Correlation between copy number variation genes and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation of 70 peak regions and 8 molecular subtypes across 352 patients, 113 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 2(2q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 4(3q26.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 6(5p12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 7(6p12.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 8(6q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 10(7q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 12(8q11.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 14(9p23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 15(9p13.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 16(11p13) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 17(11q13.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 18(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 19(12q15) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 20(13q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 21(15q26.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 22(17q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 23(18p11.31) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 25(20q11.22) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • Del Peak 4(2q21.2) cnvs correlated to 'MIRSEQ_CNMF'.

  • Del Peak 6(2q36.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 7(3p25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 8(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 9(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 10(3p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 11(4p15.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 12(4q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 15(5q35.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 16(6p25.3) cnvs correlated to 'METHLYATION_CNMF'.

  • Del Peak 18(7q36.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 19(8p23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 20(9p23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 21(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 22(9q21.11) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(9q34.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 24(10p15.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 25(10p11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 26(10q23.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 27(11p15.4) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • Del Peak 28(11q14.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 29(11q23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 31(13q12.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 32(13q14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 34(14q32.32) cnvs correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 36(16q12.1) cnvs correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Del Peak 37(16q23.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 39(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 40(18q23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 41(19p13.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 42(19q13.43) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 43(Xp21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 44(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 45(Xq21.33) cnvs correlated to 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 113 significant findings detected.

