Correlation between copy number variations of arm-level result and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JW8CRF
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 80 arm-level events and 8 molecular subtypes across 184 patients, 57 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level 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, 57 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
22q gain 31 (17%) 153 2e-05
(0.0125)
2e-05
(0.0125)
0.0002
(0.119)
0.00016
(0.0957)
2e-05
(0.0125)
3e-05
(0.0185)
1e-05
(0.0064)
2e-05
(0.0125)
16q loss 53 (29%) 131 1e-05
(0.0064)
2e-05
(0.0125)
0.00041
(0.239)
0.00015
(0.0898)
1e-05
(0.0064)
3e-05
(0.0185)
1e-05
(0.0064)
1e-05
(0.0064)
13q gain 43 (23%) 141 0.00248
(1.00)
1e-05
(0.0064)
0.00112
(0.637)
1e-05
(0.0064)
1e-05
(0.0064)
5e-05
(0.0305)
0.00018
(0.107)
1e-05
(0.0064)
5p loss 46 (25%) 138 0.00028
(0.165)
1e-05
(0.0064)
0.00513
(1.00)
0.0357
(1.00)
8e-05
(0.0483)
2e-05
(0.0125)
0.00026
(0.154)
4e-05
(0.0245)
16p loss 54 (29%) 130 0.00048
(0.279)
0.00014
(0.084)
0.00204
(1.00)
0.00032
(0.188)
0.00024
(0.142)
0.00016
(0.0957)
0.00032
(0.188)
0.00013
(0.0781)
22q loss 72 (39%) 112 5e-05
(0.0305)
1e-05
(0.0064)
0.0198
(1.00)
0.0872
(1.00)
6e-05
(0.0364)
0.00016
(0.0957)
3e-05
(0.0185)
2e-05
(0.0125)
3p loss 93 (51%) 91 2e-05
(0.0125)
7e-05
(0.0424)
0.00254
(1.00)
0.00302
(1.00)
1e-05
(0.0064)
1e-05
(0.0064)
0.00117
(0.663)
1e-05
(0.0064)
20q gain 115 (62%) 69 5e-05
(0.0305)
0.00031
(0.183)
0.0452
(1.00)
0.0813
(1.00)
0.0004
(0.234)
0.00065
(0.375)
0.00585
(1.00)
4e-05
(0.0245)
17p loss 71 (39%) 113 0.00237
(1.00)
0.0001
(0.0603)
0.00323
(1.00)
0.00165
(0.931)
1e-05
(0.0064)
0.00131
(0.741)
0.062
(1.00)
0.00011
(0.0662)
3q gain 77 (42%) 107 1e-05
(0.0064)
0.0203
(1.00)
0.286
(1.00)
0.0301
(1.00)
0.308
(1.00)
0.241
(1.00)
0.167
(1.00)
0.411
(1.00)
5p gain 76 (41%) 108 4e-05
(0.0245)
0.0273
(1.00)
0.092
(1.00)
0.158
(1.00)
0.0134
(1.00)
0.0333
(1.00)
0.0501
(1.00)
0.0164
(1.00)
10q loss 49 (27%) 135 7e-05
(0.0424)
0.00103
(0.588)
0.096
(1.00)
0.0278
(1.00)
0.00161
(0.91)
0.0023
(1.00)
0.0169
(1.00)
0.00173
(0.974)
12p loss 33 (18%) 151 0.0971
(1.00)
0.00102
(0.583)
0.0284
(1.00)
0.0011
(0.627)
