Correlation between copy number variation genes and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C16D5R76
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16D5R76
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 48 peak regions and 12 molecular subtypes across 269 patients, 116 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1q22) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 6(7p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 7(7q32.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 8(8q24.12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 9(10p15.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 11(12p13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 12(12p12.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 13(12q14.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 14(13q33.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 15(17q25.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 16(18q23) cnvs correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 17(19p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 18(19q13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 19(Xp22.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 20(Xp11.22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 1(1p36.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 2(1p32.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 4(2p25.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 6(2q37.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 7(3p21.1) cnvs correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • Del Peak 8(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 9(5q35.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 11(6q24.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 13(10q26.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 14(11p15.5) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 15(11q25) cnvs correlated to 'CN_CNMF'.

  • Del Peak 16(12q12) cnvs correlated to 'CN_CNMF'.

  • Del Peak 17(13q14.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 18(13q21.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 19(13q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 20(13q34) cnvs correlated to 'CN_CNMF'.

  • Del Peak 21(14q24.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 25(19q13.42) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 26(22q13.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 27(Xp22.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 28(Xq21.1) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 48 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 116 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test
Del Peak 1(1p36 31) 0 (0%) 173 0.000549
(0.239) 		5.86e-05
(0.0274) 		8.49e-14
(4.53e-11) 		4.92e-43
(2.7e-40) 		0.000732
(0.313) 		0.54
(1.00) 		7.9e-06
(0.00382) 		3.23e-23
(1.75e-20) 		8.86e-06
(0.00426) 		0.000303
(0.134) 		1.15e-08
(5.91e-06) 		0.000104
(0.0479)
Del Peak 2(1p32 3) 0 (0%) 181 0.0286
(1.00) 		0.000173
(0.0782) 		2.21e-17
