Correlation between copy number variations of arm-level result and molecular subtypes
Rectum Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1930SMG
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 12 molecular subtypes across 165 patients, 70 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MRNA_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 8p gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 13q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 18p gain cnv correlated to 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'RPPA_CNMF'.

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

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 9q loss cnv correlated to 'MRNA_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 11q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to '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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 70 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
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 Fisher's exact test Fisher's exact test
7p gain 102 (62%) 63 0.0362
(0.36)
0.00504
(0.131)
1e-05
(0.00107)
0.137
(0.62)
0.841
(1.00)
0.0175
(0.241)
0.00079
(0.033)
1e-05
(0.00107)
0.0387
(0.364)
0.097
(0.523)
0.597
(0.884)
0.371
(0.768)
7q gain 87 (53%) 78 0.0787
(0.494)
0.0114
(0.189)
2e-05
(0.00192)
0.21
(0.658)
0.954
(1.00)
0.0234
(0.28)
0.00503
(0.131)
0.00101
(0.0388)
0.248
(0.68)
0.486
(0.846)
1
(1.00)
0.553
(0.877)
16q gain 41 (25%) 124 0.188
(0.658)
0.509
(0.855)
1e-05
(0.00107)
0.0065
(0.152)
0.698
(0.932)
0.0499
(0.39)
0.00939
(0.173)
0.105
(0.548)
0.00879
(0.169)
0.245
(0.678)
0.59
(0.881)
0.76
(0.961)
11q loss 30 (18%) 135 0.00787
(0.162)
0.314
(0.715)
0.00091
(0.0364)
0.275
(0.687)
0.944
(1.00)
0.436
(0.821)
0.00717
(0.156)
0.00795
(0.162)
0.222
(0.659)
0.377
(0.774)
0.277
(0.687)
0.22
(0.659)
2p gain 40 (24%) 125 0.758
(0.961)
0.00736
(0.157)
0.00021
(0.0134)
0.0946
(0.52)
0.547
(0.877)
0.676
(0.928)
0.0227
(0.276)
0.0132
(0.204)
0.178
(0.658)
0.0515
(0.395)
0.667
(0.925)
0.612
(0.891)
13q gain 114 (69%) 51 0.314
(0.715)
0.299
(0.7)
1e-05
(0.00107)
0.0582
(0.419)
0.562
(0.877)
0.106
(0.551)
0.00609
(0.15)
0.00029
(0.0155)
0.042
(0.373)
0.0394
(0.367)
1
(1.00)
0.828
(0.997)
2q gain 41 (25%) 124 0.365
(0.768)
0.032
(0.344)
0.00162
(0.0555)
0.0287
(0.32)
0.793
(0.977)
0.582
(0.881)
0.0424
(0.373)
0.00197
(0.0591)
0.269
(0.687)
0.235
(0.669)
0.134
(0.62)
0.192
(0.658)
8p gain 40 (24%) 125 0.448
(0.823)
0.252
(0.683)
0.0069
(0.155)
0.0379
(0.364)
0.207
(0.658)
0.00625
(0.15)
0.579
(0.881)
0.299
(0.7)
0.966
(1.00)
0.0823
(0.497)
0.827
(0.997)
0.0529
(0.397)
8q gain 90 (55%) 75 0.0884
(0.511)
0.195
(0.658)
1e-05
(0.00107)
0.0213
(0.269)
0.556
(0.877)
0.21
(0.658)
0.372
(0.768)
0.205
(0.658)
0.573
(0.88)
0.0806
(0.496)
0.0114
(0.189)
0.499
(0.855)
11q gain 27 (16%) 138 0.142
(0.63)
0.432
(0.817)
0.0189
(0.251)
0.121
(0.596)
0.991
(1.00)
0.262
(0.687)
0.00495
(0.131)
0.0018
(0.0576)
0.168
(0.658)
0.443
(0.821)
0.178
(0.658)
0.274
(0.687)
16p gain 41 (25%) 124 0.453
(0.826)
0.777
(0.967)
0.00023
(0.0138)
0.0161
(0.227)
