Correlation between copy number variation genes (focal events) and molecular subtypes
Adrenocortical Carcinoma (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/C1PZ584X
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 44 focal events and 10 molecular subtypes across 90 patients, 160 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_4p16.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5q35.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_6p21.31 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q24.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_7p22.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_9q31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12q14.1 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_14q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_16p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_16q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_16q24.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF'.

  • amp_19p13.12 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'CN_CNMF'.

  • del_2q37.3 cnv correlated to 'CN_CNMF'.

  • del_3q13.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_6p24.3 cnv correlated to 'CN_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_11p15.5 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_11q14.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_12q14.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_14q21.2 cnv correlated to 'CN_CNMF'.

  • del_15q15.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q21.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q24.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_20p12.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_22q12.1 cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 44 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 160 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 14q11 2 27 (30%) 63 0.00047
(0.00517)
0.00065
(0.00696)
0.0309
(0.102)
0.0279
(0.0964)
2e-05
(0.000463)
1e-05
(0.000275)
0.00037
(0.0044)
0.00738
(0.0382)
4e-05
(8e-04)
0.00624
(0.0344)
amp 5q35 3 63 (70%) 27 1e-05
(0.000275)
5e-05
(0.000957)
0.123
(0.269)
0.0068
(0.0365)
1e-05
(0.000275)
1e-05
(0.000275)
0.0146
(0.0629)
0.0464
(0.131)
4e-05
(8e-04)
0.0537
(0.142)
amp 16q24 2 49 (54%) 41 1e-05
(0.000275)
0.0001
(0.00157)
1
(1.00)
0.325
(0.485)
0.00028
(0.00362)
1e-05
(0.000275)
0.108
(0.237)
0.00284
(0.0215)
0.00416
(0.0265)
0.0244
(0.0903)
del 4q34 3 25 (28%) 65 0.00042
(0.00486)
0.0183
(0.072)
0.809
(0.87)
0.635
(0.741)
0.0201
(0.0764)
0.0391
(0.123)
0.0531
(0.141)
0.0419
(0.127)
0.0257
(0.0937)
0.00471
(0.0276)
del 9p23 23 (26%) 67 2e-05
(0.000463)
0.00368
(0.0257)
0.167
(0.324)
0.05
(0.137)
3e-05
(0.00066)
0.00025
(0.00333)
0.0324
(0.106)
0.0464
(0.131)
0.00179
(0.0143)
0.277
(0.438)
amp 1q22 17 (19%) 73 0.00167
(0.0139)
0.00034
(0.00416)
0.564
(0.698)
0.4
(0.549)
0.00244
(0.0188)
0.00017
(0.00241)
0.048
(0.133)
0.155
(0.31)
0.0644
(0.164)
0.026
(0.0937)
amp 9q31 3 34 (38%) 56 0.0001
(0.00157)
0.0283
(0.0964)
0.129
(0.274)
0.138
(0.286)
0.0158
(0.0644)
0.0189
(0.0723)
0.00625
(0.0344)
0.202
(0.364)
0.0158
(0.0644)
0.185
(0.343)
amp 16p13 3 50 (56%) 40 1e-05
(0.000275)
0.00076
(0.00743)
0.707
(0.794)
0.0528
(0.141)
0.00014
(0.00212)
1e-05
(0.000275)
0.181
(0.34)
0.00931
(0.0465)
0.135
(0.283)
0.0156
(0.0644)
amp 16q22 1 56 (62%) 34 1e-05
(0.000275)
0.00391
(0.0261)
0.875
(0.922)
0.801
(0.87)
0.0296
(0.1)
8e-05
(0.00135)
0.132
(0.278)
0.0223
(0.0839)
0.0372
(0.118)
0.235
(0.403)
del 9p21 3 26 (29%) 64 1e-05
(0.000275)
0.00388
(0.0261)
0.22
(0.387)
0.226
(0.395)
1e-05
(0.000275)
0.00019
(0.00261)
0.0602
(0.155)
0.0437
(0.129)
0.0112
(0.0526)
0.129
(0.274)
amp 5p15 33 65 (72%) 25 1e-05
(0.000275)
0.174
(0.333)
0.811
(0.87)
0.89
(0.93)
0.0123
(0.0558)
0.00068
(0.00696)
0.095
(0.225)
0.18
(0.339)
0.00455
(0.0271)
0.0366
(0.117)
amp xq28 46 (51%) 44 2e-05
(0.000463)
0.0141
(0.0614)
0.102
(0.231)
0.044
(0.129)
0.00717
(0.0379)
0.0119
(0.0547)
0.846
(0.899)
0.259
(0.421)
0.623
(0.733)
0.104
(0.234)
del 17q21 2 26 (29%) 64 0.0022
(0.0173)
0.00723
(0.0379)
0.383
(0.54)
0.54
(0.678)
0.101
(0.231)
0.035
(0.112)
0.061
(0.156)
0.0088
(0.0445)
0.415
(0.562)
0.0103
(0.0495)
amp 4p16 3 41 (46%) 49 0.0044
(0.0269)
0.268
(0.432)
0.955
(0.976)
0.189
(0.349)
0.0148
(0.0632)
0.00611
(0.0344)
0.883
(0.925)
0.0461
(0.131)
0.72
(0.806)
0.592
(0.721)
amp 6p21 31 19 (21%) 71 0.0235
(0.0876)
0.535
(0.675)
0.61
(0.731)
0.801
(0.87)
0.0507
(0.138)
1
(1.00)
0.0923
(0.222)
0.0259
(0.0937)
0.00413
(0.0265)
0.0424
(0.128)
amp 12q14 1 70 (78%) 20 1e-05
(0.000275)
0.0515
(0.138)
0.0584
(0.152)
0.0101
(0.0493)
0.017
(0.068)
0.00177
(0.0143)
0.316
(0.476)
0.486
(0.636)
0.0994
(0.23)
0.203
