0927)
0.00483
(0.0258)
0.0725
(0.186)
0.973
(0.982)
0.435
(0.577)
0.745
(0.81)
14q gain 57 (14%) 351 0.00669
(0.0325)
0.0254
(0.0879)
0.552
(0.659)
0.458
(0.589)
0.0114
(0.0466)
0.0296
(0.1)
0.374
(0.526)
0.322
(0.483)
0.306
(0.467)
0.16
(0.308)
18q gain 61 (15%) 347 0.0069
(0.0331)
0.184
(0.338)
0.32
(0.481)
0.173
(0.323)
0.0463
(0.139)
0.451
(0.587)
0.0423
(0.13)
0.293
(0.457)
0.559
(0.661)
0.00284
(0.0171)
5p loss 54 (13%) 354 0.00114
(0.00827)
0.00015
(0.00166)
0.0848
(0.205)
0.00221
(0.0137)
0.0536
(0.152)
0.00049
(0.00437)
0.713
(0.787)
0.672
(0.751)
0.0973
(0.229)
0.208
(0.36)
5q loss 160 (39%) 248 1e-05
(0.000155)
0.00172
(0.0115)
0.42
(0.565)
0.22
(0.375)
0.416
(0.562)
0.0203
(0.0741)
0.0468
(0.139)
0.0944
(0.222)
0.473
(0.599)
0.101
(0.235)
6q loss 159 (39%) 249 1e-05
(0.000155)
0.00892
(0.04)
0.018
(0.0666)
0.4
(0.548)
0.678
(0.754)
0.0354
(0.116)
0.0816
(0.201)
0.154
(0.301)
0.509
(0.626)
0.432
(0.574)
12p loss 54 (13%) 354 0.00028
(0.00277)
0.0161
(0.0613)
0.39
(0.541)
0.122
(0.261)
0.025
(0.0873)
0.022
(0.0796)
0.275
(0.44)
0.362
(0.517)
0.181
(0.336)
0.941
(0.958)
18q loss 146 (36%) 262 1e-05
(0.000155)
0.938
(0.956)
0.571
(0.669)
0.423
(0.568)
0.776
(0.836)
0.0472
(0.139)
0.0375
(0.12)
0.00385
(0.0216)
0.084
(0.204)
0.127
(0.268)
xq loss 83 (20%) 325 0.0849
(0.205)
0.0091
(0.0401)
0.521
(0.636)
0.08
(0.199)
0.0212
(0.0771)
0.218
(0.373)
0.109
(0.245)
0.295
(0.458)
0.0161
(0.0613)
0.0339
(0.112)
5q gain 51 (12%) 357 0.00077
(0.00585)
0.054
(0.153)
0.00215
(0.0135)
0.0356
(0.116)
0.805
(0.856)
0.258
(0.42)
0.0892
(0.213)
0.521
(0.636)
0.496
(0.616)
0.0799
(0.199)
8p gain 90 (22%) 318 1e-05
(0.000155)
0.48
(0.605)
0.00137
(0.00936)
0.133
(0.276)
0.299
(0.461)
0.832
(0.88)
0.247
(0.407)
0.0153
(0.0593)
0.622
(0.714)
0.314
(0.475)
8q gain 200 (49%) 208 1e-05
(0.000155)
0.00388
(0.0216)
0.00021
(0.0021)
0.539
(0.647)
0.536
(0.644)
1
(1.00)
0.222
(0.375)
0.0514
(0.149)
0.509
(0.626)
0.454
(0.587)
10q gain 44 (11%) 364 0.00189
(0.0123)
0.00176
(0.0116)
0.725
(0.793)
0.464
(0.592)
0.396
(0.546)
0.0512
(0.149)
0.00723
(0.0343)
0.459
(0.589)
0.0679
(0.177)
0.453
(0.587)
11q gain 47 (12%) 361 0.00331
(0.019)
0.627
(0.717)
0.367
(0.52)
0.0179
(0.0665)
0.0753
(0.192)
0.0791
(0.199)
0.297
(0.46)
0.778
(0.837)
0.00512
(0.0268)
0.166
(0.316)
15q gain 35 (9%) 373 0.168
(0.318)
0.00134
(0.00923)
0.00062
(0.00508)
0.0691
(0.179)
0.102
(0.237)
0.0319
(0.106)
0.446
(0.587)
0.725
(0.793)
0.122
(0.261)
0.141
(0.285)
xq gain 45 (11%) 363 0.137
(0.28)
0.138
(0.28)
0.0228
(0.082)
0.204
(0.356)
0.044
(0.133)
0.567
(0.667)
0.0631
(0.169)
0.0309
(0.104)
0.527
(0.639)
0.168
(0.318)
16q loss 107 (26%) 301 1e-05
(0.000155)
0.403
(0.551)
0.0148
(0.0578)
0.34
(0.497)
0.0417
(0.129)
0.389
(0.541)
0.199
(0.353)
0.89
(0.921)
0.564
(0.665)
0.467
(0.593)
19p loss 95 (23%) 313 3e-05
(0.000397)
0.052
(0.149)
0.084
(0.204)
0.194
(0.348)
0.00193
(0.0125)
0.00486
(0.0258)
0.146
(0.292)
0.239
(0.398)
0.671
(0.75)
0.447
(0.587)
19q loss 59 (14%) 349 0.00095
(0.00708)
0.221
(0.375)
0.0365
(0.118)
0.31
(0.472)
0.00687
(0.0331)
0.204
(0.356)
0.371
(0.523)
0.496
(0.616)
0.4
(0.548)
0.519
(0.635)
6q gain 39 (10%) 369 0.00296
(0.0176)
0.948
(0.961)
0.618
(0.711)
0.26
(0.422)
0.12
(0.261)
0.3
(0.461)
0.415
(0.562)
0.153
(0.301)
0.0467
(0.139)
0.361
(0.516)
12p gain 116 (28%) 292 0.00094
(0.00707)
0.323
(0.483)
0.204
(0.356)
0.981
(0.99)
0.143
(0.287)
0.858
(0.902)
0.519
(0.635)
0.723
(0.792)
0.463
(0.592)
0.0389
(0.123)
17q gain 135 (33%) 273 1e-05
(0.000155)
0.072
(0.185)
0.0444
(0.133)
0.924
(0.948)
0.555
(0.659)
0.185
(0.339)
0.247
(0.407)
0.268
(0.431)
0.166
(0.316)
0.334
(0.493)
19q gain 132 (32%) 276 1e-05
(0.000155)
0.025
(0.0873)
0.131
(0.272)
0.957
(0.967)
0.235
(0.395)
0.492
(0.616)
0.0979
(0.229)
0.432
(0.574)
0.201
(0.353)
0.608
(0.703)
20p gain 201 (49%) 207 1e-05
(0.000155)
0.187
(0.341)
0.329
(0.488)
0.0648
(0.173)
0.156
(0.303)
0.0414
(0.128)
0.125
(0.264)
0.19
(0.344)
0.0578
(0.16)
0.345
(0.502)
3q loss 23 (6%) 385 0.541
(0.649)
0.351
(0.508)
0.3
(0.461)
0.0617
(0.167)
0.00661
(0.0323)
0.156
(0.303)
0.0857
(0.207)
0.454
(0.587)
0.00124
(0.00862)
0.105
(0.24)
6p loss 103 (25%) 305 1e-05
(0.000155)
0.0233
(0.0829)
0.079
(0.199)
0.723
(0.792)
0.56
(0.661)
0.0607
(0.165)
0.234
(0.395)
0.2
(0.353)
0.147
(0.292)
0.263
(0.425)
8q loss 38 (9%) 370 0.00033
(0.00318)
0.448
(0.587)
0.508
(0.626)
0.0607
(0.165)
0.0189
(0.0695)
0.387
(0.54)
0.108
(0.244)
0.0616
(0.167)
0.533
(0.643)
0.618
(0.711)
10p loss 73 (18%) 335 0.0137
(0.0544)
0.252
(0.411)
0.34
(0.497)
0.878
(0.915)
0.0161
(0.0613)
0.138
(0.28)
0.714
(0.787)
0.324
(0.484)
0.199
(0.353)
0.218
(0.373)
10q loss 129 (32%) 279 1e-05
(0.000155)
0.00203
(0.0128)
0.345
(0.502)
0.416
(0.562)
0.45
(0.587)
0.556
(0.659)
0.661