0.887
(1.00)
0.347
(0.757)
0.127
(0.601)
0.368
(0.768)
0.351
(0.757)
0.678
(0.928)
0.638
(0.906)
0.944
(1.00)
20q gain 146 (88%) 19 0.126
(0.6)
0.165
(0.656)
5e-05
(0.004)
0.0792
(0.494)
0.0374
(0.364)
0.244
(0.678)
0.609
(0.889)
0.00072
(0.0314)
0.332
(0.739)
0.398
(0.789)
0.501
(0.855)
0.695
(0.932)
6q loss 23 (14%) 142 0.0503
(0.39)
0.737
(0.954)
0.0157
(0.225)
0.137
(0.62)
0.206
(0.658)
0.898
(1.00)
0.0778
(0.494)
0.145
(0.632)
0.142
(0.63)
0.298
(0.7)
0.011
(0.189)
0.483
(0.845)
8p loss 75 (45%) 90 0.096
(0.523)
0.424
(0.814)
0.00158
(0.0555)
0.479
(0.842)
0.17
(0.658)
0.278
(0.687)
0.0174
(0.241)
0.182
(0.658)
1
(1.00)
0.852
(1.00)
0.661
(0.922)
0.0503
(0.39)
9q loss 23 (14%) 142 0.0134
(0.204)
0.805
(0.978)
0.286
(0.694)
0.223
(0.659)
0.755
(0.961)
0.948
(1.00)
0.534
(0.866)
0.197
(0.658)
0.667
(0.925)
0.00191
(0.0591)
0.76
(0.961)
0.068
(0.46)
10q loss 38 (23%) 127 0.0133
(0.204)
0.126
(0.6)
0.0196
(0.251)
0.087
(0.506)
0.0924
(0.513)
0.0156
(0.225)
0.406
(0.798)
0.0731
(0.481)
0.93
(1.00)
0.0868
(0.506)
0.89
(1.00)
0.737
(0.954)
11p loss 24 (15%) 141 0.0275
(0.314)
0.485
(0.846)
0.00066
(0.0302)
0.196
(0.658)
0.589
(0.881)
0.568
(0.879)
0.0106
(0.185)
0.204
(0.658)
0.913
(1.00)
0.713
(0.944)
0.218
(0.658)
0.229
(0.664)
18p loss 128 (78%) 37 0.15
(0.633)
0.672
(0.926)
1e-05
(0.00107)
0.0357
(0.36)
0.551
(0.877)
0.316
(0.717)
0.0809
(0.496)
0.0141
(0.212)
0.0845
(0.5)
0.164
(0.656)
0.8
(0.978)
0.833
(1)
1p gain 12 (7%) 153 0.00837
(0.167)
0.609
(0.889)
0.409
(0.801)
0.232
(0.664)
0.251
(0.683)
0.264
(0.687)
0.391
(0.782)
0.594
(0.883)
1
(1.00)
0.461
(0.829)
0.576
(0.881)
0.586
(0.881)
1q gain 33 (20%) 132 0.178
(0.658)
0.272
(0.687)
0.012
(0.195)
0.284
(0.693)
0.23
(0.664)
0.179
(0.658)
0.0774
(0.494)
0.953
(1.00)
0.919
(1.00)
0.841
(1.00)
1
(1.00)
0.35
(0.757)
5p gain 35 (21%) 130 0.804
(0.978)
0.119
(0.592)
0.0195
(0.251)
0.0841
(0.5)
0.518
(0.855)
0.726
(0.947)
0.11
(0.564)
0.00042
(0.0202)
0.479
(0.842)
1
(1.00)
0.757
(0.961)
0.602
(0.884)
6p gain 40 (24%) 125 0.153
(0.64)
0.594
(0.883)
0.00011
(0.00812)
0.351
(0.757)
0.518
(0.855)
0.329
(0.737)
0.901
(1.00)
0.501
(0.855)
0.16
(0.648)
0.494
(0.855)
0.461
(0.829)
0.962
(1.00)
6q gain 35 (21%) 130 0.447
(0.823)
0.193
(0.658)
3e-05
(0.00262)
0.26
(0.687)
0.631
(0.9)
0.453
(0.826)
0.501
(0.855)
0.53
(0.86)
0.0529
(0.397)
0.422
(0.813)
0.206
(0.658)
0.558
(0.877)
18p gain 8 (5%) 157 0.503
(0.855)
0.731
(0.949)
0.261
(0.687)
0.0127
(0.203)
0.936
(1.00)
0.907
(1.00)
0.878
(1.00)
0.384
(0.78)
0.632
(0.9)
0.558
(0.877)
1
(1.00)
1
(1.00)
19p gain 33 (20%) 132 0.26
(0.687)
0.455
(0.827)
0.00212
(0.0617)
0.828
(0.997)
0.984
(1.00)
0.196
(0.658)
0.856
(1.00)
0.0622
(0.433)
0.882
(1.00)
0.918
(1.00)
0.516
(0.855)
0.277
(0.687)
19q gain 33 (20%) 132 0.572
(0.88)
0.653
(0.915)
0.0145
(0.214)
0.289
(0.699)
0.882
(1.00)
0.664
(0.924)
0.803
(0.978)
0.149
(0.633)
0.523
(0.855)
0.496
(0.855)
0.518
(0.855)
0.279
(0.687)
20p gain 105 (64%) 60 0.355
(0.762)
0.285
(0.693)
0.0548
(0.408)
0.588
(0.881)
0.00242
(0.0683)
0.441
(0.821)
0.216
(0.658)
0.823
(0.997)
0.175
(0.658)
0.148
(0.633)
0.187
(0.658)
0.524
(0.856)
