Correlation between copy number variations of arm-level result and molecular subtypes
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 367 patients, 181 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 4p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF'.

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

  • 8p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 9p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'METHLYATION_CNMF'.

  • 11p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 16q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'METHLYATION_CNMF'.

  • 17q gain cnv correlated to 'METHLYATION_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 2p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MIRSEQ_CNMF'.

  • 3q loss cnv correlated to 'MIRSEQ_CNMF'.

  • 4p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 6p loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 7q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 8p loss cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CNMF'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 9q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

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

  • 12q loss cnv correlated to 'CN_CNMF'.

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

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

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'METHLYATION_CNMF'.

  • 17q loss cnv correlated to 'RPPA_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_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, 181 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
6p gain 148 (40%) 219 0.00077
(0.0186) 		0.0129
(0.0982) 		0.584
(0.787) 		0.209
(0.505) 		0.0169
(0.119) 		0.0384
(0.195) 		0.04
(0.199) 		0.00036
(0.0102) 		3e-05
(0.00145) 		0.0001
(0.0039)
2p gain 67 (18%) 300 0.00194
(0.0325) 		0.00285
(0.0399) 		0.832
(0.917) 		0.417
(0.673) 		0.00831
(0.0741) 		0.00423
(0.051) 		0.311
(0.588) 		0.00096
(0.0199) 		0.212
(0.507) 		0.00122
(0.0238)
2q gain 65 (18%) 302 0.00131
(0.025) 		0.00222
(0.035) 		0.943
(0.971) 		0.132
(0.398) 		0.00152
(0.0271) 		0.0052
(0.0566) 		0.228
(0.511) 		0.0003
(0.00946) 		0.283
(0.557) 		0.00243
(0.0367)
xp loss 96 (26%) 271 0.036
(0.187) 		1e-05
(0.000683) 		0.0865
(0.303) 		0.175
(0.468) 		0.0014
(0.0259) 		0.00179
(0.0306) 		0.0201
(0.134) 		0.0622
(0.254) 		0.0937
(0.318) 		0.0251
(0.151)
xq loss 92 (25%) 275 0.0469
(0.214) 		2e-05
(0.00109) 		0.0829
(0.295) 		0.584
(0.787) 		0.00092
(0.0199) 		0.00429
(0.051) 		0.0463
(0.214) 		0.344
(0.611) 		0.0569
(0.24) 		0.0197
(0.134)
1q gain 173 (47%) 194 3e-05
(0.00145) 		0.608
(0.806) 		0.0137
(0.102) 		0.154
(0.429) 		0.0032
(0.0426) 		0.119
(0.372) 		0.0185
(0.129) 		0.0682
(0.263) 		0.0195
(0.133) 		0.33
(0.597)
11p gain 34 (9%) 333 0.0799
(0.29) 		0.0378
(0.192) 		0.118
(0.372) 		0.0283
(0.164) 		0.00401
(0.0498) 		0.00243
(0.0367) 		0.192
(0.491) 		0.00707
(0.0659) 		0.631
(0.821) 		0.0891
(0.308)
13q gain 92 (25%) 275 4e-05
(0.00182) 		0.00012
(0.00428) 		0.102
(0.336) 		0.187
(0.487) 		0.00011
(0.0041) 		0.057
(0.24) 		0.221
(0.507) 		0.966
(0.984) 		0.0305
(0.17) 		0.0325
(0.177)
15q gain 84 (23%) 283 0.047
(0.214) 		0.275
(0.555) 		0.834
(0.917) 		0.635
(0.822) 		0.0058
(0.058) 		0.00652
(0.0622) 		0.0303
(0.17) 		0.118
(0.372) 		0.144
(0.415) 		0.0441
(0.211)
16q gain 45 (12%) 322 2e-05
(0.00109) 		0.0055
(0.0574) 		0.685
(0.855) 		0.457
(0.692) 		0.00337
(0.0439) 		0.0152
(0.11) 		0.209
(0.505) 		0.217
(0.507) 		0.39
(0.663) 		0.00097
(0.0199)
xq gain 44 (12%) 323 0.0461
(0.214) 		0.00505
(0.0566) 		0.404
(0.668) 		0.691
(0.855) 		0.00215
(0.035) 		0.00524
(0.0566) 		0.287
(0.56) 		0.717
(0.873) 		0.00057
(0.0146) 		0.603
(0.803)
9p loss 235 (64%) 132 0.00034
(0.00996) 		0.0351
(0.186) 		0.0112
(0.0908) 		0.057
(0.24) 		0.0809
(0.291) 		0.0496
(0.225) 		0.443
(0.685) 		0.0991
(0.326) 		0.968
(0.985) 		0.00818
(0.0741)
8q gain 172 (47%) 195 5e-05
(0.00216) 		1e-05
(0.000683) 		0.499
(0.719) 		0.691
(0.855) 		0.00046
(0.0122) 		0.0187
(0.129) 		0.811
(0.911) 		0.324
(0.592) 		0.43
(0.68) 		0.387
(0.662)
11q gain 28 (8%) 339 0.127
(0.388) 		0.0966
