Correlation between copy number variation genes (focal events) and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1HT2N4D
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HT2N4D
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 62 focal events and 10 molecular subtypes across 419 patients, 146 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_3q21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF'.

  • amp_4q13.3 cnv correlated to 'CN_CNMF'.

  • amp_5q33.3 cnv correlated to 'CN_CNMF'.

  • amp_7p14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_9q34.11 cnv correlated to 'CN_CNMF'.

  • amp_11q13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_12q23.1 cnv correlated to 'CN_CNMF'.

  • amp_13q12.11 cnv correlated to 'CN_CNMF'.

  • amp_14q21.1 cnv correlated to 'CN_CNMF'.

  • amp_16q11.2 cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • amp_17q23.2 cnv correlated to 'CN_CNMF'.

  • amp_18q21.31 cnv correlated to 'CN_CNMF'.

  • amp_19q13.43 cnv correlated to 'CN_CNMF'.

  • amp_20q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp22.2 cnv correlated to 'CN_CNMF'.

  • amp_xp22.11 cnv correlated to 'CN_CNMF'.

  • amp_xp22.11 cnv correlated to 'CN_CNMF'.

  • amp_xp21.1 cnv correlated to 'CN_CNMF'.

  • amp_xq21.31 cnv correlated to 'CN_CNMF'.

  • del_1p31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p22.1 cnv correlated to 'CN_CNMF'.

  • del_1q42.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_2q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p13 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q28.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_5q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_5q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_5q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_8p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p11.2 cnv correlated to 'CN_CNMF'.

  • del_12p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q24.31 cnv correlated to 'CN_CNMF'.