1p loss 46 (28%) 119 0.384
(0.78)
0.0694
(0.46)
0.00134
(0.0495)
0.213
(0.658)
0.395
(0.785)
0.173
(0.658)
0.252
(0.683)
0.17
(0.658)
0.329
(0.737)
0.61
(0.889)
0.926
(1.00)
0.443
(0.821)
1q loss 28 (17%) 137 0.651
(0.915)
0.194
(0.658)
0.00041
(0.0202)
0.222
(0.659)
0.762
(0.961)
0.151
(0.634)
0.0336
(0.351)
0.382
(0.779)
0.389
(0.781)
0.372
(0.768)
0.914
(1.00)
0.122
(0.597)
3q loss 10 (6%) 155 0.504
(0.855)
0.856
(1.00)
0.105
(0.548)
0.154
(0.641)
0.231
(0.664)
0.515
(0.855)
0.21
(0.658)
0.22
(0.659)
0.465
(0.829)
0.0101
(0.184)
0.293
(0.7)
0.615
(0.893)
4p loss 60 (36%) 105 0.218
(0.658)
0.5
(0.855)
0.00027
(0.0152)
0.559
(0.877)
0.429
(0.816)
0.231
(0.664)
0.685
(0.931)
0.56
(0.877)
0.678
(0.928)
0.1
(0.532)
0.259
(0.687)
0.372
(0.768)
4q loss 67 (41%) 98 0.463
(0.829)
0.368
(0.768)
1e-05
(0.00107)
0.18
(0.658)
0.425
(0.814)
0.0412
(0.373)
0.764
(0.961)
0.438
(0.821)
0.655
(0.915)
0.217
(0.658)
0.609
(0.889)
0.852
(1.00)
5q loss 40 (24%) 125 0.0427
(0.373)
0.0265
(0.311)
0.0017
(0.0563)
0.704
(0.938)
0.731
(0.949)
0.878
(1.00)
0.918
(1.00)
0.221
(0.659)
0.846
(1.00)
0.21
(0.658)
0.272
(0.687)
0.112
(0.567)
14q loss 67 (41%) 98 0.487
(0.846)
0.187
(0.658)
1e-05
(0.00107)
0.123
(0.597)
0.957
(1.00)
0.897
(1.00)
0.364
(0.768)
0.077
(0.494)
0.314
(0.715)
0.199
(0.658)
0.601
(0.884)
0.952
(1.00)
15q loss 72 (44%) 93 0.0466
(0.389)
0.15
(0.633)
0.00014
(0.0096)
0.864
(1.00)
0.0989
(0.528)
0.629
(0.9)
0.448
(0.823)
0.404
(0.797)
0.792
(0.977)
0.563
(0.877)
0.845
(1.00)
0.755
(0.961)
16q loss 14 (8%) 151 0.0913
(0.512)
0.852
(1.00)
0.00546
(0.138)
0.937
(1.00)
0.389
(0.781)
0.668
(0.925)
0.251
(0.683)
0.955
(1.00)
0.246
(0.678)
0.858
(1.00)
0.726
(0.947)
0.569
(0.88)
17p loss 105 (64%) 60 0.562
(0.877)
0.137
(0.62)
0.00856
(0.168)
0.44
(0.821)
0.573
(0.88)
0.59
(0.881)
0.435
(0.821)
0.566
(0.879)
0.972
(1.00)
0.268
(0.687)
0.519
(0.855)
0.866
(1.00)
18q loss 138 (84%) 27 0.0363
(0.36)
0.2
(0.658)
1e-05
(0.00107)
0.0814
(0.496)
0.78
(0.97)
0.138
(0.621)
0.0321
(0.344)
0.0194
(0.251)
0.225
(0.664)
0.0274
(0.314)
0.558
(0.877)
0.824
(0.997)
19q loss 22 (13%) 143 0.214
(0.658)
0.577
(0.881)
0.309
(0.711)
0.893
(1.00)
0.64
(0.906)
0.68
(0.928)
0.352
(0.757)
0.514
(0.855)
0.0617
(0.433)
0.00923
(0.173)
0.763
(0.961)
0.766
(0.961)
20p loss 24 (15%) 141 0.616
(0.893)
0.702
(0.936)
0.00696
(0.155)
0.495
(0.855)
0.161
(0.648)
0.889
(1.00)
0.191
(0.658)
0.685
(0.931)
0.774
(0.967)
0.183
(0.658)
0.723
(0.947)
0.179
(0.658)
22q loss 58 (35%) 107 0.439
(0.821)
0.238
(0.671)
0.11
(0.564)
0.872
(1.00)
0.65
(0.914)
0.297
(0.7)
0.463
(0.829)
0.168
(0.658)
0.322
(0.727)
0.181
(0.658)
0.124
(0.6)
0.0104
(0.185)
3p gain 27 (16%) 138 0.457
(0.829)
0.89
(1.00)
0.245
(0.678)
0.233
(0.666)
0.238
(0.671)
0.448
(0.823)
0.177
(0.658)
0.929
(1.00)
0.299
(0.7)
0.359
(0.768)
0.655
(0.915)
0.71
(0.943)
3q gain 33 (20%) 132 0.73
(0.949)
0.55
(0.877)
0.0216
(0.269)
0.276
(0.687)
0.392
(0.782)
0.179
(0.658)
0.124
(0.6)
0.732
(0.949)
0.307
(0.709)
0.253
(0.683)
0.627
(0.9)
0.96
(1.00)
4p gain 9 (5%) 156 0.423
(0.814)
0.941
(1.00)
0.697
(0.932)
0.918
(1.00)
0.0694
(0.46)
0.0323
(0.344)
0.513
