Correlation between copy number variation genes (focal events) 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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C15B01Z1
Overview
Introduction

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

Summary

Testing the association between copy number variation 58 focal events and 12 molecular subtypes across 165 patients, 98 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • amp_6p21.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF'.

  • amp_11p15.5 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_12p12.1 cnv correlated to 'RPPA_CNMF'.

  • amp_13q12.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_13q12.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_13q22.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_16p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_17q12 cnv correlated to 'CN_CNMF'.

  • amp_17q24.1 cnv correlated to 'CN_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20q11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_xq27.3 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.11 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p33 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_1p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_2p12 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • del_3q26.31 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_4p13 cnv correlated to 'CN_CNMF'.

  • del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_4q35.1 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_5q22.2 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_7q31.1 cnv correlated to 'CN_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_8q11.1 cnv correlated to 'CN_CNMF'.

  • del_10q25.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_11q22.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q11.2 cnv correlated to 'CN_CNMF'.

  • del_14q31.1 cnv correlated to 'CN_CNMF'.

  • del_15q21.1 cnv correlated to 'CN_CNMF'.

  • del_15q22.33 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • del_17p11.2 cnv correlated to 'CN_CNMF'.

  • del_18p11.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q21.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • del_22q13.31 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp22.33 cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 58 focal 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, 98 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
amp 13q12 13 126 (76%) 39 0.279
(0.592)
0.182
(0.506)
1e-05
(0.000535)
0.104
(0.413)
0.399
(0.681)
0.12
(0.43)
0.00675
(0.0839)
1e-05
(0.000535)
0.00033
(0.00763)
0.00414
(0.0605)
1
(1.00)
1
(1.00)
amp 13q12 2 125 (76%) 40 0.404
(0.683)
0.285
(0.592)
3e-05
(0.0011)
0.0459
(0.288)
0.456
(0.719)
0.0888
(0.396)
0.00358
(0.0579)
0.0001
(0.0029)
0.00651
(0.0824)
0.0215
(0.178)
1
(1.00)
1
(1.00)
amp 13q22 1 120 (73%) 45 0.255
(0.581)
0.0521
(0.305)
1e-05
(0.000535)
0.111
(0.415)
0.485
(0.749)
0.274
(0.592)
0.00378
(0.0585)
3e-05
(0.0011)
0.0249
(0.201)
0.0108
(0.118)
1
(1.00)
0.829
(0.943)
del 11q22 3 38 (23%) 127 0.00157
(0.028)
0.0422
(0.274)
6e-05
(0.00199)
0.193
(0.52)
0.852
(0.95)
0.388
(0.675)
0.00541
(0.0738)
0.0077
(0.094)
0.291
(0.595)
0.966
(1.00)
0.28
(0.592)
0.221
(0.538)
del 18q22 1 141 (85%) 24 0.108
(0.415)
0.119
(0.428)
1e-05
(0.000535)
0.0129
(0.129)
0.911
(0.98)
0.169
(0.491)
0.028
(0.219)
0.0116
(0.12)
0.112
(0.415)
0.297
(0.601)
0.635
(0.834)
0.879
(0.963)
amp 6p21 1 54 (33%) 111 0.0125
(0.128)
0.135
(0.45)
0.00034
(0.00763)
0.495
(0.752)
0.182
(0.506)
0.0341
(0.244)
0.657
(0.849)
0.145
(0.465)
0.225
(0.541)
0.389
(0.675)
0.498
(0.752)
0.403
(0.683)
amp 8p11 23 53 (32%) 112 0.0728
(0.361)
0.282
(0.592)
1e-05
(0.000535)
0.16
(0.482)
0.473
(0.735)
0.148
(0.467)
0.112
(0.415)
0.0724
(0.361)
0.0185
(0.17)
0.0274
(0.217)
0.933
(0.983)
0.133
(0.45)
amp 11q13 3 28 (17%) 137 0.0738
(0.362)
0.208
(0.538)
0.0356
(0.251)
0.0267
(0.213)
0.929
(0.98)
0.288
(0.592)
0.00411
(0.0605)
0.0112
(0.118)
0.0807
(0.384)
0.34
(0.635)
0.0438
(0.277)
0.125
(0.441)
amp 20q11 21 146 (88%) 19 0.127
(0.441)
0.165
(0.486)
5e-05
(0.00174)
0.00507
(0.0706)
0.0376
(0.261)
0.243
(0.568)
0.155
(0.478)
0.00027
(0.00648)
0.333
(0.629)
0.397
(0.679)
0.328
(0.625)
0.432
(0.711)
amp 20q11 23 147 (89%) 18 0.127
(0.441)
0.167
(0.486)
8e-05
(0.00242)
0.0232
(0.19)
0.0379
(0.261)
0.245
(0.57)
0.213
(0.538)
0.00021
(0.00522)
0.177
(0.503)
0.278
(0.592)
0.501
(0.752)
0.692
(0.872)
del 8p23 2 100 (61%) 65 0.187
(0.516)
0.0621
(0.332)
1e-05
(0.000535)
0.439
(0.714)
0.915
(0.98)
0.774
(0.915)