(0.364)
amp 19p13 12 58 (64%) 32 1e-05
(0.000275)
0.142
(0.292)
0.242
(0.407)
0.0102
(0.0495)
0.0015
(0.0127)
0.00045
(0.00508)
0.307
(0.469)
0.48
(0.632)
0.106
(0.235)
0.621
(0.733)
amp xp11 22 49 (54%) 41 0.00016
(0.00235)
0.162
(0.319)
0.366
(0.525)
0.0165
(0.0666)
0.0307
(0.102)
0.0951
(0.225)
0.958
(0.976)
0.145
(0.294)
0.105
(0.234)
0.0271
(0.0953)
del 4q34 3 28 (31%) 62 6e-05
(0.0011)
0.0282
(0.0964)
0.706
(0.794)
0.147
(0.295)
0.208
(0.371)
0.185
(0.343)
0.127
(0.274)
0.19
(0.35)
0.0154
(0.0644)
0.0139
(0.0612)
del 4q35 1 30 (33%) 60 0.00079
(0.00756)
0.0472
(0.131)
0.389
(0.54)
0.393
(0.542)
0.0907
(0.222)
0.0415
(0.127)
0.275
(0.438)
0.167
(0.324)
0.0971
(0.227)
0.0309
(0.102)
del 15q15 1 25 (28%) 65 8e-05
(0.00135)
0.506
(0.653)
0.904
(0.936)
0.242
(0.407)
0.0467
(0.131)
0.241
(0.407)
0.809
(0.87)
0.0482
(0.133)
0.454
(0.604)
0.00401
(0.0263)
del 17q11 2 24 (27%) 66 0.0134
(0.0596)
0.0431
(0.129)
0.621
(0.733)
0.629
(0.736)
0.0806
(0.201)
0.105
(0.234)
0.221
(0.387)
0.0182
(0.072)
0.254
(0.418)
0.00438
(0.0269)
del 17q24 2 24 (27%) 66 0.0345
(0.112)
0.00378
(0.026)
0.702
(0.791)
0.29
(0.454)
0.137
(0.286)
0.0396
(0.123)
0.341
(0.497)
0.0268
(0.095)
0.235
(0.403)
0.302
(0.467)
del 20p12 1 12 (13%) 78 0.00507
(0.029)
0.255
(0.418)
0.518
(0.658)
0.621
(0.733)
0.0451
(0.13)
0.0266
(0.095)
0.0443
(0.129)
0.516
(0.657)
0.0599
(0.155)
0.402
(0.55)
amp 7p22 1 54 (60%) 36 0.00294
(0.0219)
0.244
(0.407)
0.333
(0.493)
0.674
(0.773)
0.00649
(0.0353)
0.0327
(0.107)
0.44
(0.591)
0.491
(0.637)
0.0961
(0.226)
0.37
(0.529)
amp 19q12 56 (62%) 34 1e-05
(0.000275)
0.111
(0.242)
0.444
(0.591)
0.168
(0.324)
0.00135
(0.0116)
0.00118
(0.0104)
0.203
(0.364)
0.253
(0.417)
0.157
(0.311)
0.239
(0.405)
del 12q14 2 5 (6%) 85 0.072
(0.182)
0.195
(0.357)
0.178
(0.339)
0.00095
(0.00889)
0.0512
(0.138)
0.306
(0.469)
0.0189
(0.0723)
0.00424
(0.0267)
del 16q23 1 11 (12%) 79 0.0157
(0.0644)
0.391
(0.541)
0.573
(0.707)
0.233
(0.402)
0.0442
(0.129)
0.0111
(0.0526)
0.0553
(0.145)
0.139
(0.287)
0.337
(0.494)
0.0754
(0.189)
amp 6q24 3 19 (21%) 71 0.0127
(0.057)
0.809
(0.87)
0.903
(0.936)
0.64
(0.745)
0.028
(0.0964)
0.934
(0.963)
0.261
(0.422)
0.231
(0.402)
0.1
(0.23)
0.399
(0.548)
del 1p36 23 38 (42%) 52 1e-05
(0.000275)
0.145
(0.294)
0.802
(0.87)
0.145
(0.294)
0.0923
(0.222)
0.00358
(0.0257)
1
(1.00)
0.559
(0.693)
0.353
(0.511)
0.0923
(0.222)
del 3q13 31 25 (28%) 65 0.00986
(0.0487)
0.61
(0.731)
0.338
(0.494)
0.47
(0.622)
0.104
(0.234)
0.0402
(0.124)
0.2
(0.363)
0.2
(0.363)
0.125
(0.271)
0.0883
(0.218)
del 11p15 5 26 (29%) 64 0.00029
(0.00365)
0.179
(0.339)
0.387
(0.54)
0.671
(0.772)
0.127
(0.274)
0.0395
(0.123)
0.215
(0.381)
0.596
(0.724)
0.598
(0.725)
0.49
(0.637)
del 11q14 1 24 (27%) 66 0.00453
(0.0271)
0.0186
(0.0723)
0.968
(0.983)
0.551
(0.687)
0.293
(0.454)
0.374
(0.531)
0.332
(0.493)
0.645
(0.749)
0.544
(0.679)
0.603
(0.729)
del 13q14 2 42 (47%) 48 0.00115
(0.0103)
0.0454
(0.13)
0.58
(0.71)
0.839
(0.896)
0.275
(0.438)
0.559
(0.693)
0.958
(0.976)
0.529
(0.669)
0.605
(0.729)
0.357
(0.514)
amp 17q25 3 18 (20%) 72 0.00487
(0.0282)
0.876
(0.922)
0.614
(0.733)
0.1
(0.23)
0.164
(0.321)
0.672
(0.772)
0.92
(0.95)
0.696
(0.787)
0.259
(0.421)
0.69
(0.787)
del 2q22 1 18 (20%) 72 0.00365
(0.0257)
0.158
(0.312)
0.761
(0.843)
0.796
(0.87)
0.233
(0.402)
0.0893
(0.219)
0.274
(0.438)
0.663
(0.766)
0.389
(0.54)
0.507
(0.653)
del 2q37 3 21 (23%) 69 0.00313
(0.023)
0.151
(0.303)
0.693
(0.787)
0.83
(0.889)
0.322
(0.482)
0.0929
(0.222)
0.43
(0.581)
0.528
(0.669)
0.76
(0.843)
0.949
(0.973)
del 6p24 3 20 (22%) 70 0.00099
(0.00907)
0.762
(0.843)
0.616
(0.733)
0.318
(0.478)
0.614
(0.733)
0.483
(0.634)
0.505
(0.653)
0.0987
(0.23)
0.47
(0.622)
0.245
(0.407)
del 6q26 21 (23%) 69 0.00068
(0.00696)
0.146
(0.295)
0.512
(0.655)
0.313
(0.475)
0.315
(0.476)
0.308
(0.469)
0.276
(0.438)
0.348
(0.505)
0.387
(0.54)
0.253
(0.417)
del 14q21 2 20 (22%) 70 0.0115
(0.0532)
0.541
(0.678)
0.388
(0.54)
0.579
(0.71)
0.293
(0.454)
0.285
(0.449)
0.244
(0.407)
0.735
(0.82)
0.512
(0.655)
0.859
(0.91)
del 16p13 3 8 (9%) 82 0.306
(0.469)
0.628
(0.736)
0.938
(0.964)
0.286
(0.449)
0.13
(0.276)
0.00782
(0.04)
0.0846
(0.21)
0.785
(0.863)
0.336
(0.494)
0.196
(0.358)
del 22q12 1 50 (56%) 40 0.00076
(0.00743)
0.384
(0.54)
0.791
(0.868)
0.291
(0.454)
0.844
(0.899)
0.184
(0.343)
0.364
(0.523)
0.88
(0.924)
0.898
(0.936)
0.442
(0.591)
del 7q36 3 11 (12%) 79 0.215
(0.381)
0.587
(0.718)
0.409
(0.556)
0.66
(0.765)
0.171
(0.328)
0.336
(0.494)
0.901
(0.936)
0.736
(0.82)
0.676
(0.773)
0.372
(0.53)
del 10q23 1 10 (11%) 80 0.438
(0.589)
0.78
(0.86)
1
(1.00)
0.239
(0.405)
0.409
(0.556)
1
(1.00)
0.695
(0.787)
0.801
(0.87)
0.865
(0.914)
0.49
(0.637)
'amp_1q22' versus 'CN_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.014

