Correlation between copy number variation genes (focal events) and molecular subtypes
Testicular Germ Cell Tumors (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/C1930SNX
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 50 focal events and 10 molecular subtypes across 150 patients, 267 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_2p24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3p13 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q27.3 cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'CN_CNMF'.

  • amp_7p22.1 cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q11.22 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q11.23 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_8q23.3 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p13.33 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • amp_12p11.21 cnv correlated to 'RPPA_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_16q21 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_20q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_22q11.21 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.31 cnv correlated to 'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p31.1 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_1q42.12 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_3p26.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q22.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5p15.2 cnv correlated to 'CN_CNMF'.

  • del_5p14.3 cnv correlated to 'RPPA_CNMF'.

  • del_5q12.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p22.3 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'.

  • del_6q26 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q11.22 cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q35 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p24.3 cnv correlated to 'CN_CNMF'.

  • del_9p23 cnv correlated to 'CN_CNMF'.

  • del_9q33.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_9q34.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_10p15.3 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'.

  • del_10q23.1 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'.

  • del_10q26.3 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'.

  • del_11p15.5 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p12 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q12.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q24.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q34 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18p11.32 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_18q22.3 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q13.33 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'.

  • del_19q13.42 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'.

  • del_20p12.1 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq27.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 50 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, 267 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 8q11 23 122 (81%) 28 0.00015
(0.00142)
0.00834
(0.0253)
0.00061
(0.00401)
0.00013
(0.00127)
1e-05
(0.000161)
2e-05
(0.000303)
9e-05
(0.001)
1e-05
(0.000161)
3e-05
(0.000417)
5e-05
(0.000581)
amp 16q21 21 (14%) 129 0.00532
(0.018)
0.0191
(0.0466)
0.00335
(0.0131)
0.00119
(0.00626)
0.0465
(0.088)
0.00777
(0.0242)
0.0014
(0.0068)
0.00841
(0.0253)
0.00234
(0.00975)
0.00287
(0.0117)
del 6p22 3 24 (16%) 126 0.00024
(0.00197)
0.00233
(0.00975)
0.00017
(0.00152)
0.00078
(0.00459)
0.022
(0.0509)
0.0116
(0.0323)
0.00501
(0.0175)
0.00345
(0.0133)
0.00334
(0.0131)
0.00553
(0.0184)
del 10p15 3 84 (56%) 66 0.00015
(0.00142)
0.0201
(0.0479)
0.00408
(0.0151)
0.00267
(0.0109)
0.00542
(0.0182)
0.00126
(0.00649)
0.0346
(0.071)
0.00065
(0.00411)
0.0003
(0.00238)
0.00144
(0.00686)
del 10q23 1 71 (47%) 79 0.00052
(0.00366)
0.00403
(0.015)
0.0244
(0.0542)
0.0136
(0.0356)
0.00216
(0.00927)
0.00037
(0.00276)
0.0234
(0.0529)
3e-05
(0.000417)
0.0001
(0.00104)
3e-05
(0.000417)
del 10q26 3 76 (51%) 74 1e-05
(0.000161)
0.00078
(0.00459)
0.0122
(0.0325)
0.00308
(0.0123)
0.00041
(0.00301)
0.00011
(0.00112)
0.0441
(0.0845)
5e-05
(0.000581)
5e-05
(0.000581)
4e-05
(0.000513)
del 19q13 33 58 (39%) 92 1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
del 19q13 42 57 (38%) 93 1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
amp 8q23 3 108 (72%) 42 0.103
(0.163)
0.00183
(0.00832)
0.0241
(0.0538)
0.011
(0.0318)
0.00033
(0.0025)
0.00057
(0.00396)
2e-05
(0.000303)
0.0001
(0.00104)
0.00032
(0.00246)
0.00886
(0.0265)
amp 20q11 21 51 (34%) 99 0.0366
(0.0741)
0.00099
(0.00544)
0.0195
(0.047)
0.0145
(0.037)
0.0835
(0.137)
0.0337
(0.0694)
0.0115
(0.0322)
0.00687
(0.0219)
0.0102
(0.0296)
0.0421
(0.082)
amp 22q11 21 57 (38%) 93 1e-05
(0.000161)
0.0749
(0.127)
0.0118
(0.0323)
0.00574
(0.019)
1e-05
(0.000161)
1e-05
(0.000161)
0.0249
(0.0543)
0.00019
(0.00161)
0.00025
(0.00202)
5e-05
(0.000581)
del 6q26 26 (17%) 124 0.102
(0.162)
0.0397
(0.078)
0.0247
(0.0542)
0.0144
(0.0368)
0.00077
(0.00459)
0.0013
(0.0065)
0.0179
(0.0438)
0.00505
(0.0175)
0.00446
(0.0159)
0.0234
(0.0529)
del 11q12 3 114 (76%) 36 0.0009
(0.00506)
0.188
(0.26)
0.0324
(0.0672)
0.0217
(0.0507)
4e-05
(0.000513)
1e-05
(0.000161)
1e-05
(0.000161)
1e-05
(0.000161)
8e-05
(0.000909)
1e-05
(0.000161)
amp 2p24 1 62 (41%) 88 0.00838
(0.0253)
0.00031
(0.00242)
0.194
(0.265)
0.129
(0.193)
0.0391
(0.0776)
0.0436
(0.0842)
0.0274
(0.0593)
0.0389
(0.0775)
0.0433
(0.0838)
0.012
(0.0323)
amp 3p13 34 (23%) 116 0.0162
(0.0402)
0.153
(0.219)
0.00012
(0.0012)
0.00159
(0.00743)
0.00059
(0.00399)
0.0176
(0.0433)
0.141
(0.206)
0.0207
(0.049)
0.0169
(0.0418)
0.0336
(0.0694)
amp 3q27 3 49 (33%) 101 0.419
(0.492)
0.0592
(0.105)
0.00233
(0.00975)
0.00088
(0.00506)
0.00018
(0.00155)
0.00784
(0.0242)
0.00135
(0.00668)
0.00242
(0.01)
0.00106
(0.00575)
0.00972
(0.0286)
amp 7q11 22 120 (80%) 30 0.0633
(0.111)
0.0246
(0.0542)
0.0114
(0.0322)
0.058
(0.104)
1e-05
(0.000161)
0.00203
(0.00891)
0.0002
(0.00167)
0.00018
(0.00155)
0.0001
(0.00104)
0.00089
(0.00506)
del 3p26 2 41 (27%) 109 0.0246
(0.0542)
0.00349
(0.0133)
0.0897
(0.146)
0.505
(0.565)
0.00789
(0.0242)
0.00442
(0.0159)
0.0037
(0.014)
0.00348
(0.0133)
0.0013
(0.0065)
0.00016
(0.00148)
del 4q22 2 110 (73%) 40 0.025
(0.0544)
0.0867
(0.141)
0.68
(0.719)
0.559
(0.616)
0.00924
(0.0273)
0.00142
(0.00683)
0.00066
(0.00412)
0.00421
(0.0155)
0.0294
(0.0624)
0.00494
(0.0174)
del 5q12 1 105 (70%) 45 0.00063
(0.00404)
0.0667
(0.115)
0.0111
(0.0319)
0.332
(0.409)
0.0118
(0.0323)
0.00745
(0.0236)
0.451
(0.521)
0.0239
(0.0536)
0.029
(0.0621)
0.0395
(0.078)
del 11q24 3 122 (81%) 28 0.00061
(0.00401)
0.572
(0.624)
0.588
(0.638)
0.309
(0.388)
0.00205
(0.00891)
0.00059
(0.00399)
0.00314
(0.0125)
0.00608
(0.02)
0.0155
(0.0391)
0.00047
(0.00341)
del 7q11 22 4 (3%) 146 0.101
(0.162)
0.0627
(0.11)
0.12
(0.184)
0.0282
(0.0607)
0.0792
(0.132)
0.0293
(0.0623)
0.00531
(0.018)
0.00894
(0.0266)
0.0102
(0.0296)
0.0226
(0.0517)
del 11p15 5 94 (63%) 56 0.18
(0.249)
0.0486
(0.0917)
0.159
(0.225)
0.45
(0.521)
0.0828
(0.137)
0.00427
(0.0156)
0.00217
(0.00927)
0.00204
(0.00891)
0.00618
(0.0202)
0.0119
(0.0323)
del 11p12 99 (66%) 51 0.421
(0.493)
0.0465
(0.088)
0.138
(0.203)
0.489
(0.553)
0.109
(0.17)
0.00529
(0.018)
0.00077
(0.00459)
0.00128
(0.0065)
0.00634
(0.0205)
0.0126
(0.0336)
del 16q23 3 67 (45%) 83 0.00138
(0.00676)
0.00304
(0.0123)
0.764
(0.794)
0.192
(0.265)
0.045
(0.0858)
0.0854
(0.14)
0.00177
(0.00819)
0.0218
(0.0508)
0.172
(0.239)
0.0142
(0.0366)
del xq27 3 30 (20%) 120 0.00149
(0.00703)
0.00124
(0.00646)
0.117
(0.181)
0.744
(0.775)
0.00631
(0.0205)
0.0631
(0.111)
0.0137
(0.0356)
0.012
(0.0323)
0.102
(0.162)
0.0212
(0.0498)
amp 7p22 1 126 (84%) 24 0.208
(0.279)
0.0721
(0.122)
0.125
(0.19)
0.091
(0.147)
0.0316
(0.0661)
0.104
(0.164)
0.012
(0.0323)
0.0113
(0.0322)
0.0221
(0.051)
0.0386
(0.0771)
del 1p36 31 34 (23%) 116 0.64
(0.686)
0.0561
(0.103)
0.158
(0.224)
0.0574
(0.104)
0.0668
(0.115)
0.0502
(0.0936)
0.00524
(0.018)
0.00473
(0.0168)
0.00195
(0.00878)
0.0146
(0.0371)
del 13q34 113 (75%) 37 0.0132
(0.0348)
0.316
(0.395)
0.112
(0.174)
0.159
(0.225)
0.00074
(0.00457)
0.00198
(0.00884)
0.165
(0.23)
0.131
(0.195)
0.219
(0.291)
0.00112
(0.00596)
del 18q22 3 125 (83%) 25 0.0119
(0.0323)
0.138
(0.203)
0.72
(0.755)
0.952
(0.958)
0.207
(0.278)
0.135
(0.199)
0.0236
(0.0532)
0.0405
(0.0791)
0.235
(0.311)
0.00765
(0.0241)
amp 12p11 21 144 (96%) 6 0.096
(0.154)
0.193
(0.265)
0.153
(0.219)
0.0361
(0.0734)
0.156
(0.221)
0.496
(0.56)
0.206
(0.278)
0.0361
(0.0734)
0.0382
(0.0767)
0.194
(0.265)
del 1p31 1 27 (18%) 123 0.02
(0.0479)
0.272
(0.351)
0.355
(0.431)
0.0489
(0.0917)
0.676
(0.719)
0.727
(0.76)
0.00787
(0.0242)
0.153
(0.219)
0.0642
(0.112)
0.43
(0.499)
del 7q35 13 (9%) 137 0.0137
(0.0356)
0.404
(0.479)
0.587
(0.638)
0.0578
(0.104)
0.142
(0.207)
0.0115
(0.0322)
0.267
(0.346)
0.808
(0.831)
0.43
(0.499)
0.0322
(0.0672)
del 9q34 2 60 (40%) 90 0.00099
(0.00544)
0.0682
(0.116)
0.128
(0.193)
0.0554
(0.102)
0.0593
(0.105)
0.00402
(0.015)
0.537
(0.595)
0.0284
(0.061)
0.143
(0.207)
0.131
(0.195)
del 16q23 1 66 (44%) 84 0.00063
(0.00404)
0.0223
(0.0511)
0.679
(0.719)
0.381
(0.459)
0.295
(0.37)
0.395
(0.472)
0.0562
(0.103)
0.207
(0.278)
0.568
(0.622)
0.0161
(0.0402)
del xp21 1 28 (19%) 122 0.0754
(0.127)
0.00441
(0.0159)
0.901
(0.915)
0.622
(0.67)
0.0762
(0.128)
0.0513
(0.0954)
0.0572
(0.104)
0.0722
(0.122)
0.049
(0.0917)
0.00675
(0.0216)
amp 1q21 2 69 (46%) 81 0.00107
(0.00575)
0.395
(0.472)
0.319
(0.398)
0.916
(0.927)
0.141
(0.206)
0.00086
(0.005)
0.134
(0.199)
0.933
(0.94)
0.673
(0.719)
0.13
(0.194)
del 9q33 3 60 (40%) 90 0.00017
(0.00152)
0.123
(0.188)
0.127
(0.192)
0.0549
(0.102)
0.0679
(0.116)
0.0156
(0.0391)
0.678
(0.719)
0.0553
(0.102)
0.164
(0.23)
0.242
(0.316)
del 18p11 32 118 (79%) 32 0.502
(0.563)
0.155
(0.22)
0.71
(0.746)
0.959
(0.963)
0.627
(0.674)
0.248
(0.322)
0.044
(0.0845)
0.0193
(0.0469)
0.281
(0.36)
0.0676
(0.116)
del 20p12 1 29 (19%) 121 0.219
(0.291)
0.397
(0.472)
0.414
(0.487)
0.454
(0.523)
0.0783
(0.13)
0.0938
(0.151)
0.0312
(0.0656)
0.241
(0.316)
0.0611
(0.108)
0.00179
(0.00821)
amp 4q12 20 (13%) 130 4e-05
(0.000513)
0.807
(0.831)
0.804
(0.83)
0.457
(0.525)
0.197
(0.267)
0.396
(0.472)
0.339
(0.415)
0.333
(0.41)
0.278
(0.357)
0.242
(0.316)
amp 12p13 33 145 (97%) 5 0.195
(0.266)
0.397
(0.472)
0.15
(0.217)
0.0373
(0.0753)
0.216
(0.288)
0.685
(0.723)
0.32
(0.398)
0.0828
(0.137)
0.0868
(0.141)
0.473
(0.54)
del 1q42 12 9 (6%) 141 0.0943
(0.152)
0.0667
(0.115)
0.831
(0.853)
0.288
(0.365)
0.62
(0.67)
0.196
(0.266)
0.123
(0.188)
0.127
(0.192)
0.501
(0.562)
0.013
(0.0345)
del 2q37 3 15 (10%) 135 0.561
(0.616)
0.02
(0.0479)
0.411
(0.485)
0.252
(0.327)
0.344
(0.418)
0.173
(0.241)
0.381
(0.459)
0.117
(0.181)
0.109
(0.17)
0.242
(0.316)
del 5p15 2 101 (67%) 49 0.0398
(0.078)
0.407
(0.481)
0.119
(0.183)
0.488
(0.553)
0.489
(0.553)
0.458
(0.525)
0.55
(0.607)
0.241
(0.316)
0.284
(0.362)
0.286
(0.363)
del 5p14 3 103 (69%) 47 0.0591
(0.105)
0.168
(0.235)
0.0209
(0.0494)
0.705
(0.742)
0.278
(0.357)
0.295
(0.37)
0.795
(0.825)
0.152
(0.219)
0.198
(0.267)
0.282
(0.36)
del 9p24 3 70 (47%) 80 0.0308
(0.0649)
0.329
(0.407)
0.668
(0.715)
0.424
(0.495)
0.465
(0.532)
0.803
(0.83)
0.339
(0.415)
0.678
(0.719)
1
(1.00)
0.871
(0.891)
del 9p23 66 (44%) 84 0.00049
(0.0035)
0.608
(0.658)
0.52
(0.579)
0.342
(0.417)
0.377
(0.457)
0.527
(0.584)
0.585
(0.637)
0.91
(0.923)
0.932
(0.94)
0.888
(0.904)
amp 12p12 1 147 (98%) 3 0.108
(0.169)
0.104
(0.163)
0.294
(0.37)
0.234
(0.309)
0.0775
(0.13)
0.562
(0.616)
0.0589
(0.105)
0.339
(0.415)
0.326
(0.405)
0.125
(0.189)
amp 12q15 100 (67%) 50 0.869
(0.89)
0.887
(0.904)
0.39
(0.468)
1
(1.00)
0.497
(0.56)
0.735
(0.767)
0.43
(0.499)
0.512
(0.571)
0.524
(0.583)
0.478
(0.544)
'amp_1q21.2' versus 'CN_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0058