  • del_13q14.13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_13q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_15q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_16q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_17p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17q21.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_21q22.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_21q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 62 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 146 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
del 16q22 3 158 (38%) 261 1e-05
(0.00616) 		1e-05
(0.00616) 		0.423
(1.00) 		0.213
(1.00) 		3e-05
(0.0157) 		1e-05
(0.00616) 		5e-05
(0.0256) 		1e-05
(0.00616) 		0.00012
(0.0599) 		0.00031
(0.149)
amp 8q24 21 118 (28%) 301 1e-05
(0.00616) 		6e-05
(0.0305) 		0.00561
(1.00) 		0.00646
(1.00) 		1e-05
(0.00616) 		0.00012
(0.0599) 		4e-05
(0.0206) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.00184
(0.815)
del 8p21 3 242 (58%) 177 1e-05
(0.00616) 		1e-05
(0.00616) 		0.0315
(1.00) 		0.0526
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		1e-05
(0.00616) 		3e-05
(0.0157) 		3e-05
(0.0157) 		0.0222
(1.00)
del 8p11 21 136 (32%) 283 1e-05
(0.00616) 		1e-05
(0.00616) 		0.865
(1.00) 		0.434
(1.00) 		1e-05
(0.00616) 		8e-05
(0.0402) 		0.00025
(0.121) 		2e-05
(0.0105) 		0.0007
(0.327) 		0.00039
(0.185)
del 10q23 31 126 (30%) 293 1e-05
(0.00616) 		1e-05
(0.00616) 		0.0659
(1.00) 		0.142
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.339
(1.00) 		0.00033
(0.157)
del 16q24 1 174 (42%) 245 1e-05
(0.00616) 		1e-05
(0.00616) 		0.68
(1.00) 		0.496
(1.00) 		1e-05
(0.00616) 		5e-05
(0.0256) 		0.0026
(1.00) 		1e-05
(0.00616) 		0.00032
(0.153) 		0.00222
(0.963)
del 2q22 1 72 (17%) 347 1e-05
(0.00616) 		1e-05
(0.00616) 		0.0249
(1.00) 		0.0633
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.0152
(1.00) 		0.00636
(1.00) 		0.0366
(1.00) 		8e-05
(0.0402)
del 13q14 13 180 (43%) 239 1e-05
(0.00616) 		1e-05
(0.00616) 		0.0773
(1.00) 		0.225
(1.00) 		4e-05
(0.0206) 		0.00021
(0.102) 		0.00034
(0.162) 		0.0153
(1.00) 		0.00732
(1.00) 		0.0886
(1.00)
del 15q21 3 48 (11%) 371 1e-05
(0.00616) 		6e-05
(0.0305) 		0.00195
(0.854) 		0.00637
(1.00) 		6e-05
(0.0305) 		0.00082
(0.38) 		0.0129
(1.00) 		0.0001
(0.0501) 		1e-05
(0.00616) 		0.00672
(1.00)
del 17p13 1 131 (31%) 288 1e-05
(0.00616) 		1e-05
(0.00616) 		0.0312
(1.00) 		0.05
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.0146
(1.00) 		7e-05
(0.0354) 		0.00108
(0.492) 		0.00228
(0.985)
del 21q22 3 119 (28%) 300 1e-05
(0.00616) 		1e-05
(0.00616) 		0.118
(1.00) 		0.448
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.0012
(0.544) 		0.00343
(1.00) 		0.249
(1.00) 		0.00026
(0.126)
del 1p31 3 48 (11%) 371 1e-05
(0.00616) 		1e-05
(0.00616) 		0.335
(1.00) 		0.532
(1.00) 		5e-05
(0.0256) 		2e-05
(0.0105) 		0.00074
(0.345) 		0.00257
(1.00) 		0.00796
(1.00) 		0.0342
(1.00)
del 2q22 3 66 (16%) 353 1e-05
(0.00616) 		1e-05
(0.00616) 		0.224
(1.00) 		0.0712
(1.00) 		2e-05
(0.0105) 		1e-05
(0.00616) 		0.142
(1.00) 		0.0298
(1.00) 		0.241
(1.00) 		0.0646
(1.00)
del 5q11 2 74 (18%) 345 1e-05
(0.00616) 		1e-05
(0.00616) 		0.00427
(1.00) 		0.0314
(1.00) 		0.00157
(0.702) 		0.0025
(1.00) 		0.0013
(0.585) 		0.00012
(0.0599) 		0.00014
(0.0692) 		0.0237
(1.00)
del 5q21 1 82 (20%) 337 1e-05
(0.00616) 		1e-05
(0.00616) 		0.121
(1.00) 		0.0952
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.00199
(0.87) 		0.0142
(1.00) 		0.0135
(1.00) 		0.0117
(1.00)
del 6q14 3 148 (35%) 271 1e-05
(0.00616) 		1e-05
(0.00616) 		0.00793
(1.00) 		0.00224
(0.97) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.00321
(1.00) 		0.00078
(0.362) 		0.00058
(0.273) 		0.0248
(1.00)
del 12p13 1 100 (24%) 319 1e-05
(0.00616) 		0.00011
(0.055) 		0.0598
(1.00) 		0.0804
(1.00) 		0.00335
(1.00) 		0.00215
(0.937) 		0.00012
(0.0599) 		1e-05
(0.00616) 		0.0217
(1.00) 		0.0523
(1.00)
del 17q21 31 85 (20%) 334 1e-05
(0.00616) 		1e-05
(0.00616) 		0.523
(1.00) 		0.751
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.17
(1.00) 		0.0512
(1.00) 		0.014
(1.00) 		0.383
(1.00)
amp 7p14 3 86 (21%) 333 1e-05
(0.00616) 		1e-05
(0.00616) 		0.356
(1.00) 		0.562
(1.00) 		1e-05
(0.00616) 		0.00636
(1.00) 		0.0251
(1.00) 		0.00151
(0.676) 		0.00669
(1.00) 		0.0276
(1.00)
amp 8p11 23 50 (12%) 369 1e-05
(0.00616) 		7e-05
(0.0354) 		0.0961
(1.00) 		0.163
(1.00) 		3e-05
(0.0157) 		0.00847
(1.00) 		0.108
(1.00) 		0.0561
(1.00) 		0.00354
(1.00) 		0.308
(1.00)
amp 20q13 2 34 (8%) 385 1e-05
(0.00616) 		0.00041
(0.194) 		0.305
(1.00) 		0.328
(1.00) 		0.0032
(1.00) 		0.00891
(1.00) 		0.157
(1.00) 		0.0161
(1.00) 		0.0188
(1.00) 		0.00016
(0.0787)
del 3p13 67 (16%) 352 0.00108
(0.492) 		1e-05
(0.00616) 		0.84
(1.00) 		0.92
(1.00) 		1e-05
(0.00616) 		1e-05
(0.00616) 		0.106
(1.00) 		0.544
(1.00) 		0.0179
(1.00) 		0.0191
(1.00)
del 5q13 2 76 (18%) 343 1e-05
(0.00616) 		1e-05
(0.00616) 		0.0207
(1.00) 		0.183
(1.00) 		0.00106
(0.487) 		0.058
(1.00) 		0.00274
(1.00) 		0.00051
(0.24) 		0.00344
(1.00) 		0.00813
(1.00)
del 13q22 1 139 (33%) 280 1e-05
(0.00616) 		3e-05
(0.0157) 		0.00864
(1.00) 		0.0426
(1.00) 		0.00031
(0.149) 		0.00512
(1.00) 		0.0145
(1.00) 		0.0367
(1.00) 		0.0326
(1.00) 		0.0498
(1.00)
amp 3q21 3 60 (14%) 359 1e-05
(0.00616) 		0.00448
(1.00) 		0.172
(1.00) 		0.2
(1.00) 		0.00044
(0.208) 		0.00191
(0.838) 		0.0662
(1.00) 		0.0209
(1.00) 		0.0576
(1.00) 		0.0193
(1.00)
amp 11q13 2 35 (8%) 384 1e-05
(0.00616) 		0.055
(1.00) 		0.521
(1.00) 		0.523
(1.00) 		0.00017
(0.0833) 		0.0661
(1.00) 		0.311
(1.00) 		0.0856
(1.00) 		0.0384
(1.00) 		0.00136
(0.611)
amp 16q11 2 24 (6%) 395 0.00095
(0.438) 		0.106
(1.00) 		1
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.0684
(1.00) 		0.0352
(1.00) 		0.0003
(0.145) 		7e-05
(0.0354) 		0.0188
(1.00)
del 1q42 2 39 (9%) 380 1e-05
(0.00616) 		0.00026
(0.126) 		0.932
(1.00) 		0.106
(1.00) 		0.919
(1.00) 		0.0242
(1.00) 		0.21
(1.00) 		0.298
(1.00) 		0.0665
(1.00) 		0.832
(1.00)
del 4q28 1 34 (8%) 385 2e-05
(0.0105) 		0.0003
(0.145) 		0.0882
(1.00) 		0.0996
(1.00) 		0.00084
(0.388) 		0.033
(1.00) 		0.0107