(0.855)
0.63
(0.9)
0.184
(0.658)
0.374
(0.77)
0.726
(0.947)
0.913
(1.00)
4q gain 5 (3%) 160 0.277
(0.687)
0.783
(0.971)
0.686
(0.931)
0.0453
(0.384)
0.161
(0.648)
0.621
(0.897)
1
(1.00)
0.845
(1.00)
1
(1.00)
5q gain 24 (15%) 141 0.269
(0.687)
0.036
(0.36)
0.211
(0.658)
0.348
(0.757)
0.429
(0.816)
0.604
(0.886)
0.48
(0.842)
0.0903
(0.512)
1
(1.00)
0.523
(0.855)
1
(1.00)
0.481
(0.842)
9p gain 43 (26%) 122 0.189
(0.658)
0.387
(0.78)
0.0478
(0.39)
0.0326
(0.344)
0.441
(0.821)
0.191
(0.658)
0.0565
(0.414)
0.297
(0.7)
0.191
(0.658)
0.217
(0.658)
0.959
(1.00)
0.745
(0.96)
9q gain 35 (21%) 130 0.469
(0.832)
0.526
(0.858)
0.21
(0.658)
0.0918
(0.512)
0.19
(0.658)
0.0988
(0.528)
0.335
(0.744)
0.302
(0.703)
0.599
(0.884)
0.589
(0.881)
0.864
(1.00)
0.841
(1.00)
10p gain 12 (7%) 153 0.716
(0.946)
0.159
(0.648)
0.428
(0.816)
0.27
(0.687)
0.368
(0.768)
0.894
(1.00)
0.142
(0.63)
0.203
(0.658)
0.83
(0.999)
1
(1.00)
0.842
(1.00)
0.694
(0.932)
10q gain 7 (4%) 158 0.276
(0.687)
0.166
(0.658)
0.255
(0.686)
0.794
(0.977)
0.452
(0.826)
0.712
(0.944)
0.832
(1)
0.501
(0.855)
0.639
(0.906)
0.861
(1.00)
11p gain 32 (19%) 133 0.0948
(0.52)
0.43
(0.816)
0.112
(0.567)
0.416
(0.812)
0.989
(1.00)
0.751
(0.961)
0.187
(0.658)
0.146
(0.632)
0.085
(0.5)
0.208
(0.658)
0.263
(0.687)
0.718
(0.946)
12p gain 33 (20%) 132 0.21
(0.658)
0.136
(0.62)
0.188
(0.658)
0.246
(0.678)
0.161
(0.648)
0.692
(0.932)
0.0437
(0.378)
0.201
(0.658)
0.765
(0.961)
0.549
(0.877)
0.312
(0.715)
0.67
(0.926)
12q gain 21 (13%) 144 0.205
(0.658)
0.265
(0.687)
0.96
(1.00)
0.66
(0.921)
0.274
(0.687)
0.548
(0.877)
0.028
(0.316)
0.387
(0.78)
0.347
(0.757)
0.802
(0.978)
0.156
(0.644)
1
(1.00)
14q gain 8 (5%) 157 0.601
(0.884)
0.687
(0.931)
0.0969
(0.523)
0.253
(0.683)
0.722
(0.947)
0.861
(1.00)
0.473
(0.837)
0.912
(1.00)
0.64
(0.906)
0.861
(1.00)
15q gain 4 (2%) 161 0.293
(0.7)
0.102
(0.54)
0.506
(0.855)
1
(1.00)
0.539
(0.871)
0.599
(0.884)
0.392
(0.782)
0.761
(0.961)
17p gain 10 (6%) 155 0.0252
(0.298)
0.0816
(0.496)
0.586
(0.881)
0.182
(0.658)
0.925
(1.00)
0.468
(0.832)
0.427
(0.816)
0.422
(0.813)
0.275
(0.687)
0.332
(0.739)
17q gain 31 (19%) 134 0.754
(0.961)
0.697
(0.932)
0.0194
(0.251)
0.256
(0.686)
0.798
(0.978)
0.28
(0.687)
0.783
(0.971)
0.221
(0.659)
0.8
(0.978)
0.277
(0.687)
0.389
(0.781)
0.37
(0.768)
18q gain 6 (4%) 159 0.464
(0.829)
0.0325
(0.344)
0.863
(1.00)
0.587
(0.881)
0.648
(0.914)
0.229
(0.664)
0.555
(0.877)
0.627
(0.9)
1
(1.00)
1
(1.00)
21q gain 10 (6%) 155 0.048
(0.39)
0.992
(1.00)
0.116
(0.581)
0.565
(0.879)
0.0785
(0.494)
0.304
(0.704)
0.451
(0.826)
0.921
(1.00)
1
(1.00)
0.726
(0.947)
22q gain 9 (5%) 156 0.228
(0.664)
0.0491
(0.39)
0.0674
(0.459)
0.546
(0.877)
0.0905
(0.512)
0.936
(1.00)
0.366
(0.768)
0.197
(0.658)
0.873
(1.00)
1
(1.00)
xp gain 31 (19%) 134 0.041
(0.373)
0.137
(0.62)
0.133
(0.62)
0.52
(0.855)
0.514
(0.855)
0.942
(1.00)
0.3
(0.7)
0.573
(0.88)
0.643
(0.908)
0.763
(0.961)
0.344
(0.757)
0.405
(0.798)
xq gain 32 (19%) 133 0.293
(0.7)
0.509
(0.855)
0.198
(0.658)
0.52
(0.855)
0.134
(0.62)
0.68
(0.928)
0.0572
(0.416)
0.642
(0.908)
0.596
(0.884)
0.805
(0.978)
0.237
(0.671)
0.3
(0.7)
