Correlation between copy number variations of arm-level result and molecular subtypes
Pancreatic Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1GH9GV0
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1GH9GV0
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 79 arm-level events and 10 molecular subtypes across 184 patients, 49 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

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

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xq loss 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 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 49 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
17p loss 80 (43%) 104 1e-05
(0.00782) 		1e-05
(0.00782) 		0.00302
(1.00) 		0.00628
(1.00) 		1e-05
(0.00782) 		1e-05
(0.00782) 		1e-05
(0.00782) 		2e-05
(0.0151) 		1e-05
(0.00782) 		3e-05
(0.0225)
6q loss 83 (45%) 101 1e-05
(0.00782) 		2e-05
(0.0151) 		0.00832
(1.00) 		0.0697
(1.00) 		0.00031
(0.228) 		0.00048
(0.349) 		0.00139
(0.972) 		2e-05
(0.0151) 		1e-05
(0.00782) 		2e-05
(0.0151)
6p loss 64 (35%) 120 1e-05
(0.00782) 		3e-05
(0.0225) 		0.0716
(1.00) 		0.388
(1.00) 		0.135
(1.00) 		0.0142
(1.00) 		0.221
(1.00) 		0.00101
(0.714) 		0.00266
(1.00) 		0.00013
(0.0965)
18q loss 106 (58%) 78 1e-05
(0.00782) 		0.0008
(0.567) 		0.0162
(1.00) 		0.00851
(1.00) 		0.00239
(1.00) 		0.00523
(1.00) 		0.0149
(1.00) 		0.00344
(1.00) 		0.0473
(1.00) 		2e-05
(0.0151)
1q gain 50 (27%) 134 0.0079
(1.00) 		0.00162
(1.00) 		0.235
(1.00) 		0.366
(1.00) 		0.0126
(1.00) 		0.0619
(1.00) 		0.00551
(1.00) 		0.0387
(1.00) 		0.00032
(0.235) 		0.0114
(1.00)
5p gain 28 (15%) 156 1e-05
(0.00782) 		0.776
(1.00) 		0.6
(1.00) 		0.37
(1.00) 		0.668
(1.00) 		0.157
(1.00) 		0.241
(1.00) 		0.124
(1.00) 		0.00639
(1.00) 		0.457
(1.00)
5q gain 20 (11%) 164 1e-05
(0.00782) 		0.6
(1.00) 		0.711
(1.00) 		0.22
(1.00) 		0.325
(1.00) 		0.0103
(1.00) 		0.11
(1.00) 		0.0339
(1.00) 		0.115
(1.00) 		0.145
(1.00)
7p gain 52 (28%) 132 1e-05
(0.00782) 		0.0104
(1.00) 		0.0718
(1.00) 		0.292
(1.00) 		0.353
(1.00) 		0.268
(1.00) 		0.276
(1.00) 		0.0472
(1.00) 		0.00547
(1.00) 		0.164
(1.00)
7q gain 48 (26%) 136 1e-05
(0.00782) 		0.0553
(1.00) 		0.213
(1.00) 		0.673
(1.00) 		0.758
(1.00) 		0.259
(1.00) 		0.669
(1.00) 		0.34
(1.00) 		0.0224
(1.00) 		0.451
(1.00)
8q gain 48 (26%) 136 6e-05
(0.0447) 		0.00072
(0.515) 		0.469
(1.00) 		0.493
(1.00) 		0.294
(1.00) 		0.544