(1.00) 		0.157
(1.00) 		0.0165
(1.00) 		0.323
(1.00)
del 18q22 1 115 (27%) 304 1e-05
(0.00616) 		0.108
(1.00) 		0.309
(1.00) 		0.0509
(1.00) 		0.00173
(0.768) 		0.0422
(1.00) 		0.506
(1.00) 		0.00015
(0.0739) 		0.0462
(1.00) 		0.0542
(1.00)
amp 1q21 3 31 (7%) 388 1e-05
(0.00616) 		0.00188
(0.829) 		0.00218
(0.948) 		0.0687
(1.00) 		0.00107
(0.49) 		0.00875
(1.00) 		0.00286
(1.00) 		0.147
(1.00) 		0.00274
(1.00) 		0.00129
(0.582)
amp 3q26 2 66 (16%) 353 1e-05
(0.00616) 		0.156
(1.00) 		0.152
(1.00) 		0.397
(1.00) 		0.00301
(1.00) 		0.0882
(1.00) 		0.162
(1.00) 		0.233
(1.00) 		0.324
(1.00) 		0.0173
(1.00)
amp 4q13 3 15 (4%) 404 1e-05
(0.00616) 		0.219
(1.00) 		0.472
(1.00) 		0.781
(1.00) 		0.0533
(1.00) 		0.32
(1.00) 		0.0346
(1.00) 		0.477
(1.00) 		0.00111
(0.504) 		0.0023
(0.991)
amp 5q33 3 23 (5%) 396 1e-05
(0.00616) 		0.0963
(1.00) 		0.076
(1.00) 		0.114
(1.00) 		0.0339
(1.00) 		0.592
(1.00) 		0.491
(1.00) 		0.312
(1.00) 		0.0978
(1.00) 		0.0874
(1.00)
amp 9q34 11 47 (11%) 372 1e-05
(0.00616) 		0.0362
(1.00) 		0.0557
(1.00) 		0.0437
(1.00) 		0.0449
(1.00) 		0.00507
(1.00) 		0.0685
(1.00) 		0.00059
(0.277) 		0.313
(1.00) 		0.00535
(1.00)
amp 12q23 1 26 (6%) 393 0.00016
(0.0787) 		0.00862
(1.00) 		0.0559
(1.00) 		0.112
(1.00) 		0.0503
(1.00) 		0.302
(1.00) 		0.0864
(1.00) 		0.37
(1.00) 		0.228
(1.00) 		0.271
(1.00)
amp 13q12 11 21 (5%) 398 0.00012
(0.0599) 		0.0555
(1.00) 		0.0437
(1.00) 		0.0342
(1.00) 		0.0337
(1.00) 		0.0915
(1.00) 		0.458
(1.00) 		0.0455
(1.00) 		0.0133
(1.00) 		0.00063
(0.295)
amp 14q21 1 21 (5%) 398 1e-05
(0.00616) 		0.00997
(1.00) 		0.167
(1.00) 		0.177
(1.00) 		0.081
(1.00) 		0.283
(1.00) 		0.856
(1.00) 		0.182
(1.00) 		0.232
(1.00) 		0.441
(1.00)
amp 17q23 2 18 (4%) 401 5e-05
(0.0256) 		0.578
(1.00) 		1
(1.00) 		0.325
(1.00) 		0.304
(1.00) 		0.174
(1.00) 		0.282
(1.00) 		0.0332
(1.00) 		0.331
(1.00) 		0.283
(1.00)
amp 18q21 31 10 (2%) 409 0.00021
(0.102) 		0.568
(1.00) 		0.847
(1.00) 		0.452
(1.00) 		0.105
(1.00) 		0.443
(1.00) 		0.859
(1.00) 		0.479
(1.00) 		0.478
(1.00) 		0.17
(1.00)
amp 19q13 43 14 (3%) 405 1e-05
(0.00616) 		0.101
(1.00) 		0.454
(1.00) 		0.387
(1.00) 		0.0303
(1.00) 		0.17
(1.00) 		0.201
(1.00) 		0.00468
(1.00) 		0.194
(1.00) 		0.00186
(0.822)
amp xp22 2 20 (5%) 399 1e-05
(0.00616) 		0.296
(1.00) 		0.096
(1.00) 		0.207
(1.00) 		0.359
(1.00) 		0.14
(1.00) 		0.0204
(1.00) 		0.0263
(1.00)
amp xp22 11 17 (4%) 402 3e-05
(0.0157) 		0.872
(1.00) 		0.118
(1.00) 		0.4
(1.00) 		0.502
(1.00) 		0.174
(1.00) 		0.0118
(1.00) 		0.13
(1.00)
amp xp22 11 17 (4%) 402 1e-05
(0.00616) 		0.933
(1.00) 		0.0943
(1.00) 		0.189
(1.00) 		0.0751
(1.00) 		0.344
(1.00) 		0.218
(1.00) 		0.221
(1.00) 		0.139
(1.00) 		0.0856
(1.00)
amp xp21 1 17 (4%) 402 3e-05
(0.0157) 		0.233
(1.00) 		0.85
(1.00) 		0.734
(1.00) 		0.133
(1.00) 		0.813
(1.00) 		0.0798
(1.00) 		0.572
(1.00) 		0.00726
(1.00) 		0.0178
(1.00)
amp xq21 31 11 (3%) 408 4e-05
(0.0206) 		0.307
(1.00) 		0.848
(1.00) 		0.736
(1.00) 		0.0621
(1.00) 		0.302
(1.00) 		0.15
(1.00) 		0.134
(1.00) 		0.323
(1.00) 		0.118
(1.00)
del 1p22 1 48 (11%) 371 1e-05
(0.00616) 		0.0195
(1.00) 		0.227
(1.00) 		0.0933
(1.00) 		0.0249
(1.00) 		0.00781
(1.00) 		0.00324
(1.00) 		0.0107
(1.00) 		0.00251
(1.00) 		0.042
(1.00)
del 9p23 38 (9%) 381 1e-05
(0.00616) 		0.214
(1.00) 		0.00328
(1.00) 		0.0294
(1.00) 		0.00096
(0.442) 		0.0229
(1.00) 		0.0952
(1.00) 		0.532
(1.00) 		0.0175
(1.00) 		0.222
(1.00)
del 11p11 2 28 (7%) 391 0.00034
(0.162) 		0.339
(1.00) 		0.00295
(1.00) 		0.044
(1.00) 		0.038
(1.00) 		0.0117
(1.00) 		0.191
(1.00) 		0.566
(1.00) 		0.00802
(1.00) 		0.265
(1.00)
del 12q24 31 39 (9%) 380 0.00025
(0.121) 		0.0886
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.00923
(1.00) 		0.0774
(1.00) 		0.539
(1.00) 		0.173
(1.00) 		0.0643
(1.00) 		0.778
(1.00)
del 21q22 2 40 (10%) 379 0.018
(1.00) 		0.00883
(1.00) 		0.423
(1.00) 		0.767
(1.00) 		0.0023
(0.991) 		0.00018
(0.088) 		0.405
(1.00) 		0.232
(1.00) 		0.064
(1.00) 		0.804
(1.00)
amp 15q11 2 13 (3%) 406 0.121
(1.00) 		0.314
(1.00) 		0.784
(1.00) 		0.78
(1.00) 		0.482
(1.00) 		0.441
(1.00) 		0.765
(1.00) 		0.863
(1.00) 		0.53
(1.00) 		0.553
(1.00)
amp xq21 1 12 (3%) 407 0.0019
(0.836) 		0.361
(1.00) 		0.486
(1.00) 		0.642
(1.00) 		0.0938
(1.00) 		0.489
(1.00) 		0.0412
(1.00) 		0.58
(1.00) 		0.463
(1.00) 		0.0772
(1.00)
amp xq21 1 10 (2%) 409 0.00328
(1.00) 		0.00159
(0.709) 		0.451
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.237
(1.00) 		0.896
(1.00) 		0.625
(1.00) 		0.151
(1.00) 		0.363
(1.00)
amp xq25 10 (2%) 409 0.00168
(0.748) 		0.0364
(1.00) 		0.621
(1.00) 		0.492
(1.00) 		0.1
(1.00) 		0.172
(1.00) 		0.297
(1.00) 		0.0258
(1.00) 		0.0267
(1.00) 		0.119
(1.00)
amp xq25 13 (3%) 406 0.00124
(0.56) 		0.194
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.0564
(1.00) 		0.192
(1.00) 		0.472
(1.00) 		0.808
(1.00) 		0.776
(1.00) 		0.0719
(1.00)
amp xq27 1 14 (3%) 405 0.00296
(1.00) 		0.121
(1.00) 		0.417
(1.00) 		0.216
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.00395
(1.00) 		0.0771
(1.00) 		0.00077
(0.358) 		0.00324
(1.00)
del 2p22 1 34 (8%) 385 0.03
(1.00) 		0.0573
(1.00) 		0.0391
(1.00) 		0.0653
(1.00) 		0.0101
(1.00) 		0.00306
(1.00) 		0.0776
(1.00) 		0.229
(1.00) 		0.689
(1.00) 		0.0239
(1.00)
del 3q29 26 (6%) 393 0.724
(1.00) 		0.0377
(1.00) 		0.728
(1.00) 		0.138
(1.00) 		0.00739
(1.00) 		0.127
(1.00) 		0.705
(1.00) 		0.623
(1.00) 		0.842
(1.00) 		0.955
(1.00)
del 7q31 33 23 (5%) 396 0.0335
(1.00) 		0.0541
(1.00) 		0.0271
(1.00) 		0.0138
(1.00) 		0.00315
(1.00) 		0.0123
(1.00) 		0.135
(1.00) 		0.0759
(1.00) 		0.067
(1.00) 		0.0388
(1.00)
del 11q23 2 43 (10%) 376 0.0386
(1.00) 		0.0741
(1.00) 		0.167
(1.00) 		0.192
(1.00) 		0.91
(1.00) 		0.976
(1.00) 		0.12
(1.00) 		0.663
(1.00) 		0.662
(1.00) 		0.592
(1.00)
del 19q13 2 39 (9%) 380 0.00107
(0.49) 		0.159
(1.00) 		0.35
(1.00) 		0.361
(1.00) 		0.0613
(1.00) 		0.176
(1.00) 		0.0482
(1.00) 		0.00451
(1.00) 		0.0144
(1.00) 		0.067
(1.00)
'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S1.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 1(1Q21.3) MUTATED 7 23 1
AMP PEAK 1(1Q21.3) WILD-TYPE 228 93 67