2p loss 11 (7%) 154 0.18
(0.658)
0.516
(0.855)
0.12
(0.596)
0.757
(0.961)
0.592
(0.882)
0.402
(0.795)
0.478
(0.842)
0.0593
(0.422)
0.421
(0.813)
0.605
(0.887)
2q loss 7 (4%) 158 0.362
(0.768)
0.157
(0.646)
0.204
(0.658)
0.278
(0.687)
0.521
(0.855)
0.468
(0.832)
0.0501
(0.39)
0.0645
(0.442)
0.266
(0.687)
3p loss 15 (9%) 150 0.889
(1.00)
0.797
(0.978)
0.0627
(0.433)
0.126
(0.6)
0.243
(0.678)
0.218
(0.658)
0.245
(0.678)
0.556
(0.877)
0.478
(0.842)
0.135
(0.62)
0.0627
(0.433)
0.113
(0.567)
5p loss 27 (16%) 138 0.0738
(0.482)
0.924
(1.00)
0.052
(0.396)
0.581
(0.881)
0.406
(0.798)
0.823
(0.997)
0.87
(1.00)
0.247
(0.68)
0.301
(0.7)
0.679
(0.928)
0.347
(0.757)
0.0384
(0.364)
6p loss 14 (8%) 151 0.381
(0.779)
0.418
(0.813)
0.37
(0.768)
0.149
(0.633)
0.385
(0.78)
0.694
(0.932)
0.624
(0.9)
0.167
(0.658)
0.859
(1.00)
0.578
(0.881)
7q loss 3 (2%) 162 0.11
(0.564)
0.718
(0.946)
0.439
(0.821)
0.0455
(0.384)
0.76
(0.961)
0.773
(0.967)
1
(1.00)
8q loss 10 (6%) 155 1
(1.00)
0.446
(0.823)
0.415
(0.812)
0.161
(0.648)
0.761
(0.961)
0.145
(0.632)
0.585
(0.881)
0.339
(0.751)
0.903
(1.00)
0.421
(0.813)
0.0913
(0.512)
0.367
(0.768)
9p loss 23 (14%) 142 0.0343
(0.354)
0.933
(1.00)
0.495
(0.855)
0.316
(0.717)
0.707
(0.94)
0.81
(0.984)
0.458
(0.829)
0.513
(0.855)
0.905
(1.00)
0.0474
(0.39)
0.91
(1.00)
0.149
(0.633)
10p loss 34 (21%) 131 0.149
(0.633)
0.0687
(0.46)
0.0382
(0.364)
0.0499
(0.39)
0.0906
(0.512)
0.0442
(0.379)
0.306
(0.708)
0.574
(0.88)
0.789
(0.976)
0.137
(0.62)
0.845
(1.00)
0.883
(1.00)
12p loss 23 (14%) 142 0.554
(0.877)
0.626
(0.9)
0.18
(0.658)
0.28
(0.687)
0.918
(1.00)
0.567
(0.879)
0.695
(0.932)
0.34
(0.751)
0.486
(0.846)
0.776
(0.967)
0.145
(0.632)
0.617
(0.893)
12q loss 24 (15%) 141 0.585
(0.881)
0.631
(0.9)
0.0403
(0.372)
0.38
(0.779)
0.34
(0.751)
0.837
(1.00)
0.786
(0.974)
0.28
(0.687)
0.269
(0.687)
0.269
(0.687)
0.774
(0.967)
1
(1.00)
13q loss 6 (4%) 159 0.0419
(0.373)
0.228
(0.664)
0.285
(0.693)
0.754
(0.961)
1
(1.00)
0.348
(0.757)
0.74
(0.956)
0.861
(1.00)
16p loss 9 (5%) 156 0.215
(0.658)
0.893
(1.00)
0.229
(0.664)
0.284
(0.693)
0.356
(0.764)
0.517
(0.855)
0.175
(0.658)
0.912
(1.00)
0.561
(0.877)
1
(1.00)
0.653
(0.915)
0.535
(0.867)
17q loss 28 (17%) 137 0.674
(0.927)
0.665
(0.924)
0.0559
(0.413)
0.462
(0.829)
0.672
(0.926)
0.238
(0.671)
0.352
(0.757)
0.362
(0.768)
0.529
(0.86)
0.547
(0.877)
0.33
(0.738)
1
(1.00)
19p loss 24 (15%) 141 0.51
(0.855)
0.835
(1.00)
0.0585
(0.419)
0.957
(1.00)
0.718
(0.946)
0.854
(1.00)
0.325
(0.733)
0.296
(0.7)
0.293
(0.7)
0.0223
(0.275)
0.562
(0.877)
0.689
(0.932)
21q loss 68 (41%) 97 0.174
(0.658)
0.367
(0.768)
0.42
(0.813)
0.964
(1.00)
0.382
(0.779)
0.744
(0.96)
0.931
(1.00)
0.691
(0.932)
0.589
(0.881)
0.182
(0.658)
0.208
(0.658)
0.0793
(0.494)
xp loss 28 (17%) 137 0.916
(1.00)
0.75
(0.961)
0.0845
(0.5)
0.216
(0.658)
0.436
(0.821)
0.297
(0.7)
0.791
(0.977)
0.693
(0.932)
0.804
(0.978)
0.459
(0.829)
0.942
(1.00)
0.774
(0.967)
xq loss 26 (16%) 139 0.983
(1.00)
0.523
(0.855)
0.191
(0.658)
0.214
(0.658)
0.884
(1.00)
0.63
(0.9)
0.723
(0.947)
0.884
(1.00)
0.87
(1.00)
0.31
(0.712)
0.863
(1.00)
0.859
(1.00)
'1p gain' versus 'MRNA_CNMF'