0.00266
(1.00)
0.00199
(1.00)
0.0143
(1.00)
0.00022
(0.13)
18q loss 102 (55%) 82 0.0974
(1.00)
0.0114
(1.00)
0.118
(1.00)
0.237
(1.00)
0.0213
(1.00)
0.00229
(1.00)
0.0474
(1.00)
0.00035
(0.205)
1p gain 37 (20%) 147 0.648
(1.00)
0.224
(1.00)
0.673
(1.00)
0.692
(1.00)
1
(1.00)
0.884
(1.00)
0.453
(1.00)
0.965
(1.00)
1q gain 63 (34%) 121 0.0618
(1.00)
0.207
(1.00)
0.24
(1.00)
0.113
(1.00)
0.383
(1.00)
0.488
(1.00)
0.507
(1.00)
0.628
(1.00)
2p gain 61 (33%) 123 0.012
(1.00)
0.0314
(1.00)
0.147
(1.00)
0.416
(1.00)
0.037
(1.00)
0.342
(1.00)
0.00283
(1.00)
0.507
(1.00)
2q gain 46 (25%) 138 0.267
(1.00)
0.0701
(1.00)
0.502
(1.00)
0.178
(1.00)
0.486
(1.00)
0.768
(1.00)
0.256
(1.00)
0.886
(1.00)
3p gain 31 (17%) 153 0.305
(1.00)
0.447
(1.00)
0.274
(1.00)
0.935
(1.00)
0.779
(1.00)
0.609
(1.00)
0.862
(1.00)
0.616
(1.00)
4p gain 19 (10%) 165 0.529
(1.00)
0.857
(1.00)
0.113
(1.00)
1
(1.00)
1
(1.00)
0.959
(1.00)
0.98
(1.00)
1
(1.00)
4q gain 18 (10%) 166 0.0869
(1.00)
0.327
(1.00)
0.00261
(1.00)
0.367
(1.00)
0.306
(1.00)
0.545
(1.00)
0.558
(1.00)
0.491
(1.00)
5q gain 20 (11%) 164 0.409
(1.00)
0.779
(1.00)
0.469
(1.00)
0.604
(1.00)
0.699
(1.00)
0.986
(1.00)
0.752
(1.00)
0.793
(1.00)
6p gain 38 (21%) 146 0.241
(1.00)
0.369
(1.00)
0.7
(1.00)
0.388
(1.00)
0.251
(1.00)
0.103
(1.00)
0.115
(1.00)
0.0303
(1.00)
6q gain 33 (18%) 151 0.235
(1.00)
0.328
(1.00)
0.706
(1.00)
0.247
(1.00)
0.377
(1.00)
0.286
(1.00)
0.149
(1.00)
0.0829
(1.00)
7p gain 110 (60%) 74 0.348
(1.00)
0.235
(1.00)
0.115
(1.00)
0.0273
(1.00)
0.0748
(1.00)
0.208
(1.00)
0.555
(1.00)
0.11
(1.00)
7q gain 89 (48%) 95 0.666
(1.00)
0.289
(1.00)
0.697
(1.00)
0.0231
(1.00)
0.423
(1.00)
0.745
(1.00)
0.836
(1.00)
0.124
(1.00)
8p gain 68 (37%) 116 0.317
(1.00)
0.537
(1.00)
0.773
(1.00)
0.625
(1.00)
0.373
(1.00)
0.834
(1.00)
0.56
(1.00)
0.737
(1.00)
8q gain 101 (55%) 83 0.466
(1.00)
0.286
(1.00)
0.406
(1.00)
0.406
(1.00)
0.292
(1.00)
0.726
(1.00)
0.913
(1.00)
0.976
(1.00)
9p gain 16 (9%) 168 0.799
(1.00)
0.482
(1.00)
0.451
(1.00)
0.795
(1.00)
0.564
(1.00)
0.184
(1.00)
0.587
(1.00)
0.468
(1.00)
9q gain 33 (18%) 151 0.394
(1.00)
0.257
(1.00)
0.335
(1.00)
0.942
(1.00)
0.384
(1.00)
0.029
(1.00)
0.673
(1.00)
0.0798
(1.00)