Table S1.  Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 1(1Q22) MUTATED 8 0 0 6 3 0 0
AMP PEAK 1(1Q22) WILD-TYPE 11 18 13 12 8 6 5

Figure S1.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 1(1Q22) MUTATED 8 5 2 0 0 0 0
AMP PEAK 1(1Q22) WILD-TYPE 8 9 6 17 9 12 2

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

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.019

Table S3.  Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 1(1Q22) MUTATED 11 1 1 2
AMP PEAK 1(1Q22) WILD-TYPE 13 13 15 21

Figure S3.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0024

Table S4.  Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 1(1Q22) MUTATED 11 1 2 1
AMP PEAK 1(1Q22) WILD-TYPE 12 22 5 23

Figure S4.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.13

Table S5.  Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 24 25
AMP PEAK 1(1Q22) MUTATED 7 7 1
AMP PEAK 1(1Q22) WILD-TYPE 22 17 24

Figure S5.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.094

Table S6.  Gene #1: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 1(1Q22) MUTATED 1 3 1 7 3 0
AMP PEAK 1(1Q22) WILD-TYPE 5 21 10 7 8 11

Figure S6.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #2: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 2(4P16.3) MUTATED 4 8 9 6 4 5 5
AMP PEAK 2(4P16.3) WILD-TYPE 15 10 4 12 7 1 0

Figure S7.  Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.063

Table S8.  Gene #2: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 2(4P16.3) MUTATED 5 8 11 10
AMP PEAK 2(4P16.3) WILD-TYPE 19 6 5 13

Figure S8.  Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.034

Table S9.  Gene #2: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 2(4P16.3) MUTATED 5 15 1 13
AMP PEAK 2(4P16.3) WILD-TYPE 18 8 6 11

Figure S9.  Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.13

Table S10.  Gene #2: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 2(4P16.3) MUTATED 11 10 6 5 3
AMP PEAK 2(4P16.3) WILD-TYPE 5 17 5 15 1

Figure S10.  Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S11.  Gene #3: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 3(5P15.33) MUTATED 5 18 11 14 7 5 5
AMP PEAK 3(5P15.33) WILD-TYPE 14 0 2 4 4 1 0

Figure S11.  Get High-res Image Gene #3: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.056

Table S12.  Gene #3: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 3(5P15.33) MUTATED 12 11 15 19
AMP PEAK 3(5P15.33) WILD-TYPE 12 3 1 4

Figure S12.  Get High-res Image Gene #3: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.007

Table S13.  Gene #3: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 3(5P15.33) MUTATED 13 20 2 22
AMP PEAK 3(5P15.33) WILD-TYPE 10 3 5 2

Figure S13.  Get High-res Image Gene #3: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.027

Table S14.  Gene #3: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 3(5P15.33) MUTATED 9 11 16 21
AMP PEAK 3(5P15.33) WILD-TYPE 7 8 0 5

Figure S14.  Get High-res Image Gene #3: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.12

Table S15.  Gene #3: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 3(5P15.33) MUTATED 6 19 11 8 6 7
AMP PEAK 3(5P15.33) WILD-TYPE 0 5 0 6 5 4

Figure S15.  Get High-res Image Gene #3: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S16.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 4(5Q35.3) MUTATED 6 18 13 9 7 5 5
AMP PEAK 4(5Q35.3) WILD-TYPE 13 0 0 9 4 1 0

Figure S16.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00096

Table S17.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 4(5Q35.3) MUTATED 5 7 6 16 8 12 2
AMP PEAK 4(5Q35.3) WILD-TYPE 11 7 2 1 1 0 0

Figure S17.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.036

Table S18.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
AMP PEAK 4(5Q35.3) MUTATED 4 7 7 1 2 4 6 3
AMP PEAK 4(5Q35.3) WILD-TYPE 4 0 0 2 2 0 0 3

Figure S18.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S19.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 4(5Q35.3) MUTATED 7 13 15 20
AMP PEAK 4(5Q35.3) WILD-TYPE 17 1 1 3

Figure S19.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S20.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 4(5Q35.3) MUTATED 8 22 2 23
AMP PEAK 4(5Q35.3) WILD-TYPE 15 1 5 1

Figure S20.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.063

Table S21.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 24 25
AMP PEAK 4(5Q35.3) MUTATED 19 14 23
AMP PEAK 4(5Q35.3) WILD-TYPE 10 10 2

Figure S21.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.13

Table S22.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 4(5Q35.3) MUTATED 14 21 9 9 3
AMP PEAK 4(5Q35.3) WILD-TYPE 2 6 2 11 1

Figure S22.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8e-04

Table S23.  Gene #4: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 4(5Q35.3) MUTATED 4 14 15 22
AMP PEAK 4(5Q35.3) WILD-TYPE 12 5 1 4

Figure S23.  Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.31' versus 'CN_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.088

Table S24.  Gene #5: 'amp_6p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 5(6P21.31) MUTATED 2 2 2 3 7 1 2
AMP PEAK 5(6P21.31) WILD-TYPE 17 16 11 15 4 5 3

Figure S24.  Get High-res Image Gene #5: 'amp_6p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.094

Table S25.  Gene #5: 'amp_6p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 5(6P21.31) MUTATED 5 2 5 2 0
AMP PEAK 5(6P21.31) WILD-TYPE 11 25 6 18 4

Figure S25.  Get High-res Image Gene #5: 'amp_6p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00413 (Fisher's exact test), Q value = 0.027

Table S26.  Gene #5: 'amp_6p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 5(6P21.31) MUTATED 3 0 7 3
AMP PEAK 5(6P21.31) WILD-TYPE 13 19 9 23

Figure S26.  Get High-res Image Gene #5: 'amp_6p21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #5: 'amp_6p21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 5(6P21.31) MUTATED 2 2 5 2 0 2
AMP PEAK 5(6P21.31) WILD-TYPE 4 22 6 12 11 9

Figure S27.  Get High-res Image Gene #5: 'amp_6p21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q24.3' versus 'CN_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.057

Table S28.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 6(6Q24.3) MUTATED 4 1 2 2 7 1 2
AMP PEAK 6(6Q24.3) WILD-TYPE 15 17 11 16 4 5 3