Table S1.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 1(1Q21.2) MUTATED 16 23 28 2
AMP PEAK 1(1Q21.2) WILD-TYPE 32 11 26 12

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.005

Table S2.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 1(1Q21.2) MUTATED 12 19 3 16 3 13 3
AMP PEAK 1(1Q21.2) WILD-TYPE 31 8 9 8 5 10 10

Figure S2.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'CN_CNMF'

P value = 0.00838 (Fisher's exact test), Q value = 0.025

Table S3.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 2(2P24.1) MUTATED 11 17 29 5
AMP PEAK 2(2P24.1) WILD-TYPE 37 17 25 9

Figure S3.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.1' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0024

Table S4.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
AMP PEAK 2(2P24.1) MUTATED 9 7 14 32
AMP PEAK 2(2P24.1) WILD-TYPE 36 13 20 19

Figure S4.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.078

Table S5.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 2(2P24.1) MUTATED 8 14 12 10 3 15 0
AMP PEAK 2(2P24.1) WILD-TYPE 26 16 21 12 5 7 1

Figure S5.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.084

Table S6.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 2(2P24.1) MUTATED 10 13 6 14 2 9 8
AMP PEAK 2(2P24.1) WILD-TYPE 33 14 6 10 6 14 5

Figure S6.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.059

Table S7.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 2(2P24.1) MUTATED 15 23 24
AMP PEAK 2(2P24.1) WILD-TYPE 36 34 18

Figure S7.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.077

Table S8.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 2(2P24.1) MUTATED 23 15 24
AMP PEAK 2(2P24.1) WILD-TYPE 47 23 18

Figure S8.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.084

Table S9.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 2(2P24.1) MUTATED 22 15 25
AMP PEAK 2(2P24.1) WILD-TYPE 47 21 20

Figure S9.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S10.  Gene #2: 'amp_2p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 2(2P24.1) MUTATED 7 16 10 17 5 7
AMP PEAK 2(2P24.1) WILD-TYPE 27 20 9 10 14 8

Figure S10.  Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p13' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.04

Table S11.  Gene #3: 'amp_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 3(3P13) MUTATED 8 7 19 0
AMP PEAK 3(3P13) WILD-TYPE 40 27 35 14

Figure S11.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p13' versus 'RPPA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S12.  Gene #3: 'amp_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 3(3P13) MUTATED 4 0 0 17 6
AMP PEAK 3(3P13) WILD-TYPE 41 8 10 20 12