P value = 0.00837 (Fisher's exact test), Q value = 0.17

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
1P GAIN MUTATED 0 3 2 0 0
1P GAIN WILD-TYPE 13 5 18 13 15

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
1Q GAIN MUTATED 5 4 7 15 2
1Q GAIN WILD-TYPE 21 36 20 27 28

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00736 (Fisher's exact test), Q value = 0.16

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 6 10 7 9 9 8 9 8 3
2P GAIN MUTATED 3 0 0 1 0 3 0 3 0
2P GAIN WILD-TYPE 3 10 7 8 9 5 9 5 3

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.013

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
2P GAIN MUTATED 9 19 2 8 2
2P GAIN WILD-TYPE 17 21 25 34 28

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
2P GAIN MUTATED 12 8 2 7 7 0 3
2P GAIN WILD-TYPE 15 28 10 12 25 18 17

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.056

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
2Q GAIN MUTATED 7 19 5 8 2
2Q GAIN WILD-TYPE 19 21 22 34 28

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.059

Table S7.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
2Q GAIN MUTATED 14 6 2 6 9 0 3
2Q GAIN WILD-TYPE 13 30 10 13 23 18 17

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.02

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
5P GAIN MUTATED 8 2 8 2 10 2 3
5P GAIN WILD-TYPE 19 34 4 17 22 16 17

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0081

Table S9.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
6P GAIN MUTATED 9 12 13 5 1
6P GAIN WILD-TYPE 17 28 14 37 29

Figure S9.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0026

Table S10.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
6Q GAIN MUTATED 6 13 13 3 0
6Q GAIN WILD-TYPE 20 27 14 39 30

Figure S10.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.13

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 6 10 7 9 9 8 9 8 3
7P GAIN MUTATED 1 6 2 2 7 7 5 7 0
7P GAIN WILD-TYPE 5 4 5 7 2 1 4 1 3

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
7P GAIN MUTATED 12 35 21 25 9
7P GAIN WILD-TYPE 14 5 6 17 21

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.24

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 20 20 24 18 29 16
7P GAIN MUTATED 14 13 17 9 13 15
7P GAIN WILD-TYPE 6 7 7 9 16 1