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S2.  Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 2(3Q21.3) MUTATED 10 41 9
AMP PEAK 2(3Q21.3) WILD-TYPE 225 75 59

Figure S2.  Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.21

Table S3.  Gene #2: 'amp_3q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
AMP PEAK 2(3Q21.3) MUTATED 28 6 17
AMP PEAK 2(3Q21.3) WILD-TYPE 96 106 117

Figure S3.  Get High-res Image Gene #2: 'amp_3q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S4.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 3(3Q26.2) MUTATED 15 39 12
AMP PEAK 3(3Q26.2) WILD-TYPE 220 77 56

Figure S4.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S5.  Gene #4: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 4(4Q13.3) MUTATED 2 13 0
AMP PEAK 4(4Q13.3) WILD-TYPE 233 103 68

Figure S5.  Get High-res Image Gene #4: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S6.  Gene #5: 'amp_5q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 5(5Q33.3) MUTATED 2 21 0
AMP PEAK 5(5Q33.3) WILD-TYPE 233 95 68

Figure S6.  Get High-res Image Gene #5: 'amp_5q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S7.  Gene #6: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 6(7P14.3) MUTATED 14 53 19
AMP PEAK 6(7P14.3) WILD-TYPE 221 63 49

Figure S7.  Get High-res Image Gene #6: 'amp_7p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S8.  Gene #6: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 6(7P14.3) MUTATED 36 6 20
AMP PEAK 6(7P14.3) WILD-TYPE 60 100 109

Figure S8.  Get High-res Image Gene #6: 'amp_7p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S9.  Gene #6: 'amp_7p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
AMP PEAK 6(7P14.3) MUTATED 44 7 21
AMP PEAK 6(7P14.3) WILD-TYPE 80 105 113

Figure S9.  Get High-res Image Gene #6: 'amp_7p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S10.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 7(8P11.23) MUTATED 6 32 12
AMP PEAK 7(8P11.23) WILD-TYPE 229 84 56

Figure S10.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S11.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 7(8P11.23) MUTATED 20 3 9
AMP PEAK 7(8P11.23) WILD-TYPE 76 103 120

Figure S11.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S12.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
AMP PEAK 7(8P11.23) MUTATED 27 5 10
AMP PEAK 7(8P11.23) WILD-TYPE 97 107 124

Figure S12.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S13.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 8(8Q24.21) MUTATED 34 71 13
AMP PEAK 8(8Q24.21) WILD-TYPE 201 45 55

Figure S13.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.031

Table S14.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 8(8Q24.21) MUTATED 39 13 32
AMP PEAK 8(8Q24.21) WILD-TYPE 57 93 97

Figure S14.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S15.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
AMP PEAK 8(8Q24.21) MUTATED 53 13 35
AMP PEAK 8(8Q24.21) WILD-TYPE 71 99 99

Figure S15.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.06

Table S16.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
AMP PEAK 8(8Q24.21) MUTATED 47 11 43
AMP PEAK 8(8Q24.21) WILD-TYPE 91 86 92

Figure S16.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S17.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
AMP PEAK 8(8Q24.21) MUTATED 9 9 52 22 24
AMP PEAK 8(8Q24.21) WILD-TYPE 79 31 71 51 67

Figure S17.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S18.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
AMP PEAK 8(8Q24.21) MUTATED 23 13 80
AMP PEAK 8(8Q24.21) WILD-TYPE 126 57 116

Figure S18.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S19.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
AMP PEAK 8(8Q24.21) MUTATED 62 33 21
AMP PEAK 8(8Q24.21) WILD-TYPE 84 85 130

Figure S19.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9q34.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S20.  Gene #9: 'amp_9q34.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 9(9Q34.11) MUTATED 7 39 1
AMP PEAK 9(9Q34.11) WILD-TYPE 228 77 67

Figure S20.  Get High-res Image Gene #9: 'amp_9q34.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S21.  Gene #10: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 10(11Q13.2) MUTATED 3 30 2
AMP PEAK 10(11Q13.2) WILD-TYPE 232 86 66

Figure S21.  Get High-res Image Gene #10: 'amp_11q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.083

Table S22.  Gene #10: 'amp_11q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
AMP PEAK 10(11Q13.2) MUTATED 17 1 7
AMP PEAK 10(11Q13.2) WILD-TYPE 107 111 127