Molecular
subtypes
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Chi-square 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 Peak 13(8q24 21) 0 (0%) 98 3.31e-10
(1.76e-07)
0.000106
(0.0496)
0.19
(1.00)
0.917
(1.00)
0.000102
(0.0482)
0.000135
(0.0632)
0.0159
(1.00)
0.000223
(0.103)
Amp Peak 1(1q21 2) 0 (0%) 270 8.51e-11
(4.55e-08)
2.63e-08
(1.36e-05)
0.473
(1.00)
0.718
(1.00)
0.000509
(0.229)
0.00316
(1.00)
0.000167
(0.0775)
0.698
(1.00)
Del Peak 1(1p36 13) 0 (0%) 283 1.44e-11
(7.71e-09)
5.38e-15
(2.94e-12)
0.0225
(1.00)
0.739
(1.00)
3.03e-05
(0.0148)
0.000716
(0.317)
0.000136
(0.0632)
0.137
(1.00)
Del Peak 32(13q14 2) 0 (0%) 203 2.86e-06
(0.00142)
5.88e-07
(0.000298)
0.151
(1.00)
0.275
(1.00)
5.7e-05
(0.0274)
6.46e-05
(0.0309)
0.00618
(1.00)
0.979
(1.00)
Del Peak 36(16q12 1) 0 (0%) 290 0.00922
(1.00)
1.13e-07
(5.74e-05)
0.746
(1.00)
0.0896
(1.00)
7.1e-08
(3.64e-05)
3.91e-07
(0.000199)
0.000104
(0.0488)
0.0137
(1.00)
Amp Peak 4(3q26 33) 0 (0%) 88 2.94e-13
(1.6e-10)
8.71e-05
(0.0413)
0.244
(1.00)
0.193
(1.00)
0.00128
(0.55)
0.000468
(0.212)
0.000917
(0.402)
0.165
(1.00)
Del Peak 2(1p13 2) 0 (0%) 267 3.1e-10
(1.65e-07)
8.62e-10
(4.56e-07)
0.0124
(1.00)
0.118
(1.00)
0.00546
(1.00)
0.0927
(1.00)
4.41e-05
(0.0213)
0.614
(1.00)
Del Peak 15(5q35 3) 0 (0%) 218 7.2e-18
(3.98e-15)
4.25e-14
(2.32e-11)
0.419
(1.00)
0.0645
(1.00)
0.0146
(1.00)
0.000477
(0.216)
0.204
(1.00)
0.649
(1.00)
Del Peak 27(11p15 4) 0 (0%) 242 1.6e-08
(8.32e-06)
0.000523
(0.234)
0.471
(1.00)
0.458
(1.00)
0.00228
(0.954)
0.0071
(1.00)
0.000501
(0.226)
0.54
(1.00)
Del Peak 29(11q23 1) 0 (0%) 183 7.7e-18
(4.25e-15)
8.45e-07
(0.000423)
0.169
(1.00)
0.254
(1.00)
0.000815
(0.359)
0.00023
(0.106)
0.103
(1.00)
0.35
(1.00)
Del Peak 34(14q32 32) 0 (0%) 299 0.0267
(1.00)
1.42e-07
(7.23e-05)
0.0984
(1.00)
0.413
(1.00)
0.000242
(0.111)
9.8e-05
(0.0462)
0.00137
(0.584)
0.0924
(1.00)
Amp Peak 2(2q11 2) 0 (0%) 278 2.5e-08
(1.29e-05)
1.71e-08
(8.87e-06)
0.991
(1.00)
0.295
(1.00)
0.0119
(1.00)
0.0807
(1.00)
0.00172
(0.727)
0.296
(1.00)
Amp Peak 3(2q31 2) 0 (0%) 280 1.26e-10
(6.74e-08)
9.37e-09
(4.89e-06)
0.803
(1.00)
0.509
(1.00)
0.318
(1.00)
0.11
(1.00)
0.206
(1.00)
0.391
(1.00)
Amp Peak 9(7p11 2) 0 (0%) 205 1.12e-08
(5.84e-06)
6.87e-07
(0.000346)
0.26
(1.00)
0.832
(1.00)
0.5
(1.00)
0.923
(1.00)
0.934
(1.00)
0.0261
(1.00)
Amp Peak 10(7q22 1) 0 (0%) 231 6.99e-15
(3.81e-12)
5.46e-08
(2.8e-05)
0.599
(1.00)
0.567
(1.00)
0.235
(1.00)
0.335
(1.00)
0.011
(1.00)
0.67
(1.00)
Amp Peak 18(12p13 33) 0 (0%) 234 2.85e-10
(1.52e-07)
1.28e-05
(0.00628)
0.276
(1.00)
0.352
(1.00)
0.00912
(1.00)
0.00101
(0.44)
0.00117
(0.507)
0.323
(1.00)
Amp Peak 20(13q22 1) 0 (0%) 280 0.000262
(0.12)
8.43e-05
(0.04)
0.0181
(1.00)
0.205
(1.00)
0.233
(1.00)
0.0924
(1.00)
0.0822
(1.00)
0.135
(1.00)
Amp Peak 22(17q12) 0 (0%) 289 8.2e-08
(4.2e-05)
0.000112
(0.0522)
0.623
(1.00)
0.73
(1.00)
0.0168
(1.00)
0.0308
(1.00)
0.0161
(1.00)
0.167
(1.00)
Del Peak 6(2q36 2) 0 (0%) 248 5.4e-08
(2.78e-05)
5.69e-06
(0.0028)
0.114
(1.00)
0.531
(1.00)
0.000636
(0.283)
0.00125
(0.539)
0.00452
(1.00)
0.232
(1.00)
Del Peak 7(3p25 3) 0 (0%) 105 7.67e-25
(4.25e-22)
2.92e-10
(1.55e-07)
0.213
(1.00)
0.39
(1.00)
0.0134
(1.00)
0.0632
(1.00)
0.146
(1.00)
0.00212
(0.892)
Del Peak 8(3p14 2) 0 (0%) 89 2.49e-29
(1.4e-26)
8.81e-08
(4.5e-05)
0.259
(1.00)
0.5
(1.00)
0.115
(1.00)
0.161
(1.00)
0.534
(1.00)
0.0592
(1.00)
Del Peak 9(3p14 2) 0 (0%) 89 2.49e-29
(1.4e-26)
5.71e-07
(0.000289)
0.216
(1.00)
0.386
(1.00)
0.115
(1.00)
0.161
(1.00)
0.534
(1.00)
0.0592
(1.00)
Del Peak 10(3p12 2) 0 (0%) 103 6.77e-29
(3.78e-26)
4.04e-09
(2.13e-06)
0.853
(1.00)
0.684
(1.00)
0.241
(1.00)
0.463
(1.00)
0.287
(1.00)
0.273
(1.00)
Del Peak 11(4p15 2) 0 (0%) 202 3.05e-12
(1.65e-09)
5.98e-07
(0.000302)
0.0483
(1.00)
0.13
(1.00)
0.0406
(1.00)
0.0129
(1.00)
0.00483
(1.00)
0.678
(1.00)
Del Peak 12(4q22 1) 0 (0%) 235 8.67e-09
(4.54e-06)
6.5e-07
(0.000327)
0.13
(1.00)
0.651
(1.00)
0.371
(1.00)
0.205
(1.00)
0.334
(1.00)
0.578
(1.00)
Del Peak 13(4q35 2) 0 (0%) 207 7.51e-09
(3.94e-06)
2.97e-05
(0.0145)
0.0962
(1.00)
0.534
(1.00)
0.275
(1.00)
0.353
(1.00)
0.218
(1.00)
0.482
(1.00)
Del Peak 14(5q11 2) 0 (0%) 210 5.27e-17
(2.91e-14)
1.35e-12
(7.3e-10)
0.0186
(1.00)
0.615
(1.00)
0.0401
(1.00)
0.000767
(0.339)
0.0647
(1.00)
0.457
(1.00)
Del Peak 19(8p23 2) 0 (0%) 151 2.17e-15
(1.19e-12)
3.84e-05
(0.0186)
0.134
(1.00)
0.188
(1.00)
0.0166
(1.00)
0.00353
(1.00)
0.143
(1.00)
0.0273
(1.00)
Del Peak 20(9p23) 0 (0%) 191 1.16e-16
(6.36e-14)
5.42e-09
(2.85e-06)
0.538
(1.00)
0.851
(1.00)
0.74
(1.00)
0.493
(1.00)
0.834
(1.00)
0.845
(1.00)
Del Peak 21(9p21 3) 0 (0%) 148 2.71e-13
(1.47e-10)
2.83e-09
(1.49e-06)
0.707
(1.00)
0.423
(1.00)
0.39
(1.00)
0.462
(1.00)
0.746
(1.00)
0.432
(1.00)
Del Peak 31(13q12 11) 0 (0%) 193 2.63e-11
(1.41e-08)
7.28e-07
(0.000366)
0.272
(1.00)
0.371
(1.00)
0.053
(1.00)
0.0289
(1.00)
0.456
(1.00)
0.758
(1.00)
Del Peak 39(18q21 2) 0 (0%) 170 7.27e-17
(4e-14)
1.69e-09
(8.92e-07)
0.603
(1.00)
0.642
(1.00)
0.00268
(1.00)
0.0073
(1.00)
0.00342
(1.00)
0.00548
(1.00)
Del Peak 40(18q23) 0 (0%) 154 8.57e-20
(4.75e-17)
1.38e-11
(7.41e-09)
0.183
(1.00)
0.385
(1.00)
0.00216
(0.908)
0.00333
(1.00)
0.0125
(1.00)
0.0184
(1.00)
Del Peak 42(19q13 43) 0 (0%) 284 1.03e-05
(0.00506)
6.93e-05