(0.321) 		0.191
(0.491) 		0.0113
(0.0908) 		0.00142
(0.0259) 		0.00353
(0.0452) 		0.14
(0.411) 		0.00032
(0.00972) 		0.221
(0.507) 		0.0671
(0.263)
16p gain 57 (16%) 310 7e-05
(0.00287) 		0.00086
(0.0198) 		0.959
(0.98) 		0.877
(0.934) 		0.00567
(0.0574) 		0.0624
(0.254) 		0.307
(0.581) 		0.193
(0.491) 		0.364
(0.632) 		0.00825
(0.0741)
20p gain 147 (40%) 220 1e-05
(0.000683) 		0.00041
(0.0112) 		0.257
(0.539) 		0.11
(0.353) 		0.00087
(0.0198) 		0.0132
(0.0991) 		0.127
(0.388) 		0.257
(0.539) 		0.413
(0.67) 		0.0592
(0.247)
20q gain 180 (49%) 187 1e-05
(0.000683) 		0.00848
(0.0745) 		0.149
(0.421) 		0.0455
(0.214) 		0.0842
(0.298) 		0.0469
(0.214) 		0.454
(0.692) 		0.21
(0.505) 		0.932
(0.966) 		0.148
(0.421)
xp gain 42 (11%) 325 0.199
(0.494) 		0.00489
(0.0566) 		0.633
(0.821) 		0.281
(0.557) 		0.0126
(0.0978) 		0.00975
(0.0824) 		0.341
(0.608) 		0.679
(0.854) 		0.0118
(0.094) 		0.486
(0.713)
2q loss 51 (14%) 316 0.151
(0.428) 		0.0256
(0.153) 		0.0671
(0.263) 		0.0392
(0.197) 		0.221
(0.507) 		0.14
(0.411) 		0.00854
(0.0745) 		0.0357
(0.187) 		0.107
(0.346) 		0.714
(0.871)
8q loss 25 (7%) 342 0.163
(0.447) 		0.0236
(0.146) 		0.0206
(0.135) 		0.174
(0.467) 		0.323
(0.592) 		0.834
(0.917) 		0.0917
(0.313) 		0.251
(0.533) 		0.021
(0.135) 		0.0202
(0.134)
10p loss 204 (56%) 163 1e-05
(0.000683) 		0.00427
(0.051) 		0.63
(0.821) 		0.828
(0.917) 		0.0259
(0.153) 		0.00987
(0.0826) 		0.884
(0.935) 		0.194
(0.491) 		0.154
(0.429) 		0.409
(0.669)
10q loss 224 (61%) 143 1e-05
(0.000683) 		0.00122
(0.0238) 		0.818
(0.917) 		0.91
(0.951) 		0.00522
(0.0566) 		0.0029
(0.0399) 		0.593
(0.795) 		0.192
(0.491) 		0.234
(0.515) 		0.211
(0.505)
7q gain 199 (54%) 168 0.00559
(0.0574) 		0.181
(0.477) 		0.223
(0.507) 		0.243
(0.527) 		0.0146
(0.108) 		0.0809
(0.291) 		0.952
(0.976) 		0.418
(0.673) 		0.0682
(0.263) 		0.0465
(0.214)
8p gain 123 (34%) 244 2e-05
(0.00109) 		0.0905
(0.312) 		0.195
(0.491) 		0.258
(0.539) 		0.0336
(0.18) 		0.023
(0.146) 		0.485
(0.713) 		0.933
(0.966) 		0.498
(0.719) 		0.796
(0.905)
19q gain 56 (15%) 311 0.00375
(0.0473) 		0.0731
(0.273) 		0.567
(0.774) 		0.169
(0.458) 		0.0248
(0.15) 		0.0239
(0.146) 		0.945
(0.971) 		0.296
(0.572) 		0.0734
(0.273) 		0.401
(0.668)
1p loss 51 (14%) 316 0.00284
(0.0399) 		0.00563
(0.0574) 		0.684
(0.855) 		0.304
(0.578) 		0.506
(0.724) 		0.275
(0.555) 		0.205
(0.502) 		0.848
(0.922) 		0.0097
(0.0824) 		0.125
(0.384)
2p loss 50 (14%) 317 0.317
(0.59) 		0.0848
(0.299) 		0.136
(0.402) 		0.252
(0.533) 		0.298
(0.573) 		0.0313
(0.172) 		0.00292
(0.0399) 		0.0218
(0.14) 		0.153
(0.429) 		0.633
(0.821)
6q loss 172 (47%) 195 1e-05
(0.000683) 		0.0446
(0.212) 		0.0966
(0.321) 		0.532
(0.748) 		0.00513
(0.0566) 		0.0561
(0.24) 		0.526
(0.742) 		0.235
(0.515) 		0.451
(0.689) 		0.289
(0.56)
9q loss 185 (50%) 182 0.0207
(0.135) 		0.141
(0.412) 		0.0916
(0.313) 		0.562
(0.771) 		0.146
(0.418) 		0.748
(0.885) 		0.218
(0.507) 		0.0287
(0.164) 		0.87
(0.934) 		0.00905
(0.0781)
14q loss 112 (31%) 255 0.00013
(0.00444) 		0.0617
(0.254) 		0.409
(0.669) 		0.0355
(0.187) 		0.0258
(0.153) 		0.0571
(0.24) 		0.322
(0.592) 		0.825
(0.917) 		0.422
(0.676) 		0.692
(0.855)
5p gain 74 (20%) 293 1e-05
(0.000683) 		0.353
(0.618) 		0.643
(0.829) 		0.393
(0.663) 		0.406
(0.668) 		0.217
(0.507) 		0.079
(0.289) 		0.54
(0.751) 		0.304
(0.578) 		0.031
(0.172)
18p gain 56 (15%) 311 0.0129
(0.0982) 		0.0541
(0.237) 		0.384
(0.659) 		0.727
(0.876) 		0.69
(0.855) 		0.457
(0.692) 		0.856
(0.928) 		0.813
(0.912) 		0.00664
(0.0626) 		0.458
(0.692)
19p gain 58 (16%) 309 0.0236
(0.146) 		0.18
(0.477) 		0.536
(0.749) 		0.494
(0.719) 		0.0261
(0.153) 		0.0604
(0.25) 		0.986
(0.995) 		0.499
(0.719) 		0.0626
(0.254) 		0.415
(0.671)
22q gain 126 (34%) 241 0.00604
(0.059) 		0.0556
(0.24) 		0.262
(0.544) 		0.258
(0.539) 		0.0822
(0.294) 		0.154
(0.429) 		0.444
(0.685) 		0.147
(0.42) 		0.723
(0.876) 		0.043
(0.209)
4p loss 80 (22%) 287 0.276
(0.555) 		0.593
(0.795) 		0.739
(0.88) 		0.465
(0.696) 		0.353
(0.618) 		0.015
(0.11) 		0.498
(0.719) 		0.00596
(0.0589) 		0.727
(0.876) 		0.834
(0.917)
4q loss 85 (23%) 282 0.249
(0.533) 		0.748
(0.885) 		0.823
(0.917) 		0.557
(0.764) 		0.234
(0.515) 		0.0163
(0.116) 		0.481
(0.709) 		0.00322