Figure S12.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0074

Table S13.  Gene #3: 'amp_3p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 3(3P13) MUTATED 4 7 16
AMP PEAK 3(3P13) WILD-TYPE 47 18 26

Figure S13.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3p13' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.004

Table S14.  Gene #3: 'amp_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 3(3P13) MUTATED 4 4 7 4 1 14 0
AMP PEAK 3(3P13) WILD-TYPE 30 26 26 18 7 8 1

Figure S14.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.043

Table S15.  Gene #3: 'amp_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 3(3P13) MUTATED 5 4 4 6 2 5 8
AMP PEAK 3(3P13) WILD-TYPE 38 23 8 18 6 18 5

Figure S15.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.049

Table S16.  Gene #3: 'amp_3p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 3(3P13) MUTATED 9 11 14
AMP PEAK 3(3P13) WILD-TYPE 61 27 28

Figure S16.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.042

Table S17.  Gene #3: 'amp_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 3(3P13) MUTATED 9 9 16
AMP PEAK 3(3P13) WILD-TYPE 60 27 29

Figure S17.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.069

Table S18.  Gene #3: 'amp_3p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 3(3P13) MUTATED 6 3 7 10 3 5
AMP PEAK 3(3P13) WILD-TYPE 28 33 12 17 16 10

Figure S18.  Get High-res Image Gene #3: 'amp_3p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q27.3' versus 'RPPA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0097

Table S19.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 4(3Q27.3) MUTATED 6 1 5 18 7
AMP PEAK 4(3Q27.3) WILD-TYPE 39 7 5 19 11

Figure S19.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3q27.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0051

Table S20.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 4(3Q27.3) MUTATED 7 11 19
AMP PEAK 4(3Q27.3) WILD-TYPE 44 14 23

Figure S20.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q27.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S21.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 4(3Q27.3) MUTATED 2 10 13 7 3 14 0
AMP PEAK 4(3Q27.3) WILD-TYPE 32 20 20 15 5 8 1

Figure S21.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00784 (Fisher's exact test), Q value = 0.024

Table S22.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 4(3Q27.3) MUTATED 5 8 6 9 4 10 7
AMP PEAK 4(3Q27.3) WILD-TYPE 38 19 6 15 4 13 6

Figure S22.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q27.3' versus 'MIRSEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0067

Table S23.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 4(3Q27.3) MUTATED 7 24 18
AMP PEAK 4(3Q27.3) WILD-TYPE 44 33 24

Figure S23.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q27.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.01

Table S24.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 4(3Q27.3) MUTATED 13 18 18
AMP PEAK 4(3Q27.3) WILD-TYPE 57 20 24

Figure S24.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q27.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0058

Table S25.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 4(3Q27.3) MUTATED 12 17 20
AMP PEAK 4(3Q27.3) WILD-TYPE 57 19 25

Figure S25.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00972 (Fisher's exact test), Q value = 0.029

Table S26.  Gene #4: 'amp_3q27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 4(3Q27.3) MUTATED 4 9 9 11 8 8
AMP PEAK 4(3Q27.3) WILD-TYPE 30 27 10 16 11 7

Figure S26.  Get High-res Image Gene #4: 'amp_3q27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S27.  Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 5(4Q12) MUTATED 1 13 4 2
AMP PEAK 5(4Q12) WILD-TYPE 47 21 50 12

Figure S27.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.066

Table S28.  Gene #6: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 6(7P22.1) MUTATED 32 26 29 14 7 18 0
AMP PEAK 6(7P22.1) WILD-TYPE 2 4 4 8 1 4 1

Figure S28.  Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S29.  Gene #6: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 6(7P22.1) MUTATED 45 52 29
AMP PEAK 6(7P22.1) WILD-TYPE 6 5 13

Figure S29.  Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.032

Table S30.  Gene #6: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 6(7P22.1) MUTATED 62 35 29
AMP PEAK 6(7P22.1) WILD-TYPE 8 3 13

Figure S30.  Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.051

Table S31.  Gene #6: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 6(7P22.1) MUTATED 61 33 32
AMP PEAK 6(7P22.1) WILD-TYPE 8 3 13

Figure S31.  Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.077

Table S32.  Gene #6: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 6(7P22.1) MUTATED 32 30 17 18 18 11
AMP PEAK 6(7P22.1) WILD-TYPE 2 6 2 9 1 4

Figure S32.  Get High-res Image Gene #6: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q11.22' versus 'METHLYATION_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.054

Table S33.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
AMP PEAK 7(7Q11.22) MUTATED 39 16 31 34
AMP PEAK 7(7Q11.22) WILD-TYPE 6 4 3 17

Figure S33.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q11.22' versus 'RPPA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.032

Table S34.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 7(7Q11.22) MUTATED 39 8 7 22 16
AMP PEAK 7(7Q11.22) WILD-TYPE 6 0 3 15 2

Figure S34.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S35.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 7(7Q11.22) MUTATED 32 27 29 9 7 16 0
AMP PEAK 7(7Q11.22) WILD-TYPE 2 3 4 13 1 6 1

Figure S35.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.0089

Table S36.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 7(7Q11.22) MUTATED 39 24 8 14 7 21 7
AMP PEAK 7(7Q11.22) WILD-TYPE 4 3 4 10 1 2 6

Figure S36.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.22' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0017

Table S37.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 7(7Q11.22) MUTATED 45 51 24
AMP PEAK 7(7Q11.22) WILD-TYPE 6 6 18

Figure S37.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S38.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 7(7Q11.22) MUTATED 63 33 24
AMP PEAK 7(7Q11.22) WILD-TYPE 7 5 18

Figure S38.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S39.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 7(7Q11.22) MUTATED 62 32 26
AMP PEAK 7(7Q11.22) WILD-TYPE 7 4 19

Figure S39.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0051

Table S40.  Gene #7: 'amp_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 7(7Q11.22) MUTATED 31 32 15 14 18 10
AMP PEAK 7(7Q11.22) WILD-TYPE 3 4 4 13 1 5

Figure S40.  Get High-res Image Gene #7: 'amp_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.23' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S41.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 8(8Q11.23) MUTATED 33 34 41 14
AMP PEAK 8(8Q11.23) WILD-TYPE 15 0 13 0

Figure S41.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.23' versus 'METHLYATION_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.025

Table S42.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
AMP PEAK 8(8Q11.23) MUTATED 40 20 26 36
AMP PEAK 8(8Q11.23) WILD-TYPE 5 0 8 15

Figure S42.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.23' versus 'RPPA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.004

Table S43.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 8(8Q11.23) MUTATED 44 6 6 25 14
AMP PEAK 8(8Q11.23) WILD-TYPE 1 2 4 12 4

Figure S43.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q11.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S44.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 8(8Q11.23) MUTATED 49 15 31
AMP PEAK 8(8Q11.23) WILD-TYPE 2 10 11

Figure S44.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S45.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 8(8Q11.23) MUTATED 33 30 27 17 5 9 1
AMP PEAK 8(8Q11.23) WILD-TYPE 1 0 6 5 3 13 0

Figure S45.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S46.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 8(8Q11.23) MUTATED 40 27 8 18 6 19 4
AMP PEAK 8(8Q11.23) WILD-TYPE 3 0 4 6 2 4 9

Figure S46.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.23' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.001

Table S47.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 8(8Q11.23) MUTATED 48 49 25
AMP PEAK 8(8Q11.23) WILD-TYPE 3 8 17

Figure S47.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S48.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 8(8Q11.23) MUTATED 67 30 25
AMP PEAK 8(8Q11.23) WILD-TYPE 3 8 17

Figure S48.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S49.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 8(8Q11.23) MUTATED 66 28 28
AMP PEAK 8(8Q11.23) WILD-TYPE 3 8 17

Figure S49.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S50.  Gene #8: 'amp_8q11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 8(8Q11.23) MUTATED 31 36 16 16 14 9
AMP PEAK 8(8Q11.23) WILD-TYPE 3 0 3 11 5 6

Figure S50.  Get High-res Image Gene #8: 'amp_8q11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q23.3' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0083

Table S51.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
AMP PEAK 9(8Q23.3) MUTATED 41 15 22 30
AMP PEAK 9(8Q23.3) WILD-TYPE 4 5 12 21

Figure S51.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q23.3' versus 'RPPA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.054

Table S52.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 9(8Q23.3) MUTATED 38 7 6 20 12
AMP PEAK 9(8Q23.3) WILD-TYPE 7 1 4 17 6

Figure S52.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.032

Table S53.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 9(8Q23.3) MUTATED 43 14 26
AMP PEAK 9(8Q23.3) WILD-TYPE 8 11 16

Figure S53.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0025

Table S54.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 9(8Q23.3) MUTATED 32 24 24 13 5 9 1
AMP PEAK 9(8Q23.3) WILD-TYPE 2 6 9 9 3 13 0

Figure S54.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.004

Table S55.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 9(8Q23.3) MUTATED 38 22 9 15 5 16 3
AMP PEAK 9(8Q23.3) WILD-TYPE 5 5 3 9 3 7 10

Figure S55.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-04

Table S56.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 9(8Q23.3) MUTATED 46 42 20
AMP PEAK 9(8Q23.3) WILD-TYPE 5 15 22

Figure S56.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S57.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 9(8Q23.3) MUTATED 60 28 20
AMP PEAK 9(8Q23.3) WILD-TYPE 10 10 22