(0.033)
0.256
(1.00)
0.0841
(1.00)
0.584
(1.00)
0.262
(1.00)
0.058
(1.00)
0.495
(1.00)
Del Peak 44(Xp11 3) 0 (0%) 238 4.65e-06
(0.0023)
5.8e-05
(0.0278)
0.346
(1.00)
0.00914
(1.00)
0.211
(1.00)
0.0598
(1.00)
0.099
(1.00)
0.931
(1.00)
Amp Peak 5(5p15 33) 0 (0%) 195 1.31e-11
(7.08e-09)
0.0256
(1.00)
0.624
(1.00)
0.282
(1.00)
0.683
(1.00)
0.32
(1.00)
0.687
(1.00)
0.757
(1.00)
Amp Peak 6(5p12) 0 (0%) 221 3.48e-12
(1.88e-09)
0.0182
(1.00)
0.478
(1.00)
1
(1.00)
0.9
(1.00)
0.388
(1.00)
0.784
(1.00)
0.746
(1.00)
Amp Peak 7(6p12 1) 0 (0%) 282 0.000195
(0.0905)
0.0028
(1.00)
0.303
(1.00)
0.47
(1.00)
0.983
(1.00)
0.802
(1.00)
0.928
(1.00)
0.00123
(0.531)
Amp Peak 8(6q12) 0 (0%) 290 0.0004
(0.182)
0.0138
(1.00)
0.811
(1.00)
0.373
(1.00)
1
(1.00)
0.822
(1.00)
0.674
(1.00)
0.00726
(1.00)
Amp Peak 12(8q11 21) 0 (0%) 145 1.8e-06
(0.000895)
0.0111
(1.00)
0.0323
(1.00)
0.518
(1.00)
0.00113
(0.49)
0.000664
(0.295)
0.00334
(1.00)
0.00122
(0.529)
Amp Peak 14(9p23) 0 (0%) 269 3.19e-05
(0.0155)
0.786
(1.00)
0.655
(1.00)
0.888
(1.00)
0.0993
(1.00)
0.227
(1.00)
0.406
(1.00)
0.943
(1.00)
Amp Peak 15(9p13 3) 0 (0%) 257 5.06e-05
(0.0244)
0.222
(1.00)
0.39
(1.00)
0.254
(1.00)
0.00708
(1.00)
0.0379
(1.00)
0.0113
(1.00)
0.085
(1.00)
Amp Peak 16(11p13) 0 (0%) 283 5.66e-05
(0.0272)
0.0971
(1.00)
0.187
(1.00)
0.0539
(1.00)
0.631
(1.00)
0.163
(1.00)
0.384
(1.00)
0.0655
(1.00)
Amp Peak 17(11q13 3) 0 (0%) 188 1.73e-27
(9.63e-25)
0.000897
(0.394)
0.901
(1.00)
0.284
(1.00)
0.361
(1.00)
0.504
(1.00)
0.67
(1.00)
0.0874
(1.00)
Amp Peak 19(12q15) 0 (0%) 280 0.000508
(0.229)
0.00842
(1.00)
0.0609
(1.00)
0.193
(1.00)
0.09
(1.00)
0.0459
(1.00)
0.463
(1.00)
0.726
(1.00)
Amp Peak 21(15q26 3) 0 (0%) 277 0.000327
(0.15)
0.217
(1.00)
0.263
(1.00)
0.624
(1.00)
0.923
(1.00)
0.416
(1.00)
0.918
(1.00)
0.599
(1.00)
Amp Peak 23(18p11 31) 0 (0%) 244 7.58e-07
(0.00038)
0.00315
(1.00)
0.962
(1.00)
0.766
(1.00)
0.262
(1.00)
0.206
(1.00)
0.5
(1.00)
0.927
(1.00)
Amp Peak 25(20q11 22) 0 (0%) 197 4.86e-06
(0.0024)
0.0222
(1.00)
0.845
(1.00)
0.442
(1.00)
0.0128
(1.00)
0.0854
(1.00)
0.308
(1.00)
0.0129
(1.00)
Del Peak 4(2q21 2) 0 (0%) 306 0.717
(1.00)
0.0278
(1.00)
0.91
(1.00)
1
(1.00)
0.0154
(1.00)
0.00564
(1.00)
0.000377
(0.172)
0.155
(1.00)
Del Peak 16(6p25 3) 0 (0%) 284 0.00195
(0.821)
0.00033
(0.151)
0.0727
(1.00)
0.133
(1.00)
0.00752
(1.00)
0.38
(1.00)
0.101
(1.00)
0.667
(1.00)
Del Peak 18(7q36 1) 0 (0%) 266 0.000182
(0.0844)
0.33
(1.00)
0.00511
(1.00)
0.277
(1.00)
0.957
(1.00)
0.674
(1.00)
0.914
(1.00)
0.135
(1.00)
Del Peak 22(9q21 11) 0 (0%) 287 2.86e-08
(1.48e-05)
0.000962
(0.42)
0.96
(1.00)
0.926
(1.00)
0.882
(1.00)
0.673
(1.00)
0.72
(1.00)
0.0485
(1.00)
Del Peak 23(9q34 3) 0 (0%) 296 0.000333
(0.152)
0.0316
(1.00)
0.712
(1.00)
0.108
(1.00)
0.851
(1.00)
0.409
(1.00)
0.29
(1.00)
0.14
(1.00)
Del Peak 24(10p15 3) 0 (0%) 238 5.46e-06
(0.00269)
0.0293
(1.00)
0.504
(1.00)
0.155
(1.00)
0.327
(1.00)
0.307
(1.00)
0.313
(1.00)
0.469
(1.00)
Del Peak 25(10p11 21) 0 (0%) 245 9.79e-06
(0.00481)
0.145
(1.00)
0.225
(1.00)
0.0652
(1.00)
0.702
(1.00)
0.975
(1.00)
0.511
(1.00)
0.705
(1.00)
Del Peak 26(10q23 31) 0 (0%) 263 1.55e-06
(0.000771)
0.00416
(1.00)
0.179
(1.00)
0.548
(1.00)
0.0249
(1.00)
0.0128
(1.00)
0.0224
(1.00)
0.947
(1.00)
Del Peak 28(11q14 1) 0 (0%) 240 4.77e-25
(2.65e-22)
0.0851
(1.00)
0.193
(1.00)
0.769
(1.00)
0.0105
(1.00)
0.0369
(1.00)
0.38
(1.00)
0.821
(1.00)
Del Peak 37(16q23 3) 0 (0%) 280 0.0167
(1.00)
0.000839
(0.369)
0.504
(1.00)
0.0196
(1.00)
0.000601
(0.269)
8.88e-05
(0.042)
0.00604
(1.00)
0.218
(1.00)
Del Peak 41(19p13 3) 0 (0%) 235 3.57e-06
(0.00177)
0.0368
(1.00)
0.31
(1.00)
0.0817
(1.00)
0.0876
(1.00)
0.761
(1.00)
0.487
(1.00)
0.0959
(1.00)
Del Peak 43(Xp21 3) 0 (0%) 236 4.3e-05
(0.0208)
0.00532
(1.00)
0.424
(1.00)
0.0649
(1.00)
0.275
(1.00)
0.0415
(1.00)
0.2
(1.00)
0.564
(1.00)
Del Peak 45(Xq21 33) 0 (0%) 296 0.00168
(0.711)
0.00166
(0.705)
0.0255
(1.00)
0.444
(1.00)
0.00131
(0.56)
0.0123
(1.00)
6.6e-05
(0.0315)
0.00424
(1.00)
Amp Peak 11(8p11 23) 0 (0%) 241 0.0352
(1.00)
0.0369
(1.00)
0.897
(1.00)
0.629
(1.00)
0.15
(1.00)
0.0182
(1.00)
0.0229
(1.00)
0.332
(1.00)
Amp Peak 24(18q11 2) 0 (0%) 278 0.0174
(1.00)
0.033
(1.00)
0.157
(1.00)
0.462
(1.00)
1
(1.00)
0.689
(1.00)
0.182
(1.00)
0.259
(1.00)
Del Peak 3(1q44) 0 (0%) 322 0.139
(1.00)
0.175
(1.00)
0.859
(1.00)
0.931
(1.00)
0.0628
(1.00)
0.0133
(1.00)
0.00447
(1.00)
0.157
(1.00)
Del Peak 5(2q22 1) 0 (0%) 274 0.297
(1.00)
0.00648
(1.00)
0.29
(1.00)
0.522
(1.00)
0.0513
(1.00)
0.0292
(1.00)
0.109
(1.00)
0.139
(1.00)
Del Peak 17(7q31 1) 0 (0%) 298 0.000918
(0.402)
0.0261
(1.00)
0.17
(1.00)
0.581
(1.00)
0.363
(1.00)
0.609
(1.00)
0.635
(1.00)
0.0823
(1.00)
Del Peak 30(12q24 33) 0 (0%) 312 0.0427
(1.00)
0.0646
(1.00)
0.082
(1.00)
0.748
(1.00)
0.859
(1.00)
0.775
(1.00)
0.977
(1.00)
0.387
(1.00)
Del Peak 33(14q11 2) 0 (0%) 301 0.000613
(0.274)
0.00616
(1.00)
0.38
(1.00)
0.515
(1.00)
0.463
(1.00)
0.329
(1.00)
0.0268
(1.00)
0.199
(1.00)
Del Peak 35(15q15 1) 0 (0%) 273 0.0014
(0.598)
0.778
(1.00)
0.293
(1.00)
0.161
(1.00)
0.0226
(1.00)
0.0628
(1.00)
0.2
(1.00)
0.26
(1.00)
Del Peak 38(17q25 3) 0 (0%) 310 0.477
(1.00)
0.123
(1.00)
0.474
(1.00)
1
(1.00)
0.037
(1.00)
0.0612
(1.00)
0.0361
(1.00)
0.073
(1.00)
'Amp Peak 1(1q21.2)' versus 'CN_CNMF'

