Correlation between copy number variation genes (focal events) and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1J9659H
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/C1J9659H
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 8 molecular subtypes across 370 patients, 121 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p22.3 cnv correlated to 'CN_CNMF'.

  • amp_1q22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_1q42.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_2q33.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • amp_3q26.31 cnv correlated to 'CN_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF'.

  • amp_5q35.3 cnv correlated to 'CN_CNMF'.

  • amp_6p25.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_6q12 cnv correlated to 'CN_CNMF'.

  • amp_6q12 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_8q13.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q32.3 cnv correlated to 'CN_CNMF'.

  • amp_13q33.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF'.

  • amp_19p13.12 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_19q12 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_19q13.11 cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_xq28 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • del_1p36.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_4p16.3 cnv correlated to 'CN_CNMF'.

  • del_4q21.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q22.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q35.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF'.

  • del_8p12 cnv correlated to 'CN_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_9q31.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q26.13 cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q14.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_11q24.2 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12p12.1 cnv correlated to 'CN_CNMF'.

  • del_12q24.33 cnv correlated to 'CN_CNMF'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q23.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q32.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q26.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p13.1 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p11.2 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q21.2 cnv correlated to 'METHLYATION_CNMF'.

  • del_19p13.3 cnv correlated to 'CN_CNMF'.