(0.744)
0.159
(0.306)
0.122
(0.261)
0.512
(0.629)
11q loss 129 (32%) 279 1e-05
(0.000155)
0.0525
(0.149)
0.302
(0.462)
0.0344
(0.113)
0.36
(0.516)
0.154
(0.302)
0.305
(0.467)
0.151
(0.297)
0.291
(0.454)
0.343
(0.501)
16p loss 110 (27%) 298 1e-05
(0.000155)
0.443
(0.586)
0.00066
(0.00525)
0.278
(0.442)
0.0517
(0.149)
0.235
(0.395)
0.24
(0.399)
0.667
(0.748)
0.171
(0.321)
0.127
(0.268)
1p gain 89 (22%) 319 1e-05
(0.000155)
0.103
(0.238)
0.314
(0.475)
0.529
(0.64)
0.251
(0.411)
0.495
(0.616)
0.915
(0.944)
0.636
(0.723)
0.462
(0.592)
0.554
(0.659)
1q gain 126 (31%) 282 1e-05
(0.000155)
0.929
(0.949)
0.594
(0.693)
0.486
(0.612)
0.498
(0.618)
0.841
(0.886)
0.623
(0.715)
0.253
(0.412)
0.152
(0.298)
0.451
(0.587)
2q gain 55 (13%) 353 3e-05
(0.000397)
0.113
(0.25)
0.617
(0.711)
0.556
(0.659)
0.0926
(0.219)
0.231
(0.39)
0.103
(0.238)
0.188
(0.341)
0.29
(0.453)
0.374
(0.526)
4q gain 26 (6%) 382 0.024
(0.085)
0.187
(0.341)
0.676
(0.753)
0.552
(0.659)
0.607
(0.703)
0.113
(0.25)
0.069
(0.179)
0.334
(0.493)
0.334
(0.493)
0.383
(0.537)
6p gain 73 (18%) 335 1e-05
(0.000155)
0.884
(0.92)
0.346
(0.502)
0.2
(0.353)
0.297
(0.46)
0.58
(0.68)
0.365
(0.519)
0.525
(0.639)
0.592
(0.691)
0.875
(0.912)
7q gain 148 (36%) 260 1e-05
(0.000155)
0.13
(0.271)
0.0769
(0.196)
0.755
(0.817)
0.265
(0.427)
0.644
(0.731)
0.669
(0.749)
0.319
(0.48)
0.827
(0.876)
0.716
(0.788)
12q gain 91 (22%) 317 0.0619
(0.167)
0.287
(0.452)
0.275
(0.44)
0.786
(0.843)
0.151
(0.297)
0.0991
(0.231)
0.369
(0.522)
0.364
(0.518)
0.989
(0.994)
0.00224
(0.0138)
13q gain 100 (25%) 308 0.00072
(0.00568)
0.808
(0.857)
0.325
(0.484)
0.889
(0.921)
0.17
(0.32)
0.47
(0.595)
0.947
(0.961)
0.794
(0.848)
0.252
(0.411)
0.348
(0.504)
16p gain 75 (18%) 333 1e-05
(0.000155)
0.262
(0.425)
0.582
(0.68)
0.475
(0.599)
0.692
(0.765)
0.128
(0.268)
0.493
(0.616)
0.193
(0.347)
0.399
(0.548)
0.747
(0.812)
16q gain 82 (20%) 326 1e-05
(0.000155)
0.137
(0.28)
0.398
(0.547)
0.283
(0.449)
0.8
(0.851)
0.107
(0.244)
0.509
(0.626)
0.282
(0.448)
0.395
(0.545)
0.474
(0.599)
17p gain 56 (14%) 352 0.00106
(0.00776)
0.206
(0.358)
0.653
(0.738)
0.648
(0.734)
0.536
(0.644)
0.207
(0.359)
0.149
(0.296)
0.125
(0.265)
0.13
(0.271)
0.295
(0.458)
19p gain 87 (21%) 321 0.00077
(0.00585)
0.176
(0.328)
0.0781
(0.198)
0.466
(0.593)
0.229
(0.388)
0.108
(0.244)
0.367
(0.52)
0.79
(0.846)
0.352
(0.509)
0.784
(0.842)
20q gain 230 (56%) 178 1e-05
(0.000155)
0.137
(0.28)
0.467
(0.593)
0.636
(0.723)
0.39
(0.541)
0.141
(0.285)
0.192
(0.346)
0.149
(0.296)
0.0927
(0.219)
0.113
(0.25)
22q gain 48 (12%) 360 0.314
(0.475)
0.0677
(0.177)
0.745
(0.81)
0.237
(0.397)
0.109
(0.245)
0.0395
(0.124)
0.0835
(0.204)
0.646
(0.733)
0.125
(0.264)
0.357
(0.514)
1q loss 31 (8%) 377 0.0827
(0.203)
0.247
(0.407)
0.869
(0.91)
0.719
(0.791)
0.891
(0.921)
0.427
(0.572)
0.992
(0.996)
0.923
(0.948)
0.0465
(0.139)
0.383
(0.537)
2p loss 45 (11%) 363 0.337
(0.494)
0.0812
(0.201)
0.691
(0.765)
0.925
(0.948)
0.533
(0.643)
0.0271
(0.0927)
0.115
(0.253)
0.943
(0.958)
0.157
(0.304)
0.763
(0.825)
7q loss 28 (7%) 380 0.00747
(0.0352)
0.414
(0.562)
0.451
(0.587)
0.211
(0.365)
0.989
(0.994)
0.726
(0.793)
0.489
(0.614)
0.191
(0.345)
0.599
(0.698)
0.833
(0.88)
12q loss 58 (14%) 350 0.00044
(0.00396)
0.772
(0.833)
0.393
(0.543)
0.214
(0.368)
0.167
(0.317)
0.465
(0.593)
0.66
(0.743)
0.794
(0.848)
0.865
(0.907)
0.683
(0.759)
17p loss 182 (45%) 226 1e-05
(0.000155)
0.454
(0.587)
0.0872
(0.21)
0.113
(0.251)
0.872
(0.912)
0.0914
(0.217)
0.3
(0.461)
0.391
(0.541)
0.196
(0.348)
0.353
(0.509)
18p loss 98 (24%) 310 0.00012
(0.00137)
0.117
(0.257)
0.701
(0.774)
0.433
(0.575)
0.077
(0.196)
0.051
(0.149)
0.183
(0.338)
0.336
(0.494)
0.0695
(0.18)
0.12
(0.261)
20q loss 15 (4%) 393 0.181
(0.336)
0.919
(0.945)
0.0522
(0.149)
0.136
(0.28)
0.0478
(0.141)
0.842
(0.887)
0.753
(0.815)
1
(1.00)
0.874
(0.912)
0.943
(0.958)
1p loss 31 (8%) 377 0.103
(0.238)
0.311
(0.472)
0.569
(0.669)
0.386
(0.539)
0.863
(0.906)
0.222
(0.375)
0.789
(0.846)
0.463
(0.592)
0.728
(0.793)
0.287
(0.452)
7p loss 20 (5%) 388 0.453
(0.587)
0.658
(0.742)
0.657
(0.742)
0.898
(0.928)
0.276
(0.441)
0.415
(0.562)
0.545
(0.653)
0.0579
(0.16)
0.494
(0.616)
0.501
(0.62)
17q loss 46 (11%) 362 0.0887
(0.213)
0.603
(0.701)
0.928
(0.949)
0.265
(0.427)
0.141
(0.285)
0.798
(0.851)
0.685
(0.76)
0.918
(0.945)
1
(1.00)
0.985
(0.993)
20p loss 32 (8%) 376 0.105
(0.24)
0.195
(0.348)
0.131
(0.272)
0.236
(0.395)
0.674
(0.752)
0.329
(0.488)
0.38
(0.533)
0.495
(0.616)
0.249
(0.409)
0.458
(0.589)
xp loss 73 (18%) 335 0.196
(0.348)
0.284
(0.449)
0.361
(0.516)
0.316
(0.476)
0.0816
(0.201)
0.635
(0.723)
0.84
(0.886)
0.215
(0.369)
0.147
(0.292)
0.12
(0.261)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
1P GAIN MUTATED 23 44 4 16 2
1P GAIN WILD-TYPE 55 102 117 45 0