(0.0426) 		0.645
(0.829) 		0.473
(0.7)
5q loss 97 (26%) 270 1e-05
(0.000683) 		0.437
(0.683) 		0.0345
(0.184) 		0.934
(0.966) 		0.356
(0.622) 		0.272
(0.554) 		0.948
(0.973) 		0.667
(0.847) 		0.833
(0.917) 		0.988
(0.995)
6p loss 70 (19%) 297 0.0635
(0.255) 		0.867
(0.933) 		0.469
(0.697) 		0.88
(0.935) 		0.00073
(0.0181) 		0.051
(0.23) 		0.502
(0.721) 		0.0698
(0.266) 		0.121
(0.374) 		0.0125
(0.0978)
8p loss 66 (18%) 301 0.068
(0.263) 		0.367
(0.636) 		0.0183
(0.128) 		0.0728
(0.273) 		0.0376
(0.192) 		0.84
(0.919) 		0.245
(0.528) 		0.0523
(0.233) 		0.519
(0.738) 		0.584
(0.787)
11q loss 149 (41%) 218 0.0017
(0.0297) 		0.859
(0.929) 		0.897
(0.943) 		0.405
(0.668) 		0.481
(0.709) 		0.263
(0.545) 		0.754
(0.885) 		0.245
(0.528) 		0.301
(0.576) 		0.0297
(0.168)
16p loss 69 (19%) 298 0.00028
(0.00918) 		0.0293
(0.167) 		0.318
(0.59) 		0.546
(0.755) 		0.159
(0.438) 		0.27
(0.554) 		0.197
(0.494) 		0.142
(0.412) 		0.112
(0.359) 		0.673
(0.85)
20q loss 9 (2%) 358 0.762
(0.885) 		0.106
(0.345) 		0.445
(0.685) 		0.0408
(0.201) 		0.47
(0.697) 		0.00525
(0.0566) 		0.26
(0.542) 		0.39
(0.663) 		0.575
(0.781) 		0.457
(0.692)
21q loss 70 (19%) 297 0.0106
(0.0869) 		0.394
(0.663) 		0.533
(0.748) 		0.67
(0.848) 		0.252
(0.533) 		0.336
(0.604) 		0.0159
(0.115) 		0.727
(0.876) 		0.132
(0.398) 		0.737
(0.878)
4p gain 57 (16%) 310 0.21
(0.505) 		0.0528
(0.234) 		0.744
(0.883) 		0.621
(0.818) 		0.436
(0.683) 		0.238
(0.519) 		0.136
(0.402) 		0.00246
(0.0367) 		0.232
(0.515) 		0.614
(0.813)
4q gain 48 (13%) 319 0.371
(0.639) 		0.115
(0.366) 		0.177
(0.472) 		0.614
(0.813) 		0.312
(0.588) 		0.412
(0.67) 		0.107
(0.346) 		0.00559
(0.0574) 		0.325
(0.592) 		0.798
(0.906)
5q gain 52 (14%) 315 1e-05
(0.000683) 		0.33
(0.597) 		0.796
(0.905) 		0.302
(0.576) 		0.342
(0.608) 		0.875
(0.934) 		0.214
(0.507) 		0.434
(0.682) 		0.106
(0.346) 		0.443
(0.685)
7p gain 204 (56%) 163 0.00096
(0.0199) 		0.273
(0.555) 		0.18
(0.477) 		0.161
(0.442) 		0.0972
(0.321) 		0.2
(0.495) 		0.96
(0.98) 		0.737
(0.878) 		0.515
(0.736) 		0.288
(0.56)
9p gain 16 (4%) 351 0.524
(0.742) 		0.277
(0.555) 		0.0833
(0.296) 		0.046
(0.214) 		0.574
(0.781) 		0.899
(0.944) 		0.495
(0.719) 		0.721
(0.876) 		0.495
(0.719) 		0.523
(0.742)
10q gain 3 (1%) 364 0.19
(0.49) 		0.0432
(0.209) 		0.698
(0.859) 		1
(1.00) 		0.864
(0.932) 		0.85
(0.923) 		0.356
(0.622) 		0.501
(0.721)
12p gain 64 (17%) 303 0.00822
(0.0741) 		0.17
(0.459) 		0.449
(0.687) 		0.095
(0.321) 		0.233
(0.515) 		0.938
(0.968) 		0.883
(0.935) 		0.414
(0.671) 		0.318
(0.59) 		0.467
(0.696)
12q gain 40 (11%) 327 0.055
(0.239) 		0.64
(0.827) 		0.974
(0.986) 		0.159
(0.438) 		0.798
(0.906) 		0.699
(0.86) 		0.956
(0.979) 		0.222
(0.507) 		0.579
(0.785) 		0.0332
(0.179)
14q gain 42 (11%) 325 0.876
(0.934) 		0.893
(0.941) 		0.395
(0.663) 		0.043
(0.209) 		0.828
(0.917) 		0.727
(0.876) 		0.534
(0.748) 		0.824
(0.917) 		0.49
(0.717) 		0.234
(0.515)
17p gain 40 (11%) 327 0.0939
(0.318) 		0.0101
(0.0834) 		0.569
(0.776) 		0.244
(0.527) 		0.734
(0.878) 		0.348
(0.614) 		0.27
(0.554) 		0.438
(0.683) 		0.908
(0.951) 		0.456
(0.692)
17q gain 67 (18%) 300 0.224
(0.507) 		0.0422
(0.207) 		0.847
(0.922) 		0.905
(0.949) 		0.989
(0.996) 		0.422
(0.676) 		0.198
(0.494) 		0.357
(0.622) 		0.463
(0.695) 		0.157
(0.435)
18q gain 45 (12%) 322 0.00271
(0.0397) 		0.37
(0.639) 		0.323
(0.592) 		0.406
(0.668) 		0.545
(0.755) 		0.585
(0.787) 		0.811
(0.911) 		0.867
(0.933) 		0.196
(0.492) 		0.618
(0.815)
3p loss 60 (16%) 307 0.314
(0.588) 		0.79
(0.904) 		0.803
(0.907) 		0.438
(0.683) 		0.207
(0.504) 		0.464
(0.696) 		0.00652
(0.0622) 		0.662
(0.842) 		0.931
(0.966) 		0.143
(0.413)
3q loss 51 (14%) 316 0.195
(0.491) 		0.395
(0.663) 		0.59
(0.794) 		0.143
(0.413) 		0.423
(0.677) 		0.603
(0.803) 		0.0234
(0.146) 		0.428
(0.677) 		0.215
(0.507) 		0.535
(0.748)
5p loss 79 (22%) 288 1e-05
(0.000683) 		0.756
(0.885) 		0.0963
(0.321) 		0.86
(0.929) 		0.42
(0.676) 		0.759
(0.885) 		0.76
(0.885) 		0.345
(0.611) 		0.403
(0.668) 		0.467
(0.696)
7q loss 17 (5%) 350 0.398
(0.666) 		0.533
(0.748) 		0.599
(0.802) 		0.201
(0.496) 		0.0237
(0.146) 		0.485
(0.713) 		0.828
(0.917) 		0.834
(0.917) 		0.142
(0.412) 		0.97
(0.985)