  • del_xq26.2 cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 62 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 121 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
del 1p36 11 142 (38%) 228 2e-05
(0.0089) 		1e-05
(0.00496) 		1e-05
(0.00496) 		2e-05
(0.0089) 		0.00166
(0.586) 		5e-05
(0.021) 		0.00017
(0.0694) 		0.00035
(0.135)
del 16q23 1 162 (44%) 208 1e-05
(0.00496) 		3e-05
(0.0129) 		1e-05
(0.00496) 		1e-05
(0.00496) 		0.706
(1.00) 		1e-05
(0.00496) 		3e-05
(0.0129) 		4e-05
(0.017)
amp 19p13 12 69 (19%) 301 0.0816
(1.00) 		2e-05
(0.0089) 		1e-05
(0.00496) 		0.00018
(0.0733) 		0.00012
(0.0494) 		0.00219
(0.747) 		0.0006
(0.226) 		0.00142
(0.514)
del 4q35 1 172 (46%) 198 1e-05
(0.00496) 		4e-05
(0.017) 		0.0006
(0.226) 		0.00034
(0.133) 		0.155
(1.00) 		0.00614
(1.00) 		0.00022
(0.0882) 		0.00488
(1.00)
amp 1q22 283 (76%) 87 1e-05
(0.00496) 		1e-05
(0.00496) 		1e-05
(0.00496) 		0.0001
(0.0413) 		0.828
(1.00) 		0.0123
(1.00) 		0.208
(1.00) 		0.303
(1.00)
amp 1q42 3 270 (73%) 100 1e-05
(0.00496) 		1e-05
(0.00496) 		1e-05
(0.00496) 		5e-05
(0.021) 		0.492
(1.00) 		0.0382
(1.00) 		0.392
(1.00) 		0.559
(1.00)
amp 19q12 78 (21%) 292 0.0555
(1.00) 		0.00033
(0.129) 		2e-05
(0.0089) 		0.00021
(0.0848) 		0.00121
(0.443) 		0.0112
(1.00) 		0.00032
(0.125) 		0.00214
(0.732)
amp 20q13 33 128 (35%) 242 1e-05
(0.00496) 		0.00351
(1.00) 		2e-05
(0.0089) 		1e-05
(0.00496) 		0.191
(1.00) 		0.0618
(1.00) 		2e-05
(0.0089) 		0.124
(1.00)
del 4q21 3 171 (46%) 199 1e-05
(0.00496) 		0.00487
(1.00) 		9e-05
(0.0373) 		0.00144
(0.52) 		0.187
(1.00) 		0.00175
(0.612) 		4e-05
(0.017) 		0.00041
(0.157)
del 4q22 3 172 (46%) 198 1e-05
(0.00496) 		0.00509
(1.00) 		0.00021
(0.0848) 		0.00126
(0.459) 		0.21
(1.00) 		0.00132
(0.479) 		0.00012
(0.0494) 		0.00056
(0.212)
del 17p11 2 195 (53%) 175 1e-05
(0.00496) 		0.0371
(1.00) 		0.0345
(1.00) 		0.162
(1.00) 		0.00012
(0.0494) 		0.00038
(0.146) 		0.278
(1.00) 		0.00024
(0.0955)
amp 8q13 3 207 (56%) 163 1e-05
(0.00496) 		0.612
(1.00) 		1e-05
(0.00496) 		0.00864
(1.00) 		0.0978
(1.00) 		0.00251
(0.838) 		0.0388
(1.00) 		2e-05
(0.0089)
amp 8q24 21 231 (62%) 139 1e-05
(0.00496) 		0.122
(1.00) 		1e-05
(0.00496) 		0.004
(1.00) 		0.0149
(1.00) 		0.00715
(1.00) 		0.081
(1.00) 		3e-05
(0.0129)
amp 19q13 11 91 (25%) 279 0.032
(1.00) 		0.0515
(1.00) 		0.00203
(0.698) 		0.00034
(0.133) 		0.0076
(1.00) 		0.00188
(0.65) 		2e-05
(0.0089) 		0.00046
(0.175)
amp 20q13 13 124 (34%) 246 1e-05
(0.00496) 		0.059
(1.00) 		0.00147
(0.529) 		2e-05
(0.0089) 		0.109
(1.00) 		0.0114
(1.00) 		1e-05
(0.00496) 		0.0605
(1.00)
del 3p13 73 (20%) 297 0.00556
(1.00) 		0.0494
(1.00) 		1e-05
(0.00496) 		1e-05
(0.00496) 		0.00163
(0.579) 		0.0337
(1.00) 		0.00038
(0.146) 		0.00204
(0.7)
del 10q23 31 97 (26%) 273 0.0317
(1.00) 		0.0325
(1.00) 		1e-05
(0.00496) 		0.0472
(1.00) 		0.0305
(1.00) 		2e-05
(0.0089) 		0.0494
(1.00) 		1e-05
(0.00496)
del 10q26 13 105 (28%) 265 0.00818
(1.00) 		0.28
(1.00) 		2e-05
(0.0089) 		0.0139
(1.00) 		0.136
(1.00) 		1e-05
(0.00496) 		0.205
(1.00) 		1e-05
(0.00496)
del 13q14 2 179 (48%) 191 1e-05
(0.00496) 		0.0811
(1.00) 		0.00191
(0.659) 		6e-05
(0.025) 		0.00229
(0.774) 		0.00073
(0.274) 		0.101
(1.00) 		6e-05
(0.025)
del 14q23 3 131 (35%) 239 1e-05
(0.00496) 		0.135
(1.00) 		0.00018
(0.0733) 		3e-05
(0.0129) 		0.872
(1.00) 		0.0979
(1.00) 		0.00658
(1.00) 		0.0598
(1.00)
del 14q32 33 132 (36%) 238 1e-05
(0.00496) 		0.0473
(1.00) 		0.00021
(0.0848) 		1e-05
(0.00496) 		0.758
(1.00) 		0.242
(1.00) 		0.0144
(1.00) 		0.0308
(1.00)
del 17p13 1 226 (61%) 144 1e-05
(0.00496) 		0.0095
(1.00) 		0.00117
(0.429) 		0.193
(1.00) 		0.00164
(0.581) 		6e-05
(0.025) 		0.628
(1.00) 		1e-05
(0.00496)
amp 6p25 2 159 (43%) 211 1e-05
(0.00496) 		2e-05
(0.0089) 		0.00652
(1.00) 		0.00301
(0.996) 		0.668
(1.00) 		0.062
(1.00) 		0.21
(1.00) 		0.399
(1.00)
amp 6p21 1 158 (43%) 212 1e-05
(0.00496) 		2e-05
(0.0089) 		0.00082
(0.304) 		0.175
(1.00) 		0.117
(1.00) 		0.0634
(1.00) 		0.276
(1.00) 		0.505
(1.00)
amp 6q12 83 (22%) 287 1e-05
(0.00496) 		0.00158
(0.562) 		0.00025
(0.0992) 		0.00107
(0.395) 		0.878
(1.00) 		0.548
(1.00) 		0.00411
(1.00) 		0.073
(1.00)
amp 13q33 3 67 (18%) 303 1e-05
(0.00496) 		0.00037
(0.142) 		0.00233
(0.785) 		0.0387
(1.00) 		0.151
(1.00) 		0.18
(1.00) 		0.0737
(1.00) 		0.0495
(1.00)
amp xq28 85 (23%) 285 4e-05
(0.017) 		0.0751
(1.00) 		0.0128
(1.00) 		0.0752
(1.00) 		0.00945
(1.00) 		0.00492
(1.00) 		0.0464
(1.00) 		0.00036
(0.139)
del 1p36 31 162 (44%) 208 0.00155
(0.556) 		1e-05
(0.00496) 		1e-05
(0.00496) 		0.00078
(0.291) 		0.0536
(1.00) 		0.00122
(0.445) 		0.0125
(1.00) 		0.00992
(1.00)
del 9p21 3 150 (41%) 220 4e-05
(0.017) 		0.00185
(0.644) 		0.00248
(0.831) 		0.00025
(0.0992) 		0.265
(1.00) 		0.00178
(0.621) 		0.0194
(1.00) 		0.00804
(1.00)
del 9q31 3 119 (32%) 251 0.0022
(0.748) 		0.00663
(1.00) 		0.00378
(1.00) 		0.00023
(0.0918) 		0.16
(1.00) 		0.00647
(1.00) 		0.0645
(1.00) 		0.00028
(0.111)