10p gain 40 (22%) 144 0.0363
(1.00)
0.0274
(1.00)
0.201
(1.00)
0.31
(1.00)
0.119
(1.00)
0.218
(1.00)
0.0556
(1.00)
0.0753
(1.00)
10q gain 30 (16%) 154 0.015
(1.00)
0.0342
(1.00)
0.15
(1.00)
0.232
(1.00)
0.0804
(1.00)
0.0701
(1.00)
0.0518
(1.00)
0.0224
(1.00)
11p gain 39 (21%) 145 0.646
(1.00)
0.917
(1.00)
0.149
(1.00)
0.677
(1.00)
0.345
(1.00)
0.318
(1.00)
0.875
(1.00)
0.481
(1.00)
11q gain 29 (16%) 155 0.288
(1.00)
0.316
(1.00)
0.105
(1.00)
0.0228
(1.00)
0.0477
(1.00)
0.174
(1.00)
0.0816
(1.00)
0.0772
(1.00)
12p gain 58 (32%) 126 0.0226
(1.00)
0.00385
(1.00)
0.00857
(1.00)
0.00555
(1.00)
0.00592
(1.00)
0.00283
(1.00)
0.0033
(1.00)
0.00938
(1.00)
12q gain 38 (21%) 146 0.174
(1.00)
0.321
(1.00)
0.427
(1.00)
0.28
(1.00)
0.393
(1.00)
0.45
(1.00)
0.268
(1.00)
0.258
(1.00)
14q gain 48 (26%) 136 0.0351
(1.00)
0.084
(1.00)
0.139
(1.00)
0.0577
(1.00)
0.0385
(1.00)
0.035
(1.00)
0.138
(1.00)
0.0526
(1.00)
15q gain 30 (16%) 154 0.389
(1.00)
0.28
(1.00)
0.35
(1.00)
0.034
(1.00)
0.454
(1.00)
0.375
(1.00)
0.319
(1.00)
0.365
(1.00)
16p gain 41 (22%) 143 0.00378
(1.00)
0.0981
(1.00)
0.0195
(1.00)
0.00451
(1.00)
0.0257
(1.00)
0.0345
(1.00)
0.0829
(1.00)
0.0566
(1.00)
16q gain 38 (21%) 146 0.00082
(0.471)
0.0272
(1.00)
0.00905
(1.00)
0.0032
(1.00)
0.0123
(1.00)
0.00619
(1.00)
0.00289
(1.00)
0.00677
(1.00)
17p gain 33 (18%) 151 0.0507
(1.00)
0.0314
(1.00)
0.302
(1.00)
0.243
(1.00)
0.366
(1.00)
0.451
(1.00)
0.543
(1.00)
0.552
(1.00)
17q gain 45 (24%) 139 0.14
(1.00)
0.206
(1.00)
0.37
(1.00)
0.411
(1.00)
0.854
(1.00)
0.938
(1.00)
0.992
(1.00)
0.637
(1.00)
18p gain 50 (27%) 134 0.0617
(1.00)
0.377
(1.00)
0.644
(1.00)
0.333
(1.00)
0.0228
(1.00)
0.873
(1.00)
0.937
(1.00)
0.812
(1.00)
18q gain 26 (14%) 158 0.738
(1.00)
0.815
(1.00)
0.972
(1.00)
0.772
(1.00)
0.398
(1.00)
0.303
(1.00)
0.382
(1.00)
0.227
(1.00)
19p gain 28 (15%) 156 0.43
(1.00)
0.282
(1.00)
0.263
(1.00)
0.62
(1.00)
0.381
(1.00)
0.906
(1.00)
0.537
(1.00)
0.497
(1.00)
19q gain 38 (21%) 146 0.101
(1.00)
0.14
(1.00)
0.178
(1.00)
0.101
(1.00)
0.0442
(1.00)
0.353
(1.00)
0.398
(1.00)
0.111
(1.00)
20p gain 108 (59%) 76 0.00464
(1.00)
0.0582
(1.00)
0.182
(1.00)
0.532
(1.00)
0.0991
(1.00)
0.263
(1.00)
0.385
(1.00)
0.0577
(1.00)
21q gain 18 (10%) 166 1