11p loss 126 (34%) 241 0.00222
(0.035) 		0.385
(0.659) 		0.874
(0.934) 		0.705
(0.865) 		0.887
(0.937) 		0.882
(0.935) 		0.629
(0.821) 		0.134
(0.401) 		0.445
(0.685) 		0.281
(0.557)
12q loss 68 (19%) 299 0.0205
(0.135) 		0.0514
(0.23) 		0.448
(0.687) 		0.313
(0.588) 		0.298
(0.573) 		0.713
(0.871) 		0.27
(0.554) 		0.333
(0.602) 		0.631
(0.821) 		0.277
(0.555)
16q loss 105 (29%) 262 1e-05
(0.000683) 		0.08
(0.29) 		0.0873
(0.304) 		0.554
(0.762) 		0.0593
(0.247) 		0.0663
(0.263) 		0.225
(0.507) 		0.202
(0.497) 		0.181
(0.477) 		0.134
(0.401)
17p loss 124 (34%) 243 0.444
(0.685) 		0.0315
(0.172) 		0.0702
(0.266) 		0.0693
(0.266) 		0.428
(0.677) 		0.205
(0.502) 		0.757
(0.885) 		0.633
(0.821) 		0.729
(0.877) 		0.223
(0.507)
17q loss 62 (17%) 305 0.689
(0.855) 		0.972
(0.985) 		0.0277
(0.161) 		0.206
(0.502) 		0.677
(0.853) 		0.426
(0.677) 		0.846
(0.922) 		0.518
(0.737) 		0.235
(0.515) 		0.809
(0.911)
19p loss 77 (21%) 290 0.0397
(0.198) 		0.743
(0.883) 		0.537
(0.749) 		0.724
(0.876) 		0.12
(0.374) 		0.665
(0.845) 		0.223
(0.507) 		0.94
(0.969) 		0.661
(0.842) 		0.765
(0.885)
19q loss 73 (20%) 294 0.0372
(0.192) 		0.121
(0.374) 		0.241
(0.525) 		0.336
(0.604) 		0.121
(0.374) 		0.425
(0.677) 		0.174
(0.467) 		0.964
(0.983) 		0.341
(0.608) 		0.732
(0.878)
20p loss 25 (7%) 342 0.752
(0.885) 		0.111
(0.355) 		0.375
(0.645) 		0.222
(0.507) 		0.321
(0.592) 		0.064
(0.256) 		0.0676
(0.263) 		0.0124
(0.0978) 		0.791
(0.904) 		0.187
(0.487)
1p gain 93 (25%) 274 0.338
(0.606) 		0.444
(0.685) 		0.315
(0.588) 		0.402
(0.668) 		0.0534
(0.236) 		0.706
(0.865) 		0.633
(0.821) 		0.986
(0.995) 		0.281
(0.557) 		0.607
(0.806)
3p gain 64 (17%) 303 0.328
(0.596) 		0.693
(0.855) 		0.711
(0.87) 		0.801
(0.907) 		0.655
(0.837) 		0.736
(0.878) 		0.287
(0.56) 		0.266
(0.549) 		0.838
(0.919) 		0.876
(0.934)
3q gain 74 (20%) 293 0.76
(0.885) 		0.225
(0.507) 		0.468
(0.697) 		0.538
(0.749) 		0.313
(0.588) 		0.505
(0.724) 		0.188
(0.487) 		0.496
(0.719) 		0.405
(0.668) 		0.819
(0.917)
6q gain 50 (14%) 317 0.525
(0.742) 		0.913
(0.954) 		0.769
(0.888) 		0.692
(0.855) 		1
(1.00) 		0.394
(0.663) 		0.553
(0.762) 		0.254
(0.536) 		0.227
(0.509) 		0.552
(0.761)
9q gain 20 (5%) 347 0.132
(0.398) 		0.323
(0.592) 		0.0763
(0.282) 		0.0956
(0.321) 		0.917
(0.956) 		0.339
(0.608) 		0.839
(0.919) 		0.761
(0.885) 		0.752
(0.885) 		0.567
(0.774)
10p gain 12 (3%) 355 0.276
(0.555) 		0.972
(0.985) 		0.725
(0.876) 		0.774
(0.892) 		0.935
(0.966) 		0.933
(0.966) 		0.234
(0.515) 		0.323
(0.592) 		0.684
(0.855) 		0.454
(0.692)
21q gain 67 (18%) 300 0.19
(0.49) 		0.194
(0.491) 		0.287
(0.56) 		0.285
(0.559) 		0.271
(0.554) 		0.754
(0.885) 		0.432
(0.681) 		0.772
(0.891) 		0.761
(0.885) 		0.411
(0.67)
1q loss 27 (7%) 340 0.0735
(0.273) 		0.0549
(0.239) 		0.897
(0.943) 		0.651
(0.836) 		0.686
(0.855) 		0.765
(0.885) 		0.644
(0.829) 		0.939
(0.968) 		0.675
(0.851) 		0.625
(0.819)
7p loss 18 (5%) 349 0.461
(0.694) 		0.252
(0.533) 		0.292
(0.565) 		0.567
(0.774) 		0.0681
(0.263) 		0.784
(0.9) 		0.409
(0.669) 		0.778
(0.894) 		0.218
(0.507) 		0.824
(0.917)
12p loss 61 (17%) 306 0.249
(0.533) 		0.188
(0.487) 		0.993
(0.998) 		0.765
(0.885) 		0.351
(0.617) 		0.792
(0.904) 		0.285
(0.559) 		0.131
(0.396) 		0.802
(0.907) 		0.174
(0.467)
13q loss 82 (22%) 285 0.37
(0.639) 		0.623
(0.818) 		0.283
(0.557) 		0.811
(0.911) 		0.223
(0.507) 		0.393
(0.663) 		0.432
(0.681) 		0.389
(0.663) 		0.281
(0.557) 		0.118
(0.372)
15q loss 54 (15%) 313 0.517
(0.737) 		0.733
(0.878) 		0.152
(0.429) 		0.0635
(0.255) 		0.346
(0.612) 		0.616
(0.813) 		0.869
(0.934) 		0.67
(0.848) 		0.225
(0.507) 		0.876
(0.934)
18p loss 104 (28%) 263 0.251
(0.533) 		0.493
(0.719) 		0.301
(0.576) 		0.46
(0.694) 		0.0783
(0.288) 		0.236
(0.515) 		0.988
(0.995) 		0.0724
(0.273) 		0.69
(0.855) 		0.759
(0.885)
18q loss 100 (27%) 267 0.221
(0.507) 		0.277
(0.555) 		0.168
(0.458) 		0.837
(0.919) 		0.545
(0.755) 		0.858
(0.929) 		0.88
(0.935) 		0.0886
(0.308) 		0.915
(0.954) 		0.846
(0.922)
22q loss 39 (11%) 328 0.787
(0.901) 		0.406
(0.668) 		0.659
(0.842) 		0.602
(0.803) 		0.219
(0.507) 		0.692
(0.855) 		0.785
(0.9) 		0.654
(0.837) 		0.425
(0.677) 		0.89
(0.94)
'1q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0014