(1.00) 		0.396
(1.00) 		0.0793
(1.00) 		0.00104
(0.734) 		0.0676
(1.00)
9q gain 12 (7%) 172 7e-05
(0.052) 		0.671
(1.00) 		0.766
(1.00) 		0.684
(1.00) 		0.926
(1.00) 		0.612
(1.00) 		0.628
(1.00) 		0.263
(1.00) 		0.263
(1.00) 		0.28
(1.00)
12p gain 30 (16%) 154 1e-05
(0.00782) 		0.00645
(1.00) 		0.321
(1.00) 		0.251
(1.00) 		0.677
(1.00) 		0.255
(1.00) 		0.11
(1.00) 		0.0693
(1.00) 		0.0022
(1.00) 		0.457
(1.00)
12q gain 22 (12%) 162 1e-05
(0.00782) 		0.0227
(1.00) 		0.353
(1.00) 		0.306
(1.00) 		0.586
(1.00) 		0.111
(1.00) 		0.207
(1.00) 		0.0405
(1.00) 		0.00403
(1.00) 		0.156
(1.00)
14q gain 26 (14%) 158 1e-05
(0.00782) 		0.33
(1.00) 		0.585
(1.00) 		0.894
(1.00) 		0.276
(1.00) 		0.576
(1.00) 		0.169
(1.00) 		0.267
(1.00) 		0.103
(1.00) 		0.925
(1.00)
16p gain 22 (12%) 162 2e-05
(0.0151) 		0.0042
(1.00) 		0.0165
(1.00) 		0.25
(1.00) 		0.153
(1.00) 		0.0585
(1.00) 		0.0668
(1.00) 		0.0145
(1.00) 		0.00205
(1.00) 		0.0289
(1.00)
16q gain 23 (12%) 161 1e-05
(0.00782) 		0.00766
(1.00) 		0.26
(1.00) 		0.528
(1.00) 		0.106
(1.00) 		0.0557
(1.00) 		0.0131
(1.00) 		0.00076
(0.54) 		0.00269
(1.00) 		0.00322
(1.00)
17p gain 9 (5%) 175 4e-05
(0.0299) 		0.0394
(1.00) 		0.892
(1.00) 		0.495
(1.00) 		0.0027
(1.00) 		0.00058
(0.419) 		0.00085
(0.602) 		0.00252
(1.00) 		0.225
(1.00) 		0.01
(1.00)
18p gain 28 (15%) 156 1e-05
(0.00782) 		0.0449
(1.00) 		0.211
(1.00) 		0.0532
(1.00) 		0.0268
(1.00) 		0.197
(1.00) 		0.147
(1.00) 		0.0218
(1.00) 		0.0337
(1.00) 		0.102
(1.00)
18q gain 12 (7%) 172 5e-05
(0.0373) 		0.601
(1.00) 		0.641
(1.00) 		0.0421
(1.00) 		0.38
(1.00) 		0.491
(1.00) 		0.479
(1.00) 		0.124
(1.00) 		0.363
(1.00) 		0.0884
(1.00)
20p gain 34 (18%) 150 1e-05
(0.00782) 		0.217
(1.00) 		0.135
(1.00) 		0.455
(1.00) 		0.227
(1.00) 		0.154
(1.00) 		0.219
(1.00) 		0.0162
(1.00) 		0.00643
(1.00) 		0.257
(1.00)
20q gain 45 (24%) 139 1e-05
(0.00782) 		0.126
(1.00) 		0.412
(1.00) 		0.333
(1.00) 		0.545
(1.00) 		0.175
(1.00) 		0.331
(1.00) 		0.0234
(1.00) 		0.00052
(0.376) 		0.208
(1.00)
xq gain 13 (7%) 171 0.00027
(0.199) 		1
(1.00) 		0.699
(1.00) 		0.407
(1.00) 		0.126
(1.00) 		0.00932
(1.00) 		0.16
(1.00) 		0.0367
(1.00) 		0.813
(1.00) 		0.0871
(1.00)
1p loss 36 (20%) 148 6e-05
(0.0447) 		0.00433
(1.00) 		0.00045
(0.328) 		0.00161
(1.00) 		0.0103
(1.00) 		0.0642
(1.00) 		0.166
(1.00) 		0.0511
(1.00) 		0.0285
(1.00) 		0.024
(1.00)
9p loss 75 (41%) 109 1e-05
(0.00782) 		0.13
(1.00) 		0.00879