0.00145
(0.0266)
0.00973
(0.111)
0.647
(0.842)
0.329
(0.625)
0.452
(0.719)
0.525
(0.77)
del 18p11 31 125 (76%) 40 0.0608
(0.328)
0.502
(0.752)
1e-05
(0.000535)
0.00931
(0.11)
0.261
(0.582)
0.326
(0.625)
0.0471
(0.29)
0.0057
(0.075)
0.189
(0.516)
0.222
(0.538)
0.8
(0.925)
0.349
(0.639)
del 18q21 2 145 (88%) 20 0.132
(0.45)
0.407
(0.683)
1e-05
(0.000535)
0.0522
(0.305)
1
(1.00)
0.0864
(0.39)
0.00603
(0.0777)
0.0297
(0.227)
0.223
(0.538)
0.124
(0.441)
0.892
(0.972)
0.698
(0.872)
del 18q23 141 (85%) 24 0.336
(0.632)
0.256
(0.582)
1e-05
(0.000535)
0.053
(0.305)
0.792
(0.919)
0.149
(0.467)
0.0322
(0.241)
0.0293
(0.227)
0.155
(0.478)
0.532
(0.773)
0.635
(0.834)
0.88
(0.963)
amp 1q32 1 49 (30%) 116 0.1
(0.413)
0.528
(0.771)
0.00204
(0.0355)
0.217
(0.538)
0.0206
(0.178)
0.16
(0.482)
0.658
(0.849)
0.898
(0.973)
0.637
(0.834)
0.769
(0.912)
0.5
(0.752)
0.247
(0.57)
amp 8p11 21 70 (42%) 95 0.042
(0.274)
0.212
(0.538)
1e-05
(0.000535)
0.0207
(0.178)
0.396
(0.679)
0.705
(0.874)
0.455
(0.719)
0.126
(0.441)
0.0429
(0.276)
0.275
(0.592)
0.214
(0.538)
0.199
(0.531)
amp 16p11 2 47 (28%) 118 0.487
(0.749)
0.528
(0.771)
1e-05
(0.000535)
0.0085
(0.102)
0.475
(0.737)
0.27
(0.589)
0.0415
(0.274)
0.159
(0.482)
0.208
(0.538)
0.851
(0.95)
0.364
(0.652)
0.939
(0.984)
amp 20q13 33 146 (88%) 19 0.199
(0.531)
0.211
(0.538)
0.00012
(0.00321)
0.0793
(0.383)
0.105
(0.413)
0.465
(0.726)
0.612
(0.819)
0.00066
(0.0135)
0.33
(0.627)
0.395
(0.679)
0.176
(0.503)
0.697
(0.872)
amp xq27 3 37 (22%) 128 0.746
(0.893)
0.441
(0.714)
0.102
(0.413)
0.0343
(0.244)
0.0714
(0.361)
0.513
(0.76)
0.0404
(0.273)
0.238
(0.564)
0.216
(0.538)
0.277
(0.592)
0.0961
(0.409)
0.0196
(0.175)
del 1p36 11 75 (45%) 90 0.3
(0.602)
0.07
(0.361)
0.0163
(0.153)
0.13
(0.449)
0.587
(0.806)
0.791
(0.919)
0.192
(0.52)
0.0146
(0.14)
0.77
(0.912)
0.0637
(0.336)
0.736
(0.888)
0.791
(0.919)
del 1p33 53 (32%) 112 0.367
(0.656)
0.0146
(0.14)
0.00013
(0.00335)
0.112
(0.415)
0.299
(0.601)
0.264
(0.582)
0.311
(0.615)
0.186
(0.515)
0.563
(0.791)
0.266
(0.582)
0.924
(0.98)
0.44
(0.714)
del 1p13 2 54 (33%) 111 0.776
(0.915)
0.0527
(0.305)
0.00104
(0.0207)
0.0821
(0.384)
0.544
(0.782)
0.582
(0.802)
0.489
(0.749)
0.0195
(0.175)
0.312
(0.615)
0.214
(0.538)
0.582
(0.802)
0.693
(0.872)
del 2p12 13 (8%) 152 0.0146
(0.14)
0.672
(0.861)
0.021
(0.178)
1
(1.00)
0.277
(0.592)
0.38
(0.668)
0.716
(0.876)
0.141
(0.461)
0.104
(0.413)
0.145
(0.465)
del 3q26 31 18 (11%) 147 0.55
(0.783)
0.928
(0.98)
0.321
(0.621)
0.0211
(0.178)
0.36
(0.652)
0.611
(0.819)
0.562
(0.791)
0.432
(0.711)
0.551
(0.783)
0.0343
(0.244)
0.63
(0.833)
0.612
(0.819)
del 4q22 1 73 (44%) 92 0.551
(0.783)
0.0329
(0.244)
7e-05
(0.00221)
0.78
(0.917)
0.109
(0.415)
0.0829
(0.385)
0.388
(0.675)
0.318
(0.617)
0.833
(0.945)
0.257
(0.582)
0.684
(0.872)
0.674
(0.862)
del 4q35 1 72 (44%) 93 0.462
(0.724)
0.106
(0.413)
1e-05
(0.000535)
0.912
(0.98)
0.282
(0.592)
0.013
(0.129)
0.603
(0.815)
0.049
(0.299)
0.292
(0.595)
0.0503
(0.304)
0.571
(0.793)
0.863
(0.956)
del 5q12 1 53 (32%) 112 0.111
(0.415)
0.00431
(0.0612)
0.00123
(0.0235)
0.0861
(0.39)
0.446
(0.714)
0.712
(0.874)
0.582
(0.802)
0.0935
(0.405)
0.23
(0.551)
0.288
(0.592)
0.159
(0.482)
0.119
(0.428)
del 5q22 2 59 (36%) 106 0.161
(0.482)
0.00125
(0.0235)
0.00965
(0.111)
0.338
(0.634)
0.389
(0.675)
0.894
(0.972)
0.733
(0.887)
0.188
(0.516)
0.513
(0.76)
0.239
(0.564)
0.0403
(0.273)
0.0963
(0.409)
del 16q23 1 23 (14%) 142 0.0214
(0.178)
0.524
(0.769)
0.0037
(0.0585)
0.599
(0.814)
0.448
(0.714)
0.501
(0.752)
0.422
(0.703)
0.739
(0.889)
1
(1.00)
0.844
(0.948)
0.809
(0.933)
0.925
(0.98)
amp 1q21 3 48 (29%) 117 0.0513
(0.305)
0.316
(0.617)
0.0112
(0.118)
0.146
(0.466)
0.202
(0.534)
0.405
(0.683)
0.418
(0.698)
0.397
(0.679)
0.571
(0.793)
0.15
(0.468)
0.922
(0.98)
0.356
(0.648)
amp 8q24 21 109 (66%) 56 0.0432
(0.276)
0.26
(0.582)
1e-05
(0.000535)
0.054
(0.306)
0.937
(0.984)
0.69
(0.872)
0.167
(0.486)
0.047
(0.29)
0.26
(0.582)
0.263
(0.582)
0.0732
(0.361)
0.447
(0.714)
amp 11p15 5 45 (27%) 120 0.785
(0.918)
0.135
(0.45)
0.138
(0.456)
0.0975
(0.409)
0.71
(0.874)
0.789
(0.919)
0.125
(0.441)
0.00358
(0.0579)
0.242
(0.567)
0.538
(0.775)
0.506
(0.755)
0.363
(0.652)
amp 12p12 1 40 (24%) 125 0.447
(0.714)
0.136
(0.45)
0.0627
(0.333)
0.104
(0.413)
0.0175
(0.162)
0.515
(0.76)
0.424
(0.703)
0.368
(0.657)
1
(1.00)
0.76
(0.904)
0.427
(0.707)
0.215
(0.538)
amp 17q12 46 (28%) 119 0.317
(0.617)
0.0798
(0.383)
0.00417
(0.0605)
0.284
(0.592)
0.309
(0.614)
0.0552
(0.31)
0.439
(0.714)
0.0688
(0.358)
0.587
(0.806)
0.597
(0.813)
0.118
(0.428)
0.562
(0.791)
amp 17q24 1 39 (24%) 126 0.723
(0.879)
0.74
(0.89)
0.00056
(0.0118)