(1.19e-14) 		2.3e-48
(1.27e-45) 		0.000477
(0.209) 		0.235
(1.00) 		2.73e-09
(1.42e-06) 		3.06e-27
(1.67e-24) 		5.78e-08
(2.93e-05) 		3.2e-05
(0.0151) 		1.54e-09
(8.09e-07) 		1.09e-06
(0.00054)
Del Peak 13(10q26 3) 0 (0%) 188 0.179
(1.00) 		0.022
(1.00) 		6.21e-19
(3.35e-16) 		1.3e-20
(7.03e-18) 		1.56e-07
(7.9e-05) 		0.000214
(0.0967) 		2.13e-08
(1.08e-05) 		2.92e-09
(1.52e-06) 		0.00461
(1.00) 		5.98e-06
(0.00292) 		4.5e-09
(2.32e-06) 		1.26e-11
(6.69e-09)
Del Peak 25(19q13 42) 0 (0%) 133 0.0353
(1.00) 		0.127
(1.00) 		1.55e-15
(8.27e-13) 		9.49e-28
(5.17e-25) 		0.00212
(0.877) 		0.6
(1.00) 		7.99e-07
(0.000399) 		9.06e-15
(4.84e-12) 		8.24e-05
(0.0382) 		0.000298
(0.132) 		2.28e-05
(0.0108) 		5.19e-08
(2.64e-05)
Amp Peak 6(7p11 2) 0 (0%) 196 0.864
(1.00) 		0.726
(1.00) 		2.06e-29
(1.12e-26) 		4.41e-16
(2.36e-13) 		0.000113
(0.052) 		0.00626
(1.00) 		1.96e-05
(0.00933) 		0.000756
(0.322) 		0.00133
(0.558) 		6.43e-06
(0.00312) 		4.5e-07
(0.000226) 		3.1e-12
(1.65e-09)
Amp Peak 18(19q13 2) 0 (0%) 250 0.369
(1.00) 		0.194
(1.00) 		7.29e-07
(0.000365) 		1.01e-05
(0.00485) 		0.0381
(1.00) 		0.34
(1.00) 		0.000122
(0.0558) 		0.00316
(1.00) 		0.00251
(1.00) 		0.00397
(1.00) 		5.25e-06
(0.00258) 		5.89e-06
(0.00288)
Del Peak 12(9p21 3) 0 (0%) 170 0.333
(1.00) 		0.0153
(1.00) 		3.04e-11
(1.61e-08) 		2.66e-08
(1.36e-05) 		8.67e-06
(0.00418) 		9.22e-05
(0.0425) 		0.0237
(1.00) 		0.00935
(1.00) 		0.177
(1.00) 		0.206
(1.00) 		0.0574
(1.00) 		0.000199
(0.0899)
Del Peak 26(22q13 31) 0 (0%) 229 0.25
(1.00) 		0.0588
(1.00) 		1.41e-09
(7.41e-07) 		2.85e-06
(0.00141) 		6.75e-05
(0.0315) 		0.0187
(1.00) 		6.92e-06
(0.00336) 		3.77e-05
(0.0178) 		0.011
(1.00) 		0.0269
(1.00) 		0.0161
(1.00) 		0.00779
(1.00)
Amp Peak 2(1q32 1) 0 (0%) 242 2.14e-07
(0.000108) 		2.28e-06
(0.00113) 		0.104
(1.00) 		0.846
(1.00) 		0.00996
(1.00) 		0.249
(1.00) 		0.618
(1.00) 		8.96e-05
(0.0415) 		0.0219
(1.00) 		2.79e-05
(0.0132)
Amp Peak 7(7q32 3) 0 (0%) 169 0.764
(1.00) 		0.755
(1.00) 		5.19e-23
(2.81e-20) 		2.11e-08
(1.08e-05) 		0.00814
(1.00) 		0.0242
(1.00) 		0.000267
(0.119) 		0.0012
(0.507) 		0.068
(1.00) 		0.00428
(1.00) 		0.00282
(1.00) 		1.02e-05
(0.00489)
Amp Peak 8(8q24 12) 0 (0%) 214 0.37
(1.00) 		0.164
(1.00) 		2.32e-12
(1.23e-09) 		5.52e-09
(2.85e-06) 		0.0287
(1.00) 		0.884
(1.00) 		0.225
(1.00) 		0.00715
(1.00) 		0.221
(1.00) 		0.18
(1.00) 		0.000257
(0.115) 		0.00178
(0.736)
Amp Peak 9(10p15 3) 0 (0%) 228 0.526
(1.00) 		0.207
(1.00) 		1e-09
(5.27e-07) 		2.97e-09
(1.54e-06) 		0.0343
(1.00) 		0.244
(1.00) 		0.352
(1.00) 		0.000605
(0.262) 		0.0993
(1.00) 		0.225
(1.00) 		0.000284
(0.126) 		0.0465
(1.00)
Amp Peak 12(12p12 1) 0 (0%) 241 1
(1.00) 		0.0138
(1.00) 		4.75e-06
(0.00234) 		0.0256
(1.00) 		0.169
(1.00) 		0.688
(1.00) 		0.000601
(0.261) 		0.000392
(0.173) 		0.00479
(1.00) 		0.023
(1.00) 		6.84e-05
(0.0318) 		0.161
(1.00)
Amp Peak 20(Xp11 22) 0 (0%) 231 0.651
(1.00) 		0.892
(1.00) 		1.84e-09
(9.65e-07) 		1.54e-06
(0.000762) 		0.0268
(1.00) 		0.143
(1.00) 		0.0835
(1.00) 		0.000355
(0.156) 		0.132
(1.00) 		0.0575
(1.00) 		0.292