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
1Q GAIN MUTATED 35 58 17 14 2
1Q GAIN WILD-TYPE 43 88 104 47 0

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
2P GAIN MUTATED 32 60 6 13 0
2P GAIN WILD-TYPE 46 86 115 48 2

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
2P GAIN MUTATED 31 54 10 16
2P GAIN WILD-TYPE 107 73 53 64

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
2P GAIN MUTATED 17 43 5 24 22
2P GAIN WILD-TYPE 55 92 33 79 34

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.043

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
2P GAIN MUTATED 45 25 41
2P GAIN WILD-TYPE 73 87 133

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00653 (Fisher's exact test), Q value = 0.032

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
2P GAIN MUTATED 21 29 28 12 20
2P GAIN WILD-TYPE 84 45 86 13 67

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.066

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
2P GAIN MUTATED 64 33 13
2P GAIN WILD-TYPE 202 50 43

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.014

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
2P GAIN MUTATED 19 23 18 37 11
2P GAIN WILD-TYPE 68 37 23 95 63

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
2Q GAIN MUTATED 16 31 4 4 0
2Q GAIN WILD-TYPE 62 115 117 57 2

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S11.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
3P GAIN MUTATED 44 62 20 17 0
3P GAIN WILD-TYPE 34 84 101 44 2

Figure S11.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.06

Table S12.  Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
3P GAIN MUTATED 28 56 7 27 23
3P GAIN WILD-TYPE 44 79 31 76 33

Figure S12.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.052

Table S13.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
3P GAIN MUTATED 52 41 48
3P GAIN WILD-TYPE 66 71 126

Figure S13.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.14

Table S14.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
3P GAIN MUTATED 33 37 34 10 28
3P GAIN WILD-TYPE 72 37 80 15 59

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00828 (Fisher's exact test), Q value = 0.038

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
3P GAIN MUTATED 80 40 22
3P GAIN WILD-TYPE 186 43 34

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.073

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
3P GAIN MUTATED 32 32 13 41 20
3P GAIN WILD-TYPE 55 28 28 91 54

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S17.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
3Q GAIN MUTATED 50 80 24 23 2
3Q GAIN WILD-TYPE 28 66 97 38 0

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.038

Table S18.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
3Q GAIN MUTATED 41 46 43 13 35
3Q GAIN WILD-TYPE 64 28 71 12 52

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.037

Table S19.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
3Q GAIN MUTATED 103 48 27
3Q GAIN WILD-TYPE 163 35 29

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00964 (Fisher's exact test), Q value = 0.042

Table S20.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
3Q GAIN MUTATED 37 39 18 50 29
3Q GAIN WILD-TYPE 50 21 23 82 45

Figure S20.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0046

Table S21.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
4P GAIN MUTATED 9 24 3 2 0
4P GAIN WILD-TYPE 69 122 118 59 2

Figure S21.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00908 (Fisher's exact test), Q value = 0.04

Table S22.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
4P GAIN MUTATED 7 21 3 7
4P GAIN WILD-TYPE 131 106 60 73

Figure S22.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.026

Table S23.  Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
4P GAIN MUTATED 4 12 16
4P GAIN WILD-TYPE 118 102 88

Figure S23.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.13

Table S24.  Gene #7: '4p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
4P GAIN MUTATED 5 19 6 2
4P GAIN WILD-TYPE 85 102 92 29

Figure S24.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00974 (Fisher's exact test), Q value = 0.042

Table S25.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
4P GAIN MUTATED 11 18 9
4P GAIN WILD-TYPE 107 94 165

Figure S25.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.056

Table S26.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
4P GAIN MUTATED 7 8 19 0 4
4P GAIN WILD-TYPE 98 66 95 25 83

Figure S26.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.085

Table S27.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
4Q GAIN MUTATED 6 16 3 1 0
4Q GAIN WILD-TYPE 72 130 118 60 2

Figure S27.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S28.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
5P GAIN MUTATED 43 70 19 32 2
5P GAIN WILD-TYPE 35 76 102 29 0

Figure S28.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.088

Table S29.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
5P GAIN MUTATED 66 45 18 37
5P GAIN WILD-TYPE 72 82 45 43

Figure S29.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0033

Table S30.  Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
5P GAIN MUTATED 43 32 56
5P GAIN WILD-TYPE 79 82 48

Figure S30.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00288 (Fisher's exact test), Q value = 0.017

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
5P GAIN MUTATED 27 38 51 15
5P GAIN WILD-TYPE 63 83 47 16

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.023

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
5P GAIN MUTATED 27 48 9 57 23
5P GAIN WILD-TYPE 45 87 29 46 33

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0046

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
5P GAIN MUTATED 34 41 89
5P GAIN WILD-TYPE 84 71 85

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.12

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
5P GAIN MUTATED 46 36 33 12 38
5P GAIN WILD-TYPE 59 38 81 13 49

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.087

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
5P GAIN MUTATED 44 21 46 50
5P GAIN WILD-TYPE 80 30 81 42

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00454 (Fisher's exact test), Q value = 0.025

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
5P GAIN MUTATED 26 27 23 46 39
5P GAIN WILD-TYPE 61 33 18 86 35

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0058

Table S37.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
5Q GAIN MUTATED 20 17 8 5 1
5Q GAIN WILD-TYPE 58 129 113 56 1

Figure S37.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.013

Table S38.  Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
5Q GAIN MUTATED 8 12 23
5Q GAIN WILD-TYPE 114 102 81

Figure S38.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #10: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
5Q GAIN MUTATED 5 15 19 4
5Q GAIN WILD-TYPE 85 106 79 27

Figure S39.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
6P GAIN MUTATED 15 35 6 16 1
6P GAIN WILD-TYPE 63 111 115 45 1

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.018

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
6Q GAIN MUTATED 8 16 5 8 2
6Q GAIN WILD-TYPE 70 130 116 53 0