P value = 8.51e-11 (Chi-square test), Q value = 4.6e-08

Table S1.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 1(1Q21.2) CNV 32 5 26 12 4 3
AMP PEAK 1(1Q21.2) WILD-TYPE 50 36 24 80 70 10

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 1(1q21.2)' versus 'METHLYATION_CNMF'

P value = 2.63e-08 (Chi-square test), Q value = 1.4e-05

Table S2.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 1(1Q21.2) CNV 8 13 4 10 31 1 0 4
AMP PEAK 1(1Q21.2) WILD-TYPE 35 34 35 35 27 50 4 15

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 1(1q21.2)' versus 'MRNASEQ_CNMF'

P value = 0.000509 (Fisher's exact test), Q value = 0.23

Table S3.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
AMP PEAK 1(1Q21.2) CNV 41 16 12
AMP PEAK 1(1Q21.2) WILD-TYPE 77 75 78

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 1(1q21.2)' versus 'MIRSEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.077

Table S4.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
AMP PEAK 1(1Q21.2) CNV 15 48 19
AMP PEAK 1(1Q21.2) WILD-TYPE 98 90 81

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 2(2q11.2)' versus 'CN_CNMF'

P value = 2.5e-08 (Chi-square test), Q value = 1.3e-05

Table S5.  Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 2(2Q11.2) CNV 23 10 24 3 11 3
AMP PEAK 2(2Q11.2) WILD-TYPE 59 31 26 89 63 10

Figure S5.  Get High-res Image Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 2(2q11.2)' versus 'METHLYATION_CNMF'

P value = 1.71e-08 (Chi-square test), Q value = 8.9e-06

Table S6.  Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 2(2Q11.2) CNV 19 9 4 1 26 5 1 2
AMP PEAK 2(2Q11.2) WILD-TYPE 24 38 35 44 32 46 3 17

Figure S6.  Get High-res Image Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 3(2q31.2)' versus 'CN_CNMF'

P value = 1.26e-10 (Chi-square test), Q value = 6.7e-08

Table S7.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 3(2Q31.2) CNV 26 9 25 4 6 2
AMP PEAK 3(2Q31.2) WILD-TYPE 56 32 25 88 68 11

Figure S7.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(2q31.2)' versus 'METHLYATION_CNMF'

P value = 9.37e-09 (Chi-square test), Q value = 4.9e-06

Table S8.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 3(2Q31.2) CNV 13 8 5 2 30 5 1 1
AMP PEAK 3(2Q31.2) WILD-TYPE 30 39 34 43 28 46 3 18

Figure S8.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(3q26.33)' versus 'CN_CNMF'

P value = 2.94e-13 (Chi-square test), Q value = 1.6e-10

Table S9.  Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 4(3Q26.33) CNV 70 38 48 42 54 12
AMP PEAK 4(3Q26.33) WILD-TYPE 12 3 2 50 20 1

Figure S9.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q26.33)' versus 'METHLYATION_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.041

Table S10.  Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 4(3Q26.33) CNV 34 38 25 36 54 30 2 9
AMP PEAK 4(3Q26.33) WILD-TYPE 9 9 14 9 4 21 2 10

Figure S10.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(3q26.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000468 (Fisher's exact test), Q value = 0.21

Table S11.  Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
AMP PEAK 4(3Q26.33) CNV 75 50 100
AMP PEAK 4(3Q26.33) WILD-TYPE 20 34 20

Figure S11.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(5p15.33)' versus 'CN_CNMF'

P value = 1.31e-11 (Chi-square test), Q value = 7.1e-09

Table S12.  Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 5(5P15.33) CNV 45 37 25 27 18 5
AMP PEAK 5(5P15.33) WILD-TYPE 37 4 25 65 56 8

Figure S12.  Get High-res Image Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(5p12)' versus 'CN_CNMF'

P value = 3.48e-12 (Chi-square test), Q value = 1.9e-09

Table S13.  Gene #6: 'Amp Peak 6(5p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 6(5P12) CNV 33 35 24 18 19 2
AMP PEAK 6(5P12) WILD-TYPE 49 6 26 74 55 11

Figure S13.  Get High-res Image Gene #6: 'Amp Peak 6(5p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(6p12.1)' versus 'CN_CNMF'

P value = 0.000195 (Chi-square test), Q value = 0.09

Table S14.  Gene #7: 'Amp Peak 7(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 7(6P12.1) CNV 23 14 15 6 10 2
AMP PEAK 7(6P12.1) WILD-TYPE 59 27 35 86 64 11

Figure S14.  Get High-res Image Gene #7: 'Amp Peak 7(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(6q12)' versus 'CN_CNMF'

P value = 4e-04 (Chi-square test), Q value = 0.18

Table S15.  Gene #8: 'Amp Peak 8(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 8(6Q12) CNV 15 16 12 6 11 2
AMP PEAK 8(6Q12) WILD-TYPE 67 25 38 86 63 11

Figure S15.  Get High-res Image Gene #8: 'Amp Peak 8(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7p11.2)' versus 'CN_CNMF'

P value = 1.12e-08 (Chi-square test), Q value = 5.8e-06

Table S16.  Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 9(7P11.2) CNV 42 30 27 18 28 2
AMP PEAK 9(7P11.2) WILD-TYPE 40 11 23 74 46 11

Figure S16.  Get High-res Image Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7p11.2)' versus 'METHLYATION_CNMF'

P value = 6.87e-07 (Chi-square test), Q value = 0.00035

Table S17.  Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 9(7P11.2) CNV 27 24 21 3 31 15 1 9
AMP PEAK 9(7P11.2) WILD-TYPE 16 23 18 42 27 36 3 10

Figure S17.  Get High-res Image Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 10(7q22.1)' versus 'CN_CNMF'

P value = 6.99e-15 (Chi-square test), Q value = 3.8e-12

Table S18.  Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 10(7Q22.1) CNV 48 13 33 9 16 2
AMP PEAK 10(7Q22.1) WILD-TYPE 34 28 17 83 58 11

Figure S18.  Get High-res Image Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 10(7q22.1)' versus 'METHLYATION_CNMF'

P value = 5.46e-08 (Chi-square test), Q value = 2.8e-05

Table S19.  Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 10(7Q22.1) CNV 16 11 15 6 40 11 2 5
AMP PEAK 10(7Q22.1) WILD-TYPE 27 36 24 39 18 40 2 14

Figure S19.  Get High-res Image Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 12(8q11.21)' versus 'CN_CNMF'

P value = 1.8e-06 (Chi-square test), Q value = 0.00089

Table S20.  Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 12(8Q11.21) CNV 53 33 25 34 52 10
AMP PEAK 12(8Q11.21) WILD-TYPE 29 8 25 58 22 3

Figure S20.  Get High-res Image Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'CN_CNMF'

P value = 3.31e-10 (Chi-square test), Q value = 1.8e-07

Table S21.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 13(8Q24.21) CNV 73 37 32 43 57 12
AMP PEAK 13(8Q24.21) WILD-TYPE 9 4 18 49 17 1

Figure S21.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'METHLYATION_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.05

Table S22.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 13(8Q24.21) CNV 30 42 32 20 40 33 4 16
AMP PEAK 13(8Q24.21) WILD-TYPE 13 5 7 25 18 18 0 3

Figure S22.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.048

Table S23.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
AMP PEAK 13(8Q24.21) CNV 69 77 68
AMP PEAK 13(8Q24.21) WILD-TYPE 49 14 22

Figure S23.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.063

Table S24.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
AMP PEAK 13(8Q24.21) CNV 79 65 70
AMP PEAK 13(8Q24.21) WILD-TYPE 16 19 50

Figure S24.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.1

Table S25.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 11 208
AMP PEAK 13(8Q24.21) CNV 111 8 134
AMP PEAK 13(8Q24.21) WILD-TYPE 21 3 74

Figure S25.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(9p23)' versus 'CN_CNMF'

P value = 3.19e-05 (Chi-square test), Q value = 0.015

Table S26.  Gene #14: 'Amp Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 14(9P23) CNV 17 9 11 21 14 11
AMP PEAK 14(9P23) WILD-TYPE 65 32 39 71 60 2