Figure S28.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.096

Table S29.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 6(6Q24.3) MUTATED 5 0 7 4
AMP PEAK 6(6Q24.3) WILD-TYPE 19 14 9 19

Figure S29.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'CN_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.022

Table S30.  Gene #7: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 7(7P22.1) MUTATED 6 12 12 12 4 3 5
AMP PEAK 7(7P22.1) WILD-TYPE 13 6 1 6 7 3 0

Figure S30.  Get High-res Image Gene #7: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.035

Table S31.  Gene #7: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 7(7P22.1) MUTATED 10 13 12 12
AMP PEAK 7(7P22.1) WILD-TYPE 14 1 4 11

Figure S31.  Get High-res Image Gene #7: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #7: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 7(7P22.1) MUTATED 12 19 2 14
AMP PEAK 7(7P22.1) WILD-TYPE 11 4 5 10

Figure S32.  Get High-res Image Gene #7: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q31.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0016

Table S33.  Gene #8: 'amp_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 8(9Q31.3) MUTATED 4 1 11 9 5 3 1
AMP PEAK 8(9Q31.3) WILD-TYPE 15 17 2 9 6 3 4

Figure S33.  Get High-res Image Gene #8: 'amp_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q31.3' versus 'METHLYATION_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.096

Table S34.  Gene #8: 'amp_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 8(9Q31.3) MUTATED 7 2 3 9 2 1 2
AMP PEAK 8(9Q31.3) WILD-TYPE 9 12 5 8 7 11 0

Figure S34.  Get High-res Image Gene #8: 'amp_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q31.3' versus 'MRNASEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.064

Table S35.  Gene #8: 'amp_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 8(9Q31.3) MUTATED 8 9 5 3
AMP PEAK 8(9Q31.3) WILD-TYPE 16 5 11 20

Figure S35.  Get High-res Image Gene #8: 'amp_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.072

Table S36.  Gene #8: 'amp_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 8(9Q31.3) MUTATED 9 12 1 3
AMP PEAK 8(9Q31.3) WILD-TYPE 14 11 6 21

Figure S36.  Get High-res Image Gene #8: 'amp_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q31.3' versus 'MIRSEQ_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.034

Table S37.  Gene #8: 'amp_9q31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 24 25
AMP PEAK 8(9Q31.3) MUTATED 10 13 3
AMP PEAK 8(9Q31.3) WILD-TYPE 19 11 22

Figure S37.  Get High-res Image Gene #8: 'amp_9q31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9q31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.064

Table S38.  Gene #8: 'amp_9q31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 8(9Q31.3) MUTATED 7 10 6 3
AMP PEAK 8(9Q31.3) WILD-TYPE 9 9 10 23

Figure S38.  Get High-res Image Gene #8: 'amp_9q31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S39.  Gene #9: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 9(12Q14.1) MUTATED 4 18 12 17 9 5 5
AMP PEAK 9(12Q14.1) WILD-TYPE 15 0 1 1 2 1 0

Figure S39.  Get High-res Image Gene #9: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.049

Table S40.  Gene #9: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
AMP PEAK 9(12Q14.1) MUTATED 7 6 7 3 3 4 5 1
AMP PEAK 9(12Q14.1) WILD-TYPE 1 1 0 0 1 0 1 5

Figure S40.  Get High-res Image Gene #9: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.068

Table S41.  Gene #9: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 9(12Q14.1) MUTATED 14 14 13 19
AMP PEAK 9(12Q14.1) WILD-TYPE 10 0 3 4

Figure S41.  Get High-res Image Gene #9: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.014

Table S42.  Gene #9: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 9(12Q14.1) MUTATED 14 20 3 23
AMP PEAK 9(12Q14.1) WILD-TYPE 9 3 4 1

Figure S42.  Get High-res Image Gene #9: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0052

Table S43.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 10(14Q11.2) MUTATED 1 3 9 6 6 0 2
AMP PEAK 10(14Q11.2) WILD-TYPE 18 15 4 12 5 6 3

Figure S43.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.007

Table S44.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 10(14Q11.2) MUTATED 5 0 4 11 2 1 1
AMP PEAK 10(14Q11.2) WILD-TYPE 11 14 4 6 7 11 1

Figure S44.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q11.2' versus 'RPPA_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.1

Table S45.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 11 10 14
AMP PEAK 10(14Q11.2) MUTATED 2 6 0 5
AMP PEAK 10(14Q11.2) WILD-TYPE 8 5 10 9

Figure S45.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.096

Table S46.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
AMP PEAK 10(14Q11.2) MUTATED 3 5 0 2 0 0 1 2
AMP PEAK 10(14Q11.2) WILD-TYPE 5 2 7 1 4 4 5 4

Figure S46.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_14q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00046

Table S47.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 10(14Q11.2) MUTATED 4 8 10 1
AMP PEAK 10(14Q11.2) WILD-TYPE 20 6 6 22

Figure S47.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S48.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 10(14Q11.2) MUTATED 5 16 0 2
AMP PEAK 10(14Q11.2) WILD-TYPE 18 7 7 22

Figure S48.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0044

Table S49.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 24 25
AMP PEAK 10(14Q11.2) MUTATED 15 8 1
AMP PEAK 10(14Q11.2) WILD-TYPE 14 16 24

Figure S49.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.038

Table S50.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 10(14Q11.2) MUTATED 9 3 3 6 3
AMP PEAK 10(14Q11.2) WILD-TYPE 7 24 8 14 1

Figure S50.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8e-04

Table S51.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 10(14Q11.2) MUTATED 5 6 11 1
AMP PEAK 10(14Q11.2) WILD-TYPE 11 13 5 25

Figure S51.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.034

Table S52.  Gene #10: 'amp_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 10(14Q11.2) MUTATED 4 3 7 4 4 1
AMP PEAK 10(14Q11.2) WILD-TYPE 2 21 4 10 7 10

Figure S52.  Get High-res Image Gene #10: 'amp_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S53.  Gene #11: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 11(16P13.3) MUTATED 2 18 13 6 5 4 2
AMP PEAK 11(16P13.3) WILD-TYPE 17 0 0 12 6 2 3

Figure S53.  Get High-res Image Gene #11: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0074

Table S54.  Gene #11: 'amp_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 11(16P13.3) MUTATED 5 4 5 12 6 12 1
AMP PEAK 11(16P13.3) WILD-TYPE 11 10 3 5 3 0 1

Figure S54.  Get High-res Image Gene #11: 'amp_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0021

Table S55.  Gene #11: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 11(16P13.3) MUTATED 5 10 13 16
AMP PEAK 11(16P13.3) WILD-TYPE 19 4 3 7

Figure S55.  Get High-res Image Gene #11: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S56.  Gene #11: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 11(16P13.3) MUTATED 6 19 0 19
AMP PEAK 11(16P13.3) WILD-TYPE 17 4 7 5