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.14

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
6Q GAIN MUTATED 5 7 14 12
6Q GAIN WILD-TYPE 119 44 113 80

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S43.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
7P GAIN MUTATED 51 71 17 30 2
7P GAIN WILD-TYPE 27 75 104 31 0

Figure S43.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.11

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
7P GAIN MUTATED 62 62 18 29
7P GAIN WILD-TYPE 76 65 45 51

Figure S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.019

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
7P GAIN MUTATED 41 40 56
7P GAIN WILD-TYPE 81 74 48

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.13

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
7P GAIN MUTATED 29 25 15 53 42
7P GAIN WILD-TYPE 58 35 26 79 32

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S47.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
7Q GAIN MUTATED 50 60 17 19 2
7Q GAIN WILD-TYPE 28 86 104 42 0

Figure S47.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S48.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
8P GAIN MUTATED 44 26 16 3 1
8P GAIN WILD-TYPE 34 120 105 58 1

Figure S48.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0094

Table S49.  Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
8P GAIN MUTATED 19 22 37
8P GAIN WILD-TYPE 103 92 67

Figure S49.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.059

Table S50.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
8P GAIN MUTATED 68 16 5
8P GAIN WILD-TYPE 198 67 51

Figure S50.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S51.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
8Q GAIN MUTATED 64 72 35 28 1
8Q GAIN WILD-TYPE 14 74 86 33 1

Figure S51.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00388 (Fisher's exact test), Q value = 0.022

Table S52.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
8Q GAIN MUTATED 61 75 21 43
8Q GAIN WILD-TYPE 77 52 42 37

Figure S52.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0021

Table S53.  Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
8Q GAIN MUTATED 52 48 69
8Q GAIN WILD-TYPE 70 66 35

Figure S53.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S54.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
9P GAIN MUTATED 19 18 5 26 1
9P GAIN WILD-TYPE 59 128 116 35 1

Figure S54.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.063

Table S55.  Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
9P GAIN MUTATED 18 11 19 9
9P GAIN WILD-TYPE 72 110 79 22

Figure S55.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.00971 (Fisher's exact test), Q value = 0.042

Table S56.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
9P GAIN MUTATED 30 9 17 4 9
9P GAIN WILD-TYPE 75 65 97 21 78

Figure S56.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0016

Table S57.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
9P GAIN MUTATED 14 8 14 30
9P GAIN WILD-TYPE 110 43 113 62

Figure S57.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S58.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
9P GAIN MUTATED 13 8 2 16 27
9P GAIN WILD-TYPE 74 52 39 116 47

Figure S58.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S59.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
9Q GAIN MUTATED 11 18 6 20 1
9Q GAIN WILD-TYPE 67 128 115 41 1

Figure S59.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.031

Table S60.  Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
9Q GAIN MUTATED 12 9 19 9
9Q GAIN WILD-TYPE 78 112 79 22

Figure S60.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.013

Table S61.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
9Q GAIN MUTATED 7 14 1 26 6
9Q GAIN WILD-TYPE 65 121 37 77 50

Figure S61.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0039

Table S62.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
9Q GAIN MUTATED 7 11 36
9Q GAIN WILD-TYPE 111 101 138

Figure S62.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.12

Table S63.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
9Q GAIN MUTATED 22 9 10 6 9
9Q GAIN WILD-TYPE 83 65 104 19 78

Figure S63.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S64.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
9Q GAIN MUTATED 11 6 9 27
9Q GAIN WILD-TYPE 113 45 118 65

Figure S64.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0085

Table S65.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
9Q GAIN MUTATED 10 6 3 12 22
9Q GAIN WILD-TYPE 77 54 38 120 52

Figure S65.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S66.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
10P GAIN MUTATED 30 58 8 21 0
10P GAIN WILD-TYPE 48 88 113 40 2

Figure S66.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0044

Table S67.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
10P GAIN MUTATED 34 54 11 18
10P GAIN WILD-TYPE 104 73 52 62

Figure S67.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.093

Table S68.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
10P GAIN MUTATED 22 39 4 29 23
10P GAIN WILD-TYPE 50 96 34 74 33

Figure S68.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.026

Table S69.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
10P GAIN MUTATED 48 26 43
10P GAIN WILD-TYPE 70 86 131

Figure S69.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.012

Table S70.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
10Q GAIN MUTATED 12 23 3 6 0
10Q GAIN WILD-TYPE 66 123 118 55 2

Figure S70.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.012

Table S71.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
10Q GAIN MUTATED 11 25 2 6
10Q GAIN WILD-TYPE 127 102 61 74

Figure S71.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.034

Table S72.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
10Q GAIN MUTATED 6 11 11 8 8
10Q GAIN WILD-TYPE 99 63 103 17 79

Figure S72.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00828 (Fisher's exact test), Q value = 0.038

Table S73.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
11P GAIN MUTATED 7 7 4 11 0
11P GAIN WILD-TYPE 71 139 117 50 2

Figure S73.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00898 (Fisher's exact test), Q value = 0.04

Table S74.  Gene #21: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
11P GAIN MUTATED 4 4 10 6
11P GAIN WILD-TYPE 86 117 88 25

Figure S74.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.012

Table S75.  Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
11P GAIN MUTATED 1 6 2 17 3
11P GAIN WILD-TYPE 71 129 36 86 53

Figure S75.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.049

Table S76.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
11P GAIN MUTATED 6 3 20
11P GAIN WILD-TYPE 112 109 154

Figure S76.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0094

Table S77.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
11P GAIN MUTATED 5 3 5 16
11P GAIN WILD-TYPE 119 48 122 76

Figure S77.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.026

Table S78.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
11P GAIN MUTATED 3 3 2 7 14
11P GAIN WILD-TYPE 84 57 39 125 60

Figure S78.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.019

Table S79.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
11Q GAIN MUTATED 12 19 4 12 0
11Q GAIN WILD-TYPE 66 127 117 49 2

Figure S79.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.066

Table S80.  Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
11Q GAIN MUTATED 6 13 10 9
11Q GAIN WILD-TYPE 84 108 88 22

Figure S80.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.027

Table S81.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
11Q GAIN MUTATED 13 8 7 19
11Q GAIN WILD-TYPE 111 43 120 73

Figure S81.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0071

Table S82.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
12P GAIN MUTATED 32 47 19 18 0
12P GAIN WILD-TYPE 46 99 102 43 2

Figure S82.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.12

Table S83.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
12P GAIN MUTATED 16 22 17 36 23
12P GAIN WILD-TYPE 71 38 24 96 51

Figure S83.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.014

Table S84.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
12Q GAIN MUTATED 11 20 16 31 12
12Q GAIN WILD-TYPE 76 40 25 101 62

Figure S84.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0057

Table S85.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
13Q GAIN MUTATED 25 45 14 16 0
13Q GAIN WILD-TYPE 53 101 107 45 2

Figure S85.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.032

Table S86.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
14Q GAIN MUTATED 15 21 7 14 0
14Q GAIN WILD-TYPE 63 125 114 47 2

Figure S86.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.088

Table S87.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
14Q GAIN MUTATED 23 18 2 14
14Q GAIN WILD-TYPE 115 109 61 66

Figure S87.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.047

Table S88.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
14Q GAIN MUTATED 8 9 6 22 10
14Q GAIN WILD-TYPE 64 126 32 81 46

Figure S88.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.1

Table S89.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
14Q GAIN MUTATED 11 11 33
14Q GAIN WILD-TYPE 107 101 141