amp 1p22 3 89 (24%) 281 1e-05
(0.00496) 		0.0102
(1.00) 		0.00541
(1.00) 		0.00989
(1.00) 		0.523
(1.00) 		0.945
(1.00) 		0.00812
(1.00) 		0.15
(1.00)
amp 2q33 1 64 (17%) 306 0.00319
(1.00) 		0.257
(1.00) 		0.384
(1.00) 		0.0225
(1.00) 		0.278
(1.00) 		0.119
(1.00) 		0.00016
(0.0654) 		0.171
(1.00)
amp 3q26 31 77 (21%) 293 0.00028
(0.111) 		0.00969
(1.00) 		0.0968
(1.00) 		0.642
(1.00) 		0.0745
(1.00) 		0.00481
(1.00) 		0.0385
(1.00) 		0.0222
(1.00)
amp 5p15 33 163 (44%) 207 1e-05
(0.00496) 		0.00476
(1.00) 		0.453
(1.00) 		0.217
(1.00) 		0.0775
(1.00) 		0.0172
(1.00) 		0.0926
(1.00) 		0.164
(1.00)
amp 5q35 3 135 (36%) 235 5e-05
(0.021) 		0.0247
(1.00) 		0.0575
(1.00) 		0.513
(1.00) 		0.938
(1.00) 		0.999
(1.00) 		0.852
(1.00) 		0.637
(1.00)
amp 6q12 109 (29%) 261 1e-05
(0.00496) 		0.0114
(1.00) 		0.00361
(1.00) 		0.00349
(1.00) 		0.458
(1.00) 		0.618
(1.00) 		0.0103
(1.00) 		0.152
(1.00)
amp 11q13 3 57 (15%) 313 0.312
(1.00) 		0.43
(1.00) 		0.0256
(1.00) 		0.119
(1.00) 		0.00871
(1.00) 		0.00332
(1.00) 		0.216
(1.00) 		0.00019
(0.0769)
amp 13q32 3 67 (18%) 303 1e-05
(0.00496) 		0.00221
(0.749) 		0.00351
(1.00) 		0.0355
(1.00) 		0.164
(1.00) 		0.2
(1.00) 		0.0122
(1.00) 		0.0189
(1.00)
amp 17q25 3 145 (39%) 225 2e-05
(0.0089) 		0.00245
(0.823) 		0.0513
(1.00) 		0.196
(1.00) 		0.00111
(0.408) 		0.00155
(0.556) 		0.0247
(1.00) 		0.0149
(1.00)
del 4p16 3 85 (23%) 285 1e-05
(0.00496) 		0.00948
(1.00) 		0.257
(1.00) 		0.0914
(1.00) 		0.706
(1.00) 		0.0276
(1.00) 		0.0446
(1.00) 		0.00668
(1.00)
del 8p23 2 247 (67%) 123 1e-05
(0.00496) 		0.0129
(1.00) 		0.00172
(0.604) 		0.399
(1.00) 		0.251
(1.00) 		0.168
(1.00) 		0.336
(1.00) 		0.146
(1.00)
del 8p12 242 (65%) 128 1e-05
(0.00496) 		0.0353
(1.00) 		0.001
(0.37) 		0.362
(1.00) 		0.19
(1.00) 		0.0998
(1.00) 		0.278
(1.00) 		0.0961
(1.00)
del 11q14 1 77 (21%) 293 0.0107
(1.00) 		0.603
(1.00) 		0.0378
(1.00) 		0.0188
(1.00) 		0.803
(1.00) 		0.26
(1.00) 		0.00034
(0.133) 		0.0136
(1.00)
del 11q24 2 95 (26%) 275 0.00462
(1.00) 		0.0867
(1.00) 		0.00335
(1.00) 		0.0108
(1.00) 		0.317
(1.00) 		0.257
(1.00) 		0.00075
(0.28) 		0.00046
(0.175)
del 12p12 1 78 (21%) 292 0.00054
(0.205) 		0.0628
(1.00) 		0.00807
(1.00) 		0.544
(1.00) 		0.217
(1.00) 		0.029
(1.00) 		0.504
(1.00) 		0.0725
(1.00)
del 12q24 33 59 (16%) 311 0.00022
(0.0882) 		0.666
(1.00) 		0.666
(1.00) 		0.865
(1.00) 		0.815
(1.00) 		0.714
(1.00) 		0.819
(1.00) 		0.29
(1.00)
del 15q26 3 79 (21%) 291 0.0352
(1.00) 		0.364
(1.00) 		0.0505
(1.00) 		0.00028
(0.111) 		0.354
(1.00) 		0.12
(1.00) 		0.00185
(0.644) 		0.0698
(1.00)
del 18q21 2 94 (25%) 276 0.00157
(0.56) 		5e-05
(0.021) 		0.0967
(1.00) 		0.463
(1.00) 		0.114
(1.00) 		0.538
(1.00) 		0.172
(1.00) 		0.249
(1.00)
del 19p13 3 87 (24%) 283 1e-05
(0.00496) 		0.333
(1.00) 		0.00933
(1.00) 		0.0178
(1.00) 		0.404
(1.00) 		0.128
(1.00) 		0.0211
(1.00) 		0.00275
(0.916)
del xq26 2 67 (18%) 303 2e-05
(0.0089) 		0.285
(1.00) 		0.313
(1.00) 		0.499
(1.00) 		0.904
(1.00) 		0.696
(1.00) 		0.315
(1.00) 		0.894
(1.00)
amp 2p24 1 65 (18%) 305 0.00489
(1.00) 		0.303
(1.00) 		0.39
(1.00) 		0.00458
(1.00) 		0.481
(1.00) 		0.0431
(1.00) 		0.144
(1.00) 		0.0919
(1.00)
amp 4p14 54 (15%) 316 0.00326
(1.00) 		0.0914
(1.00) 		0.00277
(0.92) 		0.00079
(0.294) 		0.184
(1.00) 		0.0545
(1.00) 		0.0101
(1.00) 		0.0163
(1.00)
amp 7q31 2 120 (32%) 250 0.193
(1.00) 		0.188
(1.00) 		0.698
(1.00) 		0.0166
(1.00) 		0.521
(1.00) 		0.435
(1.00) 		0.694
(1.00) 		0.421
(1.00)
amp 9q34 2 47 (13%) 323 0.03
(1.00) 		0.0895
(1.00) 		0.0662
(1.00) 		0.0497
(1.00) 		0.059
(1.00) 		0.0124
(1.00) 		0.327
(1.00) 		0.0126
(1.00)
amp 15q26 3 54 (15%) 316 0.0244
(1.00) 		0.127
(1.00) 		0.108
(1.00) 		0.0241
(1.00) 		0.839
(1.00) 		0.184
(1.00) 		0.301
(1.00) 		0.418
(1.00)
amp 17p11 2 46 (12%) 324 0.201
(1.00) 		0.0332
(1.00) 		0.128
(1.00) 		0.099
(1.00) 		0.0245
(1.00) 		0.249
(1.00) 		0.0791
(1.00) 		0.0865
(1.00)
del 2q22 1 52 (14%) 318 0.0673
(1.00) 		0.63
(1.00) 		0.363
(1.00) 		0.149
(1.00) 		0.207
(1.00) 		0.167
(1.00) 		0.634
(1.00) 		0.117
(1.00)
del 2q37 3 62 (17%) 308 0.103
(1.00) 		0.751
(1.00) 		0.0123
(1.00) 		0.00985
(1.00) 		0.0393
(1.00) 		0.00968
(1.00) 		0.238
(1.00) 		0.00171
(0.602)
del 6q27 136 (37%) 234 0.00918
(1.00) 		0.0666
(1.00) 		0.207
(1.00) 		0.47
(1.00) 		0.649
(1.00) 		0.0391
(1.00) 		0.35
(1.00) 		0.158
(1.00)
del 20p12 1 29 (8%) 341 0.0436
(1.00) 		0.959
(1.00) 		0.98
(1.00) 		0.804
(1.00) 		0.377
(1.00) 		0.737
(1.00) 		0.922
(1.00) 		0.38
(1.00)
del 22q12 1 79 (21%) 291 0.0292
(1.00) 		0.61
(1.00) 		0.0115
(1.00) 		0.305
(1.00) 		0.229
(1.00) 		0.194
(1.00) 		0.183
(1.00) 		0.503
(1.00)
del 22q13 32 83 (22%) 287 0.00547
(1.00) 		0.491
(1.00) 		0.00407
(1.00) 		0.418
(1.00) 		0.0938
(1.00) 		0.263
(1.00) 		0.18
(1.00) 		0.123
(1.00)
'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S1.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 1(1P22.3) MUTATED 22 49 18
AMP PEAK 1(1P22.3) WILD-TYPE 87 75 119