Figure S57.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0025

Table S58.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 9(8Q23.3) MUTATED 60 23 25
AMP PEAK 9(8Q23.3) WILD-TYPE 9 13 20

Figure S58.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00886 (Fisher's exact test), Q value = 0.027

Table S59.  Gene #9: 'amp_8q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 9(8Q23.3) MUTATED 30 30 13 14 13 8
AMP PEAK 9(8Q23.3) WILD-TYPE 4 6 6 13 6 7

Figure S59.  Get High-res Image Gene #9: 'amp_8q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.075

Table S60.  Gene #10: 'amp_12p13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 10(12P13.33) MUTATED 46 25 42
AMP PEAK 10(12P13.33) WILD-TYPE 5 0 0

Figure S60.  Get High-res Image Gene #10: 'amp_12p13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.073

Table S61.  Gene #12: 'amp_12p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 12(12P11.21) MUTATED 46 25 42
AMP PEAK 12(12P11.21) WILD-TYPE 5 0 0

Figure S61.  Get High-res Image Gene #12: 'amp_12p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.073

Table S62.  Gene #12: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 12(12P11.21) MUTATED 64 38 42
AMP PEAK 12(12P11.21) WILD-TYPE 6 0 0

Figure S62.  Get High-res Image Gene #12: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.077

Table S63.  Gene #12: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 12(12P11.21) MUTATED 63 36 45
AMP PEAK 12(12P11.21) WILD-TYPE 6 0 0

Figure S63.  Get High-res Image Gene #12: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q21' versus 'CN_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.018

Table S64.  Gene #14: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 14(16Q21) MUTATED 3 3 15 0
AMP PEAK 14(16Q21) WILD-TYPE 45 31 39 14

Figure S64.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q21' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.047

Table S65.  Gene #14: 'amp_16q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
AMP PEAK 14(16Q21) MUTATED 1 4 5 11
AMP PEAK 14(16Q21) WILD-TYPE 44 16 29 40

Figure S65.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q21' versus 'RPPA_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.013

Table S66.  Gene #14: 'amp_16q21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 14(16Q21) MUTATED 1 0 2 11 2
AMP PEAK 14(16Q21) WILD-TYPE 44 8 8 26 16

Figure S66.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_16q21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0063

Table S67.  Gene #14: 'amp_16q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 14(16Q21) MUTATED 1 7 8
AMP PEAK 14(16Q21) WILD-TYPE 50 18 34

Figure S67.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_16q21' versus 'MRNASEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.088

Table S68.  Gene #14: 'amp_16q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 14(16Q21) MUTATED 1 3 5 5 0 7 0
AMP PEAK 14(16Q21) WILD-TYPE 33 27 28 17 8 15 1

Figure S68.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00777 (Fisher's exact test), Q value = 0.024

Table S69.  Gene #14: 'amp_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 14(16Q21) MUTATED 1 3 3 8 0 3 3
AMP PEAK 14(16Q21) WILD-TYPE 42 24 9 16 8 20 10

Figure S69.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q21' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0068

Table S70.  Gene #14: 'amp_16q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 14(16Q21) MUTATED 1 9 11
AMP PEAK 14(16Q21) WILD-TYPE 50 48 31

Figure S70.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00841 (Fisher's exact test), Q value = 0.025

Table S71.  Gene #14: 'amp_16q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 14(16Q21) MUTATED 4 6 11
AMP PEAK 14(16Q21) WILD-TYPE 66 32 31

Figure S71.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.0097

Table S72.  Gene #14: 'amp_16q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 14(16Q21) MUTATED 4 4 13
AMP PEAK 14(16Q21) WILD-TYPE 65 32 32

Figure S72.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.012

Table S73.  Gene #14: 'amp_16q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 14(16Q21) MUTATED 0 4 4 8 1 4
AMP PEAK 14(16Q21) WILD-TYPE 34 32 15 19 18 11

Figure S73.  Get High-res Image Gene #14: 'amp_16q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.074

Table S74.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 15(20Q11.21) MUTATED 11 9 23 8
AMP PEAK 15(20Q11.21) WILD-TYPE 37 25 31 6

Figure S74.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0054

Table S75.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
AMP PEAK 15(20Q11.21) MUTATED 7 4 14 26
AMP PEAK 15(20Q11.21) WILD-TYPE 38 16 20 25

Figure S75.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.047

Table S76.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 15(20Q11.21) MUTATED 10 1 6 15 10
AMP PEAK 15(20Q11.21) WILD-TYPE 35 7 4 22 8

Figure S76.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.037

Table S77.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 15(20Q11.21) MUTATED 11 13 18
AMP PEAK 15(20Q11.21) WILD-TYPE 40 12 24

Figure S77.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.069

Table S78.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 15(20Q11.21) MUTATED 11 5 3 14 2 9 7
AMP PEAK 15(20Q11.21) WILD-TYPE 32 22 9 10 6 14 6

Figure S78.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.032

Table S79.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 15(20Q11.21) MUTATED 12 17 22
AMP PEAK 15(20Q11.21) WILD-TYPE 39 40 20

Figure S79.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00687 (Fisher's exact test), Q value = 0.022

Table S80.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 15(20Q11.21) MUTATED 16 13 22
AMP PEAK 15(20Q11.21) WILD-TYPE 54 25 20

Figure S80.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.03

Table S81.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 15(20Q11.21) MUTATED 16 12 23
AMP PEAK 15(20Q11.21) WILD-TYPE 53 24 22

Figure S81.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.082

Table S82.  Gene #15: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 15(20Q11.21) MUTATED 6 10 7 15 6 7
AMP PEAK 15(20Q11.21) WILD-TYPE 28 26 12 12 13 8

Figure S82.  Get High-res Image Gene #15: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S83.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
AMP PEAK 16(22Q11.21) MUTATED 13 27 12 5
AMP PEAK 16(22Q11.21) WILD-TYPE 35 7 42 9

Figure S83.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.032

Table S84.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
AMP PEAK 16(22Q11.21) MUTATED 24 2 4 8 3
AMP PEAK 16(22Q11.21) WILD-TYPE 21 6 6 29 15

Figure S84.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_22q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00574 (Fisher's exact test), Q value = 0.019

Table S85.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
AMP PEAK 16(22Q11.21) MUTATED 26 5 10
AMP PEAK 16(22Q11.21) WILD-TYPE 25 20 32

Figure S85.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S86.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
AMP PEAK 16(22Q11.21) MUTATED 12 25 9 4 2 5 0
AMP PEAK 16(22Q11.21) WILD-TYPE 22 5 24 18 6 17 1

Figure S86.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S87.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
AMP PEAK 16(22Q11.21) MUTATED 16 23 4 5 1 5 3
AMP PEAK 16(22Q11.21) WILD-TYPE 27 4 8 19 7 18 10

Figure S87.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.054

Table S88.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
AMP PEAK 16(22Q11.21) MUTATED 24 24 9
AMP PEAK 16(22Q11.21) WILD-TYPE 27 33 33

Figure S88.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0016

Table S89.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
AMP PEAK 16(22Q11.21) MUTATED 39 9 9
AMP PEAK 16(22Q11.21) WILD-TYPE 31 29 33

Figure S89.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.002

Table S90.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
AMP PEAK 16(22Q11.21) MUTATED 38 10 9
AMP PEAK 16(22Q11.21) WILD-TYPE 31 26 36

Figure S90.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S91.  Gene #16: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
AMP PEAK 16(22Q11.21) MUTATED 13 26 6 4 4 4
AMP PEAK 16(22Q11.21) WILD-TYPE 21 10 13 23 15 11

Figure S91.  Get High-res Image Gene #16: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.018

Table S92.  Gene #17: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 1(1P36.31) MUTATED 12 6 16
DEL PEAK 1(1P36.31) WILD-TYPE 39 51 26

Figure S92.  Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00473 (Fisher's exact test), Q value = 0.017

Table S93.  Gene #17: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 1(1P36.31) MUTATED 15 3 16
DEL PEAK 1(1P36.31) WILD-TYPE 55 35 26

Figure S93.  Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0088

Table S94.  Gene #17: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 1(1P36.31) MUTATED 15 2 17
DEL PEAK 1(1P36.31) WILD-TYPE 54 34 28

Figure S94.  Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.037

Table S95.  Gene #17: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 1(1P36.31) MUTATED 7 8 3 9 0 7
DEL PEAK 1(1P36.31) WILD-TYPE 27 28 16 18 19 8

Figure S95.  Get High-res Image Gene #17: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.048

Table S96.  Gene #18: 'del_1p31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 2(1P31.1) MUTATED 5 9 7 6
DEL PEAK 2(1P31.1) WILD-TYPE 43 25 47 8

Figure S96.  Get High-res Image Gene #18: 'del_1p31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.092

Table S97.  Gene #18: 'del_1p31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 2(1P31.1) MUTATED 13 5 3
DEL PEAK 2(1P31.1) WILD-TYPE 38 20 39

Figure S97.  Get High-res Image Gene #18: 'del_1p31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 0.00787 (Fisher's exact test), Q value = 0.024

Table S98.  Gene #18: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 2(1P31.1) MUTATED 15 4 8
DEL PEAK 2(1P31.1) WILD-TYPE 36 53 34

Figure S98.  Get High-res Image Gene #18: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q42.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.034

Table S99.  Gene #19: 'del_1q42.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 3(1Q42.12) MUTATED 0 6 2 0 0 1
DEL PEAK 3(1Q42.12) WILD-TYPE 34 30 17 27 19 14