Figure S89.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0092

Table S90.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
15Q GAIN MUTATED 4 9 11 11
15Q GAIN WILD-TYPE 134 118 52 69

Figure S90.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0051

Table S91.  Gene #27: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
15Q GAIN MUTATED 2 16 11
15Q GAIN WILD-TYPE 120 98 93

Figure S91.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.11

Table S92.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
15Q GAIN MUTATED 14 13 8
15Q GAIN WILD-TYPE 104 99 166

Figure S92.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S93.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
16P GAIN MUTATED 12 45 10 6 2
16P GAIN WILD-TYPE 66 101 111 55 0

Figure S93.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S94.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
16Q GAIN MUTATED 12 51 10 8 1
16Q GAIN WILD-TYPE 66 95 111 53 1

Figure S94.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0078

Table S95.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
17P GAIN MUTATED 11 26 5 14 0
17P GAIN WILD-TYPE 67 120 116 47 2

Figure S95.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S96.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
17Q GAIN MUTATED 44 53 21 17 0
17Q GAIN WILD-TYPE 34 93 100 44 2

Figure S96.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.13

Table S97.  Gene #31: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
17Q GAIN MUTATED 35 34 45
17Q GAIN WILD-TYPE 87 80 59

Figure S97.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S98.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
18P GAIN MUTATED 26 58 6 26 0
18P GAIN WILD-TYPE 52 88 115 35 2

Figure S98.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.036

Table S99.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
18P GAIN MUTATED 42 45 8 21
18P GAIN WILD-TYPE 96 82 55 59

Figure S99.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S100.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
18P GAIN MUTATED 21 28 3 37 27
18P GAIN WILD-TYPE 51 107 35 66 29

Figure S100.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.099

Table S101.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
18P GAIN MUTATED 29 25 62
18P GAIN WILD-TYPE 89 87 112

Figure S101.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.003

Table S102.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
18P GAIN MUTATED 37 17 24 16 21
18P GAIN WILD-TYPE 68 57 90 9 66

Figure S102.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.12

Table S103.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
18P GAIN MUTATED 16 16 16 36 28
18P GAIN WILD-TYPE 71 44 25 96 46

Figure S103.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.033

Table S104.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
18Q GAIN MUTATED 13 29 7 12 0
18Q GAIN WILD-TYPE 65 117 114 49 2

Figure S104.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.14

Table S105.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
18Q GAIN MUTATED 11 18 3 12 16
18Q GAIN WILD-TYPE 61 117 35 91 40

Figure S105.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.13

Table S106.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
18Q GAIN MUTATED 20 8 16 8 8
18Q GAIN WILD-TYPE 85 66 98 17 79

Figure S106.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.017

Table S107.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
18Q GAIN MUTATED 5 9 12 16 16
18Q GAIN WILD-TYPE 82 51 29 116 58

Figure S107.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0058

Table S108.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
19P GAIN MUTATED 19 44 13 10 1
19P GAIN WILD-TYPE 59 102 108 51 1

Figure S108.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S109.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
19Q GAIN MUTATED 30 71 16 14 1
19Q GAIN WILD-TYPE 48 75 105 47 1

Figure S109.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.087

Table S110.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
19Q GAIN MUTATED 32 50 20 30
19Q GAIN WILD-TYPE 106 77 43 50

Figure S110.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S111.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
20P GAIN MUTATED 53 83 31 33 1
20P GAIN WILD-TYPE 25 63 90 28 1

Figure S111.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S112.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
20P GAIN MUTATED 69 47 84
20P GAIN WILD-TYPE 49 65 90

Figure S112.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S113.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
20Q GAIN MUTATED 59 98 36 36 1
20Q GAIN WILD-TYPE 19 48 85 25 1

Figure S113.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
21Q GAIN MUTATED 29 64 9 13 1
21Q GAIN WILD-TYPE 49 82 112 48 1

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

'21q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
21Q GAIN MUTATED 25 56 14 21
21Q GAIN WILD-TYPE 113 71 49 59

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

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0058

Table S116.  Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
21Q GAIN MUTATED 49 31 36
21Q GAIN WILD-TYPE 69 81 138

Figure S116.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.011

Table S117.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
21Q GAIN MUTATED 18 34 31 6 25
21Q GAIN WILD-TYPE 87 40 83 19 62

Figure S117.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0035

Table S118.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
21Q GAIN MUTATED 59 37 18
21Q GAIN WILD-TYPE 207 46 38

Figure S118.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
21Q GAIN MUTATED 40 22 35 15
21Q GAIN WILD-TYPE 84 29 92 77

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

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.046

Table S120.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
21Q GAIN MUTATED 22 26 14 38 12
21Q GAIN WILD-TYPE 65 34 27 94 62

Figure S120.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.12

Table S121.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
22Q GAIN MUTATED 16 19 13
22Q GAIN WILD-TYPE 102 93 161

Figure S121.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00617 (Fisher's exact test), Q value = 0.031

Table S122.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
XP GAIN MUTATED 19 25 9 11 1
XP GAIN WILD-TYPE 59 121 112 50 1

Figure S122.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0021

Table S123.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
XP GAIN MUTATED 8 31 10 16
XP GAIN WILD-TYPE 130 96 53 64

Figure S123.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0021

Table S124.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
XP GAIN MUTATED 7 23 24
XP GAIN WILD-TYPE 115 91 80

Figure S124.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00879 (Fisher's exact test), Q value = 0.04

Table S125.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
XP GAIN MUTATED 7 28 17 2
XP GAIN WILD-TYPE 83 93 81 29

Figure S125.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S126.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
XP GAIN MUTATED 2 27 4 12 20
XP GAIN WILD-TYPE 70 108 34 91 36

Figure S126.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.12

Table S127.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
XP GAIN MUTATED 25 21 19
XP GAIN WILD-TYPE 93 91 155

Figure S127.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.13

Table S128.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
XP GAIN MUTATED 16 17 18 7 7
XP GAIN WILD-TYPE 89 57 96 18 80

Figure S128.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.13

Table S129.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
XP GAIN MUTATED 42 19 4
XP GAIN WILD-TYPE 224 64 52

Figure S129.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.059

Table S130.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
XP GAIN MUTATED 13 13 28 11
XP GAIN WILD-TYPE 111 38 99 81

Figure S130.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.12

Table S131.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
XP GAIN MUTATED 7 14 7 28 9
XP GAIN WILD-TYPE 80 46 34 104 65

Figure S131.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.082

Table S132.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
XQ GAIN MUTATED 8 15 19
XQ GAIN WILD-TYPE 114 99 85

Figure S132.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.13

Table S133.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
XQ GAIN MUTATED 2 16 3 14 10
XQ GAIN WILD-TYPE 70 119 35 89 46

Figure S133.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.1

Table S134.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
XQ GAIN MUTATED 33 11 1
XQ GAIN WILD-TYPE 233 72 55

Figure S134.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.14

Table S135.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
1Q LOSS MUTATED 12 0 13 5
1Q LOSS WILD-TYPE 112 51 114 87

Figure S135.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.093

Table S136.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
2P LOSS MUTATED 14 18 11
2P LOSS WILD-TYPE 104 94 163

Figure S136.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0051

Table S137.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
2Q LOSS MUTATED 24 38 12 17 1
2Q LOSS WILD-TYPE 54 108 109 44 1

Figure S137.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.03

Table S138.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
2Q LOSS MUTATED 22 42 10 18
2Q LOSS WILD-TYPE 116 85 53 62