(1.00) 		0.0713
(1.00) 		0.00287
(1.00) 		0.0386
(1.00) 		0.017
(1.00) 		0.0145
(1.00) 		0.00843
(1.00) 		0.00738
(1.00)
10p loss 36 (20%) 148 0.00024
(0.177) 		0.158
(1.00) 		0.454
(1.00) 		0.588
(1.00) 		0.16
(1.00) 		0.193
(1.00) 		0.369
(1.00) 		0.148
(1.00) 		0.0636
(1.00) 		0.0959
(1.00)
10q loss 30 (16%) 154 0.00017
(0.126) 		0.617
(1.00) 		0.771
(1.00) 		0.712
(1.00) 		0.184
(1.00) 		0.0169
(1.00) 		0.53
(1.00) 		0.335
(1.00) 		0.228
(1.00) 		0.0982
(1.00)
12p loss 20 (11%) 164 0.00018
(0.133) 		0.00079
(0.561) 		0.00044
(0.321) 		0.00254
(1.00) 		0.0612
(1.00) 		0.00869
(1.00) 		0.0841
(1.00) 		0.00108
(0.761) 		0.343
(1.00) 		0.00174
(1.00)
12q loss 28 (15%) 156 1e-05
(0.00782) 		0.0435
(1.00) 		0.00191
(1.00) 		0.00335
(1.00) 		0.152
(1.00) 		0.00285
(1.00) 		0.124
(1.00) 		0.117
(1.00) 		0.241
(1.00) 		0.0237
(1.00)
15q loss 30 (16%) 154 4e-05
(0.0299) 		0.00066
(0.475) 		0.295
(1.00) 		0.552
(1.00) 		0.0206
(1.00) 		0.00212
(1.00) 		0.0791
(1.00) 		0.00633
(1.00) 		0.105
(1.00) 		0.0037
(1.00)
19p loss 19 (10%) 165 0.00128
(0.896) 		0.00112
(0.787) 		0.354
(1.00) 		0.779
(1.00) 		0.0629
(1.00) 		0.0241
(1.00) 		0.39
(1.00) 		0.00638
(1.00) 		0.0002
(0.148) 		0.0195
(1.00)
20p loss 20 (11%) 164 0.00033
(0.242) 		0.00952
(1.00) 		0.728
(1.00) 		0.672
(1.00) 		0.00694
(1.00) 		0.0915
(1.00) 		0.0367
(1.00) 		0.0412
(1.00) 		0.00214
(1.00) 		0.0145
(1.00)
21q loss 58 (32%) 126 1e-05
(0.00782) 		0.00075
(0.534) 		0.18
(1.00) 		0.122
(1.00) 		0.0219
(1.00) 		0.096
(1.00) 		0.389
(1.00) 		0.0325
(1.00) 		0.0006
(0.433) 		0.0362
(1.00)
22q loss 46 (25%) 138 1e-05
(0.00782) 		0.0173
(1.00) 		0.974
(1.00) 		0.989
(1.00) 		0.218
(1.00) 		0.375
(1.00) 		0.311
(1.00) 		0.0394
(1.00) 		0.00116
(0.813) 		0.0282
(1.00)
xq loss 18 (10%) 166 1e-05
(0.00782) 		0.0336
(1.00) 		0.34
(1.00) 		0.198
(1.00) 		0.369
(1.00) 		0.328
(1.00) 		0.267
(1.00) 		0.835
(1.00) 		0.491
(1.00) 		0.583
(1.00)
1p gain 18 (10%) 166 0.426
(1.00) 		0.383
(1.00) 		0.0172
(1.00) 		0.00762
(1.00) 		0.761
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.134
(1.00) 		0.894
(1.00)
2p gain 14 (8%) 170 0.0211
(1.00) 		0.00298
(1.00) 		0.101
(1.00) 		0.592
(1.00) 		0.636
(1.00) 		0.188
(1.00) 		0.436
(1.00) 		0.0151
(1.00) 		0.129
(1.00) 		0.0998
(1.00)
2q gain 16 (9%) 168 0.0357
(1.00) 		0.00908
(1.00) 		0.1
(1.00) 		0.594
(1.00) 		0.466
(1.00) 		0.183
(1.00) 		0.516
(1.00) 		0.00476
(1.00) 		0.201
(1.00) 		0.04
(1.00)