(1.00) 		0.0226
(1.00)
Del Peak 6(2q37 3) 0 (0%) 229 0.18
(1.00) 		0.116
(1.00) 		6.07e-06
(0.00296) 		1.8e-07
(9.09e-05) 		0.0119
(1.00) 		0.0217
(1.00) 		0.227
(1.00) 		0.00405
(1.00) 		0.589
(1.00) 		0.155
(1.00) 		0.231
(1.00) 		0.000114
(0.0522)
Del Peak 14(11p15 5) 0 (0%) 212 0.642
(1.00) 		0.000741
(0.316) 		1.88e-09
(9.8e-07) 		2.11e-10
(1.11e-07) 		0.146
(1.00) 		0.849
(1.00) 		0.00267
(1.00) 		2.62e-05
(0.0124) 		0.229
(1.00) 		0.364
(1.00) 		0.147
(1.00) 		0.378
(1.00)
Amp Peak 11(12p13 32) 0 (0%) 226 0.864
(1.00) 		0.0486
(1.00) 		1.69e-10
(8.94e-08) 		5.16e-05
(0.0243) 		0.116
(1.00) 		0.218
(1.00) 		0.0218
(1.00) 		0.00214
(0.88) 		0.0142
(1.00) 		0.0371
(1.00) 		0.000803
(0.341) 		0.0776
(1.00)
Amp Peak 16(18q23) 0 (0%) 257 0.00133
(0.558) 		0.0268
(1.00) 		0.000132
(0.0601) 		1
(1.00) 		0.00594
(1.00) 		0.00296
(1.00) 		0.0543
(1.00) 		0.322
(1.00) 		0.00027
(0.12) 		0.083
(1.00)
Amp Peak 17(19p13 3) 0 (0%) 209 0.186
(1.00) 		0.41
(1.00) 		9.09e-05
(0.042) 		1.07e-08
(5.5e-06) 		0.867
(1.00) 		0.684
(1.00) 		0.654
(1.00) 		0.0121
(1.00) 		0.449
(1.00) 		0.238
(1.00) 		0.0396
(1.00) 		0.0125
(1.00)
Del Peak 5(2q37 1) 0 (0%) 236 0.651
(1.00) 		0.164
(1.00) 		9.7e-07
(0.000483) 		1.93e-05
(0.00922) 		0.00223
(0.915) 		0.024
(1.00) 		0.0249
(1.00) 		0.00127
(0.534) 		0.14
(1.00) 		0.0122
(1.00) 		0.0829
(1.00) 		0.00226
(0.924)
Del Peak 7(3p21 1) 0 (0%) 241 1
(1.00) 		0.00815
(1.00) 		5.04e-07
(0.000253) 		0.0121
(1.00) 		0.000478
(0.209) 		0.152
(1.00) 		0.0154
(1.00) 		0.00381
(1.00) 		0.00597
(1.00) 		0.0491
(1.00) 		0.0728
(1.00) 		0.0197
(1.00)
Del Peak 8(4q35 2) 0 (0%) 193 1
(1.00) 		0.602
(1.00) 		9.34e-09
(4.8e-06) 		9.66e-07
(0.000482) 		0.0826
(1.00) 		0.069
(1.00) 		0.00371
(1.00) 		0.00855
(1.00) 		0.195
(1.00) 		0.349
(1.00) 		0.0051
(1.00) 		0.00737
(1.00)
Del Peak 11(6q24 3) 0 (0%) 224 0.0479
(1.00) 		0.194
(1.00) 		0.000134
(0.0611) 		0.00125
(0.527) 		0.165
(1.00) 		0.273
(1.00) 		0.674
(1.00) 		0.0882
(1.00) 		0.000171
(0.0778) 		0.532
(1.00) 		0.507
(1.00) 		0.102
(1.00)
Del Peak 21(14q24 3) 0 (0%) 208 0.303
(1.00) 		0.171
(1.00) 		5.54e-05
(0.026) 		0.049
(1.00) 		0.00299
(1.00) 		0.0193
(1.00) 		0.00638
(1.00) 		0.071
(1.00) 		0.000514
(0.224) 		0.00345
(1.00) 		0.0747
(1.00) 		0.00259
(1.00)
Amp Peak 1(1q22) 0 (0%) 242 0.000254
(0.114) 		0.133
(1.00) 		0.251
(1.00) 		0.403
(1.00) 		0.169
(1.00) 		0.312
(1.00) 		0.937
(1.00) 		0.309
(1.00) 		0.134
(1.00) 		0.499
(1.00)
Amp Peak 13(12q14 1) 0 (0%) 250 1.97e-05
(0.00939) 		0.101
(1.00) 		0.0228
(1.00) 		0.881
(1.00) 		0.0291
(1.00) 		0.423
(1.00) 		0.0543
(1.00) 		0.192
(1.00) 		0.325
(1.00) 		0.011
(1.00)
Amp Peak 14(13q33 3) 0 (0%) 254 0.000431
(0.189) 		0.00549
(1.00) 		0.187
(1.00) 		0.293
(1.00) 		0.426
(1.00) 		0.0806
(1.00) 		0.861
(1.00) 		0.666
(1.00) 		0.408
(1.00) 		0.263
(1.00)
Amp Peak 15(17q25 1) 0 (0%) 253 0.0889
(1.00) 		0.0468
(1.00) 		7.64e-06
(0.0037) 		0.274
(1.00) 		0.208
(1.00) 		1
(1.00) 		0.468
(1.00) 		0.725
(1.00) 		0.0163
(1.00) 		0.389
(1.00) 		0.00944
(1.00) 		0.83
(1.00)
Amp Peak 19(Xp22 33) 0 (0%) 251 0.000241