Figure S56.  Get High-res Image Gene #11: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00931 (Fisher's exact test), Q value = 0.047

Table S57.  Gene #11: 'amp_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 11(16P13.3) MUTATED 14 16 7 6 2
AMP PEAK 11(16P13.3) WILD-TYPE 2 11 4 14 2

Figure S57.  Get High-res Image Gene #11: 'amp_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.064

Table S58.  Gene #11: 'amp_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 11(16P13.3) MUTATED 5 16 9 4 3 7
AMP PEAK 11(16P13.3) WILD-TYPE 1 8 2 10 8 4

Figure S58.  Get High-res Image Gene #11: 'amp_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S59.  Gene #12: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 12(16Q22.1) MUTATED 2 18 13 13 4 4 2
AMP PEAK 12(16Q22.1) WILD-TYPE 17 0 0 5 7 2 3

Figure S59.  Get High-res Image Gene #12: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q22.1' versus 'METHLYATION_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.026

Table S60.  Gene #12: 'amp_16q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 12(16Q22.1) MUTATED 7 5 6 13 5 12 1
AMP PEAK 12(16Q22.1) WILD-TYPE 9 9 2 4 4 0 1

Figure S60.  Get High-res Image Gene #12: 'amp_16q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.1

Table S61.  Gene #12: 'amp_16q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 12(16Q22.1) MUTATED 9 11 12 16
AMP PEAK 12(16Q22.1) WILD-TYPE 15 3 4 7

Figure S61.  Get High-res Image Gene #12: 'amp_16q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.0014

Table S62.  Gene #12: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 12(16Q22.1) MUTATED 9 20 1 18
AMP PEAK 12(16Q22.1) WILD-TYPE 14 3 6 6

Figure S62.  Get High-res Image Gene #12: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.084

Table S63.  Gene #12: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 12(16Q22.1) MUTATED 15 17 6 9 2
AMP PEAK 12(16Q22.1) WILD-TYPE 1 10 5 11 2

Figure S63.  Get High-res Image Gene #12: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #12: 'amp_16q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 12(16Q22.1) MUTATED 6 10 13 19
AMP PEAK 12(16Q22.1) WILD-TYPE 10 9 3 7

Figure S64.  Get High-res Image Gene #12: 'amp_16q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S65.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 13(16Q24.2) MUTATED 3 18 12 5 5 4 2
AMP PEAK 13(16Q24.2) WILD-TYPE 16 0 1 13 6 2 3

Figure S65.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q24.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0016

Table S66.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 13(16Q24.2) MUTATED 3 5 5 13 5 12 1
AMP PEAK 13(16Q24.2) WILD-TYPE 13 9 3 4 4 0 1

Figure S66.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0036

Table S67.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 13(16Q24.2) MUTATED 5 11 12 16
AMP PEAK 13(16Q24.2) WILD-TYPE 19 3 4 7

Figure S67.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S68.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 13(16Q24.2) MUTATED 5 20 1 18
AMP PEAK 13(16Q24.2) WILD-TYPE 18 3 6 6

Figure S68.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.022

Table S69.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
AMP PEAK 13(16Q24.2) MUTATED 14 17 6 5 2
AMP PEAK 13(16Q24.2) WILD-TYPE 2 10 5 15 2

Figure S69.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.027

Table S70.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
AMP PEAK 13(16Q24.2) MUTATED 3 10 12 18
AMP PEAK 13(16Q24.2) WILD-TYPE 13 9 4 8

Figure S70.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.09

Table S71.  Gene #13: 'amp_16q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 13(16Q24.2) MUTATED 5 16 8 3 4 7
AMP PEAK 13(16Q24.2) WILD-TYPE 1 8 3 11 7 4

Figure S71.  Get High-res Image Gene #13: 'amp_16q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.028

Table S72.  Gene #14: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 14(17Q25.3) MUTATED 2 1 0 8 3 3 1
AMP PEAK 14(17Q25.3) WILD-TYPE 17 17 13 10 8 3 4

Figure S72.  Get High-res Image Gene #14: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S73.  Gene #15: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 15(19P13.12) MUTATED 4 9 13 15 7 5 5
AMP PEAK 15(19P13.12) WILD-TYPE 15 9 0 3 4 1 0

Figure S73.  Get High-res Image Gene #15: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.049

Table S74.  Gene #15: 'amp_19p13.12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
AMP PEAK 15(19P13.12) MUTATED 8 7 4 3 1 3 4 2
AMP PEAK 15(19P13.12) WILD-TYPE 0 0 3 0 3 1 2 4

Figure S74.  Get High-res Image Gene #15: 'amp_19p13.12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.013

Table S75.  Gene #15: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 15(19P13.12) MUTATED 12 14 12 11
AMP PEAK 15(19P13.12) WILD-TYPE 12 0 4 12

Figure S75.  Get High-res Image Gene #15: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0051

Table S76.  Gene #15: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 15(19P13.12) MUTATED 15 21 1 12
AMP PEAK 15(19P13.12) WILD-TYPE 8 2 6 12

Figure S76.  Get High-res Image Gene #15: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S77.  Gene #16: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 16(19Q12) MUTATED 4 7 13 16 7 4 5
AMP PEAK 16(19Q12) WILD-TYPE 15 11 0 2 4 2 0

Figure S77.  Get High-res Image Gene #16: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.012

Table S78.  Gene #16: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 16(19Q12) MUTATED 12 14 11 10
AMP PEAK 16(19Q12) WILD-TYPE 12 0 5 13

Figure S78.  Get High-res Image Gene #16: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.01

Table S79.  Gene #16: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 16(19Q12) MUTATED 15 20 1 11
AMP PEAK 16(19Q12) WILD-TYPE 8 3 6 13

Figure S79.  Get High-res Image Gene #16: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0023

Table S80.  Gene #17: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 17(XP11.22) MUTATED 6 17 9 7 5 1 4
AMP PEAK 17(XP11.22) WILD-TYPE 13 1 4 11 6 5 1

Figure S80.  Get High-res Image Gene #17: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.067

Table S81.  Gene #17: 'amp_xp11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
AMP PEAK 17(XP11.22) MUTATED 7 6 5 1 3 3 4 0
AMP PEAK 17(XP11.22) WILD-TYPE 1 1 2 2 1 1 2 6

Figure S81.  Get High-res Image Gene #17: 'amp_xp11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.1

Table S82.  Gene #17: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 17(XP11.22) MUTATED 8 11 11 12
AMP PEAK 17(XP11.22) WILD-TYPE 16 3 5 11

Figure S82.  Get High-res Image Gene #17: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.095

Table S83.  Gene #17: 'amp_xp11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
AMP PEAK 17(XP11.22) MUTATED 5 17 8 4 4 4
AMP PEAK 17(XP11.22) WILD-TYPE 1 7 3 10 7 7