Figure S26.  Get High-res Image Gene #14: 'Amp Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 15(9p13.3)' versus 'CN_CNMF'

P value = 5.06e-05 (Chi-square test), Q value = 0.024

Table S27.  Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 15(9P13.3) CNV 18 8 16 19 23 11
AMP PEAK 15(9P13.3) WILD-TYPE 64 33 34 73 51 2

Figure S27.  Get High-res Image Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(11p13)' versus 'CN_CNMF'

P value = 5.66e-05 (Chi-square test), Q value = 0.027

Table S28.  Gene #16: 'Amp Peak 16(11p13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 16(11P13) CNV 17 7 6 9 22 8
AMP PEAK 16(11P13) WILD-TYPE 65 34 44 83 52 5

Figure S28.  Get High-res Image Gene #16: 'Amp Peak 16(11p13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 17(11q13.3)' versus 'CN_CNMF'

P value = 1.73e-27 (Chi-square test), Q value = 9.6e-25

Table S29.  Gene #17: 'Amp Peak 17(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 17(11Q13.3) CNV 81 18 19 12 30 4
AMP PEAK 17(11Q13.3) WILD-TYPE 1 23 31 80 44 9

Figure S29.  Get High-res Image Gene #17: 'Amp Peak 17(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 18(12p13.33)' versus 'CN_CNMF'

P value = 2.85e-10 (Chi-square test), Q value = 1.5e-07

Table S30.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 18(12P13.33) CNV 29 26 30 14 14 5
AMP PEAK 18(12P13.33) WILD-TYPE 53 15 20 78 60 8

Figure S30.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 18(12p13.33)' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0063

Table S31.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 18(12P13.33) CNV 20 20 5 14 34 12 0 3
AMP PEAK 18(12P13.33) WILD-TYPE 23 27 34 31 24 39 4 16

Figure S31.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 19(12q15)' versus 'CN_CNMF'

P value = 0.000508 (Chi-square test), Q value = 0.23

Table S32.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 19(12Q15) CNV 22 17 12 11 9 1
AMP PEAK 19(12Q15) WILD-TYPE 60 24 38 81 65 12

Figure S32.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(13q22.1)' versus 'CN_CNMF'

P value = 0.000262 (Chi-square test), Q value = 0.12

Table S33.  Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 20(13Q22.1) CNV 23 11 9 6 23 0
AMP PEAK 20(13Q22.1) WILD-TYPE 59 30 41 86 51 13

Figure S33.  Get High-res Image Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(13q22.1)' versus 'METHLYATION_CNMF'

P value = 8.43e-05 (Chi-square test), Q value = 0.04

Table S34.  Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 20(13Q22.1) CNV 7 23 7 10 12 3 0 5
AMP PEAK 20(13Q22.1) WILD-TYPE 36 24 32 35 46 48 4 14

Figure S34.  Get High-res Image Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 21(15q26.3)' versus 'CN_CNMF'

P value = 0.000327 (Chi-square test), Q value = 0.15

Table S35.  Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 21(15Q26.3) CNV 26 13 15 6 13 2
AMP PEAK 21(15Q26.3) WILD-TYPE 56 28 35 86 61 11

Figure S35.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(17q12)' versus 'CN_CNMF'

P value = 8.2e-08 (Chi-square test), Q value = 4.2e-05

Table S36.  Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 22(17Q12) CNV 25 5 19 4 6 4
AMP PEAK 22(17Q12) WILD-TYPE 57 36 31 88 68 9

Figure S36.  Get High-res Image Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(17q12)' versus 'METHLYATION_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.052

Table S37.  Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 22(17Q12) CNV 10 8 2 4 22 4 0 2
AMP PEAK 22(17Q12) WILD-TYPE 33 39 37 41 36 47 4 17

Figure S37.  Get High-res Image Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 23(18p11.31)' versus 'CN_CNMF'

P value = 7.58e-07 (Chi-square test), Q value = 0.00038

Table S38.  Gene #23: 'Amp Peak 23(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 23(18P11.31) CNV 30 21 26 14 13 4
AMP PEAK 23(18P11.31) WILD-TYPE 52 20 24 78 61 9

Figure S38.  Get High-res Image Gene #23: 'Amp Peak 23(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 25(20q11.22)' versus 'CN_CNMF'

P value = 4.86e-06 (Chi-square test), Q value = 0.0024

Table S39.  Gene #25: 'Amp Peak 25(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
AMP PEAK 25(20Q11.22) CNV 34 33 23 27 30 8
AMP PEAK 25(20Q11.22) WILD-TYPE 48 8 27 65 44 5

Figure S39.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 1.44e-11 (Chi-square test), Q value = 7.7e-09

Table S40.  Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 1(1P36.13) CNV 17 4 29 7 10 2
DEL PEAK 1(1P36.13) WILD-TYPE 65 37 21 85 64 11

Figure S40.  Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 5.38e-15 (Chi-square test), Q value = 2.9e-12

Table S41.  Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 1(1P36.13) CNV 6 4 8 5 36 1 2 2
DEL PEAK 1(1P36.13) WILD-TYPE 37 43 31 40 22 50 2 17

Figure S41.  Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.015

Table S42.  Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 1(1P36.13) CNV 39 17 7
DEL PEAK 1(1P36.13) WILD-TYPE 79 74 83

Figure S42.  Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.063

Table S43.  Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
DEL PEAK 1(1P36.13) CNV 16 42 10
DEL PEAK 1(1P36.13) WILD-TYPE 97 96 90

Figure S43.  Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 2(1p13.2)' versus 'CN_CNMF'

P value = 3.1e-10 (Chi-square test), Q value = 1.6e-07

Table S44.  Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 2(1P13.2) CNV 20 14 29 5 13 4
DEL PEAK 2(1P13.2) WILD-TYPE 62 27 21 87 61 9

Figure S44.  Get High-res Image Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(1p13.2)' versus 'METHLYATION_CNMF'

P value = 8.62e-10 (Chi-square test), Q value = 4.6e-07

Table S45.  Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 2(1P13.2) CNV 10 9 6 4 35 5 2 4
DEL PEAK 2(1P13.2) WILD-TYPE 33 38 33 41 23 46 2 15

Figure S45.  Get High-res Image Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 2(1p13.2)' versus 'MIRSEQ_CNMF'

P value = 4.41e-05 (Fisher's exact test), Q value = 0.021

Table S46.  Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
DEL PEAK 2(1P13.2) CNV 16 51 18
DEL PEAK 2(1P13.2) WILD-TYPE 97 87 82

Figure S46.  Get High-res Image Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 4(2q21.2)' versus 'MIRSEQ_CNMF'

P value = 0.000377 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #29: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
DEL PEAK 4(2Q21.2) CNV 26 15 5
DEL PEAK 4(2Q21.2) WILD-TYPE 87 123 95

Figure S47.  Get High-res Image Gene #29: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 6(2q36.2)' versus 'CN_CNMF'

P value = 5.4e-08 (Chi-square test), Q value = 2.8e-05

Table S48.  Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 6(2Q36.2) CNV 24 9 32 12 22 5
DEL PEAK 6(2Q36.2) WILD-TYPE 58 32 18 80 52 8

Figure S48.  Get High-res Image Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(2q36.2)' versus 'METHLYATION_CNMF'

P value = 5.69e-06 (Chi-square test), Q value = 0.0028

Table S49.  Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 6(2Q36.2) CNV 14 11 16 15 29 2 3 3
DEL PEAK 6(2Q36.2) WILD-TYPE 29 36 23 30 29 49 1 16