(1.00)
0.564
(1.00)
0.0291
(1.00)
0.297
(1.00)
0.213
(1.00)
0.426
(1.00)
0.387
(1.00)
0.229
(1.00)
xq gain 36 (20%) 148 0.0631
(1.00)
0.0375
(1.00)
0.221
(1.00)
0.0658
(1.00)
0.0118
(1.00)
0.0194
(1.00)
0.0641
(1.00)
0.0763
(1.00)
1p loss 38 (21%) 146 0.00904
(1.00)
0.0232
(1.00)
0.00273
(1.00)
0.234
(1.00)
0.0205
(1.00)
0.032
(1.00)
0.00961
(1.00)
0.044
(1.00)
1q loss 22 (12%) 162 0.0386
(1.00)
0.231
(1.00)
0.114
(1.00)
0.175
(1.00)
0.0745
(1.00)
0.12
(1.00)
0.0235
(1.00)
0.127
(1.00)
2p loss 11 (6%) 173 0.855
(1.00)
0.134
(1.00)
0.0885
(1.00)
0.819
(1.00)
0.381
(1.00)
0.00178
(1.00)
0.833
(1.00)
0.373
(1.00)
2q loss 18 (10%) 166 0.356
(1.00)
0.0319
(1.00)
0.272
(1.00)
0.322
(1.00)
0.0643
(1.00)
0.00705
(1.00)
0.282
(1.00)
0.0878
(1.00)
3q loss 33 (18%) 151 0.857
(1.00)
0.67
(1.00)
0.312
(1.00)
0.51
(1.00)
0.653
(1.00)
0.913
(1.00)
0.663
(1.00)
0.891
(1.00)
4p loss 105 (57%) 79 0.0006
(0.347)
0.0762
(1.00)
0.0194
(1.00)
0.153
(1.00)
0.0177
(1.00)
0.285
(1.00)
0.184
(1.00)
0.41
(1.00)
4q loss 87 (47%) 97 0.00043
(0.251)
0.0461
(1.00)
0.00372
(1.00)
0.418
(1.00)
0.0391
(1.00)
0.221
(1.00)
0.122
(1.00)
0.0857
(1.00)
5q loss 86 (47%) 98 0.0194
(1.00)
0.00897
(1.00)
0.0921
(1.00)
0.681
(1.00)
0.0201
(1.00)
0.113
(1.00)
0.211
(1.00)
0.0925
(1.00)
6p loss 39 (21%) 145 0.339
(1.00)
0.621
(1.00)
0.0761
(1.00)
0.667
(1.00)
0.369
(1.00)
0.366
(1.00)
0.861
(1.00)
0.462
(1.00)
6q loss 39 (21%) 145 0.334
(1.00)
0.662
(1.00)
0.273
(1.00)
0.456
(1.00)
0.488
(1.00)
0.68
(1.00)
0.831
(1.00)
0.275
(1.00)
7p loss 13 (7%) 171 0.817
(1.00)
0.555
(1.00)
0.00843
(1.00)
0.221
(1.00)
0.578
(1.00)
0.586
(1.00)
0.301
(1.00)
0.649
(1.00)
7q loss 22 (12%) 162 0.173
(1.00)
0.337
(1.00)
0.0485
(1.00)
0.885
(1.00)
0.585
(1.00)
0.858
(1.00)
0.227
(1.00)
0.804
(1.00)
8p loss 63 (34%) 121 0.00468
(1.00)
0.463
(1.00)
0.889
(1.00)
0.71
(1.00)
0.309
(1.00)
0.594
(1.00)
0.387
(1.00)
0.306
(1.00)
8q loss 23 (12%) 161 0.781
(1.00)
1
(1.00)
0.981
(1.00)
0.457
(1.00)
0.824
(1.00)
0.258
(1.00)
0.713
(1.00)
1
(1.00)
9p loss 101 (55%) 83 0.089
(1.00)
0.113
(1.00)
0.0519
(1.00)
0.176
(1.00)
0.529
(1.00)
0.569
(1.00)
0.785
(1.00)
0.543
(1.00)
9q loss 65 (35%) 119 0.0633
(1.00)
0.178
(1.00)
0.838