Figure S138.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.044

Table S139.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
2Q LOSS MUTATED 17 41 4 14 14
2Q LOSS WILD-TYPE 55 94 34 89 42

Figure S139.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.091

Table S140.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
2Q LOSS MUTATED 30 32 28
2Q LOSS WILD-TYPE 88 80 146

Figure S140.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.12

Table S141.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
2Q LOSS MUTATED 24 12 38 13
2Q LOSS WILD-TYPE 100 39 89 79

Figure S141.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.13

Table S142.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
3P LOSS MUTATED 9 25 8 8 1
3P LOSS WILD-TYPE 69 121 113 53 1

Figure S142.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0083 (Fisher's exact test), Q value = 0.038

Table S143.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
3P LOSS MUTATED 27 9 4 11
3P LOSS WILD-TYPE 111 118 59 69

Figure S143.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.063

Table S144.  Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
3P LOSS MUTATED 17 8 21
3P LOSS WILD-TYPE 105 106 83

Figure S144.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00661 (Fisher's exact test), Q value = 0.032

Table S145.  Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
3P LOSS MUTATED 13 7 20 6
3P LOSS WILD-TYPE 77 114 78 25

Figure S145.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S146.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
3P LOSS MUTATED 1 7 8 26 8
3P LOSS WILD-TYPE 71 128 30 77 48

Figure S146.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S147.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
3P LOSS MUTATED 4 7 39
3P LOSS WILD-TYPE 114 105 135

Figure S147.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.055

Table S148.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
3P LOSS MUTATED 24 7 10 3 7
3P LOSS WILD-TYPE 81 67 104 22 80

Figure S148.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S149.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
3P LOSS MUTATED 7 4 13 25
3P LOSS WILD-TYPE 117 47 114 67

Figure S149.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00968 (Fisher's exact test), Q value = 0.042

Table S150.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
3P LOSS MUTATED 5 4 7 16 17
3P LOSS WILD-TYPE 82 56 34 116 57

Figure S150.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.032

Table S151.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
3Q LOSS MUTATED 1 5 0 13 3
3Q LOSS WILD-TYPE 71 130 38 90 53

Figure S151.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0086

Table S152.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
3Q LOSS MUTATED 1 3 6 12
3Q LOSS WILD-TYPE 123 48 121 80

Figure S152.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S153.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
4P LOSS MUTATED 35 64 11 33 1
4P LOSS WILD-TYPE 43 82 110 28 1

Figure S153.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00332 (Fisher's exact test), Q value = 0.019

Table S154.  Gene #48: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
4P LOSS MUTATED 42 32 39 6
4P LOSS WILD-TYPE 48 89 59 25

Figure S154.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00526 (Fisher's exact test), Q value = 0.027

Table S155.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
4P LOSS MUTATED 24 38 8 50 22
4P LOSS WILD-TYPE 48 97 30 53 34

Figure S155.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00061

Table S156.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
4P LOSS MUTATED 49 20 73
4P LOSS WILD-TYPE 69 92 101

Figure S156.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0039

Table S157.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
4P LOSS MUTATED 42 31 23 15 32
4P LOSS WILD-TYPE 63 43 91 10 55

Figure S157.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S158.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
4Q LOSS MUTATED 33 61 8 33 1
4Q LOSS WILD-TYPE 45 85 113 28 1

Figure S158.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.047

Table S159.  Gene #49: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
4Q LOSS MUTATED 39 32 35 5
4Q LOSS WILD-TYPE 51 89 63 26

Figure S159.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.027

Table S160.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
4Q LOSS MUTATED 21 40 6 48 19
4Q LOSS WILD-TYPE 51 95 32 55 37

Figure S160.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0046

Table S161.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
4Q LOSS MUTATED 46 21 67
4Q LOSS WILD-TYPE 72 91 107

Figure S161.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.028

Table S162.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
4Q LOSS MUTATED 42 25 24 13 32
4Q LOSS WILD-TYPE 63 49 90 12 55

Figure S162.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.043

Table S163.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
4Q LOSS MUTATED 47 15 29 39
4Q LOSS WILD-TYPE 77 36 98 53

Figure S163.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0083

Table S164.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
5P LOSS MUTATED 12 31 6 5 0
5P LOSS WILD-TYPE 66 115 115 56 2

Figure S164.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0017

Table S165.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
5P LOSS MUTATED 16 29 7 2
5P LOSS WILD-TYPE 122 98 56 78

Figure S165.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.014

Table S166.  Gene #50: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
5P LOSS MUTATED 23 16 6 4
5P LOSS WILD-TYPE 67 105 92 27

Figure S166.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0044

Table S167.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
5P LOSS MUTATED 28 13 13
5P LOSS WILD-TYPE 90 99 161

Figure S167.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S168.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
5Q LOSS MUTATED 38 80 15 27 0
5Q LOSS WILD-TYPE 40 66 106 34 2

Figure S168.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.011

Table S169.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
5Q LOSS MUTATED 54 64 14 28
5Q LOSS WILD-TYPE 84 63 49 52

Figure S169.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.074

Table S170.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
5Q LOSS MUTATED 59 39 61
5Q LOSS WILD-TYPE 59 73 113

Figure S170.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.14

Table S171.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
5Q LOSS MUTATED 34 36 41 15 34
5Q LOSS WILD-TYPE 71 38 73 10 53

Figure S171.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S172.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
6P LOSS MUTATED 35 50 6 12 0
6P LOSS WILD-TYPE 43 96 115 49 2

Figure S172.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.083

Table S173.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
6P LOSS MUTATED 24 43 16 20
6P LOSS WILD-TYPE 114 84 47 60

Figure S173.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S174.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
6Q LOSS MUTATED 48 83 10 18 0
6Q LOSS WILD-TYPE 30 63 111 43 2

Figure S174.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00892 (Fisher's exact test), Q value = 0.04

Table S175.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
6Q LOSS MUTATED 42 64 22 31
6Q LOSS WILD-TYPE 96 63 41 49

Figure S175.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.067

Table S176.  Gene #53: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
6Q LOSS MUTATED 40 37 51
6Q LOSS WILD-TYPE 82 77 53

Figure S176.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.12

Table S177.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
6Q LOSS MUTATED 57 43 58
6Q LOSS WILD-TYPE 61 69 116

Figure S177.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.00747 (Fisher's exact test), Q value = 0.035

Table S178.  Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
7Q LOSS MUTATED 3 15 2 8 0
7Q LOSS WILD-TYPE 75 131 119 53 2

Figure S178.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S179.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
8P LOSS MUTATED 16 102 25 44 1
8P LOSS WILD-TYPE 62 44 96 17 1

Figure S179.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.022

Table S180.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
8P LOSS MUTATED 69 69 18 32
8P LOSS WILD-TYPE 69 58 45 48

Figure S180.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.054

Table S181.  Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
8P LOSS MUTATED 68 42 46
8P LOSS WILD-TYPE 54 72 58

Figure S181.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0072

Table S182.  Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
8P LOSS MUTATED 49 38 52 17
8P LOSS WILD-TYPE 41 83 46 14

Figure S182.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.017

Table S183.  Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
8P LOSS MUTATED 37 54 10 61 26
8P LOSS WILD-TYPE 35 81 28 42 30

Figure S183.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00578 (Fisher's exact test), Q value = 0.029

Table S184.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
8P LOSS MUTATED 63 38 87
8P LOSS WILD-TYPE 55 74 87

Figure S184.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.12

Table S185.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
8P LOSS MUTATED 110 46 30
8P LOSS WILD-TYPE 156 37 26