Figure S83.  Get High-res Image Gene #17: 'amp_xp11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00046

Table S84.  Gene #18: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
AMP PEAK 18(XQ28) MUTATED 3 16 8 8 5 1 5
AMP PEAK 18(XQ28) WILD-TYPE 16 2 5 10 6 5 0

Figure S84.  Get High-res Image Gene #18: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.061

Table S85.  Gene #18: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
AMP PEAK 18(XQ28) MUTATED 6 5 1 10 6 10 2
AMP PEAK 18(XQ28) WILD-TYPE 10 9 7 7 3 2 0

Figure S85.  Get High-res Image Gene #18: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.13

Table S86.  Gene #18: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
AMP PEAK 18(XQ28) MUTATED 6 5 6 1 2 3 4 0
AMP PEAK 18(XQ28) WILD-TYPE 2 2 1 2 2 1 2 6

Figure S86.  Get High-res Image Gene #18: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.038

Table S87.  Gene #18: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
AMP PEAK 18(XQ28) MUTATED 6 11 10 13
AMP PEAK 18(XQ28) WILD-TYPE 18 3 6 10

Figure S87.  Get High-res Image Gene #18: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.055

Table S88.  Gene #18: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
AMP PEAK 18(XQ28) MUTATED 8 14 1 17
AMP PEAK 18(XQ28) WILD-TYPE 15 9 6 7

Figure S88.  Get High-res Image Gene #18: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S89.  Gene #19: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 1(1P36.23) MUTATED 4 1 5 15 6 6 1
DEL PEAK 1(1P36.23) WILD-TYPE 15 17 8 3 5 0 4

Figure S89.  Get High-res Image Gene #19: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.026

Table S90.  Gene #19: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 1(1P36.23) MUTATED 16 9 0 8
DEL PEAK 1(1P36.23) WILD-TYPE 7 14 7 16

Figure S90.  Get High-res Image Gene #19: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.026

Table S91.  Gene #20: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 2(2Q22.1) MUTATED 2 0 3 3 5 4 1
DEL PEAK 2(2Q22.1) WILD-TYPE 17 18 10 15 6 2 4

Figure S91.  Get High-res Image Gene #20: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.023

Table S92.  Gene #21: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 3(2Q37.3) MUTATED 2 0 4 5 5 4 1
DEL PEAK 3(2Q37.3) WILD-TYPE 17 18 9 13 6 2 4

Figure S92.  Get High-res Image Gene #21: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.00986 (Fisher's exact test), Q value = 0.049

Table S93.  Gene #22: 'del_3q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 4(3Q13.31) MUTATED 4 1 5 7 7 0 1
DEL PEAK 4(3Q13.31) WILD-TYPE 15 17 8 11 4 6 4

Figure S93.  Get High-res Image Gene #22: 'del_3q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.12

Table S94.  Gene #22: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 4(3Q13.31) MUTATED 7 10 2 2
DEL PEAK 4(3Q13.31) WILD-TYPE 16 13 5 22

Figure S94.  Get High-res Image Gene #22: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0049

Table S95.  Gene #23: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 5(4Q34.3) MUTATED 5 0 5 11 4 0 0
DEL PEAK 5(4Q34.3) WILD-TYPE 14 18 8 7 7 6 5

Figure S95.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.072

Table S96.  Gene #23: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 5(4Q34.3) MUTATED 8 3 3 5 0 0 0
DEL PEAK 5(4Q34.3) WILD-TYPE 8 11 5 12 9 12 2

Figure S96.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.076

Table S97.  Gene #23: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
DEL PEAK 5(4Q34.3) MUTATED 11 2 3 2
DEL PEAK 5(4Q34.3) WILD-TYPE 13 12 13 21

Figure S97.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.12

Table S98.  Gene #23: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 5(4Q34.3) MUTATED 10 5 1 2
DEL PEAK 5(4Q34.3) WILD-TYPE 13 18 6 22

Figure S98.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #23: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 5(4Q34.3) MUTATED 2 7 0 9 1
DEL PEAK 5(4Q34.3) WILD-TYPE 14 20 11 11 3

Figure S99.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.094

Table S100.  Gene #23: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
DEL PEAK 5(4Q34.3) MUTATED 7 7 3 2
DEL PEAK 5(4Q34.3) WILD-TYPE 9 12 13 24

Figure S100.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.028

Table S101.  Gene #23: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 5(4Q34.3) MUTATED 1 6 1 9 2 0
DEL PEAK 5(4Q34.3) WILD-TYPE 5 18 10 5 9 11

Figure S101.  Get High-res Image Gene #23: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S102.  Gene #24: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 6(4Q34.3) MUTATED 4 0 3 14 4 2 1
DEL PEAK 6(4Q34.3) WILD-TYPE 15 18 10 4 7 4 4

Figure S102.  Get High-res Image Gene #24: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.096

Table S103.  Gene #24: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 6(4Q34.3) MUTATED 9 3 3 7 2 0 0
DEL PEAK 6(4Q34.3) WILD-TYPE 7 11 5 10 7 12 2

Figure S103.  Get High-res Image Gene #24: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.064

Table S104.  Gene #24: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
DEL PEAK 6(4Q34.3) MUTATED 10 6 4 4
DEL PEAK 6(4Q34.3) WILD-TYPE 6 13 12 22

Figure S104.  Get High-res Image Gene #24: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.061

Table S105.  Gene #24: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 6(4Q34.3) MUTATED 2 7 2 10 2 1
DEL PEAK 6(4Q34.3) WILD-TYPE 4 17 9 4 9 10

Figure S105.  Get High-res Image Gene #24: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0076

Table S106.  Gene #25: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 7(4Q35.1) MUTATED 4 1 4 13 5 1 2
DEL PEAK 7(4Q35.1) WILD-TYPE 15 17 9 5 6 5 3

Figure S106.  Get High-res Image Gene #25: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.13

Table S107.  Gene #25: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 7(4Q35.1) MUTATED 9 3 3 8 1 1 0
DEL PEAK 7(4Q35.1) WILD-TYPE 7 11 5 9 8 11 2

Figure S107.  Get High-res Image Gene #25: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.13

Table S108.  Gene #25: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 7(4Q35.1) MUTATED 10 10 1 3
DEL PEAK 7(4Q35.1) WILD-TYPE 13 13 6 21

Figure S108.  Get High-res Image Gene #25: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.1

Table S109.  Gene #25: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 7(4Q35.1) MUTATED 1 6 2 10 2 3
DEL PEAK 7(4Q35.1) WILD-TYPE 5 18 9 4 9 8

Figure S109.  Get High-res Image Gene #25: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p24.3' versus 'CN_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0091

Table S110.  Gene #26: 'del_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 8(6P24.3) MUTATED 6 0 3 7 0 4 0
DEL PEAK 8(6P24.3) WILD-TYPE 13 18 10 11 11 2 5