Figure S22.  Get High-res Image Gene #10: 'amp_11q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q23.1' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.079

Table S23.  Gene #11: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 11(12Q23.1) MUTATED 8 17 1
AMP PEAK 11(12Q23.1) WILD-TYPE 227 99 67

Figure S23.  Get High-res Image Gene #11: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.11' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.06

Table S24.  Gene #12: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 12(13Q12.11) MUTATED 5 15 1
AMP PEAK 12(13Q12.11) WILD-TYPE 230 101 67

Figure S24.  Get High-res Image Gene #12: 'amp_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S25.  Gene #13: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 13(14Q21.1) MUTATED 1 16 4
AMP PEAK 13(14Q21.1) WILD-TYPE 234 100 64

Figure S25.  Get High-res Image Gene #13: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.14

Table S26.  Gene #15: 'amp_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
AMP PEAK 15(16Q11.2) MUTATED 3 0 20
AMP PEAK 15(16Q11.2) WILD-TYPE 146 70 176

Figure S26.  Get High-res Image Gene #15: 'amp_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S27.  Gene #15: 'amp_16q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
AMP PEAK 15(16Q11.2) MUTATED 12 11 0
AMP PEAK 15(16Q11.2) WILD-TYPE 134 107 151

Figure S27.  Get High-res Image Gene #15: 'amp_16q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S28.  Gene #16: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 16(17Q23.2) MUTATED 4 14 0
AMP PEAK 16(17Q23.2) WILD-TYPE 231 102 68

Figure S28.  Get High-res Image Gene #16: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q21.31' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.1

Table S29.  Gene #17: 'amp_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 17(18Q21.31) MUTATED 1 9 0
AMP PEAK 17(18Q21.31) WILD-TYPE 234 107 68

Figure S29.  Get High-res Image Gene #17: 'amp_18q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S30.  Gene #18: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 18(19Q13.43) MUTATED 0 14 0
AMP PEAK 18(19Q13.43) WILD-TYPE 235 102 68

Figure S30.  Get High-res Image Gene #18: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S31.  Gene #19: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 19(20Q13.2) MUTATED 4 27 3
AMP PEAK 19(20Q13.2) WILD-TYPE 231 89 65

Figure S31.  Get High-res Image Gene #19: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.19

Table S32.  Gene #19: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 19(20Q13.2) MUTATED 14 1 6
AMP PEAK 19(20Q13.2) WILD-TYPE 82 105 123

Figure S32.  Get High-res Image Gene #19: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.079

Table S33.  Gene #19: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 37 125 61 97
AMP PEAK 19(20Q13.2) MUTATED 2 6 20 1 5
AMP PEAK 19(20Q13.2) WILD-TYPE 93 31 105 60 92

Figure S33.  Get High-res Image Gene #19: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S34.  Gene #20: 'amp_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 20(XP22.2) MUTATED 3 17 0
AMP PEAK 20(XP22.2) WILD-TYPE 232 99 68

Figure S34.  Get High-res Image Gene #20: 'amp_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.11' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S35.  Gene #21: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 21(XP22.11) MUTATED 3 14 0
AMP PEAK 21(XP22.11) WILD-TYPE 232 102 68

Figure S35.  Get High-res Image Gene #21: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S36.  Gene #22: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 22(XP22.11) MUTATED 3 14 0
AMP PEAK 22(XP22.11) WILD-TYPE 232 102 68

Figure S36.  Get High-res Image Gene #22: 'amp_xp22.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S37.  Gene #23: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 23(XP21.1) MUTATED 3 14 0
AMP PEAK 23(XP21.1) WILD-TYPE 232 102 68

Figure S37.  Get High-res Image Gene #23: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.31' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S38.  Gene #26: 'amp_xq21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
AMP PEAK 26(XQ21.31) MUTATED 1 10 0
AMP PEAK 26(XQ21.31) WILD-TYPE 234 106 68

Figure S38.  Get High-res Image Gene #26: 'amp_xq21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S39.  Gene #30: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 1(1P31.3) MUTATED 16 29 3
DEL PEAK 1(1P31.3) WILD-TYPE 219 87 65

Figure S39.  Get High-res Image Gene #30: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S40.  Gene #30: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 1(1P31.3) MUTATED 10 2 26
DEL PEAK 1(1P31.3) WILD-TYPE 86 104 103

Figure S40.  Get High-res Image Gene #30: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p31.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S41.  Gene #30: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 1(1P31.3) MUTATED 12 3 27
DEL PEAK 1(1P31.3) WILD-TYPE 112 109 107

Figure S41.  Get High-res Image Gene #30: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S42.  Gene #30: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 1(1P31.3) MUTATED 11 2 29
DEL PEAK 1(1P31.3) WILD-TYPE 127 95 106

Figure S42.  Get High-res Image Gene #30: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S43.  Gene #31: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 2(1P22.1) MUTATED 9 32 7
DEL PEAK 2(1P22.1) WILD-TYPE 226 84 61

Figure S43.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S44.  Gene #32: 'del_1q42.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 3(1Q42.2) MUTATED 8 18 13
DEL PEAK 3(1Q42.2) WILD-TYPE 227 98 55

Figure S44.  Get High-res Image Gene #32: 'del_1q42.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.2' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #32: 'del_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 3(1Q42.2) MUTATED 17 3 6
DEL PEAK 3(1Q42.2) WILD-TYPE 79 103 123

Figure S45.  Get High-res Image Gene #32: 'del_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S46.  Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 5(2Q22.1) MUTATED 8 39 25
DEL PEAK 5(2Q22.1) WILD-TYPE 227 77 43

Figure S46.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S47.  Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 5(2Q22.1) MUTATED 33 2 14
DEL PEAK 5(2Q22.1) WILD-TYPE 63 104 115

Figure S47.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S48.  Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 5(2Q22.1) MUTATED 38 6 15
DEL PEAK 5(2Q22.1) WILD-TYPE 86 106 119

Figure S48.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S49.  Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 5(2Q22.1) MUTATED 37 4 18
DEL PEAK 5(2Q22.1) WILD-TYPE 101 93 117

Figure S49.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S50.  Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 37 125 61 97
DEL PEAK 5(2Q22.1) MUTATED 14 5 35 1 17
DEL PEAK 5(2Q22.1) WILD-TYPE 81 32 90 60 80

Figure S50.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S51.  Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 6(2Q22.3) MUTATED 6 37 23
DEL PEAK 6(2Q22.3) WILD-TYPE 229 79 45