Figure S99.  Get High-res Image Gene #19: 'del_1q42.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.048

Table S100.  Gene #20: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 4(2Q37.3) MUTATED 2 0 8 5
DEL PEAK 4(2Q37.3) WILD-TYPE 43 20 26 46

Figure S100.  Get High-res Image Gene #20: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.054

Table S101.  Gene #21: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 5(3P26.2) MUTATED 11 8 13 9
DEL PEAK 5(3P26.2) WILD-TYPE 37 26 41 5

Figure S101.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.013

Table S102.  Gene #21: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 5(3P26.2) MUTATED 14 5 16 6
DEL PEAK 5(3P26.2) WILD-TYPE 31 15 18 45

Figure S102.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.024

Table S103.  Gene #21: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 5(3P26.2) MUTATED 14 6 14 2 3 2 0
DEL PEAK 5(3P26.2) WILD-TYPE 20 24 19 20 5 20 1

Figure S103.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.016

Table S104.  Gene #21: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 5(3P26.2) MUTATED 17 5 2 2 2 12 1
DEL PEAK 5(3P26.2) WILD-TYPE 26 22 10 22 6 11 12

Figure S104.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.014

Table S105.  Gene #21: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 5(3P26.2) MUTATED 15 22 4
DEL PEAK 5(3P26.2) WILD-TYPE 36 35 38

Figure S105.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00348 (Fisher's exact test), Q value = 0.013

Table S106.  Gene #21: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 5(3P26.2) MUTATED 22 15 4
DEL PEAK 5(3P26.2) WILD-TYPE 48 23 38

Figure S106.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0065

Table S107.  Gene #21: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 5(3P26.2) MUTATED 22 15 4
DEL PEAK 5(3P26.2) WILD-TYPE 47 21 41

Figure S107.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0015

Table S108.  Gene #21: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 5(3P26.2) MUTATED 15 7 5 1 11 2
DEL PEAK 5(3P26.2) WILD-TYPE 19 29 14 26 8 13

Figure S108.  Get High-res Image Gene #21: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.2' versus 'CN_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.054

Table S109.  Gene #22: 'del_4q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 6(4Q22.2) MUTATED 29 29 39 13
DEL PEAK 6(4Q22.2) WILD-TYPE 19 5 15 1

Figure S109.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.027

Table S110.  Gene #22: 'del_4q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 6(4Q22.2) MUTATED 21 27 29 15 5 12 1
DEL PEAK 6(4Q22.2) WILD-TYPE 13 3 4 7 3 10 0

Figure S110.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0068

Table S111.  Gene #22: 'del_4q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 6(4Q22.2) MUTATED 27 25 10 14 7 21 6
DEL PEAK 6(4Q22.2) WILD-TYPE 16 2 2 10 1 2 7

Figure S111.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0041

Table S112.  Gene #22: 'del_4q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 6(4Q22.2) MUTATED 35 51 24
DEL PEAK 6(4Q22.2) WILD-TYPE 16 6 18

Figure S112.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.015

Table S113.  Gene #22: 'del_4q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 6(4Q22.2) MUTATED 52 34 24
DEL PEAK 6(4Q22.2) WILD-TYPE 18 4 18

Figure S113.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.062

Table S114.  Gene #22: 'del_4q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 6(4Q22.2) MUTATED 52 31 27
DEL PEAK 6(4Q22.2) WILD-TYPE 17 5 18

Figure S114.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.017

Table S115.  Gene #22: 'del_4q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 6(4Q22.2) MUTATED 22 30 15 13 18 12
DEL PEAK 6(4Q22.2) WILD-TYPE 12 6 4 14 1 3

Figure S115.  Get High-res Image Gene #22: 'del_4q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.2' versus 'CN_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.078

Table S116.  Gene #23: 'del_5p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 7(5P15.2) MUTATED 32 29 33 7
DEL PEAK 7(5P15.2) WILD-TYPE 16 5 21 7

Figure S116.  Get High-res Image Gene #23: 'del_5p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5p14.3' versus 'RPPA_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.049

Table S117.  Gene #24: 'del_5p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 8(5P14.3) MUTATED 30 7 4 28 7
DEL PEAK 8(5P14.3) WILD-TYPE 15 1 6 9 11

Figure S117.  Get High-res Image Gene #24: 'del_5p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S118.  Gene #25: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 9(5Q12.1) MUTATED 31 32 36 6
DEL PEAK 9(5Q12.1) WILD-TYPE 17 2 18 8

Figure S118.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.032

Table S119.  Gene #25: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 9(5Q12.1) MUTATED 33 7 4 28 7
DEL PEAK 9(5Q12.1) WILD-TYPE 12 1 6 9 11

Figure S119.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.032

Table S120.  Gene #25: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 9(5Q12.1) MUTATED 24 28 18 16 4 14 1
DEL PEAK 9(5Q12.1) WILD-TYPE 10 2 15 6 4 8 0

Figure S120.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.024

Table S121.  Gene #25: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 9(5Q12.1) MUTATED 30 26 9 15 4 12 9
DEL PEAK 9(5Q12.1) WILD-TYPE 13 1 3 9 4 11 4

Figure S121.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.054

Table S122.  Gene #25: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 9(5Q12.1) MUTATED 56 21 28
DEL PEAK 9(5Q12.1) WILD-TYPE 14 17 14

Figure S122.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.062

Table S123.  Gene #25: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 9(5Q12.1) MUTATED 55 20 30
DEL PEAK 9(5Q12.1) WILD-TYPE 14 16 15

Figure S123.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.078

Table S124.  Gene #25: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 9(5Q12.1) MUTATED 25 31 10 17 10 12
DEL PEAK 9(5Q12.1) WILD-TYPE 9 5 9 10 9 3

Figure S124.  Get High-res Image Gene #25: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p22.3' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.002

Table S125.  Gene #26: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 10(6P22.3) MUTATED 2 3 18 1
DEL PEAK 10(6P22.3) WILD-TYPE 46 31 36 13

Figure S125.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0097

Table S126.  Gene #26: 'del_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 10(6P22.3) MUTATED 1 2 10 11
DEL PEAK 10(6P22.3) WILD-TYPE 44 18 24 40

Figure S126.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p22.3' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0015

Table S127.  Gene #26: 'del_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 10(6P22.3) MUTATED 2 0 0 11 8
DEL PEAK 10(6P22.3) WILD-TYPE 43 8 10 26 10

Figure S127.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0046

Table S128.  Gene #26: 'del_6p22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 10(6P22.3) MUTATED 2 6 13
DEL PEAK 10(6P22.3) WILD-TYPE 49 19 29

Figure S128.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p22.3' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.051

Table S129.  Gene #26: 'del_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 10(6P22.3) MUTATED 2 2 8 4 0 8 0
DEL PEAK 10(6P22.3) WILD-TYPE 32 28 25 18 8 14 1

Figure S129.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.032

Table S130.  Gene #26: 'del_6p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 10(6P22.3) MUTATED 2 2 3 4 1 7 5
DEL PEAK 10(6P22.3) WILD-TYPE 41 25 9 20 7 16 8

Figure S130.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.3' versus 'MIRSEQ_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.018

Table S131.  Gene #26: 'del_6p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 10(6P22.3) MUTATED 2 11 11
DEL PEAK 10(6P22.3) WILD-TYPE 49 46 31

Figure S131.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.013

Table S132.  Gene #26: 'del_6p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 10(6P22.3) MUTATED 4 9 11
DEL PEAK 10(6P22.3) WILD-TYPE 66 29 31

Figure S132.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.013

Table S133.  Gene #26: 'del_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 10(6P22.3) MUTATED 4 10 10
DEL PEAK 10(6P22.3) WILD-TYPE 65 26 35

Figure S133.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.018

Table S134.  Gene #26: 'del_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 10(6P22.3) MUTATED 1 3 7 8 3 2
DEL PEAK 10(6P22.3) WILD-TYPE 33 33 12 19 16 13

Figure S134.  Get High-res Image Gene #26: 'del_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.078

Table S135.  Gene #27: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 11(6Q26) MUTATED 4 1 10 11
DEL PEAK 11(6Q26) WILD-TYPE 41 19 24 40

Figure S135.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.054

Table S136.  Gene #27: 'del_6q26' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 11(6Q26) MUTATED 4 0 2 10 7
DEL PEAK 11(6Q26) WILD-TYPE 41 8 8 27 11

Figure S136.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.037

Table S137.  Gene #27: 'del_6q26' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 11(6Q26) MUTATED 4 7 12
DEL PEAK 11(6Q26) WILD-TYPE 47 18 30

Figure S137.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0046

Table S138.  Gene #27: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 11(6Q26) MUTATED 1 4 9 2 0 10 0
DEL PEAK 11(6Q26) WILD-TYPE 33 26 24 20 8 12 1

Figure S138.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0065

Table S139.  Gene #27: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 11(6Q26) MUTATED 1 4 3 3 3 6 6
DEL PEAK 11(6Q26) WILD-TYPE 42 23 9 21 5 17 7

Figure S139.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.044

Table S140.  Gene #27: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 11(6Q26) MUTATED 3 13 10
DEL PEAK 11(6Q26) WILD-TYPE 48 44 32

Figure S140.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 0.018

Table S141.  Gene #27: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 11(6Q26) MUTATED 5 11 10
DEL PEAK 11(6Q26) WILD-TYPE 65 27 32