0.0577
(0.316)
0.669
(0.859)
0.247
(0.57)
0.316
(0.617)
0.1
(0.413)
0.659
(0.849)
0.21
(0.538)
0.374
(0.664)
0.825
(0.942)
del 4p13 60 (36%) 105 0.546
(0.782)
0.0791
(0.383)
3e-05
(0.0011)
0.617
(0.822)
0.311
(0.615)
0.221
(0.538)
0.875
(0.962)
0.343
(0.635)
0.721
(0.878)
0.219
(0.538)
0.182
(0.506)
0.49
(0.749)
del 7q31 1 4 (2%) 161 0.0343
(0.244)
0.85
(0.95)
0.643
(0.838)
0.177
(0.503)
0.771
(0.912)
1
(1.00)
1
(1.00)
del 8q11 1 17 (10%) 148 0.691
(0.872)
0.283
(0.592)
0.01
(0.113)
0.081
(0.384)
0.924
(0.98)
0.709
(0.874)
0.643
(0.838)
0.102
(0.413)
0.208
(0.538)
0.0866
(0.39)
0.328
(0.625)
0.565
(0.791)
del 10q25 2 48 (29%) 117 0.402
(0.683)
0.566
(0.791)
0.162
(0.482)
0.323
(0.622)
0.603
(0.815)
0.745
(0.893)
0.206
(0.538)
0.0318
(0.24)
0.709
(0.874)
0.277
(0.592)
0.429
(0.709)
0.565
(0.791)
del 14q11 2 70 (42%) 95 0.458
(0.72)
0.0926
(0.405)
2e-05
(0.000928)
0.345
(0.635)
0.918
(0.98)
0.546
(0.782)
0.298
(0.601)
0.0982
(0.409)
0.0726
(0.361)
0.342
(0.635)
0.604
(0.815)
0.952
(0.995)
del 14q31 1 72 (44%) 93 0.458
(0.72)
0.106
(0.414)
2e-05
(0.000928)
0.303
(0.605)
0.97
(1.00)
0.59
(0.806)
0.218
(0.538)
0.0971
(0.409)
0.407
(0.683)
0.238
(0.564)
0.453
(0.719)
0.904
(0.977)
del 15q21 1 79 (48%) 86 0.0575
(0.316)
0.145
(0.465)
0.00012
(0.00321)
0.817
(0.938)
0.0936
(0.405)
0.757
(0.903)
0.38
(0.668)
0.414
(0.692)
0.433
(0.712)
0.435
(0.713)
0.346
(0.636)
0.551
(0.783)
del 15q22 33 77 (47%) 88 0.072
(0.361)
0.194
(0.522)
3e-05
(0.0011)
0.381
(0.668)
0.134
(0.45)
0.252
(0.578)
0.341
(0.635)
0.101
(0.413)
0.854
(0.951)
0.744
(0.893)
0.678
(0.866)
0.445
(0.714)
del 17p11 2 113 (68%) 52 0.0566
(0.315)
0.819
(0.938)
0.00229
(0.0389)
0.636
(0.834)
0.708
(0.874)
0.289
(0.592)
0.225
(0.541)
0.218
(0.538)
0.718
(0.876)
0.354
(0.645)
0.888
(0.969)
0.924
(0.98)
del 19p13 3 36 (22%) 129 0.988
(1.00)
0.819
(0.938)
0.139
(0.456)
0.164
(0.485)
0.728
(0.882)
0.81
(0.933)
0.874
(0.962)
0.914
(0.98)
0.495
(0.752)
0.00571
(0.075)
0.47
(0.731)
0.521
(0.766)
del 22q13 31 68 (41%) 97 0.689
(0.872)
0.339
(0.634)
0.0409
(0.274)
0.917
(0.98)
0.293
(0.596)
0.393
(0.679)
0.594
(0.811)
0.272
(0.591)
0.215
(0.538)
0.113
(0.415)
0.0982
(0.409)
0.011
(0.118)
del xp22 33 34 (21%) 131 0.959
(0.998)
0.871
(0.961)
0.266
(0.582)
0.00041
(0.00892)
0.847
(0.949)
0.876
(0.962)
0.984
(1.00)
0.531
(0.773)
0.663
(0.854)
1
(1.00)
0.777
(0.915)
0.716
(0.876)
amp 10q22 2 11 (7%) 154 0.844
(0.948)
0.838
(0.948)
0.372
(0.663)
0.653
(0.848)
0.783
(0.918)
0.936
(0.984)
0.204
(0.536)
0.0903
(0.398)
0.181
(0.506)
0.19
(0.516)
amp 12p13 33 41 (25%) 124 0.21
(0.538)
0.136
(0.45)
0.112
(0.415)
0.246
(0.57)
0.0541
(0.306)
0.625
(0.83)
0.533
(0.773)
0.486
(0.749)
0.844
(0.948)
0.816
(0.938)
0.285
(0.592)
0.148
(0.467)
amp xp22 2 32 (19%) 133 0.167
(0.486)
0.507
(0.755)
0.7
(0.873)
0.354
(0.645)
0.403
(0.683)
0.379
(0.668)
0.436
(0.713)
0.629
(0.833)
0.692
(0.872)
0.869
(0.961)
0.318
(0.617)
0.84
(0.948)
del 3p14 2 31 (19%) 134 0.943
(0.987)
0.966
(1.00)
0.838
(0.948)
0.0892
(0.396)
0.172
(0.495)
0.294
(0.596)
0.556
(0.788)
0.862
(0.956)
0.923
(0.98)
0.961
(0.998)
0.261
(0.582)
0.16
(0.482)
del 6p25 3 24 (15%) 141 0.448
(0.714)
0.632
(0.834)
0.895
(0.972)
0.119
(0.428)
0.576
(0.799)
0.445
(0.714)
0.881
(0.963)
0.697
(0.872)
0.829
(0.943)
0.784
(0.918)
0.633
(0.834)
0.613
(0.819)
del 6q26 30 (18%) 135 0.17
(0.491)
0.955
(0.997)
0.181
(0.506)
0.611
(0.819)
0.0531
(0.305)
0.148
(0.467)
0.202
(0.534)
0.324
(0.623)
0.0868
(0.39)
0.333
(0.629)
0.0668
(0.35)
0.84
(0.948)
del 10q21 1 41 (25%) 124 0.105
(0.413)
0.565
(0.791)
0.0862
(0.39)
0.142
(0.461)
0.241
(0.566)
0.204
(0.536)
0.222
(0.538)
0.537
(0.775)
0.393
(0.679)
0.189
(0.516)
0.928
(0.98)
0.695
(0.872)
del 12q13 2 20 (12%) 145 0.314
(0.617)
0.872
(0.961)
0.26
(0.582)
0.489
(0.749)
0.36
(0.652)
0.515
(0.76)
0.589
(0.806)
0.799
(0.925)
0.71
(0.874)
0.788
(0.919)
0.512
(0.76)
0.569
(0.793)
del 16p13 3 14 (8%) 151 0.162
(0.482)
0.736
(0.888)
0.265
(0.582)
0.134
(0.45)
0.501
(0.752)
0.691
(0.872)
0.239
(0.564)
0.928
(0.98)
0.155
(0.478)
0.463
(0.724)
0.654
(0.848)
0.535
(0.774)
del 20p12 1 49 (30%) 116 0.825
(0.942)
0.302
(0.605)
0.113
(0.415)
0.96
(0.998)
0.903
(0.977)
0.862
(0.956)
0.362
(0.652)
0.375
(0.664)
0.702
(0.874)
0.253
(0.579)
0.603
(0.815)
0.265
(0.582)
del 21q11 2 73 (44%) 92 0.618
(0.823)
0.108
(0.415)
0.0603
(0.328)
0.758
(0.903)
0.344
(0.635)
0.503
(0.753)
0.5
(0.752)
0.709
(0.874)
0.0822
(0.384)
0.726
(0.882)
0.28
(0.592)
0.287
(0.592)
'amp_1q21.3' versus 'CN_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 1(1Q21.3) MUTATED 11 8 12 14 3
AMP PEAK 1(1Q21.3) WILD-TYPE 15 32 15 28 27