(1.00)
0.446
(1.00)
0.648
(1.00)
0.23
(1.00)
0.0686
(1.00)
0.795
(1.00)
10p loss 50 (27%) 134 0.00193
(1.00)
0.00446
(1.00)
0.0599
(1.00)
0.112
(1.00)
0.00211
(1.00)
0.00811
(1.00)
0.0125
(1.00)
0.00239
(1.00)
11p loss 52 (28%) 132 0.1
(1.00)
0.228
(1.00)
0.76
(1.00)
0.405
(1.00)
0.901
(1.00)
0.651
(1.00)
0.822
(1.00)
0.77
(1.00)
11q loss 58 (32%) 126 0.00053
(0.308)
0.0427
(1.00)
0.362
(1.00)
0.0591
(1.00)
0.0143
(1.00)
0.133
(1.00)
0.0771
(1.00)
0.0682
(1.00)
12q loss 31 (17%) 153 0.165
(1.00)
0.0027
(1.00)
0.0747
(1.00)
0.0135
(1.00)
0.0246
(1.00)
0.0124
(1.00)
0.00905
(1.00)
0.00709
(1.00)
13q loss 67 (36%) 117 0.0163
(1.00)
0.0664
(1.00)
0.249
(1.00)
0.0481
(1.00)
0.0431
(1.00)
0.148
(1.00)
0.0584
(1.00)
0.105
(1.00)
14q loss 45 (24%) 139 0.00054
(0.313)
0.00497
(1.00)
0.00216
(1.00)
0.00254
(1.00)
0.0294
(1.00)
0.00305
(1.00)
0.0371
(1.00)
0.001
(0.573)
15q loss 57 (31%) 127 0.285
(1.00)
0.03
(1.00)
0.259
(1.00)
0.509
(1.00)
0.0969
(1.00)
0.00556
(1.00)
0.323
(1.00)
0.00081
(0.467)
17q loss 25 (14%) 159 0.792
(1.00)
0.605
(1.00)
0.871
(1.00)
0.92
(1.00)
0.516
(1.00)
0.888
(1.00)
0.363
(1.00)
0.868
(1.00)
18p loss 71 (39%) 113 0.0121
(1.00)
0.00091
(0.522)
0.222
(1.00)
0.0417
(1.00)
0.00115
(0.653)
0.0233
(1.00)
0.025
(1.00)
0.00581
(1.00)
19p loss 65 (35%) 119 0.0491
(1.00)
0.393
(1.00)
0.219
(1.00)
0.236
(1.00)
0.0623
(1.00)
0.121
(1.00)
0.0957
(1.00)
0.00943
(1.00)
19q loss 52 (28%) 132 0.00451
(1.00)
0.111
(1.00)
0.307
(1.00)
0.0602
(1.00)
0.0594
(1.00)
0.0935
(1.00)
0.0188
(1.00)
0.00909
(1.00)
20p loss 19 (10%) 165 0.582
(1.00)
0.858
(1.00)
0.555
(1.00)
0.19
(1.00)
0.598
(1.00)
0.419
(1.00)
0.687
(1.00)
0.48
(1.00)
20q loss 8 (4%) 176 0.899
(1.00)
0.704
(1.00)
0.265
(1.00)
0.317
(1.00)
1
(1.00)
0.674
(1.00)
0.747
(1.00)
0.445
(1.00)
21q loss 106 (58%) 78 0.0313
(1.00)
0.006
(1.00)
0.0588
(1.00)
0.258
(1.00)
0.0206
(1.00)
0.147
(1.00)
0.0425
(1.00)
0.0851
(1.00)
xq loss 43 (23%) 141 0.0152
(1.00)
0.0314
(1.00)
0.272
(1.00)
0.123
(1.00)
0.167
(1.00)
0.00062
(0.358)
0.0352
(1.00)
0.0146
(1.00)
'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S1.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
3Q GAIN MUTATED 29 5 43
3Q GAIN WILD-TYPE 36 39 32