Figure S1.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S2.  Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 2(1Q22) MUTATED 93 111 79
AMP PEAK 2(1Q22) WILD-TYPE 16 13 58

Figure S2.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S3.  Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 2(1Q22) MUTATED 35 104 74
AMP PEAK 2(1Q22) WILD-TYPE 41 22 8

Figure S3.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S4.  Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 2(1Q22) MUTATED 26 37 45 25 21 38
AMP PEAK 2(1Q22) WILD-TYPE 6 27 1 3 27 6

Figure S4.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S5.  Gene #2: 'amp_1q22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 2(1Q22) MUTATED 76 81 35
AMP PEAK 2(1Q22) WILD-TYPE 18 49 3

Figure S5.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S6.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 3(1Q42.3) MUTATED 90 103 77
AMP PEAK 3(1Q42.3) WILD-TYPE 19 21 60

Figure S6.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S7.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 3(1Q42.3) MUTATED 35 101 66
AMP PEAK 3(1Q42.3) WILD-TYPE 41 25 16

Figure S7.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S8.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 3(1Q42.3) MUTATED 23 32 43 24 25 36
AMP PEAK 3(1Q42.3) WILD-TYPE 9 32 3 4 23 8

Figure S8.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S9.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 3(1Q42.3) MUTATED 74 75 34
AMP PEAK 3(1Q42.3) WILD-TYPE 20 55 4

Figure S9.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.065

Table S10.  Gene #5: 'amp_2q33.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
AMP PEAK 5(2Q33.1) MUTATED 29 9 13 10
AMP PEAK 5(2Q33.1) WILD-TYPE 63 78 106 32

Figure S10.  Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.11

Table S11.  Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 6(3Q26.31) MUTATED 15 41 21
AMP PEAK 6(3Q26.31) WILD-TYPE 94 83 116

Figure S11.  Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S12.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 8(5P15.33) MUTATED 54 72 37
AMP PEAK 8(5P15.33) WILD-TYPE 55 52 100

Figure S12.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S13.  Gene #9: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 9(5Q35.3) MUTATED 56 46 33
AMP PEAK 9(5Q35.3) WILD-TYPE 53 78 104

Figure S13.  Get High-res Image Gene #9: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S14.  Gene #10: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 10(6P25.2) MUTATED 50 79 30
AMP PEAK 10(6P25.2) WILD-TYPE 59 45 107

Figure S14.  Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S15.  Gene #10: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 10(6P25.2) MUTATED 16 62 45
AMP PEAK 10(6P25.2) WILD-TYPE 60 64 37

Figure S15.  Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S16.  Gene #11: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 11(6P21.1) MUTATED 47 73 38
AMP PEAK 11(6P21.1) WILD-TYPE 62 51 99

Figure S16.  Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S17.  Gene #11: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 11(6P21.1) MUTATED 16 65 41
AMP PEAK 11(6P21.1) WILD-TYPE 60 61 41

Figure S17.  Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S18.  Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 12(6Q12) MUTATED 33 55 21
AMP PEAK 12(6Q12) WILD-TYPE 76 69 116