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

'amp_1q32.1' versus 'CN_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.035

Table S2.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 2(1Q32.1) MUTATED 11 8 11 17 2
AMP PEAK 2(1Q32.1) WILD-TYPE 15 32 16 25 28

Figure S2.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'RPPA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 27 25 30 3
AMP PEAK 2(1Q32.1) MUTATED 18 9 2 11 0
AMP PEAK 2(1Q32.1) WILD-TYPE 24 18 23 19 3

Figure S3.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p21.1' versus 'MRNA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #3: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
AMP PEAK 3(6P21.1) MUTATED 0 3 4 7 6
AMP PEAK 3(6P21.1) WILD-TYPE 13 5 16 6 9

Figure S4.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0076

Table S5.  Gene #3: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 3(6P21.1) MUTATED 11 16 15 10 2
AMP PEAK 3(6P21.1) WILD-TYPE 15 24 12 32 28

Figure S5.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.24

Table S6.  Gene #3: 'amp_6p21.1' 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
AMP PEAK 3(6P21.1) MUTATED 8 5 5 9 5 9
AMP PEAK 3(6P21.1) WILD-TYPE 12 15 19 9 24 7

Figure S6.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S7.  Gene #4: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 4(8P11.23) MUTATED 4 19 7 23 0
AMP PEAK 4(8P11.23) WILD-TYPE 22 21 20 19 30

Figure S7.  Get High-res Image Gene #4: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.17

Table S8.  Gene #4: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 55 62
AMP PEAK 4(8P11.23) MUTATED 8 25 13
AMP PEAK 4(8P11.23) WILD-TYPE 16 30 49

Figure S8.  Get High-res Image Gene #4: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.22

Table S9.  Gene #4: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 4(8P11.23) MUTATED 9 26 11
AMP PEAK 4(8P11.23) WILD-TYPE 13 37 45

Figure S9.  Get High-res Image Gene #4: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S10.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 5(8P11.21) MUTATED 9 19 9 32 1
AMP PEAK 5(8P11.21) WILD-TYPE 17 21 18 10 29