Figure S1.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
5P GAIN MUTATED 22 9 45
5P GAIN WILD-TYPE 43 35 30

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

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S3.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
13Q GAIN MUTATED 31 5 7
13Q GAIN WILD-TYPE 45 27 69

Figure S3.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S4.  Gene #25: '13q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 74 12
13Q GAIN MUTATED 12 6 8
13Q GAIN WILD-TYPE 27 68 4

Figure S4.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S5.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
13Q GAIN MUTATED 34 9 0
13Q GAIN WILD-TYPE 50 78 12

Figure S5.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S6.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
13Q GAIN MUTATED 25 9 5 4
13Q GAIN WILD-TYPE 37 17 57 29

Figure S6.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
13Q GAIN MUTATED 28 8 4 3
13Q GAIN WILD-TYPE 38 58 31 8

Figure S7.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S8.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
13Q GAIN MUTATED 26 8 9
13Q GAIN WILD-TYPE 36 14 85

Figure S8.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S9.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
20Q GAIN MUTATED 54 21 40
20Q GAIN WILD-TYPE 11 23 35

Figure S9.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.18

Table S10.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
20Q GAIN MUTATED 60 18 37
20Q GAIN WILD-TYPE 16 14 39

Figure S10.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.23

Table S11.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
20Q GAIN MUTATED 65 44 5
20Q GAIN WILD-TYPE 19 43 7

Figure S11.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S12.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
20Q GAIN MUTATED 52 15 46
20Q GAIN WILD-TYPE 10 7 48

Figure S12.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S13.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
22Q GAIN MUTATED 3 3 25
22Q GAIN WILD-TYPE 62 41 50

Figure S13.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S14.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
22Q GAIN MUTATED 3 3 25
22Q GAIN WILD-TYPE 73 29 51

Figure S14.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S15.  Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 11 26 31 11
22Q GAIN MUTATED 1 1 10 10 1
22Q GAIN WILD-TYPE 45 10 16 21 10

Figure S15.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.096

Table S16.  Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 74 12
22Q GAIN MUTATED 1 22 0
22Q GAIN WILD-TYPE 38 52 12

Figure S16.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S17.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
22Q GAIN MUTATED 3 26 2
22Q GAIN WILD-TYPE 81 61 10

Figure S17.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S18.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
22Q GAIN MUTATED 2 1 22 6
22Q GAIN WILD-TYPE 60 25 40 27

Figure S18.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S19.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
22Q GAIN MUTATED 2 25 3 1
22Q GAIN WILD-TYPE 64 41 32 10

Figure S19.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
22Q GAIN MUTATED 2 1 28
22Q GAIN WILD-TYPE 60 21 66

Figure S20.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S21.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
3P LOSS MUTATED 24 15 54
3P LOSS WILD-TYPE 41 29 21

Figure S21.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S22.  Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
3P LOSS MUTATED 24 18 51
3P LOSS WILD-TYPE 52 14 25

Figure S22.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S23.  Gene #45: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
3P LOSS MUTATED 27 60 6
3P LOSS WILD-TYPE 57 27 6

Figure S23.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S24.  Gene #45: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
3P LOSS MUTATED 20 8 42 23
3P LOSS WILD-TYPE 42 18 20 10

Figure S24.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S25.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
3P LOSS MUTATED 19 8 64
3P LOSS WILD-TYPE 43 14 30

Figure S25.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S26.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
5P LOSS MUTATED 27 10 9
5P LOSS WILD-TYPE 38 34 66

Figure S26.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S27.  Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
5P LOSS MUTATED 32 2 12
5P LOSS WILD-TYPE 44 30 64

Figure S27.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.048

Table S28.  Gene #49: '5p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
5P LOSS MUTATED 33 12 0
5P LOSS WILD-TYPE 51 75 12

Figure S28.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S29.  Gene #49: '5p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
5P LOSS MUTATED 29 5 7 4
5P LOSS WILD-TYPE 33 21 55 29

Figure S29.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

Table S30.  Gene #49: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
5P LOSS MUTATED 28 11 3 1
5P LOSS WILD-TYPE 38 55 32 10