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
1Q GAIN MUTATED 81 63 29
1Q GAIN WILD-TYPE 73 47 74

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
1Q GAIN MUTATED 11 37 18 35 22
1Q GAIN WILD-TYPE 28 41 25 34 10

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.043

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
1Q GAIN MUTATED 64 21 51 37
1Q GAIN WILD-TYPE 52 52 54 36

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
1Q GAIN MUTATED 39 53 39 34
1Q GAIN WILD-TYPE 58 50 58 20

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.13

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
1Q GAIN MUTATED 32 53 75
1Q GAIN WILD-TYPE 53 66 58

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.032

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
2P GAIN MUTATED 32 27 8
2P GAIN WILD-TYPE 122 83 95

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
2P GAIN MUTATED 15 17 4 31
2P GAIN WILD-TYPE 96 105 30 68

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.074

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
2P GAIN MUTATED 20 7 30 10
2P GAIN WILD-TYPE 96 66 75 63

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00423 (Fisher's exact test), Q value = 0.051

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
2P GAIN MUTATED 19 20 28
2P GAIN WILD-TYPE 86 145 69

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.02

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
2P GAIN MUTATED 19 27 8 11
2P GAIN WILD-TYPE 113 66 80 27

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.024

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
2P GAIN MUTATED 4 2 9 8 17 3 11 9 0
2P GAIN WILD-TYPE 32 22 42 55 21 14 53 20 15

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.025

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
2Q GAIN MUTATED 28 29 8
2Q GAIN WILD-TYPE 126 81 95

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.035

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
2Q GAIN MUTATED 13 19 3 30
2Q GAIN WILD-TYPE 98 103 31 69

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.027

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
2Q GAIN MUTATED 15 8 32 10
2Q GAIN WILD-TYPE 101 65 73 63

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0052 (Fisher's exact test), Q value = 0.057

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
2Q GAIN MUTATED 15 22 28
2Q GAIN WILD-TYPE 90 143 69

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0095

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
2Q GAIN MUTATED 18 27 7 11
2Q GAIN WILD-TYPE 114 66 81 27

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.037

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
2Q GAIN MUTATED 4 2 7 9 16 4 10 9 0
2Q GAIN WILD-TYPE 32 22 44 54 22 13 54 20 15

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.037

Table S18.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
4P GAIN MUTATED 32 6 14 4
4P GAIN WILD-TYPE 100 87 74 34

Figure S18.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.057

Table S19.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
4Q GAIN MUTATED 29 6 9 4
4Q GAIN WILD-TYPE 103 87 79 34

Figure S19.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S20.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
5P GAIN MUTATED 52 13 9
5P GAIN WILD-TYPE 102 97 94

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
5P GAIN MUTATED 2 1 12 15 6 7 12 8 3
5P GAIN WILD-TYPE 34 23 39 48 32 10 52 21 12

Figure S21.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S22.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
5Q GAIN MUTATED 41 4 7
5Q GAIN WILD-TYPE 113 106 96

Figure S22.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.019

Table S23.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
6P GAIN MUTATED 73 49 26
6P GAIN WILD-TYPE 81 61 77

Figure S23.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.098

Table S24.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
6P GAIN MUTATED 48 35 16 48
6P GAIN WILD-TYPE 63 87 18 51

Figure S24.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.12

Table S25.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
6P GAIN MUTATED 49 25 34 40
6P GAIN WILD-TYPE 67 48 71 33

Figure S25.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.19

Table S26.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
6P GAIN MUTATED 49 70 29
6P GAIN WILD-TYPE 56 95 68

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.2

Table S27.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
6P GAIN MUTATED 37 53 31 23
6P GAIN WILD-TYPE 60 50 66 31

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.01

Table S28.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
6P GAIN MUTATED 71 24 36 13
6P GAIN WILD-TYPE 61 69 52 25

Figure S28.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0014

Table S29.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
6P GAIN MUTATED 23 40 75
6P GAIN WILD-TYPE 62 79 58

Figure S29.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0039

Table S30.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
6P GAIN MUTATED 11 4 20 38 9 3 33 10 10
6P GAIN WILD-TYPE 25 20 31 25 29 14 31 19 5

Figure S30.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.02

Table S31.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
7P GAIN MUTATED 99 63 42
7P GAIN WILD-TYPE 55 47 61

Figure S31.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.057

Table S32.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
7Q GAIN MUTATED 96 60 43
7Q GAIN WILD-TYPE 58 50 60

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.11

Table S33.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
7Q GAIN MUTATED 53 42 69 35
7Q GAIN WILD-TYPE 63 31 36 38

Figure S33.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
7Q GAIN MUTATED 17 11 35 24 24 12 33 17 8
7Q GAIN WILD-TYPE 19 13 16 39 14 5 31 12 7

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

'8p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
8P GAIN MUTATED 55 51 17
8P GAIN WILD-TYPE 99 59 86

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

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.18

Table S36.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
8P GAIN MUTATED 31 19 43 30
8P GAIN WILD-TYPE 85 54 62 43

Figure S36.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.15

Table S37.  Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
8P GAIN MUTATED 42 43 38
8P GAIN WILD-TYPE 63 122 59

Figure S37.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0022

Table S38.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
8Q GAIN MUTATED 82 61 29
8Q GAIN WILD-TYPE 72 49 74

Figure S38.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S39.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
8Q GAIN MUTATED 34 54 24 59
8Q GAIN WILD-TYPE 77 68 10 40

Figure S39.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.012

Table S40.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
8Q GAIN MUTATED 44 26 55 47
8Q GAIN WILD-TYPE 72 47 50 26

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.13

Table S41.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
8Q GAIN MUTATED 55 64 53
8Q GAIN WILD-TYPE 50 101 44

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.21

Table S42.  Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
9P GAIN MUTATED 8 1 4
9P GAIN WILD-TYPE 78 83 87

Figure S42.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.21

Table S43.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
10Q GAIN MUTATED 0 0 0 3
10Q GAIN WILD-TYPE 111 122 34 96

Figure S43.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.19

Table S44.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
11P GAIN MUTATED 6 8 5 15
11P GAIN WILD-TYPE 105 114 29 84

Figure S44.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.16

Table S45.  Gene #21: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
11P GAIN MUTATED 14 7 4
11P GAIN WILD-TYPE 72 77 87

Figure S45.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.05

Table S46.  Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
11P GAIN MUTATED 6 3 19 6
11P GAIN WILD-TYPE 110 70 86 67

Figure S46.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.037

Table S47.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
11P GAIN MUTATED 7 9 18
11P GAIN WILD-TYPE 98 156 79

Figure S47.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.066

Table S48.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
11P GAIN MUTATED 16 13 2 1
11P GAIN WILD-TYPE 116 80 86 37

Figure S48.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.091

Table S49.  Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
11Q GAIN MUTATED 12 7 2
11Q GAIN WILD-TYPE 74 77 89

Figure S49.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.026

Table S50.  Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
11Q GAIN MUTATED 2 4 16 6
11Q GAIN WILD-TYPE 114 69 89 67

Figure S50.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00353 (Fisher's exact test), Q value = 0.045

Table S51.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
11Q GAIN MUTATED 3 10 15
11Q GAIN WILD-TYPE 102 155 82

Figure S51.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0097

Table S52.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
11Q GAIN MUTATED 14 11 0 0
11Q GAIN WILD-TYPE 118 82 88 38

Figure S52.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00822 (Fisher's exact test), Q value = 0.074