3p gain 10 (5%) 174 0.0133
(1.00) 		0.188
(1.00) 		0.265
(1.00) 		0.685
(1.00) 		0.542
(1.00) 		0.618
(1.00) 		0.84
(1.00) 		0.442
(1.00) 		0.53
(1.00) 		0.527
(1.00)
3q gain 20 (11%) 164 0.00049
(0.356) 		0.00225
(1.00) 		0.333
(1.00) 		0.161
(1.00) 		0.266
(1.00) 		0.278
(1.00) 		0.773
(1.00) 		0.059
(1.00) 		0.175
(1.00) 		0.265
(1.00)
4p gain 11 (6%) 173 0.0154
(1.00) 		0.783
(1.00) 		0.859
(1.00) 		0.24
(1.00) 		0.00148
(1.00) 		0.00967
(1.00) 		0.0354
(1.00) 		0.0211
(1.00) 		0.78
(1.00) 		0.208
(1.00)
4q gain 8 (4%) 176 0.00072
(0.515) 		0.411
(1.00) 		0.861
(1.00) 		0.239
(1.00) 		0.0221
(1.00) 		0.0341
(1.00) 		0.0217
(1.00) 		0.0404
(1.00) 		0.521
(1.00) 		0.154
(1.00)
6p gain 7 (4%) 177 0.00041
(0.3) 		0.679
(1.00) 		0.494
(1.00) 		0.486
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.875
(1.00) 		0.0592
(1.00) 		1
(1.00)
6q gain 5 (3%) 179 0.0165
(1.00) 		0.441
(1.00) 		0.851
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0311
(1.00) 		0.453
(1.00)
8p gain 26 (14%) 158 0.00364
(1.00) 		0.0421
(1.00) 		0.558
(1.00) 		0.492
(1.00) 		0.758
(1.00) 		0.958
(1.00) 		0.222
(1.00) 		0.552
(1.00) 		0.0128
(1.00) 		0.662
(1.00)
9p gain 8 (4%) 176 0.0117
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.522
(1.00) 		0.591
(1.00) 		0.635
(1.00) 		0.684
(1.00) 		0.787
(1.00) 		0.577
(1.00) 		0.447
(1.00)
10p gain 10 (5%) 174 0.0363
(1.00) 		0.13
(1.00) 		0.0139
(1.00) 		0.124
(1.00) 		0.214
(1.00) 		0.815
(1.00) 		0.474
(1.00) 		0.9
(1.00) 		0.0007
(0.501) 		1
(1.00)
10q gain 13 (7%) 171 0.0264
(1.00) 		0.0499
(1.00) 		0.0279
(1.00) 		0.0795
(1.00) 		0.148
(1.00) 		0.381
(1.00) 		0.297
(1.00) 		0.914
(1.00) 		0.00037
(0.271) 		1
(1.00)
11p gain 13 (7%) 171 0.00072
(0.515) 		0.0485
(1.00) 		0.0453
(1.00) 		0.674
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.792
(1.00) 		0.432
(1.00) 		0.751
(1.00)
11q gain 15 (8%) 169 0.00616
(1.00) 		0.0612
(1.00) 		0.0166
(1.00) 		0.205
(1.00) 		0.939
(1.00) 		0.937
(1.00) 		0.502
(1.00) 		0.535
(1.00) 		0.284
(1.00) 		0.18
(1.00)
13q gain 29 (16%) 155 0.0165
(1.00) 		0.602
(1.00) 		0.35
(1.00) 		0.656
(1.00) 		0.211
(1.00) 		0.472
(1.00) 		0.217
(1.00) 		0.124
(1.00) 		0.431
(1.00) 		0.795
(1.00)
15q gain 14 (8%) 170 0.0899
(1.00) 		0.108
(1.00) 		0.142
(1.00) 		0.596
(1.00) 		0.343
(1.00) 		0.131
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.866
(1.00)
17q gain 17 (9%) 167 0.00046
(0.335) 		0.388
(1.00) 		0.971