Figure S51.  Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S52.  Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 6(2Q22.3) MUTATED 29 2 14
DEL PEAK 6(2Q22.3) WILD-TYPE 67 104 115

Figure S52.  Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S53.  Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 6(2Q22.3) MUTATED 34 5 15
DEL PEAK 6(2Q22.3) WILD-TYPE 90 107 119

Figure S53.  Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S54.  Gene #35: 'del_2q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 6(2Q22.3) MUTATED 33 3 18
DEL PEAK 6(2Q22.3) WILD-TYPE 105 94 117

Figure S54.  Get High-res Image Gene #35: 'del_2q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S55.  Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 7(3P13) MUTATED 4 11 39
DEL PEAK 7(3P13) WILD-TYPE 92 95 90

Figure S55.  Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S56.  Gene #36: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 7(3P13) MUTATED 7 11 42
DEL PEAK 7(3P13) WILD-TYPE 117 101 92

Figure S56.  Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S57.  Gene #36: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 7(3P13) MUTATED 6 13 41
DEL PEAK 7(3P13) WILD-TYPE 132 84 94

Figure S57.  Get High-res Image Gene #36: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q28.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S58.  Gene #38: 'del_4q28.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 9(4Q28.1) MUTATED 6 19 9
DEL PEAK 9(4Q28.1) WILD-TYPE 229 97 59

Figure S58.  Get High-res Image Gene #38: 'del_4q28.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q28.1' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.14

Table S59.  Gene #38: 'del_4q28.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 9(4Q28.1) MUTATED 15 1 10
DEL PEAK 9(4Q28.1) WILD-TYPE 81 105 119

Figure S59.  Get High-res Image Gene #38: 'del_4q28.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S60.  Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 10(5Q11.2) MUTATED 15 48 11
DEL PEAK 10(5Q11.2) WILD-TYPE 220 68 57

Figure S60.  Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S61.  Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 10(5Q11.2) MUTATED 25 3 24
DEL PEAK 10(5Q11.2) WILD-TYPE 71 103 105

Figure S61.  Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.06

Table S62.  Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 10(5Q11.2) MUTATED 19 4 50
DEL PEAK 10(5Q11.2) WILD-TYPE 130 66 146

Figure S62.  Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.069

Table S63.  Gene #39: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
DEL PEAK 10(5Q11.2) MUTATED 38 23 12
DEL PEAK 10(5Q11.2) WILD-TYPE 108 95 139

Figure S63.  Get High-res Image Gene #39: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S64.  Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 11(5Q13.2) MUTATED 14 52 10
DEL PEAK 11(5Q13.2) WILD-TYPE 221 64 58

Figure S64.  Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S65.  Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 11(5Q13.2) MUTATED 25 4 20
DEL PEAK 11(5Q13.2) WILD-TYPE 71 102 109

Figure S65.  Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.24

Table S66.  Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 11(5Q13.2) MUTATED 26 3 46
DEL PEAK 11(5Q13.2) WILD-TYPE 123 67 150

Figure S66.  Get High-res Image Gene #40: 'del_5q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S67.  Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 12(5Q21.1) MUTATED 5 48 29
DEL PEAK 12(5Q21.1) WILD-TYPE 230 68 39

Figure S67.  Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S68.  Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 12(5Q21.1) MUTATED 38 6 13
DEL PEAK 12(5Q21.1) WILD-TYPE 58 100 116

Figure S68.  Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S69.  Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 12(5Q21.1) MUTATED 47 8 15
DEL PEAK 12(5Q21.1) WILD-TYPE 77 104 119

Figure S69.  Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S70.  Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 12(5Q21.1) MUTATED 44 7 19
DEL PEAK 12(5Q21.1) WILD-TYPE 94 90 116

Figure S70.  Get High-res Image Gene #41: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S71.  Gene #42: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 13(6Q14.3) MUTATED 31 72 45
DEL PEAK 13(6Q14.3) WILD-TYPE 204 44 23

Figure S71.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S72.  Gene #42: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 13(6Q14.3) MUTATED 68 8 29
DEL PEAK 13(6Q14.3) WILD-TYPE 28 98 100

Figure S72.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S73.  Gene #42: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 13(6Q14.3) MUTATED 70 18 36
DEL PEAK 13(6Q14.3) WILD-TYPE 54 94 98

Figure S73.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S74.  Gene #42: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 13(6Q14.3) MUTATED 76 11 37
DEL PEAK 13(6Q14.3) WILD-TYPE 62 86 98

Figure S74.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S75.  Gene #44: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 15(8P21.3) MUTATED 129 88 25
DEL PEAK 15(8P21.3) WILD-TYPE 106 28 43

Figure S75.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S76.  Gene #44: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 15(8P21.3) MUTATED 53 35 95
DEL PEAK 15(8P21.3) WILD-TYPE 43 71 34

Figure S76.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S77.  Gene #44: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 15(8P21.3) MUTATED 67 41 101
DEL PEAK 15(8P21.3) WILD-TYPE 57 71 33

Figure S77.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S78.  Gene #44: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 15(8P21.3) MUTATED 69 42 98
DEL PEAK 15(8P21.3) WILD-TYPE 69 55 37

Figure S78.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S79.  Gene #44: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
DEL PEAK 15(8P21.3) MUTATED 35 11 81 57 56
DEL PEAK 15(8P21.3) WILD-TYPE 53 29 42 16 35

Figure S79.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S80.  Gene #44: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 15(8P21.3) MUTATED 71 32 137
DEL PEAK 15(8P21.3) WILD-TYPE 78 38 59

Figure S80.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S81.  Gene #44: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
DEL PEAK 15(8P21.3) MUTATED 99 75 66
DEL PEAK 15(8P21.3) WILD-TYPE 47 43 85

Figure S81.  Get High-res Image Gene #44: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S82.  Gene #45: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 16(8P11.21) MUTATED 86 48 2
DEL PEAK 16(8P11.21) WILD-TYPE 149 68 66

Figure S82.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S83.  Gene #45: 'del_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 16(8P11.21) MUTATED 29 12 64
DEL PEAK 16(8P11.21) WILD-TYPE 67 94 65

Figure S83.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S84.  Gene #45: 'del_8p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 16(8P11.21) MUTATED 39 18 62
DEL PEAK 16(8P11.21) WILD-TYPE 85 94 72

Figure S84.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S85.  Gene #45: 'del_8p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 16(8P11.21) MUTATED 35 21 63
DEL PEAK 16(8P11.21) WILD-TYPE 103 76 72