Figure S185.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0032

Table S186.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
8Q LOSS MUTATED 1 25 6 6 0
8Q LOSS WILD-TYPE 77 121 115 55 2

Figure S186.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.069

Table S187.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
8Q LOSS MUTATED 11 5 2 13 7
8Q LOSS WILD-TYPE 61 130 36 90 49

Figure S187.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S188.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
9P LOSS MUTATED 34 85 51 4 0
9P LOSS WILD-TYPE 44 61 70 57 2

Figure S188.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0021

Table S189.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
9P LOSS MUTATED 38 65 30 41
9P LOSS WILD-TYPE 100 62 33 39

Figure S189.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.019

Table S190.  Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
9P LOSS MUTATED 40 62 42
9P LOSS WILD-TYPE 82 52 62

Figure S190.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0018

Table S191.  Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
9P LOSS MUTATED 37 69 29 9
9P LOSS WILD-TYPE 53 52 69 22

Figure S191.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S192.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
9P LOSS MUTATED 31 66 27 27 23
9P LOSS WILD-TYPE 41 69 11 76 33

Figure S192.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S193.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
9P LOSS MUTATED 63 59 52
9P LOSS WILD-TYPE 55 53 122

Figure S193.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.033

Table S194.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
9P LOSS MUTATED 30 38 58 11 37
9P LOSS WILD-TYPE 75 36 56 14 50

Figure S194.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S195.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
9P LOSS MUTATED 55 25 69 21
9P LOSS WILD-TYPE 69 26 58 71

Figure S195.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0039

Table S196.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
9P LOSS MUTATED 31 31 23 67 18
9P LOSS WILD-TYPE 56 29 18 65 56

Figure S196.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S197.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
9Q LOSS MUTATED 38 76 51 4 0
9Q LOSS WILD-TYPE 40 70 70 57 2

Figure S197.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S198.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
9Q LOSS MUTATED 34 61 32 42
9Q LOSS WILD-TYPE 104 66 31 38

Figure S198.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0044

Table S199.  Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
9Q LOSS MUTATED 42 64 34
9Q LOSS WILD-TYPE 80 50 70

Figure S199.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S200.  Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
9Q LOSS MUTATED 40 71 22 7
9Q LOSS WILD-TYPE 50 50 76 24

Figure S200.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S201.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
9Q LOSS MUTATED 32 69 27 19 22
9Q LOSS WILD-TYPE 40 66 11 84 34

Figure S201.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S202.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
9Q LOSS MUTATED 62 64 43
9Q LOSS WILD-TYPE 56 48 131

Figure S202.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00061

Table S203.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
9Q LOSS MUTATED 24 33 64 11 37
9Q LOSS WILD-TYPE 81 41 50 14 50

Figure S203.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S204.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
9Q LOSS MUTATED 52 27 73 14
9Q LOSS WILD-TYPE 72 24 54 78

Figure S204.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S205.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
9Q LOSS MUTATED 33 32 21 69 11
9Q LOSS WILD-TYPE 54 28 20 63 63

Figure S205.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.054

Table S206.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
10P LOSS MUTATED 18 32 11 11 1
10P LOSS WILD-TYPE 60 114 110 50 1

Figure S206.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.061

Table S207.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
10P LOSS MUTATED 5 20 10 24 12
10P LOSS WILD-TYPE 67 115 28 79 44

Figure S207.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S208.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
10Q LOSS MUTATED 37 57 11 23 1
10Q LOSS WILD-TYPE 41 89 110 38 1

Figure S208.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.013

Table S209.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
10Q LOSS MUTATED 30 53 16 30
10Q LOSS WILD-TYPE 108 74 47 50

Figure S209.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S210.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
11P LOSS MUTATED 42 91 31 12 2
11P LOSS WILD-TYPE 36 55 90 49 0

Figure S210.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S211.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
11P LOSS MUTATED 33 71 34 40
11P LOSS WILD-TYPE 105 56 29 40

Figure S211.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0014

Table S212.  Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
11P LOSS MUTATED 43 68 29 8
11P LOSS WILD-TYPE 47 53 69 23

Figure S212.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0021

Table S213.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
11P LOSS MUTATED 29 74 21 27 25
11P LOSS WILD-TYPE 43 61 17 76 31

Figure S213.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S214.  Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
11P LOSS MUTATED 62 62 52
11P LOSS WILD-TYPE 56 50 122

Figure S214.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S215.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
11P LOSS MUTATED 25 39 65 11 37
11P LOSS WILD-TYPE 80 35 49 14 50

Figure S215.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S216.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
11P LOSS MUTATED 58 26 68 20
11P LOSS WILD-TYPE 66 25 59 72

Figure S216.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.012

Table S217.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
11P LOSS MUTATED 34 33 22 64 19
11P LOSS WILD-TYPE 53 27 19 68 55

Figure S217.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S218.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
11Q LOSS MUTATED 36 60 17 14 2
11Q LOSS WILD-TYPE 42 86 104 47 0

Figure S218.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.11

Table S219.  Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
11Q LOSS MUTATED 34 42 26 4
11Q LOSS WILD-TYPE 56 79 72 27

Figure S219.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0028

Table S220.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
12P LOSS MUTATED 8 29 5 11 1
12P LOSS WILD-TYPE 70 117 116 50 1

Figure S220.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.061

Table S221.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
12P LOSS MUTATED 11 25 11 7
12P LOSS WILD-TYPE 127 102 52 73

Figure S221.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.087

Table S222.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
12P LOSS MUTATED 14 24 2 7 6
12P LOSS WILD-TYPE 58 111 36 96 50

Figure S222.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.08

Table S223.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
12P LOSS MUTATED 24 13 16
12P LOSS WILD-TYPE 94 99 158

Figure S223.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.004

Table S224.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
12Q LOSS MUTATED 12 26 5 15 0
12Q LOSS WILD-TYPE 66 120 116 46 2

Figure S224.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S225.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
13Q LOSS MUTATED 25 32 7 19 2
13Q LOSS WILD-TYPE 53 114 114 42 0

Figure S225.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

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

Table S226.  Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
13Q LOSS MUTATED 20 16 37
13Q LOSS WILD-TYPE 102 98 67

Figure S226.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0048

Table S227.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
13Q LOSS MUTATED 9 18 6 30 20
13Q LOSS WILD-TYPE 63 117 32 73 36

Figure S227.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00061

Table S228.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
13Q LOSS MUTATED 32 20 14 10 9
13Q LOSS WILD-TYPE 73 54 100 15 78

Figure S228.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.049

Table S229.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
13Q LOSS MUTATED 60 21 4
13Q LOSS WILD-TYPE 206 62 52

Figure S229.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00939 (Fisher's exact test), Q value = 0.041

Table S230.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
13Q LOSS MUTATED 18 13 23 30
13Q LOSS WILD-TYPE 106 38 104 62

Figure S230.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0084

Table S231.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
13Q LOSS MUTATED 10 17 7 23 27
13Q LOSS WILD-TYPE 77 43 34 109 47

Figure S231.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S232.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
14Q LOSS MUTATED 25 73 9 14 0
14Q LOSS WILD-TYPE 53 73 112 47 2

Figure S232.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00061

Table S233.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
14Q LOSS MUTATED 36 55 20 10
14Q LOSS WILD-TYPE 102 72 43 70

Figure S233.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.002

Table S234.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
14Q LOSS MUTATED 52 30 38
14Q LOSS WILD-TYPE 66 82 136