Figure S18.  Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S19.  Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 13(6Q12) MUTATED 25 45 13
AMP PEAK 13(6Q12) WILD-TYPE 84 79 124

Figure S19.  Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.099

Table S20.  Gene #13: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 13(6Q12) MUTATED 10 10 23 6 5 9
AMP PEAK 13(6Q12) WILD-TYPE 22 54 23 22 43 35

Figure S20.  Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S21.  Gene #15: 'amp_8q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 15(8Q13.3) MUTATED 105 68 34
AMP PEAK 15(8Q13.3) WILD-TYPE 4 56 103

Figure S21.  Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S22.  Gene #15: 'amp_8q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 15(8Q13.3) MUTATED 20 20 32 22 19 25
AMP PEAK 15(8Q13.3) WILD-TYPE 12 44 14 6 29 19

Figure S22.  Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S23.  Gene #15: 'amp_8q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
AMP PEAK 15(8Q13.3) MUTATED 49 32 61 16 37
AMP PEAK 15(8Q13.3) WILD-TYPE 18 54 38 19 16

Figure S23.  Get High-res Image Gene #15: 'amp_8q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S24.  Gene #16: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 16(8Q24.21) MUTATED 105 80 46
AMP PEAK 16(8Q24.21) WILD-TYPE 4 44 91

Figure S24.  Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S25.  Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 16(8Q24.21) MUTATED 19 24 33 26 25 29
AMP PEAK 16(8Q24.21) WILD-TYPE 13 40 13 2 23 15

Figure S25.  Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S26.  Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
AMP PEAK 16(8Q24.21) MUTATED 51 37 70 18 41
AMP PEAK 16(8Q24.21) WILD-TYPE 16 49 29 17 12

Figure S26.  Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.077

Table S27.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
AMP PEAK 18(11Q13.3) MUTATED 12 19 13 10 0
AMP PEAK 18(11Q13.3) WILD-TYPE 55 67 86 25 53

Figure S27.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S28.  Gene #19: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 19(13Q32.3) MUTATED 11 47 9
AMP PEAK 19(13Q32.3) WILD-TYPE 98 77 128

Figure S28.  Get High-res Image Gene #19: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S29.  Gene #20: 'amp_13q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 20(13Q33.3) MUTATED 14 44 9
AMP PEAK 20(13Q33.3) WILD-TYPE 95 80 128

Figure S29.  Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.14

Table S30.  Gene #20: 'amp_13q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 20(13Q33.3) MUTATED 5 22 25
AMP PEAK 20(13Q33.3) WILD-TYPE 71 104 57

Figure S30.  Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S31.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 23(17Q25.3) MUTATED 35 70 40
AMP PEAK 23(17Q25.3) WILD-TYPE 74 54 97

Figure S31.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S32.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 24(19P13.12) MUTATED 11 14 31
AMP PEAK 24(19P13.12) WILD-TYPE 65 112 51

Figure S32.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S33.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 24(19P13.12) MUTATED 2 5 17 13 13 2
AMP PEAK 24(19P13.12) WILD-TYPE 30 59 29 15 35 42

Figure S33.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.073

Table S34.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 24(19P13.12) MUTATED 31 19 2
AMP PEAK 24(19P13.12) WILD-TYPE 63 111 36

Figure S34.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.049

Table S35.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
AMP PEAK 24(19P13.12) MUTATED 7 13 9 39
AMP PEAK 24(19P13.12) WILD-TYPE 58 114 40 85

Figure S35.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.23

Table S36.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
AMP PEAK 24(19P13.12) MUTATED 23 23 9 9
AMP PEAK 24(19P13.12) WILD-TYPE 69 64 110 33

Figure S36.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S37.  Gene #25: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
AMP PEAK 25(19Q12) MUTATED 13 19 31
AMP PEAK 25(19Q12) WILD-TYPE 63 107 51

Figure S37.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S38.  Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 25(19Q12) MUTATED 2 7 18 11 16 4
AMP PEAK 25(19Q12) WILD-TYPE 30 57 28 17 32 40

Figure S38.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.085

Table S39.  Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 25(19Q12) MUTATED 34 21 3
AMP PEAK 25(19Q12) WILD-TYPE 60 109 35

Figure S39.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.13

Table S40.  Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
AMP PEAK 25(19Q12) MUTATED 24 27 11 10
AMP PEAK 25(19Q12) WILD-TYPE 68 60 108 32

Figure S40.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.13

Table S41.  Gene #26: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 26(19Q13.11) MUTATED 39 30 4
AMP PEAK 26(19Q13.11) WILD-TYPE 55 100 34

Figure S41.  Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S42.  Gene #26: 'amp_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
AMP PEAK 26(19Q13.11) MUTATED 32 27 11 15
AMP PEAK 26(19Q13.11) WILD-TYPE 60 60 108 27

Figure S42.  Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S43.  Gene #26: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
AMP PEAK 26(19Q13.11) MUTATED 21 22 29 11 2
AMP PEAK 26(19Q13.11) WILD-TYPE 46 64 70 24 51

Figure S43.  Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S44.  Gene #27: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 27(20Q13.13) MUTATED 34 65 25
AMP PEAK 27(20Q13.13) WILD-TYPE 75 59 112

Figure S44.  Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S45.  Gene #27: 'amp_20q13.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 27(20Q13.13) MUTATED 43 41 2
AMP PEAK 27(20Q13.13) WILD-TYPE 51 89 36