Figure S10.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.18

Table S11.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
AMP PEAK 5(8P11.21) MUTATED 6 6 10 10 13
AMP PEAK 5(8P11.21) WILD-TYPE 8 17 7 15 4

Figure S11.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S12.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 6(8Q24.21) MUTATED 20 32 13 40 4
AMP PEAK 6(8Q24.21) WILD-TYPE 6 8 14 2 26

Figure S12.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.058

Table S13.  Gene #8: 'amp_11p15.5' 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
AMP PEAK 8(11P15.5) MUTATED 7 8 2 10 14 2 1
AMP PEAK 8(11P15.5) WILD-TYPE 20 28 10 9 18 16 19

Figure S13.  Get High-res Image Gene #8: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.21

Table S14.  Gene #9: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
AMP PEAK 9(11Q13.3) MUTATED 2 3 8 2 5
AMP PEAK 9(11Q13.3) WILD-TYPE 12 20 9 23 12

Figure S14.  Get High-res Image Gene #9: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.06

Table S15.  Gene #9: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
AMP PEAK 9(11Q13.3) MUTATED 9 2 0 8 9
AMP PEAK 9(11Q13.3) WILD-TYPE 23 12 33 20 48

Figure S15.  Get High-res Image Gene #9: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.12

Table S16.  Gene #9: 'amp_11q13.3' 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
AMP PEAK 9(11Q13.3) MUTATED 8 2 2 7 7 1 1
AMP PEAK 9(11Q13.3) WILD-TYPE 19 34 10 12 25 17 19

Figure S16.  Get High-res Image Gene #9: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'RPPA_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.16

Table S17.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 27 25 30 3
AMP PEAK 11(12P12.1) MUTATED 11 3 11 3 0
AMP PEAK 11(12P12.1) WILD-TYPE 31 24 14 27 3

Figure S17.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S18.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 12(13Q12.13) MUTATED 20 35 27 30 14
AMP PEAK 12(13Q12.13) WILD-TYPE 6 5 0 12 16

Figure S18.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.084

Table S19.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
AMP PEAK 12(13Q12.13) MUTATED 26 12 20 27 40
AMP PEAK 12(13Q12.13) WILD-TYPE 6 2 13 1 17

Figure S19.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S20.  Gene #12: 'amp_13q12.13' 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
AMP PEAK 12(13Q12.13) MUTATED 26 29 7 18 26 5 14
AMP PEAK 12(13Q12.13) WILD-TYPE 1 7 5 1 6 13 6

Figure S20.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0076

Table S21.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 55 62
AMP PEAK 12(13Q12.13) MUTATED 19 51 39
AMP PEAK 12(13Q12.13) WILD-TYPE 5 4 23

Figure S21.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00414 (Fisher's exact test), Q value = 0.06

Table S22.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 12(13Q12.13) MUTATED 19 55 35
AMP PEAK 12(13Q12.13) WILD-TYPE 3 8 21

Figure S22.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0011

Table S23.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 13(13Q12.2) MUTATED 18 35 27 31 14
AMP PEAK 13(13Q12.2) WILD-TYPE 8 5 0 11 16

Figure S23.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.058

Table S24.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
AMP PEAK 13(13Q12.2) MUTATED 26 12 19 27 40
AMP PEAK 13(13Q12.2) WILD-TYPE 6 2 14 1 17

Figure S24.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0029

Table S25.  Gene #13: 'amp_13q12.2' 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
AMP PEAK 13(13Q12.2) MUTATED 26 28 7 17 26 6 14
AMP PEAK 13(13Q12.2) WILD-TYPE 1 8 5 2 6 12 6

Figure S25.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.082

Table S26.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 55 62
AMP PEAK 13(13Q12.2) MUTATED 19 49 40
AMP PEAK 13(13Q12.2) WILD-TYPE 5 6 22

Figure S26.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.18

Table S27.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 13(13Q12.2) MUTATED 19 53 36
AMP PEAK 13(13Q12.2) WILD-TYPE 3 10 20

Figure S27.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S28.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 14(13Q22.1) MUTATED 18 34 27 29 12
AMP PEAK 14(13Q22.1) WILD-TYPE 8 6 0 13 18

Figure S28.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.058

Table S29.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
AMP PEAK 14(13Q22.1) MUTATED 23 11 18 27 40
AMP PEAK 14(13Q22.1) WILD-TYPE 9 3 15 1 17

Figure S29.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0011

Table S30.  Gene #14: 'amp_13q22.1' 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
AMP PEAK 14(13Q22.1) MUTATED 23 26 8 17 28 4 13
AMP PEAK 14(13Q22.1) WILD-TYPE 4 10 4 2 4 14 7

Figure S30.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.2

Table S31.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 55 62
AMP PEAK 14(13Q22.1) MUTATED 20 46 39
AMP PEAK 14(13Q22.1) WILD-TYPE 4 9 23

Figure S31.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.12

Table S32.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 14(13Q22.1) MUTATED 18 53 34
AMP PEAK 14(13Q22.1) WILD-TYPE 4 10 22

Figure S32.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S33.  Gene #15: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 15(16P11.2) MUTATED 4 20 13 9 1
AMP PEAK 15(16P11.2) WILD-TYPE 22 20 14 33 29

Figure S33.  Get High-res Image Gene #15: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.1

Table S34.  Gene #15: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
AMP PEAK 15(16P11.2) MUTATED 1 5 11 7 4
AMP PEAK 15(16P11.2) WILD-TYPE 13 18 6 18 13

Figure S34.  Get High-res Image Gene #15: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.06

Table S35.  Gene #16: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 16(17Q12) MUTATED 5 21 4 10 6
AMP PEAK 16(17Q12) WILD-TYPE 21 19 23 32 24

Figure S35.  Get High-res Image Gene #16: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.012

Table S36.  Gene #17: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 17(17Q24.1) MUTATED 6 19 1 7 6
AMP PEAK 17(17Q24.1) WILD-TYPE 20 21 26 35 24