Table S53.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
12P GAIN MUTATED 36 19 9
12P GAIN WILD-TYPE 118 91 94

Figure S53.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.18

Table S54.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
12Q GAIN MUTATED 1 0 9 5 9 2 8 4 0
12Q GAIN WILD-TYPE 35 24 42 58 29 15 56 25 15

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0018

Table S55.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
13Q GAIN MUTATED 40 41 11
13Q GAIN WILD-TYPE 114 69 92

Figure S55.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0043

Table S56.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
13Q GAIN MUTATED 24 17 10 40
13Q GAIN WILD-TYPE 87 105 24 59

Figure S56.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0041

Table S57.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
13Q GAIN MUTATED 20 9 33 30
13Q GAIN WILD-TYPE 96 64 72 43

Figure S57.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.17

Table S58.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
13Q GAIN MUTATED 13 37 35
13Q GAIN WILD-TYPE 72 82 98

Figure S58.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.18

Table S59.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
13Q GAIN MUTATED 5 3 7 20 13 4 24 6 3
13Q GAIN WILD-TYPE 31 21 44 43 25 13 40 23 12

Figure S59.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.21

Table S60.  Gene #26: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
14Q GAIN MUTATED 5 15 9
14Q GAIN WILD-TYPE 81 69 82

Figure S60.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.21

Table S61.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
15Q GAIN MUTATED 42 27 15
15Q GAIN WILD-TYPE 112 83 88

Figure S61.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.058

Table S62.  Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
15Q GAIN MUTATED 15 18 34 17
15Q GAIN WILD-TYPE 101 55 71 56

Figure S62.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00652 (Fisher's exact test), Q value = 0.062

Table S63.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
15Q GAIN MUTATED 16 35 33
15Q GAIN WILD-TYPE 89 130 64

Figure S63.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
15Q GAIN MUTATED 22 13 28 14
15Q GAIN WILD-TYPE 75 90 69 40

Figure S64.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.21

Table S65.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
15Q GAIN MUTATED 8 3 11 7 15 7 14 6 3
15Q GAIN WILD-TYPE 28 21 40 56 23 10 50 23 12

Figure S65.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0029

Table S66.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
16P GAIN MUTATED 21 30 6
16P GAIN WILD-TYPE 133 80 97

Figure S66.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.02

Table S67.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
16P GAIN MUTATED 10 15 3 28
16P GAIN WILD-TYPE 101 107 31 71

Figure S67.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00567 (Fisher's exact test), Q value = 0.057

Table S68.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
16P GAIN MUTATED 9 9 21 18
16P GAIN WILD-TYPE 107 64 84 55

Figure S68.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00825 (Fisher's exact test), Q value = 0.074

Table S69.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
16P GAIN MUTATED 3 0 3 9 8 5 17 5 2
16P GAIN WILD-TYPE 33 24 48 54 30 12 47 24 13

Figure S69.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0011

Table S70.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
16Q GAIN MUTATED 13 28 4
16Q GAIN WILD-TYPE 141 82 99

Figure S70.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.057

Table S71.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
16Q GAIN MUTATED 8 12 2 22
16Q GAIN WILD-TYPE 103 110 32 77

Figure S71.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.044

Table S72.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
16Q GAIN MUTATED 6 6 20 13
16Q GAIN WILD-TYPE 110 67 85 60

Figure S72.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.11

Table S73.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
16Q GAIN MUTATED 11 14 20
16Q GAIN WILD-TYPE 94 151 77

Figure S73.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.02

Table S74.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
16Q GAIN MUTATED 1 0 1 7 8 4 15 4 2
16Q GAIN WILD-TYPE 35 24 50 56 30 13 49 25 13

Figure S74.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.083

Table S75.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
17P GAIN MUTATED 14 5 4 17
17P GAIN WILD-TYPE 97 117 30 82

Figure S75.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.21

Table S76.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
17Q GAIN MUTATED 26 13 6 22
17Q GAIN WILD-TYPE 85 109 28 77

Figure S76.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.098

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
18P GAIN MUTATED 29 20 7
18P GAIN WILD-TYPE 125 90 96

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

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00664 (Fisher's exact test), Q value = 0.063

Table S78.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
18P GAIN MUTATED 9 12 31
18P GAIN WILD-TYPE 76 107 102

Figure S78.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.04

Table S79.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
18Q GAIN MUTATED 21 20 4
18Q GAIN WILD-TYPE 133 90 99

Figure S79.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.15

Table S80.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
19P GAIN MUTATED 29 21 8
19P GAIN WILD-TYPE 125 89 95

Figure S80.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.15

Table S81.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
19P GAIN MUTATED 16 5 24 13
19P GAIN WILD-TYPE 100 68 81 60

Figure S81.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.047

Table S82.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
19Q GAIN MUTATED 30 20 6
19Q GAIN WILD-TYPE 124 90 97

Figure S82.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.15

Table S83.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
19Q GAIN MUTATED 15 5 24 12
19Q GAIN WILD-TYPE 101 68 81 61

Figure S83.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.15

Table S84.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
19Q GAIN MUTATED 21 16 19
19Q GAIN WILD-TYPE 84 149 78

Figure S84.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S85.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
20P GAIN MUTATED 76 52 19
20P GAIN WILD-TYPE 78 58 84

Figure S85.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.011

Table S86.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
20P GAIN MUTATED 34 41 15 56
20P GAIN WILD-TYPE 77 81 19 43

Figure S86.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.02

Table S87.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
20P GAIN MUTATED 33 24 53 37
20P GAIN WILD-TYPE 83 49 52 36

Figure S87.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.099

Table S88.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
20P GAIN MUTATED 39 57 51
20P GAIN WILD-TYPE 66 108 46

Figure S88.  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 = 0.00068

Table S89.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
20Q GAIN MUTATED 96 59 25
20Q GAIN WILD-TYPE 58 51 78

Figure S89.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00848 (Fisher's exact test), Q value = 0.074

Table S90.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
20Q GAIN MUTATED 49 50 18 62
20Q GAIN WILD-TYPE 62 72 16 37

Figure S90.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
20Q GAIN MUTATED 49 32 43
20Q GAIN WILD-TYPE 37 52 48

Figure S91.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.21

Table S92.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
20Q GAIN MUTATED 49 73 58
20Q GAIN WILD-TYPE 56 92 39

Figure S92.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00604 (Fisher's exact test), Q value = 0.059

Table S93.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
22Q GAIN MUTATED 57 46 23
22Q GAIN WILD-TYPE 97 64 80

Figure S93.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.21

Table S94.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
22Q GAIN MUTATED 6 6 26 18 13 4 24 13 4
22Q GAIN WILD-TYPE 30 18 25 45 25 13 40 16 11

Figure S94.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.057

Table S95.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
XP GAIN MUTATED 13 5 5 18
XP GAIN WILD-TYPE 98 117 29 81