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.033

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
7P GAIN MUTATED 26 7 13 23 32
7P GAIN WILD-TYPE 6 7 20 5 25

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S15.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
7P GAIN MUTATED 25 17 9 13 20 3 14
7P GAIN WILD-TYPE 2 19 3 6 12 15 6

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.19

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 6 10 7 9 9 8 9 8 3
7Q GAIN MUTATED 1 6 2 2 5 7 4 7 0
7Q GAIN WILD-TYPE 5 4 5 7 4 1 5 1 3

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0019

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
7Q GAIN MUTATED 8 30 20 21 8
7Q GAIN WILD-TYPE 18 10 7 21 22

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.13

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
7Q GAIN MUTATED 19 5 11 22 29
7Q GAIN WILD-TYPE 13 9 22 6 28

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.039

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
7Q GAIN MUTATED 19 12 8 13 19 3 12
7Q GAIN WILD-TYPE 8 24 4 6 13 15 8

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
8P GAIN MUTATED 5 10 8 16 1
8P GAIN WILD-TYPE 21 30 19 26 29

Figure S20.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.15

Table S21.  Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 20 20 24 18 29 16
8P GAIN MUTATED 3 2 11 9 4 5
8P GAIN WILD-TYPE 17 18 13 9 25 11

Figure S21.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S22.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
8Q GAIN MUTATED 16 22 12 37 3
8Q GAIN WILD-TYPE 10 18 15 5 27

Figure S22.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.19

Table S23.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 14 13 6
8Q GAIN MUTATED 12 14 7 3
8Q GAIN WILD-TYPE 5 0 6 3

Figure S23.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00495 (Fisher's exact test), Q value = 0.13

Table S24.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
11Q GAIN MUTATED 7 2 0 9 9
11Q GAIN WILD-TYPE 25 12 33 19 48

Figure S24.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.058

Table S25.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
11Q GAIN MUTATED 9 2 0 7 7 1 1
11Q GAIN WILD-TYPE 18 34 12 12 25 17 19

Figure S25.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S26.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
13Q GAIN MUTATED 17 33 26 27 11
13Q GAIN WILD-TYPE 9 7 1 15 19

Figure S26.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.15

Table S27.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
13Q GAIN MUTATED 22 11 17 26 37
13Q GAIN WILD-TYPE 10 3 16 2 20

Figure S27.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.015

Table S28.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
13Q GAIN MUTATED 22 25 7 17 25 4 13
13Q GAIN WILD-TYPE 5 11 5 2 7 14 7

Figure S28.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.014

Table S29.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
16P GAIN MUTATED 3 16 12 9 1
16P GAIN WILD-TYPE 23 24 15 33 29

Figure S29.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.23

Table S30.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
16P GAIN MUTATED 0 5 9 7 4
16P GAIN WILD-TYPE 14 18 8 18 13

Figure S30.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S31.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
16Q GAIN MUTATED 4 16 14 7 0
16Q GAIN WILD-TYPE 22 24 13 35 30

Figure S31.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.15

Table S32.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
16Q GAIN MUTATED 0 6 10 7 4
16Q GAIN WILD-TYPE 14 17 7 18 13

Figure S32.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00939 (Fisher's exact test), Q value = 0.17

Table S33.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
16Q GAIN MUTATED 13 1 4 11 11
16Q GAIN WILD-TYPE 19 13 29 17 46

Figure S33.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.17

Table S34.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 55 62
16Q GAIN MUTATED 11 15 9
16Q GAIN WILD-TYPE 13 40 53

Figure S34.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.2

Table S35.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
18P GAIN MUTATED 2 0 0 0 3
18P GAIN WILD-TYPE 12 23 17 25 14

Figure S35.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.062

Table S36.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
19P GAIN MUTATED 5 17 3 6 2
19P GAIN WILD-TYPE 21 23 24 36 28

Figure S36.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.21

Table S37.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
19Q GAIN MUTATED 5 15 6 5 2
19Q GAIN WILD-TYPE 21 25 21 37 28

Figure S37.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.068

Table S38.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 27 25 30 3
20P GAIN MUTATED 33 21 12 13 1
20P GAIN WILD-TYPE 9 6 13 17 2

Figure S38.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.004

Table S39.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
20Q GAIN MUTATED 24 40 27 35 20
20Q GAIN WILD-TYPE 2 0 0 7 10

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.031

Table S40.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
20Q GAIN MUTATED 26 33 9 18 31 10 18
20Q GAIN WILD-TYPE 1 3 3 1 1 8 2

Figure S40.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.049

Table S41.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
1P LOSS MUTATED 10 16 10 9 1
1P LOSS WILD-TYPE 16 24 17 33 29

Figure S41.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.02

Table S42.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
1Q LOSS MUTATED 8 12 5 3 0
1Q LOSS WILD-TYPE 18 28 22 39 30