Figure S85.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S86.  Gene #45: 'del_8p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
DEL PEAK 16(8P11.21) MUTATED 16 6 46 32 35
DEL PEAK 16(8P11.21) WILD-TYPE 72 34 77 41 56

Figure S86.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S87.  Gene #45: 'del_8p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 16(8P11.21) MUTATED 30 18 87
DEL PEAK 16(8P11.21) WILD-TYPE 119 52 109

Figure S87.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.18

Table S88.  Gene #45: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 37 125 61 97
DEL PEAK 16(8P11.21) MUTATED 16 9 55 22 33
DEL PEAK 16(8P11.21) WILD-TYPE 79 28 70 39 64

Figure S88.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S89.  Gene #46: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 17(9P23) MUTATED 12 25 1
DEL PEAK 17(9P23) WILD-TYPE 223 91 67

Figure S89.  Get High-res Image Gene #46: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S90.  Gene #47: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 18(10Q23.31) MUTATED 59 57 10
DEL PEAK 18(10Q23.31) WILD-TYPE 176 59 58

Figure S90.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S91.  Gene #47: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 18(10Q23.31) MUTATED 23 12 66
DEL PEAK 18(10Q23.31) WILD-TYPE 73 94 63

Figure S91.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S92.  Gene #47: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 18(10Q23.31) MUTATED 22 15 79
DEL PEAK 18(10Q23.31) WILD-TYPE 102 97 55

Figure S92.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S93.  Gene #47: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 18(10Q23.31) MUTATED 21 22 73
DEL PEAK 18(10Q23.31) WILD-TYPE 117 75 62

Figure S93.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S94.  Gene #47: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
DEL PEAK 18(10Q23.31) MUTATED 19 1 41 31 32
DEL PEAK 18(10Q23.31) WILD-TYPE 69 39 82 42 59

Figure S94.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S95.  Gene #47: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 18(10Q23.31) MUTATED 40 6 78
DEL PEAK 18(10Q23.31) WILD-TYPE 109 64 118

Figure S95.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.16

Table S96.  Gene #47: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 37 125 61 97
DEL PEAK 18(10Q23.31) MUTATED 18 4 43 27 32
DEL PEAK 18(10Q23.31) WILD-TYPE 77 33 82 34 65

Figure S96.  Get High-res Image Gene #47: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.16

Table S97.  Gene #48: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 19(11P11.2) MUTATED 7 17 4
DEL PEAK 19(11P11.2) WILD-TYPE 228 99 64

Figure S97.  Get High-res Image Gene #48: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S98.  Gene #50: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 21(12P13.1) MUTATED 43 50 7
DEL PEAK 21(12P13.1) WILD-TYPE 192 66 61

Figure S98.  Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.055

Table S99.  Gene #50: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 21(12P13.1) MUTATED 27 9 37
DEL PEAK 21(12P13.1) WILD-TYPE 69 97 92

Figure S99.  Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.06

Table S100.  Gene #50: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
DEL PEAK 21(12P13.1) MUTATED 10 3 38 25 21
DEL PEAK 21(12P13.1) WILD-TYPE 78 37 85 48 70

Figure S100.  Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S101.  Gene #50: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 21(12P13.1) MUTATED 30 4 63
DEL PEAK 21(12P13.1) WILD-TYPE 119 66 133

Figure S101.  Get High-res Image Gene #50: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.31' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S102.  Gene #51: 'del_12q24.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 22(12Q24.31) MUTATED 13 22 4
DEL PEAK 22(12Q24.31) WILD-TYPE 222 94 64

Figure S102.  Get High-res Image Gene #51: 'del_12q24.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S103.  Gene #52: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 23(13Q14.13) MUTATED 65 77 38
DEL PEAK 23(13Q14.13) WILD-TYPE 170 39 30

Figure S103.  Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S104.  Gene #52: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 23(13Q14.13) MUTATED 54 22 63
DEL PEAK 23(13Q14.13) WILD-TYPE 42 84 66

Figure S104.  Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.13' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S105.  Gene #52: 'del_13q14.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 23(13Q14.13) MUTATED 55 29 71
DEL PEAK 23(13Q14.13) WILD-TYPE 69 83 63

Figure S105.  Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.1

Table S106.  Gene #52: 'del_13q14.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 23(13Q14.13) MUTATED 63 24 68
DEL PEAK 23(13Q14.13) WILD-TYPE 75 73 67

Figure S106.  Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.13' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.16

Table S107.  Gene #52: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
DEL PEAK 23(13Q14.13) MUTATED 22 13 65 33 46
DEL PEAK 23(13Q14.13) WILD-TYPE 66 27 58 40 45

Figure S107.  Get High-res Image Gene #52: 'del_13q14.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S108.  Gene #53: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 24(13Q22.1) MUTATED 45 72 22
DEL PEAK 24(13Q22.1) WILD-TYPE 190 44 46

Figure S108.  Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S109.  Gene #53: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 24(13Q22.1) MUTATED 40 17 50
DEL PEAK 24(13Q22.1) WILD-TYPE 56 89 79

Figure S109.  Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.15

Table S110.  Gene #53: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 24(13Q22.1) MUTATED 44 21 56
DEL PEAK 24(13Q22.1) WILD-TYPE 80 91 78

Figure S110.  Get High-res Image Gene #53: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S111.  Gene #54: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 25(15Q21.3) MUTATED 12 32 4
DEL PEAK 25(15Q21.3) WILD-TYPE 223 84 64

Figure S111.  Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.031

Table S112.  Gene #54: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 25(15Q21.3) MUTATED 14 2 23
DEL PEAK 25(15Q21.3) WILD-TYPE 82 104 106

Figure S112.  Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q21.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.031

Table S113.  Gene #54: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 25(15Q21.3) MUTATED 16 2 24
DEL PEAK 25(15Q21.3) WILD-TYPE 108 110 110

Figure S113.  Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.05

Table S114.  Gene #54: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 25(15Q21.3) MUTATED 6 5 35
DEL PEAK 25(15Q21.3) WILD-TYPE 143 65 161

Figure S114.  Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S115.  Gene #54: 'del_15q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
DEL PEAK 25(15Q21.3) MUTATED 26 17 3
DEL PEAK 25(15Q21.3) WILD-TYPE 120 101 148

Figure S115.  Get High-res Image Gene #54: 'del_15q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S116.  Gene #55: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 26(16Q22.3) MUTATED 70 77 11
DEL PEAK 26(16Q22.3) WILD-TYPE 165 39 57