Figure S45.  Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S46.  Gene #27: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
AMP PEAK 27(20Q13.13) MUTATED 41 27 23 25
AMP PEAK 27(20Q13.13) WILD-TYPE 51 60 96 17

Figure S46.  Get High-res Image Gene #27: 'amp_20q13.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S47.  Gene #28: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 28(20Q13.33) MUTATED 35 66 27
AMP PEAK 28(20Q13.33) WILD-TYPE 74 58 110

Figure S47.  Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S48.  Gene #28: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
AMP PEAK 28(20Q13.33) MUTATED 11 19 28 13 13 5
AMP PEAK 28(20Q13.33) WILD-TYPE 21 45 18 15 35 39

Figure S48.  Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S49.  Gene #28: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
AMP PEAK 28(20Q13.33) MUTATED 49 38 2
AMP PEAK 28(20Q13.33) WILD-TYPE 45 92 36

Figure S49.  Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S50.  Gene #28: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
AMP PEAK 28(20Q13.33) MUTATED 42 27 26 25
AMP PEAK 28(20Q13.33) WILD-TYPE 50 60 93 17

Figure S50.  Get High-res Image Gene #28: 'amp_20q13.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S51.  Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
AMP PEAK 29(XQ28) MUTATED 41 25 19
AMP PEAK 29(XQ28) WILD-TYPE 68 99 118

Figure S51.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.14

Table S52.  Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
AMP PEAK 29(XQ28) MUTATED 16 20 16 2 23
AMP PEAK 29(XQ28) WILD-TYPE 51 66 83 33 30

Figure S52.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S53.  Gene #30: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
DEL PEAK 1(1P36.31) MUTATED 19 47 57
DEL PEAK 1(1P36.31) WILD-TYPE 57 79 25

Figure S53.  Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S54.  Gene #30: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 1(1P36.31) MUTATED 8 25 39 13 18 12
DEL PEAK 1(1P36.31) WILD-TYPE 24 39 7 15 30 32

Figure S54.  Get High-res Image Gene #30: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S55.  Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 2(1P36.11) MUTATED 40 66 36
DEL PEAK 2(1P36.11) WILD-TYPE 69 58 101

Figure S55.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S56.  Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
DEL PEAK 2(1P36.11) MUTATED 17 36 54
DEL PEAK 2(1P36.11) WILD-TYPE 59 90 28

Figure S56.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S57.  Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 2(1P36.11) MUTATED 9 18 37 9 16 11
DEL PEAK 2(1P36.11) WILD-TYPE 23 46 9 19 32 33

Figure S57.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S58.  Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 2(1P36.11) MUTATED 53 39 8
DEL PEAK 2(1P36.11) WILD-TYPE 41 91 30

Figure S58.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S59.  Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
DEL PEAK 2(1P36.11) MUTATED 9 30 25 64 11
DEL PEAK 2(1P36.11) WILD-TYPE 35 65 31 58 37

Figure S59.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.069

Table S60.  Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 2(1P36.11) MUTATED 46 37 28 21
DEL PEAK 2(1P36.11) WILD-TYPE 46 50 91 21

Figure S60.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.14

Table S61.  Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 2(1P36.11) MUTATED 28 27 55 8 14
DEL PEAK 2(1P36.11) WILD-TYPE 39 59 44 27 39

Figure S61.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S62.  Gene #34: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 5(3P13) MUTATED 6 7 20 3 19 5
DEL PEAK 5(3P13) WILD-TYPE 26 57 26 25 29 39

Figure S62.  Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S63.  Gene #34: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 5(3P13) MUTATED 42 13 5
DEL PEAK 5(3P13) WILD-TYPE 52 117 33

Figure S63.  Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.15

Table S64.  Gene #34: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 5(3P13) MUTATED 29 21 11 6
DEL PEAK 5(3P13) WILD-TYPE 63 66 108 36

Figure S64.  Get High-res Image Gene #34: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S65.  Gene #35: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 6(4P16.3) MUTATED 21 48 16
DEL PEAK 6(4P16.3) WILD-TYPE 88 76 121

Figure S65.  Get High-res Image Gene #35: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S66.  Gene #36: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 7(4Q21.3) MUTATED 38 93 40
DEL PEAK 7(4Q21.3) WILD-TYPE 71 31 97

Figure S66.  Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S67.  Gene #36: 'del_4q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 7(4Q21.3) MUTATED 19 30 34 11 16 13
DEL PEAK 7(4Q21.3) WILD-TYPE 13 34 12 17 32 31

Figure S67.  Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S68.  Gene #36: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 7(4Q21.3) MUTATED 56 38 40 29
DEL PEAK 7(4Q21.3) WILD-TYPE 36 49 79 13

Figure S68.  Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.16

Table S69.  Gene #36: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 7(4Q21.3) MUTATED 41 43 52 15 12
DEL PEAK 7(4Q21.3) WILD-TYPE 26 43 47 20 41

Figure S69.  Get High-res Image Gene #36: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S70.  Gene #37: 'del_4q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 8(4Q22.3) MUTATED 39 94 39
DEL PEAK 8(4Q22.3) WILD-TYPE 70 30 98

Figure S70.  Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.085

Table S71.  Gene #37: 'del_4q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 8(4Q22.3) MUTATED 18 30 34 11 16 13
DEL PEAK 8(4Q22.3) WILD-TYPE 14 34 12 17 32 31

Figure S71.  Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.049

Table S72.  Gene #37: 'del_4q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 8(4Q22.3) MUTATED 55 38 42 29
DEL PEAK 8(4Q22.3) WILD-TYPE 37 49 77 13