Figure S141.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.016

Table S142.  Gene #27: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 11(6Q26) MUTATED 5 11 10
DEL PEAK 11(6Q26) WILD-TYPE 64 25 35

Figure S142.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S143.  Gene #27: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 11(6Q26) MUTATED 1 4 5 7 6 3
DEL PEAK 11(6Q26) WILD-TYPE 33 32 14 20 13 12

Figure S143.  Get High-res Image Gene #27: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.061

Table S144.  Gene #28: 'del_7q11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 12(7Q11.22) MUTATED 0 0 4
DEL PEAK 12(7Q11.22) WILD-TYPE 51 25 38

Figure S144.  Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.062

Table S145.  Gene #28: 'del_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 12(7Q11.22) MUTATED 0 0 1 1 0 0 2
DEL PEAK 12(7Q11.22) WILD-TYPE 43 27 11 23 8 23 11

Figure S145.  Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 0.018

Table S146.  Gene #28: 'del_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 12(7Q11.22) MUTATED 0 0 4
DEL PEAK 12(7Q11.22) WILD-TYPE 51 57 38

Figure S146.  Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00894 (Fisher's exact test), Q value = 0.027

Table S147.  Gene #28: 'del_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 12(7Q11.22) MUTATED 0 0 4
DEL PEAK 12(7Q11.22) WILD-TYPE 70 38 38

Figure S147.  Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.03

Table S148.  Gene #28: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 12(7Q11.22) MUTATED 0 0 4
DEL PEAK 12(7Q11.22) WILD-TYPE 69 36 41

Figure S148.  Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.052

Table S149.  Gene #28: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 12(7Q11.22) MUTATED 0 0 0 2 0 2
DEL PEAK 12(7Q11.22) WILD-TYPE 34 36 19 25 19 13

Figure S149.  Get High-res Image Gene #28: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q35' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.036

Table S150.  Gene #29: 'del_7q35' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 13(7Q35) MUTATED 0 6 6 1
DEL PEAK 13(7Q35) WILD-TYPE 48 28 48 13

Figure S150.  Get High-res Image Gene #29: 'del_7q35' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.032

Table S151.  Gene #29: 'del_7q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 13(7Q35) MUTATED 0 5 3 1 0 2 2
DEL PEAK 13(7Q35) WILD-TYPE 43 22 9 23 8 21 11

Figure S151.  Get High-res Image Gene #29: 'del_7q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q35' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.067

Table S152.  Gene #29: 'del_7q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 13(7Q35) MUTATED 0 5 3 2 0 3
DEL PEAK 13(7Q35) WILD-TYPE 34 31 16 25 19 12

Figure S152.  Get High-res Image Gene #29: 'del_7q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p24.3' versus 'CN_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.065

Table S153.  Gene #30: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 14(9P24.3) MUTATED 16 19 31 4
DEL PEAK 14(9P24.3) WILD-TYPE 32 15 23 10

Figure S153.  Get High-res Image Gene #30: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0035

Table S154.  Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 15(9P23) MUTATED 15 19 31 1
DEL PEAK 15(9P23) WILD-TYPE 33 15 23 13

Figure S154.  Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0015

Table S155.  Gene #32: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 16(9Q33.3) MUTATED 11 14 33 2
DEL PEAK 16(9Q33.3) WILD-TYPE 37 20 21 12

Figure S155.  Get High-res Image Gene #32: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.039

Table S156.  Gene #32: 'del_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 16(9Q33.3) MUTATED 14 8 9 12 1 13 3
DEL PEAK 16(9Q33.3) WILD-TYPE 29 19 3 12 7 10 10

Figure S156.  Get High-res Image Gene #32: 'del_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0054

Table S157.  Gene #33: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 17(9Q34.2) MUTATED 11 14 32 3
DEL PEAK 17(9Q34.2) WILD-TYPE 37 20 22 11

Figure S157.  Get High-res Image Gene #33: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00402 (Fisher's exact test), Q value = 0.015

Table S158.  Gene #33: 'del_9q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 17(9Q34.2) MUTATED 14 8 9 12 1 14 2
DEL PEAK 17(9Q34.2) WILD-TYPE 29 19 3 12 7 9 11

Figure S158.  Get High-res Image Gene #33: 'del_9q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.061

Table S159.  Gene #33: 'del_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 17(9Q34.2) MUTATED 22 22 16
DEL PEAK 17(9Q34.2) WILD-TYPE 48 16 26

Figure S159.  Get High-res Image Gene #33: 'del_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S160.  Gene #34: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 18(10P15.3) MUTATED 20 13 42 9
DEL PEAK 18(10P15.3) WILD-TYPE 28 21 12 5

Figure S160.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.048

Table S161.  Gene #34: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 18(10P15.3) MUTATED 19 10 26 29
DEL PEAK 18(10P15.3) WILD-TYPE 26 10 8 22

Figure S161.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.015

Table S162.  Gene #34: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 18(10P15.3) MUTATED 17 3 5 25 15
DEL PEAK 18(10P15.3) WILD-TYPE 28 5 5 12 3

Figure S162.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.011

Table S163.  Gene #34: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 18(10P15.3) MUTATED 19 16 30
DEL PEAK 18(10P15.3) WILD-TYPE 32 9 12

Figure S163.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.018

Table S164.  Gene #34: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 18(10P15.3) MUTATED 13 13 26 12 4 16 0
DEL PEAK 18(10P15.3) WILD-TYPE 21 17 7 10 4 6 1

Figure S164.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0065

Table S165.  Gene #34: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 18(10P15.3) MUTATED 16 12 8 14 5 21 8
DEL PEAK 18(10P15.3) WILD-TYPE 27 15 4 10 3 2 5

Figure S165.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.071

Table S166.  Gene #34: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 18(10P15.3) MUTATED 21 36 27
DEL PEAK 18(10P15.3) WILD-TYPE 30 21 15

Figure S166.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0041

Table S167.  Gene #34: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 18(10P15.3) MUTATED 28 29 27
DEL PEAK 18(10P15.3) WILD-TYPE 42 9 15

Figure S167.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0024

Table S168.  Gene #34: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 18(10P15.3) MUTATED 28 29 27
DEL PEAK 18(10P15.3) WILD-TYPE 41 7 18

Figure S168.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0069

Table S169.  Gene #34: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 18(10P15.3) MUTATED 11 17 16 15 14 11
DEL PEAK 18(10P15.3) WILD-TYPE 23 19 3 12 5 4

Figure S169.  Get High-res Image Gene #34: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.1' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0037

Table S170.  Gene #35: 'del_10q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 19(10Q23.1) MUTATED 18 9 37 7
DEL PEAK 19(10Q23.1) WILD-TYPE 30 25 17 7

Figure S170.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.1' versus 'METHLYATION_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.015

Table S171.  Gene #35: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 19(10Q23.1) MUTATED 16 7 25 23
DEL PEAK 19(10Q23.1) WILD-TYPE 29 13 9 28

Figure S171.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.1' versus 'RPPA_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.054

Table S172.  Gene #35: 'del_10q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 19(10Q23.1) MUTATED 15 2 4 21 13
DEL PEAK 19(10Q23.1) WILD-TYPE 30 6 6 16 5

Figure S172.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.036

Table S173.  Gene #35: 'del_10q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 19(10Q23.1) MUTATED 16 14 25
DEL PEAK 19(10Q23.1) WILD-TYPE 35 11 17

Figure S173.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0093

Table S174.  Gene #35: 'del_10q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 19(10Q23.1) MUTATED 12 8 25 10 4 12 0
DEL PEAK 19(10Q23.1) WILD-TYPE 22 22 8 12 4 10 1

Figure S174.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0028

Table S175.  Gene #35: 'del_10q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 19(10Q23.1) MUTATED 14 8 9 12 5 19 4
DEL PEAK 19(10Q23.1) WILD-TYPE 29 19 3 12 3 4 9

Figure S175.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S176.  Gene #35: 'del_10q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 19(10Q23.1) MUTATED 17 34 20
DEL PEAK 19(10Q23.1) WILD-TYPE 34 23 22

Figure S176.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S177.  Gene #35: 'del_10q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 19(10Q23.1) MUTATED 22 29 20
DEL PEAK 19(10Q23.1) WILD-TYPE 48 9 22

Figure S177.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S178.  Gene #35: 'del_10q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 19(10Q23.1) MUTATED 22 27 22
DEL PEAK 19(10Q23.1) WILD-TYPE 47 9 23

Figure S178.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S179.  Gene #35: 'del_10q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 19(10Q23.1) MUTATED 9 13 15 9 14 11
DEL PEAK 19(10Q23.1) WILD-TYPE 25 23 4 18 5 4

Figure S179.  Get High-res Image Gene #35: 'del_10q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S180.  Gene #36: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 20(10Q26.3) MUTATED 17 9 41 9
DEL PEAK 20(10Q26.3) WILD-TYPE 31 25 13 5

Figure S180.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0046

Table S181.  Gene #36: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 20(10Q26.3) MUTATED 17 7 27 25
DEL PEAK 20(10Q26.3) WILD-TYPE 28 13 7 26

Figure S181.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.033

Table S182.  Gene #36: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 20(10Q26.3) MUTATED 15 2 5 23 13
DEL PEAK 20(10Q26.3) WILD-TYPE 30 6 5 14 5

Figure S182.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.012

Table S183.  Gene #36: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 20(10Q26.3) MUTATED 16 15 27
DEL PEAK 20(10Q26.3) WILD-TYPE 35 10 15