Figure S36.  Get High-res Image Gene #17: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0017

Table S37.  Gene #18: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 18(20Q11.21) MUTATED 23 40 27 36 20
AMP PEAK 18(20Q11.21) WILD-TYPE 3 0 0 6 10

Figure S37.  Get High-res Image Gene #18: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.071

Table S38.  Gene #18: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
AMP PEAK 18(20Q11.21) MUTATED 9 22 17 22 17
AMP PEAK 18(20Q11.21) WILD-TYPE 5 1 0 3 0

Figure S38.  Get High-res Image Gene #18: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0065

Table S39.  Gene #18: 'amp_20q11.21' 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
AMP PEAK 18(20Q11.21) MUTATED 26 32 9 19 31 10 18
AMP PEAK 18(20Q11.21) WILD-TYPE 1 4 3 0 1 8 2

Figure S39.  Get High-res Image Gene #18: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.23' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0024

Table S40.  Gene #19: 'amp_20q11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 19(20Q11.23) MUTATED 24 40 27 36 20
AMP PEAK 19(20Q11.23) WILD-TYPE 2 0 0 6 10

Figure S40.  Get High-res Image Gene #19: 'amp_20q11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.23' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.19

Table S41.  Gene #19: 'amp_20q11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
AMP PEAK 19(20Q11.23) MUTATED 10 22 17 22 17
AMP PEAK 19(20Q11.23) WILD-TYPE 4 1 0 3 0

Figure S41.  Get High-res Image Gene #19: 'amp_20q11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0052

Table S42.  Gene #19: 'amp_20q11.23' 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
AMP PEAK 19(20Q11.23) MUTATED 26 33 9 19 31 10 18
AMP PEAK 19(20Q11.23) WILD-TYPE 1 3 3 0 1 8 2

Figure S42.  Get High-res Image Gene #19: 'amp_20q11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0032

Table S43.  Gene #20: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
AMP PEAK 20(20Q13.33) MUTATED 25 39 27 35 20
AMP PEAK 20(20Q13.33) WILD-TYPE 1 1 0 7 10

Figure S43.  Get High-res Image Gene #20: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #20: 'amp_20q13.33' 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
AMP PEAK 20(20Q13.33) MUTATED 26 33 9 18 31 10 18
AMP PEAK 20(20Q13.33) WILD-TYPE 1 3 3 1 1 8 2

Figure S44.  Get High-res Image Gene #20: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq27.3' versus 'METHLYATION_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.24

Table S45.  Gene #22: 'amp_xq27.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
AMP PEAK 22(XQ27.3) MUTATED 1 3 6 1 5
AMP PEAK 22(XQ27.3) WILD-TYPE 13 20 11 24 12

Figure S45.  Get High-res Image Gene #22: 'amp_xq27.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.17

Table S46.  Gene #22: 'amp_xq27.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 12 16 6 5
AMP PEAK 22(XQ27.3) MUTATED 1 4 0 0 2
AMP PEAK 22(XQ27.3) WILD-TYPE 10 8 16 6 3

Figure S46.  Get High-res Image Gene #22: 'amp_xq27.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.15

Table S47.  Gene #23: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 1(1P36.11) MUTATED 15 23 12 19 6
DEL PEAK 1(1P36.11) WILD-TYPE 11 17 15 23 24

Figure S47.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #23: 'del_1p36.11' 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
DEL PEAK 1(1P36.11) MUTATED 15 14 3 8 23 5 7
DEL PEAK 1(1P36.11) WILD-TYPE 12 22 9 11 9 13 13

Figure S48.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.14

Table S49.  Gene #24: 'del_1p33' 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
DEL PEAK 2(1P33) MUTATED 1 2 2 1 5 6 0 3 0
DEL PEAK 2(1P33) WILD-TYPE 5 8 5 8 4 2 9 5 3

Figure S49.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0034

Table S50.  Gene #24: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 2(1P33) MUTATED 10 20 11 11 1
DEL PEAK 2(1P33) WILD-TYPE 16 20 16 31 29

Figure S50.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.021

Table S51.  Gene #25: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 3(1P13.2) MUTATED 9 17 11 16 1
DEL PEAK 3(1P13.2) WILD-TYPE 17 23 16 26 29

Figure S51.  Get High-res Image Gene #25: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.17

Table S52.  Gene #25: 'del_1p13.2' 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
DEL PEAK 3(1P13.2) MUTATED 16 7 3 8 12 3 5
DEL PEAK 3(1P13.2) WILD-TYPE 11 29 9 11 20 15 15

Figure S52.  Get High-res Image Gene #25: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'MRNA_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.14

Table S53.  Gene #26: 'del_2p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
DEL PEAK 4(2P12) MUTATED 2 3 0 4 1
DEL PEAK 4(2P12) WILD-TYPE 11 5 20 9 14

Figure S53.  Get High-res Image Gene #26: 'del_2p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2p12' versus 'CN_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.18

Table S54.  Gene #26: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 4(2P12) MUTATED 0 1 5 6 1
DEL PEAK 4(2P12) WILD-TYPE 26 39 22 36 29

Figure S54.  Get High-res Image Gene #26: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.18

Table S55.  Gene #28: 'del_3q26.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
DEL PEAK 6(3Q26.31) MUTATED 5 1 0 3 1
DEL PEAK 6(3Q26.31) WILD-TYPE 9 22 17 22 16

Figure S55.  Get High-res Image Gene #28: 'del_3q26.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.24

Table S56.  Gene #28: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
DEL PEAK 6(3Q26.31) MUTATED 6 5 4
DEL PEAK 6(3Q26.31) WILD-TYPE 16 58 52

Figure S56.  Get High-res Image Gene #28: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p13' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0011

Table S57.  Gene #29: 'del_4p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 7(4P13) MUTATED 13 15 17 14 1
DEL PEAK 7(4P13) WILD-TYPE 13 25 10 28 29