(1.00) 		0.832
(1.00) 		0.191
(1.00) 		0.062
(1.00) 		0.0945
(1.00) 		0.0706
(1.00) 		0.119
(1.00) 		0.245
(1.00)
19p gain 17 (9%) 167 0.00069
(0.495) 		0.143
(1.00) 		0.471
(1.00) 		0.297
(1.00) 		0.684
(1.00) 		0.622
(1.00) 		0.0125
(1.00) 		0.337
(1.00) 		0.384
(1.00) 		0.594
(1.00)
19q gain 28 (15%) 156 0.00036
(0.264) 		0.177
(1.00) 		0.612
(1.00) 		0.521
(1.00) 		0.896
(1.00) 		0.891
(1.00) 		0.0681
(1.00) 		0.686
(1.00) 		0.107
(1.00) 		1
(1.00)
22q gain 8 (4%) 176 0.348
(1.00) 		0.0542
(1.00) 		0.264
(1.00) 		0.4
(1.00) 		0.106
(1.00) 		0.0796
(1.00) 		0.367
(1.00) 		0.0649
(1.00) 		0.144
(1.00) 		0.27
(1.00)
1q loss 8 (4%) 176 0.0424
(1.00) 		0.284
(1.00) 		0.516
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.509
(1.00) 		0.76
(1.00) 		0.695
(1.00) 		0.103
(1.00) 		0.782
(1.00)
2p loss 11 (6%) 173 0.00791
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.953
(1.00) 		0.671
(1.00) 		0.191
(1.00) 		0.92
(1.00) 		0.759
(1.00) 		0.265
(1.00) 		0.847
(1.00)
2q loss 5 (3%) 179 0.00049
(0.356) 		0.602
(1.00) 		0.451
(1.00) 		0.0902
(1.00) 		0.448
(1.00) 		0.295
(1.00) 		0.159
(1.00) 		0.362
(1.00)
3p loss 36 (20%) 148 0.00184
(1.00) 		0.256
(1.00) 		0.195
(1.00) 		0.118
(1.00) 		0.65
(1.00) 		0.906
(1.00) 		0.208
(1.00) 		0.301
(1.00) 		0.107
(1.00) 		0.556
(1.00)
3q loss 19 (10%) 165 0.0309
(1.00) 		0.173
(1.00) 		0.00738
(1.00) 		0.00565
(1.00) 		0.529
(1.00) 		0.672
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.00747
(1.00) 		0.852
(1.00)
4p loss 25 (14%) 159 0.0407
(1.00) 		0.0314
(1.00) 		0.403
(1.00) 		0.526
(1.00) 		0.105
(1.00) 		0.103
(1.00) 		0.578
(1.00) 		0.0116
(1.00) 		0.958
(1.00) 		0.00331
(1.00)
4q loss 25 (14%) 159 0.244
(1.00) 		0.0492
(1.00) 		0.505
(1.00) 		0.417
(1.00) 		0.0544
(1.00) 		0.183
(1.00) 		0.199
(1.00) 		0.00273
(1.00) 		0.706
(1.00) 		0.00111
(0.781)
5p loss 9 (5%) 175 0.00361
(1.00) 		0.175
(1.00) 		0.516
(1.00) 		0.7
(1.00) 		0.911
(1.00) 		0.237
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.16
(1.00) 		0.804
(1.00)
5q loss 13 (7%) 171 0.00381
(1.00) 		0.0025
(1.00) 		0.235
(1.00) 		0.576
(1.00) 		0.935
(1.00) 		0.251
(1.00) 		0.622
(1.00) 		0.448
(1.00) 		0.139
(1.00) 		0.601
(1.00)
7p loss 3 (2%) 181 0.178
(1.00) 		0.32
(1.00) 		0.798
(1.00) 		0.774
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.43
(1.00) 		0.314
(1.00)
7q loss 4 (2%) 180 0.0707
(1.00) 		0.188
(1.00) 		0.455
(1.00) 		0.414