Figure S42.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.18

Table S43.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
3Q LOSS MUTATED 5 4 1
3Q LOSS WILD-TYPE 17 59 55

Figure S43.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
4P LOSS MUTATED 13 15 16 14 2
4P LOSS WILD-TYPE 13 25 11 28 28

Figure S44.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S45.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
4Q LOSS MUTATED 15 17 18 15 2
4Q LOSS WILD-TYPE 11 23 9 27 28

Figure S45.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.056

Table S46.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
5Q LOSS MUTATED 7 10 9 14 0
5Q LOSS WILD-TYPE 19 30 18 28 30

Figure S46.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.23

Table S47.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
6Q LOSS MUTATED 4 2 1 12 4
6Q LOSS WILD-TYPE 22 38 26 30 26

Figure S47.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.19

Table S48.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 14 13 6
6Q LOSS MUTATED 0 4 0 0
6Q LOSS WILD-TYPE 17 10 13 6

Figure S48.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.056

Table S49.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
8P LOSS MUTATED 12 22 13 24 4
8P LOSS WILD-TYPE 14 18 14 18 26

Figure S49.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.24

Table S50.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
8P LOSS MUTATED 14 6 7 14 33
8P LOSS WILD-TYPE 18 8 26 14 24

Figure S50.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.2

Table S51.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
9Q LOSS MUTATED 0 0 8 1 2
9Q LOSS WILD-TYPE 13 8 12 12 13

Figure S51.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.059

Table S52.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
9Q LOSS MUTATED 9 5 7
9Q LOSS WILD-TYPE 13 58 49

Figure S52.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.2

Table S53.  Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
10Q LOSS MUTATED 3 5 4 3 0
10Q LOSS WILD-TYPE 10 3 16 10 15

Figure S53.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.23

Table S54.  Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 20 20 24 18 29 16
10Q LOSS MUTATED 2 3 10 1 6 7
10Q LOSS WILD-TYPE 18 17 14 17 23 9

Figure S54.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.03

Table S55.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
11P LOSS MUTATED 2 1 10 9 2
11P LOSS WILD-TYPE 24 39 17 33 28

Figure S55.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.18

Table S56.  Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
11P LOSS MUTATED 4 4 9 0 7
11P LOSS WILD-TYPE 28 10 24 28 50

Figure S56.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 0.00787 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
11Q LOSS MUTATED 2 5 3 2 0
11Q LOSS WILD-TYPE 11 3 17 11 15

Figure S57.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.036

Table S58.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
11Q LOSS MUTATED 4 1 10 12 3
11Q LOSS WILD-TYPE 22 39 17 30 27

Figure S58.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.16

Table S59.  Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
11Q LOSS MUTATED 3 5 11 1 10
11Q LOSS WILD-TYPE 29 9 22 27 47

Figure S59.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00795 (Fisher's exact test), Q value = 0.16

Table S60.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
11Q LOSS MUTATED 1 11 4 2 2 6 4
11Q LOSS WILD-TYPE 26 25 8 17 30 12 16

Figure S60.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S61.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
14Q LOSS MUTATED 15 24 15 11 2
14Q LOSS WILD-TYPE 11 16 12 31 28

Figure S61.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0096

Table S62.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
15Q LOSS MUTATED 13 20 14 23 2
15Q LOSS WILD-TYPE 13 20 13 19 28

Figure S62.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.14

Table S63.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
16Q LOSS MUTATED 3 1 0 9 1
16Q LOSS WILD-TYPE 23 39 27 33 29

Figure S63.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
17P LOSS MUTATED 18 24 20 32 11
17P LOSS WILD-TYPE 8 16 7 10 19

Figure S64.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S65.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
18P LOSS MUTATED 20 39 23 34 12
18P LOSS WILD-TYPE 6 1 4 8 18

Figure S65.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.21

Table S66.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
18P LOSS MUTATED 26 27 7 17 25 10 15
18P LOSS WILD-TYPE 1 9 5 2 7 8 5

Figure S66.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S67.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
18Q LOSS MUTATED 21 40 24 39 14
18Q LOSS WILD-TYPE 5 0 3 3 16

Figure S67.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00923 (Fisher's exact test), Q value = 0.17

Table S68.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
19Q LOSS MUTATED 7 10 3
19Q LOSS WILD-TYPE 15 53 53

Figure S68.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00696 (Fisher's exact test), Q value = 0.16

Table S69.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
20P LOSS MUTATED 0 9 4 10 1
20P LOSS WILD-TYPE 26 31 23 32 29

Figure S69.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.18

Table S70.  Gene #78: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 12 16 6 5
22Q LOSS MUTATED 9 3 8 2 0
22Q LOSS WILD-TYPE 2 9 8 4 5

Figure S70.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/22532765/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/22541962/READ-TP.transferedmergedcluster.txt

  • Number of patients = 165

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • 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)