Figure S49.  Get High-res Image Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(3p25.3)' versus 'CN_CNMF'

P value = 7.67e-25 (Chi-square test), Q value = 4.3e-22

Table S50.  Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 7(3P25.3) CNV 73 36 44 23 61 10
DEL PEAK 7(3P25.3) WILD-TYPE 9 5 6 69 13 3

Figure S50.  Get High-res Image Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(3p25.3)' versus 'METHLYATION_CNMF'

P value = 2.92e-10 (Chi-square test), Q value = 1.6e-07

Table S51.  Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 7(3P25.3) CNV 36 42 27 14 50 29 4 14
DEL PEAK 7(3P25.3) WILD-TYPE 7 5 12 31 8 22 0 5

Figure S51.  Get High-res Image Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(3p14.2)' versus 'CN_CNMF'

P value = 2.49e-29 (Chi-square test), Q value = 1.4e-26

Table S52.  Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 8(3P14.2) CNV 77 38 47 26 64 11
DEL PEAK 8(3P14.2) WILD-TYPE 5 3 3 66 10 2

Figure S52.  Get High-res Image Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(3p14.2)' versus 'METHLYATION_CNMF'

P value = 8.81e-08 (Chi-square test), Q value = 4.5e-05

Table S53.  Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 8(3P14.2) CNV 41 41 27 22 52 30 4 14
DEL PEAK 8(3P14.2) WILD-TYPE 2 6 12 23 6 21 0 5

Figure S53.  Get High-res Image Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(3p14.2)' versus 'CN_CNMF'

P value = 2.49e-29 (Chi-square test), Q value = 1.4e-26

Table S54.  Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 9(3P14.2) CNV 77 38 47 26 64 11
DEL PEAK 9(3P14.2) WILD-TYPE 5 3 3 66 10 2

Figure S54.  Get High-res Image Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(3p14.2)' versus 'METHLYATION_CNMF'

P value = 5.71e-07 (Chi-square test), Q value = 0.00029

Table S55.  Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 9(3P14.2) CNV 41 41 27 23 51 30 4 14
DEL PEAK 9(3P14.2) WILD-TYPE 2 6 12 22 7 21 0 5

Figure S55.  Get High-res Image Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 10(3p12.2)' versus 'CN_CNMF'

P value = 6.77e-29 (Chi-square test), Q value = 3.8e-26

Table S56.  Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 10(3P12.2) CNV 75 36 47 21 59 11
DEL PEAK 10(3P12.2) WILD-TYPE 7 5 3 71 15 2

Figure S56.  Get High-res Image Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(3p12.2)' versus 'METHLYATION_CNMF'

P value = 4.04e-09 (Chi-square test), Q value = 2.1e-06

Table S57.  Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 10(3P12.2) CNV 38 38 27 18 53 26 4 13
DEL PEAK 10(3P12.2) WILD-TYPE 5 9 12 27 5 25 0 6

Figure S57.  Get High-res Image Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(4p15.2)' versus 'CN_CNMF'

P value = 3.05e-12 (Chi-square test), Q value = 1.7e-09

Table S58.  Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 11(4P15.2) CNV 48 13 39 15 31 4
DEL PEAK 11(4P15.2) WILD-TYPE 34 28 11 77 43 9

Figure S58.  Get High-res Image Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(4p15.2)' versus 'METHLYATION_CNMF'

P value = 5.98e-07 (Chi-square test), Q value = 3e-04

Table S59.  Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 11(4P15.2) CNV 20 15 17 13 44 12 3 7
DEL PEAK 11(4P15.2) WILD-TYPE 23 32 22 32 14 39 1 12

Figure S59.  Get High-res Image Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(4q22.1)' versus 'CN_CNMF'

P value = 8.67e-09 (Chi-square test), Q value = 4.5e-06

Table S60.  Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 12(4Q22.1) CNV 30 19 32 10 22 4
DEL PEAK 12(4Q22.1) WILD-TYPE 52 22 18 82 52 9

Figure S60.  Get High-res Image Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(4q22.1)' versus 'METHLYATION_CNMF'

P value = 6.5e-07 (Chi-square test), Q value = 0.00033

Table S61.  Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 12(4Q22.1) CNV 17 16 11 7 36 8 1 2
DEL PEAK 12(4Q22.1) WILD-TYPE 26 31 28 38 22 43 3 17

Figure S61.  Get High-res Image Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(4q35.2)' versus 'CN_CNMF'

P value = 7.51e-09 (Chi-square test), Q value = 3.9e-06

Table S62.  Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 13(4Q35.2) CNV 29 27 31 15 37 6
DEL PEAK 13(4Q35.2) WILD-TYPE 53 14 19 77 37 7

Figure S62.  Get High-res Image Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(4q35.2)' versus 'METHLYATION_CNMF'

P value = 2.97e-05 (Chi-square test), Q value = 0.014

Table S63.  Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 13(4Q35.2) CNV 17 25 19 9 36 12 0 6
DEL PEAK 13(4Q35.2) WILD-TYPE 26 22 20 36 22 39 4 13

Figure S63.  Get High-res Image Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 14(5q11.2)' versus 'CN_CNMF'

P value = 5.27e-17 (Chi-square test), Q value = 2.9e-14

Table S64.  Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 14(5Q11.2) CNV 40 30 37 8 23 4
DEL PEAK 14(5Q11.2) WILD-TYPE 42 11 13 84 51 9

Figure S64.  Get High-res Image Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.35e-12 (Chi-square test), Q value = 7.3e-10

Table S65.  Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 14(5Q11.2) CNV 30 27 8 6 41 11 1 6
DEL PEAK 14(5Q11.2) WILD-TYPE 13 20 31 39 17 40 3 13

Figure S65.  Get High-res Image Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 15(5q35.3)' versus 'CN_CNMF'

P value = 7.2e-18 (Chi-square test), Q value = 4e-15

Table S66.  Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 15(5Q35.3) CNV 32 29 40 10 19 4
DEL PEAK 15(5Q35.3) WILD-TYPE 50 12 10 82 55 9

Figure S66.  Get High-res Image Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(5q35.3)' versus 'METHLYATION_CNMF'

P value = 4.25e-14 (Chi-square test), Q value = 2.3e-11

Table S67.  Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 15(5Q35.3) CNV 33 24 5 8 37 8 0 6
DEL PEAK 15(5Q35.3) WILD-TYPE 10 23 34 37 21 43 4 13

Figure S67.  Get High-res Image Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 15(5q35.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000477 (Fisher's exact test), Q value = 0.22

Table S68.  Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 15(5Q35.3) CNV 39 20 61
DEL PEAK 15(5Q35.3) WILD-TYPE 56 64 59

Figure S68.  Get High-res Image Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(6p25.3)' versus 'METHLYATION_CNMF'

P value = 0.00033 (Chi-square test), Q value = 0.15

Table S69.  Gene #41: 'Del Peak 16(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 16(6P25.3) CNV 7 9 5 6 26 6 1 3
DEL PEAK 16(6P25.3) WILD-TYPE 36 38 34 39 32 45 3 16

Figure S69.  Get High-res Image Gene #41: 'Del Peak 16(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 18(7q36.1)' versus 'CN_CNMF'