Figure S110.  Get High-res Image Gene #26: 'del_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.007

Table S111.  Gene #27: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 9(6Q26) MUTATED 5 0 4 9 0 3 0
DEL PEAK 9(6Q26) WILD-TYPE 14 18 9 9 11 3 5

Figure S111.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00046

Table S112.  Gene #29: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 11(9P23) MUTATED 7 0 0 12 3 0 1
DEL PEAK 11(9P23) WILD-TYPE 12 18 13 6 8 6 4

Figure S112.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00368 (Fisher's exact test), Q value = 0.026

Table S113.  Gene #29: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 11(9P23) MUTATED 9 5 3 3 0 0 0
DEL PEAK 11(9P23) WILD-TYPE 7 9 5 14 9 12 2

Figure S113.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00066

Table S114.  Gene #29: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
DEL PEAK 11(9P23) MUTATED 15 1 3 1
DEL PEAK 11(9P23) WILD-TYPE 9 13 13 22

Figure S114.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0033

Table S115.  Gene #29: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 11(9P23) MUTATED 13 4 2 1
DEL PEAK 11(9P23) WILD-TYPE 10 19 5 23

Figure S115.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.11

Table S116.  Gene #29: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 24 25
DEL PEAK 11(9P23) MUTATED 9 9 2
DEL PEAK 11(9P23) WILD-TYPE 20 15 23

Figure S116.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.13

Table S117.  Gene #29: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 11(9P23) MUTATED 5 6 0 9 0
DEL PEAK 11(9P23) WILD-TYPE 11 21 11 11 4

Figure S117.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.014

Table S118.  Gene #29: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
DEL PEAK 11(9P23) MUTATED 10 4 2 3
DEL PEAK 11(9P23) WILD-TYPE 6 15 14 23

Figure S118.  Get High-res Image Gene #29: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S119.  Gene #30: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 12(9P21.3) MUTATED 8 1 0 12 4 0 1
DEL PEAK 12(9P21.3) WILD-TYPE 11 17 13 6 7 6 4

Figure S119.  Get High-res Image Gene #30: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00388 (Fisher's exact test), Q value = 0.026

Table S120.  Gene #30: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 12(9P21.3) MUTATED 10 5 4 3 0 1 0
DEL PEAK 12(9P21.3) WILD-TYPE 6 9 4 14 9 11 2

Figure S120.  Get High-res Image Gene #30: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S121.  Gene #30: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
DEL PEAK 12(9P21.3) MUTATED 17 1 3 2
DEL PEAK 12(9P21.3) WILD-TYPE 7 13 13 21

Figure S121.  Get High-res Image Gene #30: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0026

Table S122.  Gene #30: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 12(9P21.3) MUTATED 15 4 2 2
DEL PEAK 12(9P21.3) WILD-TYPE 8 19 5 22

Figure S122.  Get High-res Image Gene #30: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.13

Table S123.  Gene #30: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 12(9P21.3) MUTATED 5 7 0 10 1
DEL PEAK 12(9P21.3) WILD-TYPE 11 20 11 10 3

Figure S123.  Get High-res Image Gene #30: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.053

Table S124.  Gene #30: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
DEL PEAK 12(9P21.3) MUTATED 10 5 3 4
DEL PEAK 12(9P21.3) WILD-TYPE 6 14 13 22

Figure S124.  Get High-res Image Gene #30: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0036

Table S125.  Gene #32: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 14(11P15.5) MUTATED 2 2 5 4 6 6 1
DEL PEAK 14(11P15.5) WILD-TYPE 17 16 8 14 5 0 4

Figure S125.  Get High-res Image Gene #32: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.12

Table S126.  Gene #32: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 14(11P15.5) MUTATED 4 11 0 8
DEL PEAK 14(11P15.5) WILD-TYPE 19 12 7 16

Figure S126.  Get High-res Image Gene #32: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.027

Table S127.  Gene #33: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 15(11Q14.1) MUTATED 4 1 3 4 6 5 1
DEL PEAK 15(11Q14.1) WILD-TYPE 15 17 10 14 5 1 4

Figure S127.  Get High-res Image Gene #33: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.072

Table S128.  Gene #33: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 15(11Q14.1) MUTATED 1 3 4 9 3 1 0
DEL PEAK 15(11Q14.1) WILD-TYPE 15 11 4 8 6 11 2

Figure S128.  Get High-res Image Gene #33: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0089

Table S129.  Gene #34: 'del_12q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 16(12Q14.2) MUTATED 2 0 3 0
DEL PEAK 16(12Q14.2) WILD-TYPE 21 23 4 24

Figure S129.  Get High-res Image Gene #34: 'del_12q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.072

Table S130.  Gene #34: 'del_12q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 16 26
DEL PEAK 16(12Q14.2) MUTATED 0 4 1 0
DEL PEAK 16(12Q14.2) WILD-TYPE 16 15 15 26

Figure S130.  Get High-res Image Gene #34: 'del_12q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.027

Table S131.  Gene #34: 'del_12q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 16(12Q14.2) MUTATED 0 0 0 1 4 0
DEL PEAK 16(12Q14.2) WILD-TYPE 6 24 11 13 7 11

Figure S131.  Get High-res Image Gene #34: 'del_12q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.01

Table S132.  Gene #35: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 17(13Q14.2) MUTATED 7 2 6 11 9 5 2
DEL PEAK 17(13Q14.2) WILD-TYPE 12 16 7 7 2 1 3

Figure S132.  Get High-res Image Gene #35: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.13

Table S133.  Gene #35: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 17(13Q14.2) MUTATED 11 5 3 9 3 1 1
DEL PEAK 17(13Q14.2) WILD-TYPE 5 9 5 8 6 11 1

Figure S133.  Get High-res Image Gene #35: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q21.2' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.053

Table S134.  Gene #36: 'del_14q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 18(14Q21.2) MUTATED 5 1 2 4 3 5 0
DEL PEAK 18(14Q21.2) WILD-TYPE 14 17 11 14 8 1 5

Figure S134.  Get High-res Image Gene #36: 'del_14q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0014

Table S135.  Gene #37: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 19(15Q15.1) MUTATED 2 1 3 11 3 5 0
DEL PEAK 19(15Q15.1) WILD-TYPE 17 17 10 7 8 1 5

Figure S135.  Get High-res Image Gene #37: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.13

Table S136.  Gene #37: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
DEL PEAK 19(15Q15.1) MUTATED 11 3 1 6
DEL PEAK 19(15Q15.1) WILD-TYPE 13 11 15 17

Figure S136.  Get High-res Image Gene #37: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.13

Table S137.  Gene #37: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 19(15Q15.1) MUTATED 1 7 2 10 1
DEL PEAK 19(15Q15.1) WILD-TYPE 15 20 9 10 3

Figure S137.  Get High-res Image Gene #37: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00401 (Fisher's exact test), Q value = 0.026