Figure S72.  Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.21

Table S73.  Gene #37: 'del_4q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 8(4Q22.3) MUTATED 41 42 52 17 12
DEL PEAK 8(4Q22.3) WILD-TYPE 26 44 47 18 41

Figure S73.  Get High-res Image Gene #37: 'del_4q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S74.  Gene #38: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 9(4Q35.1) MUTATED 43 94 35
DEL PEAK 9(4Q35.1) WILD-TYPE 66 30 102

Figure S74.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S75.  Gene #38: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
DEL PEAK 9(4Q35.1) MUTATED 21 52 52
DEL PEAK 9(4Q35.1) WILD-TYPE 55 74 30

Figure S75.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.23

Table S76.  Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 9(4Q35.1) MUTATED 17 25 33 10 16 14
DEL PEAK 9(4Q35.1) WILD-TYPE 15 39 13 18 32 30

Figure S76.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.13

Table S77.  Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 9(4Q35.1) MUTATED 56 49 10
DEL PEAK 9(4Q35.1) WILD-TYPE 38 81 28

Figure S77.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.088

Table S78.  Gene #38: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 9(4Q35.1) MUTATED 53 40 40 28
DEL PEAK 9(4Q35.1) WILD-TYPE 39 47 79 14

Figure S78.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S79.  Gene #40: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 11(8P23.2) MUTATED 103 86 58
DEL PEAK 11(8P23.2) WILD-TYPE 6 38 79

Figure S79.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S80.  Gene #41: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 12(8P12) MUTATED 100 86 56
DEL PEAK 12(8P12) WILD-TYPE 9 38 81

Figure S80.  Get High-res Image Gene #41: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S81.  Gene #42: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 13(9P21.3) MUTATED 40 70 40
DEL PEAK 13(9P21.3) WILD-TYPE 69 54 97

Figure S81.  Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.099

Table S82.  Gene #42: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 13(9P21.3) MUTATED 55 42 12
DEL PEAK 13(9P21.3) WILD-TYPE 39 88 26

Figure S82.  Get High-res Image Gene #42: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.092

Table S83.  Gene #43: 'del_9q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 14(9Q31.3) MUTATED 45 39 5
DEL PEAK 14(9Q31.3) WILD-TYPE 49 91 33

Figure S83.  Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.11

Table S84.  Gene #43: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 14(9Q31.3) MUTATED 28 26 36 16 5
DEL PEAK 14(9Q31.3) WILD-TYPE 39 60 63 19 48

Figure S84.  Get High-res Image Gene #43: 'del_9q31.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S85.  Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 15(10Q23.31) MUTATED 22 22 4 5 14 5
DEL PEAK 15(10Q23.31) WILD-TYPE 10 42 42 23 34 39

Figure S85.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S86.  Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
DEL PEAK 15(10Q23.31) MUTATED 15 41 13 25 3
DEL PEAK 15(10Q23.31) WILD-TYPE 29 54 43 97 45

Figure S86.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S87.  Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 15(10Q23.31) MUTATED 21 39 19 13 2
DEL PEAK 15(10Q23.31) WILD-TYPE 46 47 80 22 51

Figure S87.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S88.  Gene #45: 'del_10q26.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 16(10Q26.13) MUTATED 20 24 7 5 19 6
DEL PEAK 16(10Q26.13) WILD-TYPE 12 40 39 23 29 38

Figure S88.  Get High-res Image Gene #45: 'del_10q26.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S89.  Gene #45: 'del_10q26.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
DEL PEAK 16(10Q26.13) MUTATED 14 45 12 31 3
DEL PEAK 16(10Q26.13) WILD-TYPE 30 50 44 91 45

Figure S89.  Get High-res Image Gene #45: 'del_10q26.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S90.  Gene #45: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 16(10Q26.13) MUTATED 22 41 24 13 2
DEL PEAK 16(10Q26.13) WILD-TYPE 45 45 75 22 51

Figure S90.  Get High-res Image Gene #45: 'del_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.13

Table S91.  Gene #46: 'del_11q14.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 17(11Q14.1) MUTATED 33 12 16 10
DEL PEAK 17(11Q14.1) WILD-TYPE 59 75 103 32

Figure S91.  Get High-res Image Gene #46: 'del_11q14.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S92.  Gene #47: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 18(11Q24.2) MUTATED 29 27 19 5 7
DEL PEAK 18(11Q24.2) WILD-TYPE 38 59 80 30 46

Figure S92.  Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p12.1' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.2

Table S93.  Gene #48: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 19(12P12.1) MUTATED 16 41 21
DEL PEAK 19(12P12.1) WILD-TYPE 93 83 116

Figure S93.  Get High-res Image Gene #48: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.088

Table S94.  Gene #49: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 20(12Q24.33) MUTATED 9 34 16
DEL PEAK 20(12Q24.33) WILD-TYPE 100 90 121

Figure S94.  Get High-res Image Gene #49: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S95.  Gene #50: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 21(13Q14.2) MUTATED 35 92 52
DEL PEAK 21(13Q14.2) WILD-TYPE 74 32 85

Figure S95.  Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S96.  Gene #50: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 21(13Q14.2) MUTATED 60 58 9
DEL PEAK 21(13Q14.2) WILD-TYPE 34 72 29

Figure S96.  Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S97.  Gene #50: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 21(13Q14.2) MUTATED 38 51 45 22 12
DEL PEAK 21(13Q14.2) WILD-TYPE 29 35 54 13 41