P value = 0.000182 (Chi-square test), Q value = 0.084

Table S70.  Gene #43: 'Del Peak 18(7q36.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 18(7Q36.1) CNV 33 13 6 12 17 5
DEL PEAK 18(7Q36.1) WILD-TYPE 49 28 44 80 57 8

Figure S70.  Get High-res Image Gene #43: 'Del Peak 18(7q36.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(8p23.2)' versus 'CN_CNMF'

P value = 2.17e-15 (Chi-square test), Q value = 1.2e-12

Table S71.  Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 19(8P23.2) CNV 67 28 25 20 54 7
DEL PEAK 19(8P23.2) WILD-TYPE 15 13 25 72 20 6

Figure S71.  Get High-res Image Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(8p23.2)' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Chi-square test), Q value = 0.019

Table S72.  Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 19(8P23.2) CNV 21 34 30 11 36 28 2 11
DEL PEAK 19(8P23.2) WILD-TYPE 22 13 9 34 22 23 2 8

Figure S72.  Get High-res Image Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 20(9p23)' versus 'CN_CNMF'

P value = 1.16e-16 (Chi-square test), Q value = 6.4e-14

Table S73.  Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 20(9P23) CNV 50 27 30 9 45 0
DEL PEAK 20(9P23) WILD-TYPE 32 14 20 83 29 13

Figure S73.  Get High-res Image Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(9p23)' versus 'METHLYATION_CNMF'

P value = 5.42e-09 (Chi-square test), Q value = 2.8e-06

Table S74.  Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 20(9P23) CNV 30 25 20 5 38 13 3 8
DEL PEAK 20(9P23) WILD-TYPE 13 22 19 40 20 38 1 11

Figure S74.  Get High-res Image Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(9p21.3)' versus 'CN_CNMF'

P value = 2.71e-13 (Chi-square test), Q value = 1.5e-10

Table S75.  Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 21(9P21.3) CNV 65 25 36 24 51 3
DEL PEAK 21(9P21.3) WILD-TYPE 17 16 14 68 23 10

Figure S75.  Get High-res Image Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.83e-09 (Chi-square test), Q value = 1.5e-06

Table S76.  Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 21(9P21.3) CNV 35 30 26 7 40 23 3 14
DEL PEAK 21(9P21.3) WILD-TYPE 8 17 13 38 18 28 1 5

Figure S76.  Get High-res Image Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 22(9q21.11)' versus 'CN_CNMF'

P value = 2.86e-08 (Chi-square test), Q value = 1.5e-05

Table S77.  Gene #47: 'Del Peak 22(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 22(9Q21.11) CNV 30 15 7 4 8 1
DEL PEAK 22(9Q21.11) WILD-TYPE 52 26 43 88 66 12

Figure S77.  Get High-res Image Gene #47: 'Del Peak 22(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(9q34.3)' versus 'CN_CNMF'

P value = 0.000333 (Chi-square test), Q value = 0.15

Table S78.  Gene #48: 'Del Peak 23(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 23(9Q34.3) CNV 21 12 7 4 12 0
DEL PEAK 23(9Q34.3) WILD-TYPE 61 29 43 88 62 13

Figure S78.  Get High-res Image Gene #48: 'Del Peak 23(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(10p15.3)' versus 'CN_CNMF'

P value = 5.46e-06 (Chi-square test), Q value = 0.0027

Table S79.  Gene #49: 'Del Peak 24(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 24(10P15.3) CNV 34 16 20 8 30 6
DEL PEAK 24(10P15.3) WILD-TYPE 48 25 30 84 44 7

Figure S79.  Get High-res Image Gene #49: 'Del Peak 24(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(10p11.21)' versus 'CN_CNMF'

P value = 9.79e-06 (Chi-square test), Q value = 0.0048

Table S80.  Gene #50: 'Del Peak 25(10p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 25(10P11.21) CNV 32 17 19 7 27 5
DEL PEAK 25(10P11.21) WILD-TYPE 50 24 31 85 47 8

Figure S80.  Get High-res Image Gene #50: 'Del Peak 25(10p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 26(10q23.31)' versus 'CN_CNMF'

P value = 1.55e-06 (Chi-square test), Q value = 0.00077

Table S81.  Gene #51: 'Del Peak 26(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 26(10Q23.31) CNV 22 10 28 11 16 2
DEL PEAK 26(10Q23.31) WILD-TYPE 60 31 22 81 58 11

Figure S81.  Get High-res Image Gene #51: 'Del Peak 26(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(11p15.4)' versus 'CN_CNMF'

P value = 1.6e-08 (Chi-square test), Q value = 8.3e-06

Table S82.  Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 27(11P15.4) CNV 43 15 24 16 10 2
DEL PEAK 27(11P15.4) WILD-TYPE 39 26 26 76 64 11

Figure S82.  Get High-res Image Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(11p15.4)' versus 'METHLYATION_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.23

Table S83.  Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 27(11P15.4) CNV 17 14 9 13 32 8 1 3
DEL PEAK 27(11P15.4) WILD-TYPE 26 33 30 32 26 43 3 16

Figure S83.  Get High-res Image Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 27(11p15.4)' versus 'MIRSEQ_CNMF'

P value = 0.000501 (Fisher's exact test), Q value = 0.23

Table S84.  Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
DEL PEAK 27(11P15.4) CNV 27 60 23
DEL PEAK 27(11P15.4) WILD-TYPE 86 78 77

Figure S84.  Get High-res Image Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 28(11q14.1)' versus 'CN_CNMF'

P value = 4.77e-25 (Chi-square test), Q value = 2.7e-22

Table S85.  Gene #53: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 28(11Q14.1) CNV 65 6 11 21 3 6
DEL PEAK 28(11Q14.1) WILD-TYPE 17 35 39 71 71 7

Figure S85.  Get High-res Image Gene #53: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(11q23.1)' versus 'CN_CNMF'

P value = 7.7e-18 (Chi-square test), Q value = 4.3e-15

Table S86.  Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 29(11Q23.1) CNV 74 13 23 36 15 8
DEL PEAK 29(11Q23.1) WILD-TYPE 8 28 27 56 59 5

Figure S86.  Get High-res Image Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(11q23.1)' versus 'METHLYATION_CNMF'

P value = 8.45e-07 (Chi-square test), Q value = 0.00042

Table S87.  Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 29(11Q23.1) CNV 18 21 16 40 31 16 1 6
DEL PEAK 29(11Q23.1) WILD-TYPE 25 26 23 5 27 35 3 13

Figure S87.  Get High-res Image Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 29(11q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S88.  Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 29(11Q23.1) CNV 37 33 76
DEL PEAK 29(11Q23.1) WILD-TYPE 58 51 44

Figure S88.  Get High-res Image Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(13q12.11)' versus 'CN_CNMF'

P value = 2.63e-11 (Chi-square test), Q value = 1.4e-08

Table S89.  Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 31(13Q12.11) CNV 44 26 39 17 27 6
DEL PEAK 31(13Q12.11) WILD-TYPE 38 15 11 75 47 7

Figure S89.  Get High-res Image Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(13q12.11)' versus 'METHLYATION_CNMF'

P value = 7.28e-07 (Chi-square test), Q value = 0.00037

Table S90.  Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 31(13Q12.11) CNV 31 22 15 13 39 12 1 6
DEL PEAK 31(13Q12.11) WILD-TYPE 12 25 24 32 19 39 3 13

Figure S90.  Get High-res Image Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(13q14.2)' versus 'CN_CNMF'