Figure S95.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.098

Table S96.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
XP GAIN MUTATED 14 2 12 14
XP GAIN WILD-TYPE 102 71 93 59

Figure S96.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.082

Table S97.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
XP GAIN MUTATED 18 10 14
XP GAIN WILD-TYPE 87 155 83

Figure S97.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.094

Table S98.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
XP GAIN MUTATED 3 15 21
XP GAIN WILD-TYPE 82 104 112

Figure S98.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.21

Table S99.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
XQ GAIN MUTATED 20 18 6
XQ GAIN WILD-TYPE 134 92 97

Figure S99.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.057

Table S100.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
XQ GAIN MUTATED 16 5 5 17
XQ GAIN WILD-TYPE 95 117 29 82

Figure S100.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.035

Table S101.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
XQ GAIN MUTATED 18 2 9 15
XQ GAIN WILD-TYPE 98 71 96 58

Figure S101.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00524 (Fisher's exact test), Q value = 0.057

Table S102.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
XQ GAIN MUTATED 21 11 12
XQ GAIN WILD-TYPE 84 154 85

Figure S102.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.015

Table S103.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
XQ GAIN MUTATED 1 16 21
XQ GAIN WILD-TYPE 84 103 112

Figure S103.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.04

Table S104.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
1P LOSS MUTATED 25 21 5
1P LOSS WILD-TYPE 129 89 98

Figure S104.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.057

Table S105.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
1P LOSS MUTATED 8 15 10 18
1P LOSS WILD-TYPE 103 107 24 81

Figure S105.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.082

Table S106.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
1P LOSS MUTATED 7 27 16
1P LOSS WILD-TYPE 78 92 117

Figure S106.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.17

Table S107.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
2P LOSS MUTATED 16 28 6
2P LOSS WILD-TYPE 89 137 91

Figure S107.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.04

Table S108.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
2P LOSS MUTATED 8 23 7 11
2P LOSS WILD-TYPE 89 80 90 43

Figure S108.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.14

Table S109.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
2P LOSS MUTATED 22 5 17 5
2P LOSS WILD-TYPE 110 88 71 33

Figure S109.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.15

Table S110.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
2Q LOSS MUTATED 24 12 6 9
2Q LOSS WILD-TYPE 87 110 28 90

Figure S110.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.2

Table S111.  Gene #45: '2q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
2Q LOSS MUTATED 11 8 21
2Q LOSS WILD-TYPE 75 76 70

Figure S111.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.074

Table S112.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
2Q LOSS MUTATED 9 23 8 11
2Q LOSS WILD-TYPE 88 80 89 43

Figure S112.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.19

Table S113.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
2Q LOSS MUTATED 22 6 18 5
2Q LOSS WILD-TYPE 110 87 70 33

Figure S113.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.062

Table S114.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
3P LOSS MUTATED 11 20 24 3
3P LOSS WILD-TYPE 86 83 73 51

Figure S114.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.15

Table S115.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
3Q LOSS MUTATED 9 21 17 3
3Q LOSS WILD-TYPE 88 82 80 51

Figure S115.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.11

Table S116.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
4P LOSS MUTATED 24 26 30
4P LOSS WILD-TYPE 81 139 67

Figure S116.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00596 (Fisher's exact test), Q value = 0.059

Table S117.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
4P LOSS MUTATED 16 28 21 10
4P LOSS WILD-TYPE 116 65 67 28

Figure S117.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.12

Table S118.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
4Q LOSS MUTATED 20 32 33
4Q LOSS WILD-TYPE 85 133 64

Figure S118.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.043

Table S119.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
4Q LOSS MUTATED 17 30 22 11
4Q LOSS WILD-TYPE 115 63 66 27

Figure S119.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S120.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
5P LOSS MUTATED 14 51 14
5P LOSS WILD-TYPE 140 59 89

Figure S120.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S121.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
5Q LOSS MUTATED 18 60 19
5Q LOSS WILD-TYPE 136 50 84

Figure S121.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.18

Table S122.  Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
5Q LOSS MUTATED 3 17 11 19 12
5Q LOSS WILD-TYPE 36 61 32 50 20

Figure S122.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.018

Table S123.  Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
6P LOSS MUTATED 25 7 31 7
6P LOSS WILD-TYPE 91 66 74 66

Figure S123.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.098

Table S124.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
6P LOSS MUTATED 7 6 8 9 14 5 6 7 0
6P LOSS WILD-TYPE 29 18 43 54 24 12 58 22 15

Figure S124.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S125.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
6Q LOSS MUTATED 100 48 24
6Q LOSS WILD-TYPE 54 62 79

Figure S125.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.21

Table S126.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
6Q LOSS MUTATED 60 45 16 51
6Q LOSS WILD-TYPE 51 77 18 48

Figure S126.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.057

Table S127.  Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
6Q LOSS MUTATED 65 23 54 30
6Q LOSS WILD-TYPE 51 50 51 43

Figure S127.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.15

Table S128.  Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
7Q LOSS MUTATED 6 1 2 8
7Q LOSS WILD-TYPE 110 72 103 65

Figure S128.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.13

Table S129.  Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
8P LOSS MUTATED 2 14 6 21 7
8P LOSS WILD-TYPE 37 64 37 48 25

Figure S129.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.19

Table S130.  Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
8P LOSS MUTATED 26 7 15 18
8P LOSS WILD-TYPE 90 66 90 55

Figure S130.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.15

Table S131.  Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
8Q LOSS MUTATED 14 4 3 4
8Q LOSS WILD-TYPE 97 118 31 95

Figure S131.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.13

Table S132.  Gene #57: '8q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
8Q LOSS MUTATED 0 6 1 11 3
8Q LOSS WILD-TYPE 39 72 42 58 29

Figure S132.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.14

Table S133.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
8Q LOSS MUTATED 4 4 16
8Q LOSS WILD-TYPE 81 115 117

Figure S133.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.13

Table S134.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
8Q LOSS MUTATED 7 0 3 8 1 0 3 0 2
8Q LOSS WILD-TYPE 29 24 48 55 37 17 61 29 13

Figure S134.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.01

Table S135.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
9P LOSS MUTATED 103 82 50
9P LOSS WILD-TYPE 51 28 53

Figure S135.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.19

Table S136.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
9P LOSS MUTATED 76 66 22 71
9P LOSS WILD-TYPE 35 56 12 28

Figure S136.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.091

Table S137.  Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
9P LOSS MUTATED 20 55 31 35 25
9P LOSS WILD-TYPE 19 23 12 34 7

Figure S137.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.22

Table S138.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
9P LOSS MUTATED 70 95 70
9P LOSS WILD-TYPE 35 70 27

Figure S138.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.074

Table S139.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
9P LOSS MUTATED 19 18 28 35 25 14 43 17 15
9P LOSS WILD-TYPE 17 6 23 28 13 3 21 12 0