Figure S116.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S117.  Gene #55: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 26(16Q22.3) MUTATED 38 17 64
DEL PEAK 26(16Q22.3) WILD-TYPE 58 89 65

Figure S117.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S118.  Gene #55: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 26(16Q22.3) MUTATED 43 26 72
DEL PEAK 26(16Q22.3) WILD-TYPE 81 86 62

Figure S118.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S119.  Gene #55: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 26(16Q22.3) MUTATED 42 24 75
DEL PEAK 26(16Q22.3) WILD-TYPE 96 73 60

Figure S119.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S120.  Gene #55: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 88 40 123 73 91
DEL PEAK 26(16Q22.3) MUTATED 25 6 65 25 35
DEL PEAK 26(16Q22.3) WILD-TYPE 63 34 58 48 56

Figure S120.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S121.  Gene #55: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 26(16Q22.3) MUTATED 49 11 96
DEL PEAK 26(16Q22.3) WILD-TYPE 100 59 100

Figure S121.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.06

Table S122.  Gene #55: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
DEL PEAK 26(16Q22.3) MUTATED 73 44 39
DEL PEAK 26(16Q22.3) WILD-TYPE 73 74 112

Figure S122.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.15

Table S123.  Gene #55: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 37 125 61 97
DEL PEAK 26(16Q22.3) MUTATED 33 6 65 17 35
DEL PEAK 26(16Q22.3) WILD-TYPE 62 31 60 44 62

Figure S123.  Get High-res Image Gene #55: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S124.  Gene #56: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 27(16Q24.1) MUTATED 83 83 8
DEL PEAK 27(16Q24.1) WILD-TYPE 152 33 60

Figure S124.  Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S125.  Gene #56: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 27(16Q24.1) MUTATED 39 20 74
DEL PEAK 27(16Q24.1) WILD-TYPE 57 86 55

Figure S125.  Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S126.  Gene #56: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 27(16Q24.1) MUTATED 48 29 78
DEL PEAK 27(16Q24.1) WILD-TYPE 76 83 56

Figure S126.  Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S127.  Gene #56: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 27(16Q24.1) MUTATED 44 34 77
DEL PEAK 27(16Q24.1) WILD-TYPE 94 63 58

Figure S127.  Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S128.  Gene #56: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 27(16Q24.1) MUTATED 54 14 103
DEL PEAK 27(16Q24.1) WILD-TYPE 95 56 93

Figure S128.  Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.15

Table S129.  Gene #56: 'del_16q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 118 151
DEL PEAK 27(16Q24.1) MUTATED 76 51 44
DEL PEAK 27(16Q24.1) WILD-TYPE 70 67 107

Figure S129.  Get High-res Image Gene #56: 'del_16q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S130.  Gene #57: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 28(17P13.1) MUTATED 58 68 5
DEL PEAK 28(17P13.1) WILD-TYPE 177 48 63

Figure S130.  Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S131.  Gene #57: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 28(17P13.1) MUTATED 17 15 58
DEL PEAK 28(17P13.1) WILD-TYPE 79 91 71

Figure S131.  Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S132.  Gene #57: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 28(17P13.1) MUTATED 22 19 71
DEL PEAK 28(17P13.1) WILD-TYPE 102 93 63

Figure S132.  Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S133.  Gene #57: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 28(17P13.1) MUTATED 17 21 74
DEL PEAK 28(17P13.1) WILD-TYPE 121 76 61

Figure S133.  Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S134.  Gene #57: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 28(17P13.1) MUTATED 39 10 80
DEL PEAK 28(17P13.1) WILD-TYPE 110 60 116

Figure S134.  Get High-res Image Gene #57: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S135.  Gene #58: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 29(17Q21.31) MUTATED 45 37 3
DEL PEAK 29(17Q21.31) WILD-TYPE 190 79 65

Figure S135.  Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S136.  Gene #58: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 29(17Q21.31) MUTATED 5 14 46
DEL PEAK 29(17Q21.31) WILD-TYPE 91 92 83

Figure S136.  Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S137.  Gene #58: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 29(17Q21.31) MUTATED 9 14 53
DEL PEAK 29(17Q21.31) WILD-TYPE 115 98 81

Figure S137.  Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S138.  Gene #58: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 29(17Q21.31) MUTATED 10 18 48
DEL PEAK 29(17Q21.31) WILD-TYPE 128 79 87

Figure S138.  Get High-res Image Gene #58: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S139.  Gene #59: 'del_18q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 30(18Q22.1) MUTATED 41 65 9
DEL PEAK 30(18Q22.1) WILD-TYPE 194 51 59

Figure S139.  Get High-res Image Gene #59: 'del_18q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.074

Table S140.  Gene #59: 'del_18q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 70 196
DEL PEAK 30(18Q22.1) MUTATED 26 15 73
DEL PEAK 30(18Q22.1) WILD-TYPE 123 55 123

Figure S140.  Get High-res Image Gene #59: 'del_18q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.088

Table S141.  Gene #61: 'del_21q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 32(21Q22.2) MUTATED 3 10 23
DEL PEAK 32(21Q22.2) WILD-TYPE 135 87 112

Figure S141.  Get High-res Image Gene #61: 'del_21q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S142.  Gene #62: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 116 68
DEL PEAK 33(21Q22.3) MUTATED 75 42 2
DEL PEAK 33(21Q22.3) WILD-TYPE 160 74 66

Figure S142.  Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S143.  Gene #62: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 33(21Q22.3) MUTATED 7 14 78
DEL PEAK 33(21Q22.3) WILD-TYPE 89 92 51

Figure S143.  Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S144.  Gene #62: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 112 134
DEL PEAK 33(21Q22.3) MUTATED 6 20 84
DEL PEAK 33(21Q22.3) WILD-TYPE 118 92 50

Figure S144.  Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0062

Table S145.  Gene #62: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 97 135
DEL PEAK 33(21Q22.3) MUTATED 6 27 77
DEL PEAK 33(21Q22.3) WILD-TYPE 132 70 58

Figure S145.  Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.13

Table S146.  Gene #62: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 37 125 61 97
DEL PEAK 33(21Q22.3) MUTATED 19 4 41 29 24
DEL PEAK 33(21Q22.3) WILD-TYPE 76 33 84 32 73

Figure S146.  Get High-res Image Gene #62: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 419

  • Number of significantly focal cnvs = 62

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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