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.539
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.561
(1.00)
8p loss 41 (22%) 143 0.00114
(0.8) 		0.0168
(1.00) 		0.249
(1.00) 		0.155
(1.00) 		0.148
(1.00) 		0.00496
(1.00) 		0.0153
(1.00) 		0.0125
(1.00) 		0.00667
(1.00) 		0.00233
(1.00)
8q loss 16 (9%) 168 0.0192
(1.00) 		0.522
(1.00) 		0.251
(1.00) 		0.23
(1.00) 		0.793
(1.00) 		0.437
(1.00) 		0.334
(1.00) 		0.456
(1.00) 		0.0501
(1.00) 		0.169
(1.00)
9q loss 43 (23%) 141 0.115
(1.00) 		0.967
(1.00) 		0.303
(1.00) 		0.387
(1.00) 		0.268
(1.00) 		0.441
(1.00) 		0.196
(1.00) 		0.266
(1.00) 		0.219
(1.00) 		0.31
(1.00)
11p loss 17 (9%) 167 0.00141
(0.984) 		0.0417
(1.00) 		0.342
(1.00) 		0.0689
(1.00) 		0.943
(1.00) 		0.683
(1.00) 		0.476
(1.00) 		0.481
(1.00) 		0.474
(1.00) 		0.728
(1.00)
11q loss 16 (9%) 168 0.00066
(0.475) 		0.452
(1.00) 		0.162
(1.00) 		0.0138
(1.00) 		0.787
(1.00) 		0.818
(1.00) 		0.93
(1.00) 		0.574
(1.00) 		0.401
(1.00) 		0.82
(1.00)
13q loss 20 (11%) 164 0.00061
(0.44) 		0.0135
(1.00) 		0.829
(1.00) 		0.832
(1.00) 		0.00296
(1.00) 		0.155
(1.00) 		0.0234
(1.00) 		0.0135
(1.00) 		0.00179
(1.00) 		0.0619
(1.00)
14q loss 16 (9%) 168 0.234
(1.00) 		0.186
(1.00) 		0.0857
(1.00) 		0.158
(1.00) 		0.496
(1.00) 		0.0742
(1.00) 		0.375
(1.00) 		0.218
(1.00) 		0.771
(1.00) 		0.578
(1.00)
16p loss 11 (6%) 173 0.00791
(1.00) 		0.282
(1.00) 		0.0122
(1.00) 		0.174
(1.00) 		0.672
(1.00) 		0.49
(1.00) 		0.631
(1.00) 		0.425
(1.00) 		0.279
(1.00) 		0.837
(1.00)
16q loss 13 (7%) 171 0.0244
(1.00) 		0.108
(1.00) 		0.496
(1.00) 		0.488
(1.00) 		0.707
(1.00) 		0.123
(1.00) 		0.43
(1.00) 		0.244
(1.00) 		0.133
(1.00) 		0.283
(1.00)
17q loss 22 (12%) 162 0.00065
(0.468) 		0.00499
(1.00) 		0.0223
(1.00) 		0.243
(1.00) 		0.156
(1.00) 		0.389
(1.00) 		0.517
(1.00) 		0.313
(1.00) 		0.178
(1.00) 		0.316
(1.00)
18p loss 55 (30%) 129 0.129
(1.00) 		0.0972
(1.00) 		0.847
(1.00) 		0.442
(1.00) 		0.645
(1.00) 		0.634
(1.00) 		0.363
(1.00) 		0.903
(1.00) 		0.269
(1.00) 		0.274
(1.00)
19q loss 12 (7%) 172 0.00695
(1.00) 		0.0619
(1.00) 		0.00481
(1.00) 		0.297
(1.00) 		0.04
(1.00) 		0.015
(1.00) 		0.486
(1.00) 		0.051
(1.00) 		0.0994
(1.00) 		0.0745
(1.00)
20q loss 5 (3%) 179 0.27
(1.00) 		0.0783
(1.00) 		0.381
(1.00) 		0.848
(1.00) 		0.92
(1.00) 		0.826
(1.00) 		0.13
(1.00) 		0.603
(1.00)
'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
1Q GAIN MUTATED 29 8 9
1Q GAIN WILD-TYPE 40 59 28