Figure S57.  Get High-res Image Gene #29: 'del_4p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.24

Table S58.  Gene #30: 'del_4q22.1' 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
DEL PEAK 8(4Q22.1) MUTATED 1 4 4 4 8 3 1 4 0
DEL PEAK 8(4Q22.1) WILD-TYPE 5 6 3 5 1 5 8 4 3

Figure S58.  Get High-res Image Gene #30: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0022

Table S59.  Gene #30: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 8(4Q22.1) MUTATED 14 20 19 17 3
DEL PEAK 8(4Q22.1) WILD-TYPE 12 20 8 25 27

Figure S59.  Get High-res Image Gene #30: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S60.  Gene #31: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 9(4Q35.1) MUTATED 16 18 18 19 1
DEL PEAK 9(4Q35.1) WILD-TYPE 10 22 9 23 29

Figure S60.  Get High-res Image Gene #31: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.13

Table S61.  Gene #31: 'del_4q35.1' 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
DEL PEAK 9(4Q35.1) MUTATED 7 7 15 10 5 8
DEL PEAK 9(4Q35.1) WILD-TYPE 13 13 9 8 24 8

Figure S61.  Get High-res Image Gene #31: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00431 (Fisher's exact test), Q value = 0.061

Table S62.  Gene #32: 'del_5q12.1' 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
DEL PEAK 10(5Q12.1) MUTATED 0 1 1 3 7 2 0 3 0
DEL PEAK 10(5Q12.1) WILD-TYPE 6 9 6 6 2 6 9 5 3

Figure S62.  Get High-res Image Gene #32: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.024

Table S63.  Gene #32: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 10(5Q12.1) MUTATED 11 13 10 18 1
DEL PEAK 10(5Q12.1) WILD-TYPE 15 27 17 24 29

Figure S63.  Get High-res Image Gene #32: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.024

Table S64.  Gene #33: 'del_5q22.2' 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
DEL PEAK 11(5Q22.2) MUTATED 0 2 2 3 8 3 0 4 0
DEL PEAK 11(5Q22.2) WILD-TYPE 6 8 5 6 1 5 9 4 3

Figure S64.  Get High-res Image Gene #33: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 0.00965 (Fisher's exact test), Q value = 0.11

Table S65.  Gene #33: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 11(5Q22.2) MUTATED 9 15 13 19 3
DEL PEAK 11(5Q22.2) WILD-TYPE 17 25 14 23 27

Figure S65.  Get High-res Image Gene #33: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.24

Table S66.  Gene #36: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 14(7Q31.1) MUTATED 0 0 0 4 0
DEL PEAK 14(7Q31.1) WILD-TYPE 26 40 27 38 30

Figure S66.  Get High-res Image Gene #36: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S67.  Gene #37: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 15(8P23.2) MUTATED 15 25 18 38 4
DEL PEAK 15(8P23.2) WILD-TYPE 11 15 9 4 26

Figure S67.  Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.027

Table S68.  Gene #37: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
DEL PEAK 15(8P23.2) MUTATED 22 8 10 17 42
DEL PEAK 15(8P23.2) WILD-TYPE 10 6 23 11 15

Figure S68.  Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.11

Table S69.  Gene #37: 'del_8p23.2' 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
DEL PEAK 15(8P23.2) MUTATED 22 16 8 8 24 8 13
DEL PEAK 15(8P23.2) WILD-TYPE 5 20 4 11 8 10 7

Figure S69.  Get High-res Image Gene #37: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8q11.1' versus 'CN_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.11

Table S70.  Gene #38: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 16(8Q11.1) MUTATED 4 4 7 2 0
DEL PEAK 16(8Q11.1) WILD-TYPE 22 36 20 40 30

Figure S70.  Get High-res Image Gene #38: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.24

Table S71.  Gene #40: 'del_10q25.2' 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
DEL PEAK 18(10Q25.2) MUTATED 14 6 2 3 8 8 6
DEL PEAK 18(10Q25.2) WILD-TYPE 13 30 10 16 24 10 14

Figure S71.  Get High-res Image Gene #40: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'MRNA_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.028

Table S72.  Gene #41: 'del_11q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
DEL PEAK 19(11Q22.3) MUTATED 3 6 4 2 0
DEL PEAK 19(11Q22.3) WILD-TYPE 10 2 16 11 15

Figure S72.  Get High-res Image Gene #41: 'del_11q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q22.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.002

Table S73.  Gene #41: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 19(11Q22.3) MUTATED 4 1 10 18 5
DEL PEAK 19(11Q22.3) WILD-TYPE 22 39 17 24 25

Figure S73.  Get High-res Image Gene #41: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.074

Table S74.  Gene #41: 'del_11q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
DEL PEAK 19(11Q22.3) MUTATED 5 6 12 1 14
DEL PEAK 19(11Q22.3) WILD-TYPE 27 8 21 27 43

Figure S74.  Get High-res Image Gene #41: 'del_11q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0077 (Fisher's exact test), Q value = 0.094

Table S75.  Gene #41: 'del_11q22.3' 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
DEL PEAK 19(11Q22.3) MUTATED 1 13 5 2 6 7 4
DEL PEAK 19(11Q22.3) WILD-TYPE 26 23 7 17 26 11 16

Figure S75.  Get High-res Image Gene #41: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00093

Table S76.  Gene #43: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 21(14Q11.2) MUTATED 16 23 17 10 4
DEL PEAK 21(14Q11.2) WILD-TYPE 10 17 10 32 26

Figure S76.  Get High-res Image Gene #43: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00093

Table S77.  Gene #44: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 22(14Q31.1) MUTATED 16 25 15 13 3
DEL PEAK 22(14Q31.1) WILD-TYPE 10 15 12 29 27

Figure S77.  Get High-res Image Gene #44: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0032