Figure S97.  Get High-res Image Gene #50: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S98.  Gene #51: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 22(14Q23.3) MUTATED 21 78 32
DEL PEAK 22(14Q23.3) WILD-TYPE 88 46 105

Figure S98.  Get High-res Image Gene #51: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.073

Table S99.  Gene #51: 'del_14q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 22(14Q23.3) MUTATED 21 14 21 8 19 9
DEL PEAK 22(14Q23.3) WILD-TYPE 11 50 25 20 29 35

Figure S99.  Get High-res Image Gene #51: 'del_14q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S100.  Gene #51: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 22(14Q23.3) MUTATED 51 33 8
DEL PEAK 22(14Q23.3) WILD-TYPE 43 97 30

Figure S100.  Get High-res Image Gene #51: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S101.  Gene #52: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 23(14Q32.33) MUTATED 20 77 35
DEL PEAK 23(14Q32.33) WILD-TYPE 89 47 102

Figure S101.  Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.085

Table S102.  Gene #52: 'del_14q32.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 23(14Q32.33) MUTATED 20 14 21 7 20 9
DEL PEAK 23(14Q32.33) WILD-TYPE 12 50 25 21 28 35

Figure S102.  Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S103.  Gene #52: 'del_14q32.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 23(14Q32.33) MUTATED 51 31 9
DEL PEAK 23(14Q32.33) WILD-TYPE 43 99 29

Figure S103.  Get High-res Image Gene #52: 'del_14q32.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.11

Table S104.  Gene #53: 'del_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 24(15Q26.3) MUTATED 34 17 7
DEL PEAK 24(15Q26.3) WILD-TYPE 60 113 31

Figure S104.  Get High-res Image Gene #53: 'del_15q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S105.  Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 25(16Q23.1) MUTATED 45 78 39
DEL PEAK 25(16Q23.1) WILD-TYPE 64 46 98

Figure S105.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S106.  Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
DEL PEAK 25(16Q23.1) MUTATED 20 49 50
DEL PEAK 25(16Q23.1) WILD-TYPE 56 77 32

Figure S106.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S107.  Gene #54: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
DEL PEAK 25(16Q23.1) MUTATED 23 26 35 6 13 6
DEL PEAK 25(16Q23.1) WILD-TYPE 9 38 11 22 35 38

Figure S107.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S108.  Gene #54: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
DEL PEAK 25(16Q23.1) MUTATED 58 47 4
DEL PEAK 25(16Q23.1) WILD-TYPE 36 83 34

Figure S108.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S109.  Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
DEL PEAK 25(16Q23.1) MUTATED 19 40 33 62 6
DEL PEAK 25(16Q23.1) WILD-TYPE 25 55 23 60 42

Figure S109.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S110.  Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
DEL PEAK 25(16Q23.1) MUTATED 54 36 36 28
DEL PEAK 25(16Q23.1) WILD-TYPE 38 51 83 14

Figure S110.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S111.  Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 25(16Q23.1) MUTATED 42 37 50 15 10
DEL PEAK 25(16Q23.1) WILD-TYPE 25 49 49 20 43

Figure S111.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S112.  Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 26(17P13.1) MUTATED 46 105 75
DEL PEAK 26(17P13.1) WILD-TYPE 63 19 62

Figure S112.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S113.  Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
DEL PEAK 26(17P13.1) MUTATED 38 67 30 66 23
DEL PEAK 26(17P13.1) WILD-TYPE 6 28 26 56 25

Figure S113.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S114.  Gene #55: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 26(17P13.1) MUTATED 36 67 55 31 25
DEL PEAK 26(17P13.1) WILD-TYPE 31 19 44 4 28

Figure S114.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S115.  Gene #56: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 27(17P11.2) MUTATED 40 90 65
DEL PEAK 27(17P11.2) WILD-TYPE 69 34 72

Figure S115.  Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.049

Table S116.  Gene #56: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
DEL PEAK 27(17P11.2) MUTATED 51 61 22 59
DEL PEAK 27(17P11.2) WILD-TYPE 14 66 27 65

Figure S116.  Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.15

Table S117.  Gene #56: 'del_17p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
DEL PEAK 27(17P11.2) MUTATED 36 54 25 56 22
DEL PEAK 27(17P11.2) WILD-TYPE 8 41 31 66 26

Figure S117.  Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.096

Table S118.  Gene #56: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
DEL PEAK 27(17P11.2) MUTATED 32 54 47 29 22
DEL PEAK 27(17P11.2) WILD-TYPE 35 32 52 6 31

Figure S118.  Get High-res Image Gene #56: 'del_17p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S119.  Gene #57: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
DEL PEAK 28(18Q21.2) MUTATED 9 29 35
DEL PEAK 28(18Q21.2) WILD-TYPE 67 97 47

Figure S119.  Get High-res Image Gene #57: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S120.  Gene #58: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 29(19P13.3) MUTATED 18 51 18
DEL PEAK 29(19P13.3) WILD-TYPE 91 73 119

Figure S120.  Get High-res Image Gene #58: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq26.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S121.  Gene #62: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
DEL PEAK 33(XQ26.2) MUTATED 8 39 20
DEL PEAK 33(XQ26.2) WILD-TYPE 101 85 117

Figure S121.  Get High-res Image Gene #62: 'del_xq26.2' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 370

  • Number of significantly focal cnvs = 62

  • Number of molecular subtypes = 8

  • 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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