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S2.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
5P GAIN MUTATED 3 11 14
5P GAIN WILD-TYPE 82 64 10

Figure S2.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S3.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
5Q GAIN MUTATED 2 7 11
5Q GAIN WILD-TYPE 83 68 13

Figure S3.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S4.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
7P GAIN MUTATED 12 23 17
7P GAIN WILD-TYPE 73 52 7

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S5.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
7Q GAIN MUTATED 12 20 16
7Q GAIN WILD-TYPE 73 55 8

Figure S5.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.045

Table S6.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
8Q GAIN MUTATED 10 25 13
8Q GAIN WILD-TYPE 75 50 11

Figure S6.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.052

Table S7.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
9Q GAIN MUTATED 0 6 6
9Q GAIN WILD-TYPE 85 69 18

Figure S7.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S8.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12P GAIN MUTATED 1 10 19
12P GAIN WILD-TYPE 84 65 5

Figure S8.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S9.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12Q GAIN MUTATED 1 4 17
12Q GAIN WILD-TYPE 84 71 7

Figure S9.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S10.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
14Q GAIN MUTATED 3 12 11
14Q GAIN WILD-TYPE 82 63 13

Figure S10.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S11.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
16P GAIN MUTATED 1 13 8
16P GAIN WILD-TYPE 84 62 16

Figure S11.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S12.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
16Q GAIN MUTATED 1 14 8
16Q GAIN WILD-TYPE 84 61 16

Figure S12.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.03

Table S13.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
17P GAIN MUTATED 3 0 6
17P GAIN WILD-TYPE 82 75 18

Figure S13.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S14.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
18P GAIN MUTATED 2 16 10
18P GAIN WILD-TYPE 83 59 14

Figure S14.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.037

Table S15.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
18Q GAIN MUTATED 1 4 7
18Q GAIN WILD-TYPE 84 71 17

Figure S15.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S16.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
20P GAIN MUTATED 7 12 15
20P GAIN WILD-TYPE 78 63 9

Figure S16.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S17.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
20Q GAIN MUTATED 8 21 16
20Q GAIN WILD-TYPE 77 54 8

Figure S17.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.2

Table S18.  Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
XQ GAIN MUTATED 2 4 7
XQ GAIN WILD-TYPE 83 71 17

Figure S18.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.045

Table S19.  Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
1P LOSS MUTATED 5 24 7
1P LOSS WILD-TYPE 80 51 17

Figure S19.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S20.  Gene #50: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
6P LOSS MUTATED 15 37 12
6P LOSS WILD-TYPE 70 38 12

Figure S20.  Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S21.  Gene #50: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 42 33
6P LOSS MUTATED 38 7 6
6P LOSS WILD-TYPE 32 35 27

Figure S21.  Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.096

Table S22.  Gene #50: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
6P LOSS MUTATED 43 11 6
6P LOSS WILD-TYPE 43 36 34