Figure S234.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0058

Table S235.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
14Q LOSS MUTATED 21 36 28 9 26
14Q LOSS WILD-TYPE 84 38 86 16 61

Figure S235.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0084

Table S236.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
14Q LOSS MUTATED 65 38 17
14Q LOSS WILD-TYPE 201 45 39

Figure S236.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.02

Table S237.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
14Q LOSS MUTATED 45 23 31 19
14Q LOSS WILD-TYPE 79 28 96 73

Figure S237.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.0083

Table S238.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
14Q LOSS MUTATED 24 30 16 34 14
14Q LOSS WILD-TYPE 63 30 25 98 60

Figure S238.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S239.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
15Q LOSS MUTATED 31 74 7 31 1
15Q LOSS WILD-TYPE 47 72 114 30 1

Figure S239.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S240.  Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
15Q LOSS MUTATED 59 57 7 21
15Q LOSS WILD-TYPE 79 70 56 59

Figure S240.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.028

Table S241.  Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
15Q LOSS MUTATED 25 42 5 45 24
15Q LOSS WILD-TYPE 47 93 33 58 32

Figure S241.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.082

Table S242.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
15Q LOSS MUTATED 38 37 30 10 29
15Q LOSS WILD-TYPE 67 37 84 15 58

Figure S242.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00929 (Fisher's exact test), Q value = 0.041

Table S243.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
15Q LOSS MUTATED 88 41 15
15Q LOSS WILD-TYPE 178 42 41

Figure S243.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.043

Table S244.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
15Q LOSS MUTATED 37 27 38 38
15Q LOSS WILD-TYPE 87 24 89 54

Figure S244.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.083

Table S245.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
15Q LOSS MUTATED 24 30 14 40 32
15Q LOSS WILD-TYPE 63 30 27 92 42

Figure S245.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S246.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
16P LOSS MUTATED 35 36 2 37 0
16P LOSS WILD-TYPE 43 110 119 24 2

Figure S246.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0053

Table S247.  Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
16P LOSS MUTATED 35 18 40
16P LOSS WILD-TYPE 87 96 64

Figure S247.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S248.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
16Q LOSS MUTATED 38 34 2 33 0
16Q LOSS WILD-TYPE 40 112 119 28 2

Figure S248.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.058

Table S249.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
16Q LOSS MUTATED 34 20 36
16Q LOSS WILD-TYPE 88 94 68

Figure S249.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.13

Table S250.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
16Q LOSS MUTATED 20 33 5 26 23
16Q LOSS WILD-TYPE 52 102 33 77 33

Figure S250.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S251.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
17P LOSS MUTATED 52 84 29 16 1
17P LOSS WILD-TYPE 26 62 92 45 1

Figure S251.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0014

Table S252.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
18P LOSS MUTATED 25 45 18 8 2
18P LOSS WILD-TYPE 53 101 103 53 0

Figure S252.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S253.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
18Q LOSS MUTATED 35 67 20 22 2
18Q LOSS WILD-TYPE 43 79 101 39 0

Figure S253.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.14

Table S254.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
18Q LOSS MUTATED 53 35 56
18Q LOSS WILD-TYPE 65 77 118

Figure S254.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

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

Table S255.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
18Q LOSS MUTATED 32 38 35 9 32
18Q LOSS WILD-TYPE 73 36 79 16 55

Figure S255.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.022

Table S256.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
18Q LOSS MUTATED 86 43 17
18Q LOSS WILD-TYPE 180 40 39

Figure S256.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S257.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
19P LOSS MUTATED 25 43 11 15 1
19P LOSS WILD-TYPE 53 103 110 46 1

Figure S257.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.012

Table S258.  Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
19P LOSS MUTATED 17 19 6 29 22
19P LOSS WILD-TYPE 55 116 32 74 34

Figure S258.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00486 (Fisher's exact test), Q value = 0.026

Table S259.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
19P LOSS MUTATED 33 14 46
19P LOSS WILD-TYPE 85 98 128

Figure S259.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0071

Table S260.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
19Q LOSS MUTATED 16 20 7 15 1
19Q LOSS WILD-TYPE 62 126 114 46 1

Figure S260.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.12

Table S261.  Gene #76: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
19Q LOSS MUTATED 20 8 18
19Q LOSS WILD-TYPE 102 106 86

Figure S261.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.033

Table S262.  Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
19Q LOSS MUTATED 9 13 1 21 13
19Q LOSS WILD-TYPE 63 122 37 82 43

Figure S262.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.14

Table S263.  Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
20Q LOSS MUTATED 3 1 2 4 5
20Q LOSS WILD-TYPE 69 134 36 99 51

Figure S263.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.066

Table S264.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
21Q LOSS MUTATED 16 32 13 17 1
21Q LOSS WILD-TYPE 62 114 108 44 1

Figure S264.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.054

Table S265.  Gene #79: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
21Q LOSS MUTATED 23 13 28
21Q LOSS WILD-TYPE 99 101 76

Figure S265.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.091

Table S266.  Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
21Q LOSS MUTATED 17 14 27 6
21Q LOSS WILD-TYPE 73 107 71 25

Figure S266.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00657 (Fisher's exact test), Q value = 0.032

Table S267.  Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
21Q LOSS MUTATED 14 19 46
21Q LOSS WILD-TYPE 104 93 128

Figure S267.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.018

Table S268.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
21Q LOSS MUTATED 33 8 18 7 13
21Q LOSS WILD-TYPE 72 66 96 18 74

Figure S268.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.046

Table S269.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
21Q LOSS MUTATED 20 6 21 29
21Q LOSS WILD-TYPE 104 45 106 63

Figure S269.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0083 (Fisher's exact test), Q value = 0.038

Table S270.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
21Q LOSS MUTATED 16 8 6 20 26
21Q LOSS WILD-TYPE 71 52 35 112 48

Figure S270.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S271.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
22Q LOSS MUTATED 36 75 9 40 0
22Q LOSS WILD-TYPE 42 71 112 21 2

Figure S271.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.044

Table S272.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
22Q LOSS MUTATED 64 49 14 33
22Q LOSS WILD-TYPE 74 78 49 47

Figure S272.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0048

Table S273.  Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
22Q LOSS MUTATED 47 32 44 9
22Q LOSS WILD-TYPE 43 89 54 22

Figure S273.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.024

Table S274.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
22Q LOSS MUTATED 27 42 10 55 23
22Q LOSS WILD-TYPE 45 93 28 48 33

Figure S274.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0051

Table S275.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
22Q LOSS MUTATED 44 29 84
22Q LOSS WILD-TYPE 74 83 90

Figure S275.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.12

Table S276.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
22Q LOSS MUTATED 49 15 44 47
22Q LOSS WILD-TYPE 75 36 83 45

Figure S276.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0091 (Fisher's exact test), Q value = 0.04

Table S277.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
XQ LOSS MUTATED 16 32 13 22
XQ LOSS WILD-TYPE 122 95 50 58

Figure S277.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.077

Table S278.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
XQ LOSS MUTATED 11 26 14 15 16
XQ LOSS WILD-TYPE 61 109 24 88 40

Figure S278.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.061

Table S279.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
XQ LOSS MUTATED 20 11 37 12
XQ LOSS WILD-TYPE 104 40 90 80

Figure S279.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.11

Table S280.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
XQ LOSS MUTATED 11 13 7 38 11
XQ LOSS WILD-TYPE 76 47 34 94 63

Figure S280.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/BLCA-TP/22507732/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/22541056/BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 408

  • 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)