Figure S139.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.13

Table S140.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
9Q LOSS MUTATED 77 66 42
9Q LOSS WILD-TYPE 77 44 61

Figure S140.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.16

Table S141.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
9Q LOSS MUTATED 78 38 39 21
9Q LOSS WILD-TYPE 54 55 49 17

Figure S141.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00905 (Fisher's exact test), Q value = 0.078

Table S142.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
9Q LOSS MUTATED 14 18 22 28 21 10 28 16 13
9Q LOSS WILD-TYPE 22 6 29 35 17 7 36 13 2

Figure S142.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S143.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
10P LOSS MUTATED 93 86 25
10P LOSS WILD-TYPE 61 24 78

Figure S143.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00427 (Fisher's exact test), Q value = 0.051

Table S144.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
10P LOSS MUTATED 58 58 18 70
10P LOSS WILD-TYPE 53 64 16 29

Figure S144.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.15

Table S145.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
10P LOSS MUTATED 55 36 69 44
10P LOSS WILD-TYPE 61 37 36 29

Figure S145.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00987 (Fisher's exact test), Q value = 0.083

Table S146.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
10P LOSS MUTATED 60 79 65
10P LOSS WILD-TYPE 45 86 32

Figure S146.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S147.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
10Q LOSS MUTATED 101 93 30
10Q LOSS WILD-TYPE 53 17 73

Figure S147.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.024

Table S148.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
10Q LOSS MUTATED 65 63 20 76
10Q LOSS WILD-TYPE 46 59 14 23

Figure S148.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.057

Table S149.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
10Q LOSS MUTATED 59 40 74 51
10Q LOSS WILD-TYPE 57 33 31 22

Figure S149.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0029 (Fisher's exact test), Q value = 0.04

Table S150.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
10Q LOSS MUTATED 60 91 73
10Q LOSS WILD-TYPE 45 74 24

Figure S150.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.035

Table S151.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
11P LOSS MUTATED 56 48 22
11P LOSS WILD-TYPE 98 62 81

Figure S151.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.03

Table S152.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
11Q LOSS MUTATED 69 53 27
11Q LOSS WILD-TYPE 85 57 76

Figure S152.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.17

Table S153.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
11Q LOSS MUTATED 12 12 24 20 8 8 34 15 7
11Q LOSS WILD-TYPE 24 12 27 43 30 9 30 14 8

Figure S153.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.13

Table S154.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
12Q LOSS MUTATED 34 24 10
12Q LOSS WILD-TYPE 120 86 93

Figure S154.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0044

Table S155.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
14Q LOSS MUTATED 55 42 15
14Q LOSS WILD-TYPE 99 68 88

Figure S155.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.19

Table S156.  Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
14Q LOSS MUTATED 35 19 26
14Q LOSS WILD-TYPE 51 65 65

Figure S156.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.15

Table S157.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
14Q LOSS MUTATED 26 23 43 20
14Q LOSS WILD-TYPE 90 50 62 53

Figure S157.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0092

Table S158.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
16P LOSS MUTATED 44 12 13
16P LOSS WILD-TYPE 110 98 90

Figure S158.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.17

Table S159.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
16P LOSS MUTATED 29 19 9 12
16P LOSS WILD-TYPE 82 103 25 87

Figure S159.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S160.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
16Q LOSS MUTATED 70 14 21
16Q LOSS WILD-TYPE 84 96 82

Figure S160.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.17

Table S161.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
17P LOSS MUTATED 48 42 10 24
17P LOSS WILD-TYPE 63 80 24 75

Figure S161.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.16

Table S162.  Gene #72: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
17Q LOSS MUTATED 2 19 11 8 6
17Q LOSS WILD-TYPE 37 59 32 61 26

Figure S162.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.2

Table S163.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
19P LOSS MUTATED 36 28 13
19P LOSS WILD-TYPE 118 82 90

Figure S163.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.19

Table S164.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
19Q LOSS MUTATED 37 24 12
19Q LOSS WILD-TYPE 117 86 91

Figure S164.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.098

Table S165.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
20P LOSS MUTATED 5 6 12 0
20P LOSS WILD-TYPE 127 87 76 38

Figure S165.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.2

Table S166.  Gene #78: '20q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
20Q LOSS MUTATED 0 1 5
20Q LOSS WILD-TYPE 86 83 86

Figure S166.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00525 (Fisher's exact test), Q value = 0.057

Table S167.  Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
20Q LOSS MUTATED 7 2 0
20Q LOSS WILD-TYPE 98 163 97

Figure S167.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.087

Table S168.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
21Q LOSS MUTATED 37 23 10
21Q LOSS WILD-TYPE 117 87 93

Figure S168.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S169.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
21Q LOSS MUTATED 29 14 14 12
21Q LOSS WILD-TYPE 68 89 83 42

Figure S169.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.19

Table S170.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
XP LOSS MUTATED 42 36 18
XP LOSS WILD-TYPE 112 74 85

Figure S170.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00068

Table S171.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
XP LOSS MUTATED 39 13 14 30
XP LOSS WILD-TYPE 72 109 20 69

Figure S171.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.026

Table S172.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
XP LOSS MUTATED 38 7 31 20
XP LOSS WILD-TYPE 78 66 74 53

Figure S172.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.031

Table S173.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
XP LOSS MUTATED 38 29 29
XP LOSS WILD-TYPE 67 136 68

Figure S173.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.13

Table S174.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
XP LOSS MUTATED 25 38 20 9
XP LOSS WILD-TYPE 72 65 77 45

Figure S174.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.15

Table S175.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
XP LOSS MUTATED 8 9 9 22 5 9 15 5 5
XP LOSS WILD-TYPE 28 15 42 41 33 8 49 24 10

Figure S175.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.21

Table S176.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
XQ LOSS MUTATED 42 33 17
XQ LOSS WILD-TYPE 112 77 86

Figure S176.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0011

Table S177.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
XQ LOSS MUTATED 36 12 13 31
XQ LOSS WILD-TYPE 75 110 21 68

Figure S177.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.02

Table S178.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
XQ LOSS MUTATED 34 6 33 19
XQ LOSS WILD-TYPE 82 67 72 54

Figure S178.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.051

Table S179.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
XQ LOSS MUTATED 34 28 30
XQ LOSS WILD-TYPE 71 137 67

Figure S179.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.21

Table S180.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
XQ LOSS MUTATED 29 33 18 9
XQ LOSS WILD-TYPE 68 70 79 45

Figure S180.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.13

Table S181.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
XQ LOSS MUTATED 11 5 9 21 5 10 15 5 5
XQ LOSS WILD-TYPE 25 19 42 42 33 7 49 24 10

Figure S181.  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/SKCM-TM/22533835/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/22546664/SKCM-TM.transferedmergedcluster.txt

  • Number of patients = 367

  • 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.

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)
Made with Nozzle