Figure S22.  Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S23.  Gene #51: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
6Q LOSS MUTATED 18 51 14
6Q LOSS WILD-TYPE 67 24 10

Figure S23.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S24.  Gene #51: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 42 33
6Q LOSS MUTATED 46 9 9
6Q LOSS WILD-TYPE 24 33 24

Figure S24.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #51: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
6Q LOSS MUTATED 49 18 11
6Q LOSS WILD-TYPE 34 30 35

Figure S25.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S26.  Gene #51: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
6Q LOSS MUTATED 61 10 7
6Q LOSS WILD-TYPE 41 32 26

Figure S26.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S27.  Gene #51: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
6Q LOSS MUTATED 46 13 19
6Q LOSS WILD-TYPE 23 54 18

Figure S27.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S28.  Gene #51: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
6Q LOSS MUTATED 54 18 6
6Q LOSS WILD-TYPE 32 29 34

Figure S28.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S29.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
9P LOSS MUTATED 18 49 8
9P LOSS WILD-TYPE 67 26 16

Figure S29.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18

Table S30.  Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
10P LOSS MUTATED 8 17 11
10P LOSS WILD-TYPE 77 58 13

Figure S30.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S31.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
10Q LOSS MUTATED 5 15 10
10Q LOSS WILD-TYPE 80 60 14

Figure S31.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.13

Table S32.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12P LOSS MUTATED 3 17 0
12P LOSS WILD-TYPE 82 58 24

Figure S32.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S33.  Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12Q LOSS MUTATED 2 25 1
12Q LOSS WILD-TYPE 83 50 23

Figure S33.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.03

Table S34.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
15Q LOSS MUTATED 3 20 7
15Q LOSS WILD-TYPE 82 55 17

Figure S34.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S35.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
17P LOSS MUTATED 7 65 8
17P LOSS WILD-TYPE 78 10 16

Figure S35.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S36.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 42 33
17P LOSS MUTATED 50 5 6
17P LOSS WILD-TYPE 20 37 27

Figure S36.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S37.  Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
17P LOSS MUTATED 49 22 6
17P LOSS WILD-TYPE 34 26 40

Figure S37.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S38.  Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
17P LOSS MUTATED 37 39 1
17P LOSS WILD-TYPE 37 36 27

Figure S38.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S39.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
17P LOSS MUTATED 47 16 8 6
17P LOSS WILD-TYPE 22 24 27 27

Figure S39.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S40.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
17P LOSS MUTATED 58 14 5
17P LOSS WILD-TYPE 44 28 28

Figure S40.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S41.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
17P LOSS MUTATED 46 13 17
17P LOSS WILD-TYPE 23 54 20

Figure S41.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S42.  Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
17P LOSS MUTATED 49 22 5
17P LOSS WILD-TYPE 37 25 35

Figure S42.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S43.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
18Q LOSS MUTATED 36 62 8
18Q LOSS WILD-TYPE 49 13 16

Figure S43.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
18Q LOSS MUTATED 59 31 11
18Q LOSS WILD-TYPE 27 16 29

Figure S44.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.15

Table S45.  Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
19P LOSS MUTATED 15 1 2
19P LOSS WILD-TYPE 54 66 35

Figure S45.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.24

Table S46.  Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
20P LOSS MUTATED 2 16 2
20P LOSS WILD-TYPE 83 59 22

Figure S46.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S47.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
21Q LOSS MUTATED 11 38 9
21Q LOSS WILD-TYPE 74 37 15

Figure S47.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S48.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
22Q LOSS MUTATED 7 30 9
22Q LOSS WILD-TYPE 78 45 15

Figure S48.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S49.  Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
XQ LOSS MUTATED 0 13 5
XQ LOSS WILD-TYPE 85 62 19

Figure S49.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

  • Molecular subtypes file = PAAD-TP.transferedmergedcluster.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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