Table S138.  Gene #37: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 19(15Q15.1) MUTATED 0 5 0 9 3 4
DEL PEAK 19(15Q15.1) WILD-TYPE 6 19 11 5 8 7

Figure S138.  Get High-res Image Gene #37: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00782 (Fisher's exact test), Q value = 0.04

Table S139.  Gene #38: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 20(16P13.3) MUTATED 3 2 3 0
DEL PEAK 20(16P13.3) WILD-TYPE 20 21 4 24

Figure S139.  Get High-res Image Gene #38: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.064

Table S140.  Gene #39: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 21(16Q23.1) MUTATED 5 0 0 5 0 0 1
DEL PEAK 21(16Q23.1) WILD-TYPE 14 18 13 13 11 6 4

Figure S140.  Get High-res Image Gene #39: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.13

Table S141.  Gene #39: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
DEL PEAK 21(16Q23.1) MUTATED 6 1 0 1
DEL PEAK 21(16Q23.1) WILD-TYPE 18 13 16 22

Figure S141.  Get High-res Image Gene #39: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.053

Table S142.  Gene #39: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 21(16Q23.1) MUTATED 5 1 2 0
DEL PEAK 21(16Q23.1) WILD-TYPE 18 22 5 24

Figure S142.  Get High-res Image Gene #39: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.06

Table S143.  Gene #40: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 22(17Q11.2) MUTATED 4 1 4 7 7 0 1
DEL PEAK 22(17Q11.2) WILD-TYPE 15 17 9 11 4 6 4

Figure S143.  Get High-res Image Gene #40: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.13

Table S144.  Gene #40: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 22(17Q11.2) MUTATED 6 4 3 9 0 1 0
DEL PEAK 22(17Q11.2) WILD-TYPE 10 10 5 8 9 11 2

Figure S144.  Get High-res Image Gene #40: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.072

Table S145.  Gene #40: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 22(17Q11.2) MUTATED 4 7 0 11 1
DEL PEAK 22(17Q11.2) WILD-TYPE 12 20 11 9 3

Figure S145.  Get High-res Image Gene #40: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00438 (Fisher's exact test), Q value = 0.027

Table S146.  Gene #40: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 22(17Q11.2) MUTATED 0 5 3 10 3 1
DEL PEAK 22(17Q11.2) WILD-TYPE 6 19 8 4 8 10

Figure S146.  Get High-res Image Gene #40: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.2' versus 'CN_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.017

Table S147.  Gene #41: 'del_17q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 23(17Q21.2) MUTATED 3 1 5 10 6 0 1
DEL PEAK 23(17Q21.2) WILD-TYPE 16 17 8 8 5 6 4

Figure S147.  Get High-res Image Gene #41: 'del_17q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.2' versus 'METHLYATION_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.038

Table S148.  Gene #41: 'del_17q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 23(17Q21.2) MUTATED 7 3 4 10 0 1 0
DEL PEAK 23(17Q21.2) WILD-TYPE 9 11 4 7 9 11 2

Figure S148.  Get High-res Image Gene #41: 'del_17q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.11

Table S149.  Gene #41: 'del_17q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 23(17Q21.2) MUTATED 9 11 1 3
DEL PEAK 23(17Q21.2) WILD-TYPE 14 12 6 21

Figure S149.  Get High-res Image Gene #41: 'del_17q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.045

Table S150.  Gene #41: 'del_17q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 23(17Q21.2) MUTATED 7 6 0 11 1
DEL PEAK 23(17Q21.2) WILD-TYPE 9 21 11 9 3

Figure S150.  Get High-res Image Gene #41: 'del_17q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.049

Table S151.  Gene #41: 'del_17q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 24 11 14 11 11
DEL PEAK 23(17Q21.2) MUTATED 2 5 4 10 2 1
DEL PEAK 23(17Q21.2) WILD-TYPE 4 19 7 4 9 10

Figure S151.  Get High-res Image Gene #41: 'del_17q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.2' versus 'CN_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.11

Table S152.  Gene #42: 'del_17q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 24(17Q24.2) MUTATED 4 1 5 6 6 0 2
DEL PEAK 24(17Q24.2) WILD-TYPE 15 17 8 12 5 6 3

Figure S152.  Get High-res Image Gene #42: 'del_17q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.2' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.026

Table S153.  Gene #42: 'del_17q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 16 14 8 17 9 12 2
DEL PEAK 24(17Q24.2) MUTATED 5 3 5 10 0 1 0
DEL PEAK 24(17Q24.2) WILD-TYPE 11 11 3 7 9 11 2

Figure S153.  Get High-res Image Gene #42: 'del_17q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.12

Table S154.  Gene #42: 'del_17q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 24(17Q24.2) MUTATED 8 11 1 3
DEL PEAK 24(17Q24.2) WILD-TYPE 15 12 6 21

Figure S154.  Get High-res Image Gene #42: 'del_17q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.095

Table S155.  Gene #42: 'del_17q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
DEL PEAK 24(17Q24.2) MUTATED 6 7 0 8 3
DEL PEAK 24(17Q24.2) WILD-TYPE 10 20 11 12 1

Figure S155.  Get High-res Image Gene #42: 'del_17q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.029

Table S156.  Gene #43: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 25(20P12.1) MUTATED 5 0 0 2 5 0 0
DEL PEAK 25(20P12.1) WILD-TYPE 14 18 13 16 6 6 5

Figure S156.  Get High-res Image Gene #43: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.13

Table S157.  Gene #43: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 14 16 23
DEL PEAK 25(20P12.1) MUTATED 6 1 2 0
DEL PEAK 25(20P12.1) WILD-TYPE 18 13 14 23

Figure S157.  Get High-res Image Gene #43: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.095

Table S158.  Gene #43: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
DEL PEAK 25(20P12.1) MUTATED 6 2 1 0
DEL PEAK 25(20P12.1) WILD-TYPE 17 21 6 24

Figure S158.  Get High-res Image Gene #43: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.13

Table S159.  Gene #43: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 24 25
DEL PEAK 25(20P12.1) MUTATED 4 5 0
DEL PEAK 25(20P12.1) WILD-TYPE 25 19 25

Figure S159.  Get High-res Image Gene #43: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q12.1' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0074

Table S160.  Gene #44: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 18 13 18 11 6 5
DEL PEAK 26(22Q12.1) MUTATED 10 3 7 14 8 6 2
DEL PEAK 26(22Q12.1) WILD-TYPE 9 15 6 4 3 0 3

Figure S160.  Get High-res Image Gene #44: 'del_22q12.1' versus Molecular Subtype #1: 'CN_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/ACC-TP/22522857/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/22541000/ACC-TP.transferedmergedcluster.txt

  • Number of patients = 90

  • Number of significantly focal cnvs = 44

  • Number of molecular subtypes = 10

  • 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)