Figure S183.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.003

Table S184.  Gene #36: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 20(10Q26.3) MUTATED 14 8 27 11 4 12 0
DEL PEAK 20(10Q26.3) WILD-TYPE 20 22 6 11 4 10 1

Figure S184.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S185.  Gene #36: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 20(10Q26.3) MUTATED 16 8 10 13 6 19 4
DEL PEAK 20(10Q26.3) WILD-TYPE 27 19 2 11 2 4 9

Figure S185.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.084

Table S186.  Gene #36: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 20(10Q26.3) MUTATED 19 35 22
DEL PEAK 20(10Q26.3) WILD-TYPE 32 22 20

Figure S186.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S187.  Gene #36: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 20(10Q26.3) MUTATED 24 30 22
DEL PEAK 20(10Q26.3) WILD-TYPE 46 8 20

Figure S187.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00058

Table S188.  Gene #36: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 20(10Q26.3) MUTATED 24 29 23
DEL PEAK 20(10Q26.3) WILD-TYPE 45 7 22

Figure S188.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S189.  Gene #36: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 20(10Q26.3) MUTATED 10 14 17 10 14 11
DEL PEAK 20(10Q26.3) WILD-TYPE 24 22 2 17 5 4

Figure S189.  Get High-res Image Gene #36: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.092

Table S190.  Gene #37: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 21(11P15.5) MUTATED 32 16 21 25
DEL PEAK 21(11P15.5) WILD-TYPE 13 4 13 26

Figure S190.  Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00427 (Fisher's exact test), Q value = 0.016

Table S191.  Gene #37: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 21(11P15.5) MUTATED 31 20 8 12 4 17 2
DEL PEAK 21(11P15.5) WILD-TYPE 12 7 4 12 4 6 11

Figure S191.  Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0093

Table S192.  Gene #37: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 21(11P15.5) MUTATED 35 42 17
DEL PEAK 21(11P15.5) WILD-TYPE 16 15 25

Figure S192.  Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.0089

Table S193.  Gene #37: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 21(11P15.5) MUTATED 51 26 17
DEL PEAK 21(11P15.5) WILD-TYPE 19 12 25

Figure S193.  Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00618 (Fisher's exact test), Q value = 0.02

Table S194.  Gene #37: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 21(11P15.5) MUTATED 51 23 20
DEL PEAK 21(11P15.5) WILD-TYPE 18 13 25

Figure S194.  Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.032

Table S195.  Gene #37: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 21(11P15.5) MUTATED 24 27 15 10 11 7
DEL PEAK 21(11P15.5) WILD-TYPE 10 9 4 17 8 8

Figure S195.  Get High-res Image Gene #37: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p12' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.088

Table S196.  Gene #38: 'del_11p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 22(11P12) MUTATED 33 16 24 26
DEL PEAK 22(11P12) WILD-TYPE 12 4 10 25

Figure S196.  Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00529 (Fisher's exact test), Q value = 0.018

Table S197.  Gene #38: 'del_11p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 22(11P12) MUTATED 31 21 8 12 5 19 3
DEL PEAK 22(11P12) WILD-TYPE 12 6 4 12 3 4 10

Figure S197.  Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p12' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0046

Table S198.  Gene #38: 'del_11p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 22(11P12) MUTATED 36 45 18
DEL PEAK 22(11P12) WILD-TYPE 15 12 24

Figure S198.  Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0065

Table S199.  Gene #38: 'del_11p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 22(11P12) MUTATED 52 29 18
DEL PEAK 22(11P12) WILD-TYPE 18 9 24

Figure S199.  Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.02

Table S200.  Gene #38: 'del_11p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 22(11P12) MUTATED 51 27 21
DEL PEAK 22(11P12) WILD-TYPE 18 9 24

Figure S200.  Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.034

Table S201.  Gene #38: 'del_11p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 22(11P12) MUTATED 25 27 15 10 14 8
DEL PEAK 22(11P12) WILD-TYPE 9 9 4 17 5 7

Figure S201.  Get High-res Image Gene #38: 'del_11p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q12.3' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0051

Table S202.  Gene #39: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 23(11Q12.3) MUTATED 29 31 40 14
DEL PEAK 23(11Q12.3) WILD-TYPE 19 3 14 0

Figure S202.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q12.3' versus 'RPPA_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.067

Table S203.  Gene #39: 'del_11q12.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 23(11Q12.3) MUTATED 39 7 5 23 13
DEL PEAK 23(11Q12.3) WILD-TYPE 6 1 5 14 5

Figure S203.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.051

Table S204.  Gene #39: 'del_11q12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 23(11Q12.3) MUTATED 44 16 27
DEL PEAK 23(11Q12.3) WILD-TYPE 7 9 15

Figure S204.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q12.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S205.  Gene #39: 'del_11q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 23(11Q12.3) MUTATED 27 30 26 13 7 11 0
DEL PEAK 23(11Q12.3) WILD-TYPE 7 0 7 9 1 11 1

Figure S205.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S206.  Gene #39: 'del_11q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 23(11Q12.3) MUTATED 35 27 9 14 6 20 3
DEL PEAK 23(11Q12.3) WILD-TYPE 8 0 3 10 2 3 10

Figure S206.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S207.  Gene #39: 'del_11q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 23(11Q12.3) MUTATED 43 51 20
DEL PEAK 23(11Q12.3) WILD-TYPE 8 6 22

Figure S207.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S208.  Gene #39: 'del_11q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 23(11Q12.3) MUTATED 62 32 20
DEL PEAK 23(11Q12.3) WILD-TYPE 8 6 22

Figure S208.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

Table S209.  Gene #39: 'del_11q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 23(11Q12.3) MUTATED 61 30 23
DEL PEAK 23(11Q12.3) WILD-TYPE 8 6 22

Figure S209.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S210.  Gene #39: 'del_11q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 23(11Q12.3) MUTATED 27 35 15 12 16 9
DEL PEAK 23(11Q12.3) WILD-TYPE 7 1 4 15 3 6

Figure S210.  Get High-res Image Gene #39: 'del_11q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.3' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.004

Table S211.  Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 24(11Q24.3) MUTATED 32 33 43 14
DEL PEAK 24(11Q24.3) WILD-TYPE 16 1 11 0

Figure S211.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0089

Table S212.  Gene #40: 'del_11q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 24(11Q24.3) MUTATED 28 30 28 16 6 14 0
DEL PEAK 24(11Q24.3) WILD-TYPE 6 0 5 6 2 8 1

Figure S212.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.004

Table S213.  Gene #40: 'del_11q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 24(11Q24.3) MUTATED 35 27 10 18 7 20 5
DEL PEAK 24(11Q24.3) WILD-TYPE 8 0 2 6 1 3 8

Figure S213.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.012

Table S214.  Gene #40: 'del_11q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 24(11Q24.3) MUTATED 43 52 27
DEL PEAK 24(11Q24.3) WILD-TYPE 8 5 15

Figure S214.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.02

Table S215.  Gene #40: 'del_11q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 24(11Q24.3) MUTATED 62 33 27
DEL PEAK 24(11Q24.3) WILD-TYPE 8 5 15

Figure S215.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.039

Table S216.  Gene #40: 'del_11q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 24(11Q24.3) MUTATED 61 31 30
DEL PEAK 24(11Q24.3) WILD-TYPE 8 5 15

Figure S216.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0034

Table S217.  Gene #40: 'del_11q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 24(11Q24.3) MUTATED 26 36 15 16 17 12
DEL PEAK 24(11Q24.3) WILD-TYPE 8 0 4 11 2 3

Figure S217.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.035

Table S218.  Gene #41: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 25(13Q34) MUTATED 32 32 40 9
DEL PEAK 25(13Q34) WILD-TYPE 16 2 14 5

Figure S218.  Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0046

Table S219.  Gene #41: 'del_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 25(13Q34) MUTATED 23 30 26 16 4 13 1
DEL PEAK 25(13Q34) WILD-TYPE 11 0 7 6 4 9 0

Figure S219.  Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.0088

Table S220.  Gene #41: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 25(13Q34) MUTATED 30 27 11 15 6 17 7
DEL PEAK 25(13Q34) WILD-TYPE 13 0 1 9 2 6 6

Figure S220.  Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.006

Table S221.  Gene #41: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 25(13Q34) MUTATED 22 35 14 15 15 12
DEL PEAK 25(13Q34) WILD-TYPE 12 1 5 12 4 3

Figure S221.  Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S222.  Gene #42: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 26(16Q23.1) MUTATED 12 20 23 11
DEL PEAK 26(16Q23.1) WILD-TYPE 36 14 31 3

Figure S222.  Get High-res Image Gene #42: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.051

Table S223.  Gene #42: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 26(16Q23.1) MUTATED 17 14 18 17
DEL PEAK 26(16Q23.1) WILD-TYPE 28 6 16 34

Figure S223.  Get High-res Image Gene #42: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.04

Table S224.  Gene #42: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 26(16Q23.1) MUTATED 11 21 8 6 10 10
DEL PEAK 26(16Q23.1) WILD-TYPE 23 15 11 21 9 5

Figure S224.  Get High-res Image Gene #42: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0068

Table S225.  Gene #43: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 27(16Q23.3) MUTATED 13 20 23 11
DEL PEAK 27(16Q23.3) WILD-TYPE 35 14 31 3

Figure S225.  Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 0.00304 (Fisher's exact test), Q value = 0.012