Figure S30.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S31.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
5P LOSS MUTATED 28 4 11
5P LOSS WILD-TYPE 34 18 83

Figure S31.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S32.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
10Q LOSS MUTATED 9 7 33
10Q LOSS WILD-TYPE 56 37 42

Figure S32.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S33.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
12P LOSS MUTATED 16 9 8
12P LOSS WILD-TYPE 46 13 86

Figure S33.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.084

Table S34.  Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
16P LOSS MUTATED 35 7 12
16P LOSS WILD-TYPE 41 25 64

Figure S34.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S35.  Gene #68: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 74 12
16P LOSS MUTATED 15 10 7
16P LOSS WILD-TYPE 24 64 5

Figure S35.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S36.  Gene #68: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
16P LOSS MUTATED 37 14 2
16P LOSS WILD-TYPE 47 73 10

Figure S36.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.096

Table S37.  Gene #68: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16P LOSS MUTATED 30 8 10 5
16P LOSS WILD-TYPE 32 18 52 28

Figure S37.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S38.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
16P LOSS MUTATED 31 10 7 3
16P LOSS WILD-TYPE 35 56 28 8

Figure S38.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S39.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
16P LOSS MUTATED 28 8 15
16P LOSS WILD-TYPE 34 14 79

Figure S39.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S40.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
16Q LOSS MUTATED 33 12 8
16Q LOSS WILD-TYPE 32 32 67

Figure S40.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S41.  Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
16Q LOSS MUTATED 35 8 10
16Q LOSS WILD-TYPE 41 24 66

Figure S41.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.24

Table S42.  Gene #69: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 11 26 31 11
16Q LOSS MUTATED 23 3 3 3 2
16Q LOSS WILD-TYPE 23 8 23 28 9

Figure S42.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.09

Table S43.  Gene #69: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 74 12
16Q LOSS MUTATED 17 10 7
16Q LOSS WILD-TYPE 22 64 5

Figure S43.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S44.  Gene #69: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
16Q LOSS MUTATED 40 12 0
16Q LOSS WILD-TYPE 44 75 12

Figure S44.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S45.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16Q LOSS MUTATED 31 9 8 4
16Q LOSS WILD-TYPE 31 17 54 29

Figure S45.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S46.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
16Q LOSS MUTATED 35 10 4 1
16Q LOSS WILD-TYPE 31 56 31 10

Figure S46.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S47.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
16Q LOSS MUTATED 31 7 12
16Q LOSS WILD-TYPE 31 15 82

Figure S47.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.06

Table S48.  Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
17P LOSS MUTATED 43 10 18
17P LOSS WILD-TYPE 33 22 58

Figure S48.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S49.  Gene #70: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
17P LOSS MUTATED 46 25 0
17P LOSS WILD-TYPE 38 62 12

Figure S49.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.066

Table S50.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
17P LOSS MUTATED 33 13 23
17P LOSS WILD-TYPE 29 9 71

Figure S50.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S51.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
18Q LOSS MUTATED 36 20 44
18Q LOSS WILD-TYPE 26 2 50

Figure S51.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S52.  Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
22Q LOSS MUTATED 40 13 19
22Q LOSS WILD-TYPE 25 31 56

Figure S52.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S53.  Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
22Q LOSS MUTATED 45 10 17
22Q LOSS WILD-TYPE 31 22 59

Figure S53.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S54.  Gene #79: '22q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
22Q LOSS MUTATED 47 24 1
22Q LOSS WILD-TYPE 37 63 11

Figure S54.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.096

Table S55.  Gene #79: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
22Q LOSS MUTATED 37 11 14 10
22Q LOSS WILD-TYPE 25 15 48 23

Figure S55.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S56.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
22Q LOSS MUTATED 43 18 7 3
22Q LOSS WILD-TYPE 23 48 28 8

Figure S56.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S57.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
22Q LOSS MUTATED 39 9 23
22Q LOSS WILD-TYPE 23 13 71

Figure S57.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 8

  • 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)