P value = 2.86e-06 (Chi-square test), Q value = 0.0014

Table S91.  Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 32(13Q14.2) CNV 38 24 35 27 21 4
DEL PEAK 32(13Q14.2) WILD-TYPE 44 17 15 65 53 9

Figure S91.  Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 32(13q14.2)' versus 'METHLYATION_CNMF'

P value = 5.88e-07 (Chi-square test), Q value = 3e-04

Table S92.  Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 32(13Q14.2) CNV 32 17 13 23 31 10 0 4
DEL PEAK 32(13Q14.2) WILD-TYPE 11 30 26 22 27 41 4 15

Figure S92.  Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Fisher's exact test), Q value = 0.027

Table S93.  Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 32(13Q14.2) CNV 66 39 23
DEL PEAK 32(13Q14.2) WILD-TYPE 52 52 67

Figure S93.  Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.031

Table S94.  Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 32(13Q14.2) CNV 38 22 68
DEL PEAK 32(13Q14.2) WILD-TYPE 57 62 52

Figure S94.  Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(14q32.32)' versus 'METHLYATION_CNMF'

P value = 1.42e-07 (Chi-square test), Q value = 7.2e-05

Table S95.  Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 34(14Q32.32) CNV 5 3 4 20 13 1 0 1
DEL PEAK 34(14Q32.32) WILD-TYPE 38 44 35 25 45 50 4 18

Figure S95.  Get High-res Image Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 34(14q32.32)' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.11

Table S96.  Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 34(14Q32.32) CNV 30 11 5
DEL PEAK 34(14Q32.32) WILD-TYPE 88 80 85

Figure S96.  Get High-res Image Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 34(14q32.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.046

Table S97.  Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 34(14Q32.32) CNV 11 4 31
DEL PEAK 34(14Q32.32) WILD-TYPE 84 80 89

Figure S97.  Get High-res Image Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(16q12.1)' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Chi-square test), Q value = 5.7e-05

Table S98.  Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 36(16Q12.1) CNV 8 1 5 21 13 2 1 1
DEL PEAK 36(16Q12.1) WILD-TYPE 35 46 34 24 45 49 3 18

Figure S98.  Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 36(16q12.1)' versus 'MRNASEQ_CNMF'

P value = 7.1e-08 (Fisher's exact test), Q value = 3.6e-05

Table S99.  Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 36(16Q12.1) CNV 38 9 4
DEL PEAK 36(16Q12.1) WILD-TYPE 80 82 86

Figure S99.  Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 36(16q12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 2e-04

Table S100.  Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 36(16Q12.1) CNV 7 6 38
DEL PEAK 36(16Q12.1) WILD-TYPE 88 78 82

Figure S100.  Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(16q12.1)' versus 'MIRSEQ_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.049

Table S101.  Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
DEL PEAK 36(16Q12.1) CNV 15 39 8
DEL PEAK 36(16Q12.1) WILD-TYPE 98 99 92

Figure S101.  Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 37(16q23.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.88e-05 (Fisher's exact test), Q value = 0.042

Table S102.  Gene #62: 'Del Peak 37(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 37(16Q23.3) CNV 11 9 38
DEL PEAK 37(16Q23.3) WILD-TYPE 84 75 82

Figure S102.  Get High-res Image Gene #62: 'Del Peak 37(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'CN_CNMF'

P value = 7.27e-17 (Chi-square test), Q value = 4e-14

Table S103.  Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 39(18Q21.2) CNV 51 28 27 11 56 9
DEL PEAK 39(18Q21.2) WILD-TYPE 31 13 23 81 18 4

Figure S103.  Get High-res Image Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 39(18q21.2)' versus 'METHLYATION_CNMF'

P value = 1.69e-09 (Chi-square test), Q value = 8.9e-07

Table S104.  Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 39(18Q21.2) CNV 30 35 22 4 34 24 4 8
DEL PEAK 39(18Q21.2) WILD-TYPE 13 12 17 41 24 27 0 11

Figure S104.  Get High-res Image Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 40(18q23)' versus 'CN_CNMF'

P value = 8.57e-20 (Chi-square test), Q value = 4.7e-17

Table S105.  Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 40(18Q23) CNV 56 31 31 12 59 9
DEL PEAK 40(18Q23) WILD-TYPE 26 10 19 80 15 4

Figure S105.  Get High-res Image Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 40(18q23)' versus 'METHLYATION_CNMF'

P value = 1.38e-11 (Chi-square test), Q value = 7.4e-09

Table S106.  Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 40(18Q23) CNV 31 40 23 5 39 23 3 8
DEL PEAK 40(18Q23) WILD-TYPE 12 7 16 40 19 28 1 11

Figure S106.  Get High-res Image Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 41(19p13.3)' versus 'CN_CNMF'

P value = 3.57e-06 (Chi-square test), Q value = 0.0018

Table S107.  Gene #66: 'Del Peak 41(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 41(19P13.3) CNV 38 16 17 10 28 8
DEL PEAK 41(19P13.3) WILD-TYPE 44 25 33 82 46 5

Figure S107.  Get High-res Image Gene #66: 'Del Peak 41(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 42(19q13.43)' versus 'CN_CNMF'

P value = 1.03e-05 (Chi-square test), Q value = 0.0051

Table S108.  Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 42(19Q13.43) CNV 18 7 20 3 16 4
DEL PEAK 42(19Q13.43) WILD-TYPE 64 34 30 89 58 9

Figure S108.  Get High-res Image Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 42(19q13.43)' versus 'METHLYATION_CNMF'

P value = 6.93e-05 (Chi-square test), Q value = 0.033

Table S109.  Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 42(19Q13.43) CNV 7 14 9 3 22 3 0 1
DEL PEAK 42(19Q13.43) WILD-TYPE 36 33 30 42 36 48 4 18

Figure S109.  Get High-res Image Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 43(Xp21.3)' versus 'CN_CNMF'

P value = 4.3e-05 (Chi-square test), Q value = 0.021

Table S110.  Gene #68: 'Del Peak 43(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 43(XP21.3) CNV 38 18 23 14 19 4
DEL PEAK 43(XP21.3) WILD-TYPE 44 23 27 78 55 9

Figure S110.  Get High-res Image Gene #68: 'Del Peak 43(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(Xp11.3)' versus 'CN_CNMF'

P value = 4.65e-06 (Chi-square test), Q value = 0.0023

Table S111.  Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 82 41 50 92 74 13
DEL PEAK 44(XP11.3) CNV 38 17 24 12 18 5
DEL PEAK 44(XP11.3) WILD-TYPE 44 24 26 80 56 8

Figure S111.  Get High-res Image Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 5.8e-05 (Chi-square test), Q value = 0.028

Table S112.  Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 44(XP11.3) CNV 15 18 13 7 34 8 2 6
DEL PEAK 44(XP11.3) WILD-TYPE 28 29 26 38 24 43 2 13

Figure S112.  Get High-res Image Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 45(Xq21.33)' versus 'MIRSEQ_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.031

Table S113.  Gene #70: 'Del Peak 45(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 138 100
DEL PEAK 45(XQ21.33) CNV 11 37 8
DEL PEAK 45(XQ21.33) WILD-TYPE 102 101 92

Figure S113.  Get High-res Image Gene #70: 'Del Peak 45(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data
Input
  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Molecular subtype file = HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 352

  • Number of copy number variation regions = 70

  • Number of molecular subtypes = 8

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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.

References
[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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)