Table S226.  Gene #43: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 27(16Q23.3) MUTATED 16 13 22 16
DEL PEAK 27(16Q23.3) WILD-TYPE 29 7 12 35

Figure S226.  Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.086

Table S227.  Gene #43: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 27(16Q23.3) MUTATED 10 17 21 9 3 7 0
DEL PEAK 27(16Q23.3) WILD-TYPE 24 13 12 13 5 15 1

Figure S227.  Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0082

Table S228.  Gene #43: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 27(16Q23.3) MUTATED 17 36 14
DEL PEAK 27(16Q23.3) WILD-TYPE 34 21 28

Figure S228.  Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.051

Table S229.  Gene #43: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 27(16Q23.3) MUTATED 29 24 14
DEL PEAK 27(16Q23.3) WILD-TYPE 41 14 28

Figure S229.  Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.037

Table S230.  Gene #43: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 27(16Q23.3) MUTATED 11 18 10 6 12 10
DEL PEAK 27(16Q23.3) WILD-TYPE 23 18 9 21 7 5

Figure S230.  Get High-res Image Gene #43: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.084

Table S231.  Gene #44: 'del_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 28(18P11.32) MUTATED 40 50 28
DEL PEAK 28(18P11.32) WILD-TYPE 11 7 14

Figure S231.  Get High-res Image Gene #44: 'del_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.047

Table S232.  Gene #44: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 28(18P11.32) MUTATED 55 35 28
DEL PEAK 28(18P11.32) WILD-TYPE 15 3 14

Figure S232.  Get High-res Image Gene #44: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.3' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.032

Table S233.  Gene #45: 'del_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 29(18Q22.3) MUTATED 33 32 48 12
DEL PEAK 29(18Q22.3) WILD-TYPE 15 2 6 2

Figure S233.  Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.053

Table S234.  Gene #45: 'del_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 29(18Q22.3) MUTATED 41 53 31
DEL PEAK 29(18Q22.3) WILD-TYPE 10 4 11

Figure S234.  Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.079

Table S235.  Gene #45: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 29(18Q22.3) MUTATED 58 36 31
DEL PEAK 29(18Q22.3) WILD-TYPE 12 2 11

Figure S235.  Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00765 (Fisher's exact test), Q value = 0.024

Table S236.  Gene #45: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 29(18Q22.3) MUTATED 24 34 17 18 18 14
DEL PEAK 29(18Q22.3) WILD-TYPE 10 2 2 9 1 1

Figure S236.  Get High-res Image Gene #45: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S237.  Gene #46: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 30(19Q13.33) MUTATED 14 1 37 6
DEL PEAK 30(19Q13.33) WILD-TYPE 34 33 17 8

Figure S237.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S238.  Gene #46: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 30(19Q13.33) MUTATED 5 0 29 24
DEL PEAK 30(19Q13.33) WILD-TYPE 40 20 5 27

Figure S238.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S239.  Gene #46: 'del_19q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 30(19Q13.33) MUTATED 1 2 4 25 15
DEL PEAK 30(19Q13.33) WILD-TYPE 44 6 6 12 3

Figure S239.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S240.  Gene #46: 'del_19q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 30(19Q13.33) MUTATED 1 15 31
DEL PEAK 30(19Q13.33) WILD-TYPE 50 10 11

Figure S240.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S241.  Gene #46: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 30(19Q13.33) MUTATED 0 1 28 14 1 14 0
DEL PEAK 30(19Q13.33) WILD-TYPE 34 29 5 8 7 8 1

Figure S241.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S242.  Gene #46: 'del_19q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 30(19Q13.33) MUTATED 0 1 11 14 5 20 7
DEL PEAK 30(19Q13.33) WILD-TYPE 43 26 1 10 3 3 6

Figure S242.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S243.  Gene #46: 'del_19q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 30(19Q13.33) MUTATED 1 32 25
DEL PEAK 30(19Q13.33) WILD-TYPE 50 25 17

Figure S243.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S244.  Gene #46: 'del_19q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 30(19Q13.33) MUTATED 1 32 25
DEL PEAK 30(19Q13.33) WILD-TYPE 69 6 17

Figure S244.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S245.  Gene #46: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 30(19Q13.33) MUTATED 1 28 29
DEL PEAK 30(19Q13.33) WILD-TYPE 68 8 16

Figure S245.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S246.  Gene #46: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 30(19Q13.33) MUTATED 0 1 15 14 16 12
DEL PEAK 30(19Q13.33) WILD-TYPE 34 35 4 13 3 3

Figure S246.  Get High-res Image Gene #46: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S247.  Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 31(19Q13.42) MUTATED 14 1 36 6
DEL PEAK 31(19Q13.42) WILD-TYPE 34 33 18 8

Figure S247.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S248.  Gene #47: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 31(19Q13.42) MUTATED 5 0 29 23
DEL PEAK 31(19Q13.42) WILD-TYPE 40 20 5 28

Figure S248.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.42' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S249.  Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
DEL PEAK 31(19Q13.42) MUTATED 1 2 4 24 15
DEL PEAK 31(19Q13.42) WILD-TYPE 44 6 6 13 3

Figure S249.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19q13.42' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S250.  Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
DEL PEAK 31(19Q13.42) MUTATED 1 15 30
DEL PEAK 31(19Q13.42) WILD-TYPE 50 10 12

Figure S250.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S251.  Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 31(19Q13.42) MUTATED 0 1 28 13 1 14 0
DEL PEAK 31(19Q13.42) WILD-TYPE 34 29 5 9 7 8 1

Figure S251.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S252.  Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
DEL PEAK 31(19Q13.42) MUTATED 0 1 11 13 5 20 7
DEL PEAK 31(19Q13.42) WILD-TYPE 43 26 1 11 3 3 6

Figure S252.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S253.  Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 31(19Q13.42) MUTATED 1 32 24
DEL PEAK 31(19Q13.42) WILD-TYPE 50 25 18

Figure S253.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S254.  Gene #47: 'del_19q13.42' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 31(19Q13.42) MUTATED 1 32 24
DEL PEAK 31(19Q13.42) WILD-TYPE 69 6 18

Figure S254.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S255.  Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 31(19Q13.42) MUTATED 1 28 28
DEL PEAK 31(19Q13.42) WILD-TYPE 68 8 17

Figure S255.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S256.  Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 31(19Q13.42) MUTATED 0 1 15 13 16 12
DEL PEAK 31(19Q13.42) WILD-TYPE 34 35 4 14 3 3

Figure S256.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.066

Table S257.  Gene #48: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 32(20P12.1) MUTATED 5 17 7
DEL PEAK 32(20P12.1) WILD-TYPE 46 40 35

Figure S257.  Get High-res Image Gene #48: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0082

Table S258.  Gene #48: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 32(20P12.1) MUTATED 1 10 9 5 3 1
DEL PEAK 32(20P12.1) WILD-TYPE 33 26 10 22 16 14

Figure S258.  Get High-res Image Gene #48: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.016

Table S259.  Gene #49: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 33(XP21.1) MUTATED 2 6 5 15
DEL PEAK 33(XP21.1) WILD-TYPE 43 14 29 36

Figure S259.  Get High-res Image Gene #49: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.092

Table S260.  Gene #49: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
DEL PEAK 33(XP21.1) MUTATED 10 4 14
DEL PEAK 33(XP21.1) WILD-TYPE 59 32 31

Figure S260.  Get High-res Image Gene #49: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00675 (Fisher's exact test), Q value = 0.022

Table S261.  Gene #49: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 33(XP21.1) MUTATED 1 9 2 10 2 4
DEL PEAK 33(XP21.1) WILD-TYPE 33 27 17 17 17 11

Figure S261.  Get High-res Image Gene #49: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq27.3' versus 'CN_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.007

Table S262.  Gene #50: 'del_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
DEL PEAK 34(XQ27.3) MUTATED 2 7 18 3
DEL PEAK 34(XQ27.3) WILD-TYPE 46 27 36 11

Figure S262.  Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq27.3' versus 'METHLYATION_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0065

Table S263.  Gene #50: 'del_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
DEL PEAK 34(XQ27.3) MUTATED 2 6 5 17
DEL PEAK 34(XQ27.3) WILD-TYPE 43 14 29 34

Figure S263.  Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.3' versus 'MRNASEQ_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.02

Table S264.  Gene #50: 'del_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
DEL PEAK 34(XQ27.3) MUTATED 4 7 3 11 0 5 0
DEL PEAK 34(XQ27.3) WILD-TYPE 30 23 30 11 8 17 1

Figure S264.  Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq27.3' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.036

Table S265.  Gene #50: 'del_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
DEL PEAK 34(XQ27.3) MUTATED 8 7 15
DEL PEAK 34(XQ27.3) WILD-TYPE 43 50 27

Figure S265.  Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq27.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S266.  Gene #50: 'del_xq27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
DEL PEAK 34(XQ27.3) MUTATED 11 4 15
DEL PEAK 34(XQ27.3) WILD-TYPE 59 34 27

Figure S266.  Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.05

Table S267.  Gene #50: 'del_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
DEL PEAK 34(XQ27.3) MUTATED 4 7 5 10 0 4
DEL PEAK 34(XQ27.3) WILD-TYPE 30 29 14 17 19 11

Figure S267.  Get High-res Image Gene #50: 'del_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/TGCT-TP/22533662/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/22541961/TGCT-TP.transferedmergedcluster.txt

  • Number of patients = 150

  • Number of significantly focal cnvs = 50

  • 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)