Table S78.  Gene #45: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 23(15Q21.1) MUTATED 14 23 14 25 3
DEL PEAK 23(15Q21.1) WILD-TYPE 12 17 13 17 27

Figure S78.  Get High-res Image Gene #45: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0011

Table S79.  Gene #46: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 24(15Q22.33) MUTATED 15 22 14 24 2
DEL PEAK 24(15Q22.33) WILD-TYPE 11 18 13 18 28

Figure S79.  Get High-res Image Gene #46: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.18

Table S80.  Gene #48: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 8 20 13 15
DEL PEAK 26(16Q23.1) MUTATED 0 1 1 5 1
DEL PEAK 26(16Q23.1) WILD-TYPE 13 7 19 8 14

Figure S80.  Get High-res Image Gene #48: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.058

Table S81.  Gene #48: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 26(16Q23.1) MUTATED 6 2 1 12 2
DEL PEAK 26(16Q23.1) WILD-TYPE 20 38 26 30 28

Figure S81.  Get High-res Image Gene #48: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'CN_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.039

Table S82.  Gene #49: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 27(17P11.2) MUTATED 19 26 21 35 12
DEL PEAK 27(17P11.2) WILD-TYPE 7 14 6 7 18

Figure S82.  Get High-res Image Gene #49: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S83.  Gene #50: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 28(18P11.31) MUTATED 21 39 21 32 12
DEL PEAK 28(18P11.31) WILD-TYPE 5 1 6 10 18

Figure S83.  Get High-res Image Gene #50: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 0.00931 (Fisher's exact test), Q value = 0.11

Table S84.  Gene #50: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
DEL PEAK 28(18P11.31) MUTATED 7 20 17 19 14
DEL PEAK 28(18P11.31) WILD-TYPE 7 3 0 6 3

Figure S84.  Get High-res Image Gene #50: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0057 (Fisher's exact test), Q value = 0.075

Table S85.  Gene #50: 'del_18p11.31' 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
DEL PEAK 28(18P11.31) MUTATED 26 26 7 17 24 9 15
DEL PEAK 28(18P11.31) WILD-TYPE 1 10 5 2 8 9 5

Figure S85.  Get High-res Image Gene #50: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S86.  Gene #51: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 29(18Q21.2) MUTATED 22 40 26 42 15
DEL PEAK 29(18Q21.2) WILD-TYPE 4 0 1 0 15

Figure S86.  Get High-res Image Gene #51: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00603 (Fisher's exact test), Q value = 0.078

Table S87.  Gene #51: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
DEL PEAK 29(18Q21.2) MUTATED 30 13 22 26 53
DEL PEAK 29(18Q21.2) WILD-TYPE 2 1 11 2 4

Figure S87.  Get High-res Image Gene #51: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.23

Table S88.  Gene #51: 'del_18q21.2' 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
DEL PEAK 29(18Q21.2) MUTATED 27 32 8 17 29 13 18
DEL PEAK 29(18Q21.2) WILD-TYPE 0 4 4 2 3 5 2

Figure S88.  Get High-res Image Gene #51: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S89.  Gene #52: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 30(18Q22.1) MUTATED 20 40 26 41 14
DEL PEAK 30(18Q22.1) WILD-TYPE 6 0 1 1 16

Figure S89.  Get High-res Image Gene #52: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.13

Table S90.  Gene #52: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
DEL PEAK 30(18Q22.1) MUTATED 8 20 17 22 16
DEL PEAK 30(18Q22.1) WILD-TYPE 6 3 0 3 1

Figure S90.  Get High-res Image Gene #52: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.22

Table S91.  Gene #52: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
DEL PEAK 30(18Q22.1) MUTATED 28 12 22 26 52
DEL PEAK 30(18Q22.1) WILD-TYPE 4 2 11 2 5

Figure S91.  Get High-res Image Gene #52: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.12

Table S92.  Gene #52: 'del_18q22.1' 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
DEL PEAK 30(18Q22.1) MUTATED 27 30 7 17 29 13 17
DEL PEAK 30(18Q22.1) WILD-TYPE 0 6 5 2 3 5 3

Figure S92.  Get High-res Image Gene #52: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S93.  Gene #53: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 40 27 42 30
DEL PEAK 31(18Q23) MUTATED 20 39 26 41 15
DEL PEAK 31(18Q23) WILD-TYPE 6 1 1 1 15

Figure S93.  Get High-res Image Gene #53: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.24

Table S94.  Gene #53: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 14 33 28 57
DEL PEAK 31(18Q23) MUTATED 29 12 22 26 51
DEL PEAK 31(18Q23) WILD-TYPE 3 2 11 2 6

Figure S94.  Get High-res Image Gene #53: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.23

Table S95.  Gene #53: 'del_18q23' 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
DEL PEAK 31(18Q23) MUTATED 27 30 8 17 29 13 16
DEL PEAK 31(18Q23) WILD-TYPE 0 6 4 2 3 5 4

Figure S95.  Get High-res Image Gene #53: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00571 (Fisher's exact test), Q value = 0.075

Table S96.  Gene #54: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
DEL PEAK 32(19P13.3) MUTATED 11 15 8
DEL PEAK 32(19P13.3) WILD-TYPE 11 48 48

Figure S96.  Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.12

Table S97.  Gene #57: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 12 16 6 5
DEL PEAK 35(22Q13.31) MUTATED 9 4 10 2 0
DEL PEAK 35(22Q13.31) WILD-TYPE 2 8 6 4 5

Figure S97.  Get High-res Image Gene #57: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.33' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0089

Table S98.  Gene #58: 'del_xp22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 23 17 25 17
DEL PEAK 36(XP22.33) MUTATED 0 9 3 0 5
DEL PEAK 36(XP22.33) WILD-TYPE 14 14 14 25 12

Figure S98.  Get High-res Image Gene #58: 'del_xp22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/22532761/transformed.cor.cli.txt

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

  • Number of patients = 165

  • Number of significantly focal cnvs = 58

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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