(0.109) 		0.00225
(0.923) 		0.341
(1.00) 		0.34
(1.00) 		0.154
(1.00) 		0.0225
(1.00) 		0.779
(1.00) 		0.00885
(1.00) 		0.59
(1.00) 		0.306
(1.00)
Del Peak 4(2p25 3) 0 (0%) 245 0.369
(1.00) 		0.407
(1.00) 		1.97e-06
(0.000973) 		0.00447
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.455
(1.00) 		0.0729
(1.00) 		0.453
(1.00) 		0.815
(1.00) 		0.56
(1.00) 		0.144
(1.00)
Del Peak 9(5q35 2) 0 (0%) 235 0.446
(1.00) 		0.0182
(1.00) 		4.08e-09
(2.11e-06) 		0.00166
(0.687) 		0.0994
(1.00) 		0.941
(1.00) 		0.0663
(1.00) 		0.00913
(1.00) 		0.393
(1.00) 		0.502
(1.00) 		0.00637
(1.00) 		0.261
(1.00)
Del Peak 15(11q25) 0 (0%) 248 0.000243
(0.109) 		0.00609
(1.00) 		0.406
(1.00) 		0.424
(1.00) 		0.11
(1.00) 		0.041
(1.00) 		0.442
(1.00) 		0.174
(1.00) 		0.725
(1.00) 		0.207
(1.00)
Del Peak 16(12q12) 0 (0%) 234 1
(1.00) 		0.0879
(1.00) 		5.28e-06
(0.00259) 		0.000714
(0.306) 		0.505
(1.00) 		0.882
(1.00) 		0.115
(1.00) 		0.0148
(1.00) 		0.922
(1.00) 		0.956
(1.00) 		0.471
(1.00) 		0.607
(1.00)
Del Peak 17(13q14 2) 0 (0%) 192 0.18
(1.00) 		0.000618
(0.267) 		3.93e-30
(2.16e-27) 		0.0078
(1.00) 		0.0343
(1.00) 		0.813
(1.00) 		0.339
(1.00) 		0.13
(1.00) 		0.203
(1.00) 		0.289
(1.00) 		0.308
(1.00) 		0.283
(1.00)
Del Peak 18(13q21 2) 0 (0%) 189 0.18
(1.00) 		0.000618
(0.267) 		1.52e-29
(8.31e-27) 		0.00278
(1.00) 		0.0185
(1.00) 		0.713
(1.00) 		0.145
(1.00) 		0.0611
(1.00) 		0.0754
(1.00) 		0.229
(1.00) 		0.34
(1.00) 		0.29
(1.00)
Del Peak 19(13q22 1) 0 (0%) 192 0.438
(1.00) 		0.000774
(0.329) 		2.75e-25
(1.49e-22) 		0.0163
(1.00) 		0.00899
(1.00) 		0.788
(1.00) 		0.457
(1.00) 		0.13
(1.00) 		0.138
(1.00) 		0.452
(1.00) 		0.611
(1.00) 		0.421
(1.00)
Del Peak 20(13q34) 0 (0%) 212 0.508
(1.00) 		0.106
(1.00) 		5.37e-17
(2.89e-14) 		0.263
(1.00) 		0.0856
(1.00) 		0.524
(1.00) 		0.454
(1.00) 		0.161
(1.00) 		0.0935
(1.00) 		0.239
(1.00) 		0.605
(1.00) 		0.699
(1.00)
Del Peak 27(Xp22 2) 0 (0%) 211 0.839
(1.00) 		0.131
(1.00) 		6.73e-09
(3.46e-06) 		0.128
(1.00) 		0.0439
(1.00) 		0.0294
(1.00) 		0.965
(1.00) 		0.0676
(1.00) 		0.491
(1.00) 		0.119
(1.00) 		0.81
(1.00) 		0.0436
(1.00)
Del Peak 28(Xq21 1) 0 (0%) 234 0.73
(1.00) 		0.00107
(0.453) 		5.92e-05
(0.0276) 		0.118
(1.00) 		0.0289
(1.00) 		0.0495
(1.00) 		0.523
(1.00) 		0.0143
(1.00) 		0.119
(1.00) 		0.176
(1.00) 		0.0416
(1.00) 		0.884
(1.00)
Amp Peak 3(3p24 3) 0 (0%) 255 0.0312
(1.00) 		0.933
(1.00) 		0.907
(1.00) 		0.0322
(1.00) 		0.0815
(1.00) 		0.252
(1.00) 		0.735
(1.00) 		0.643
(1.00) 		0.63
(1.00) 		0.621
(1.00)
Amp Peak 4(3q26 32) 0 (0%) 255 0.000655
(0.282) 		0.118
(1.00) 		0.0147
(1.00) 		0.68
(1.00) 		0.548
(1.00) 		0.434
(1.00) 		0.176
(1.00) 		0.643
(1.00) 		0.119
(1.00) 		0.276
(1.00)
Amp Peak 5(4q12) 0 (0%) 255 0.0014
(0.584) 		0.258
(1.00) 		0.0204
(1.00) 		0.737
(1.00) 		0.696
(1.00) 		0.372
(1.00) 		0.0996
(1.00) 		0.33
(1.00) 		0.191
(1.00) 		0.529
(1.00)
Amp Peak 10(11q23 3) 0 (0%) 224 0.225
(1.00) 		0.025
(1.00) 		0.185
(1.00) 		0.122
(1.00) 		0.101
(1.00) 		0.141
(1.00) 		0.603
(1.00) 		0.599
(1.00) 		0.579
(1.00) 		0.627
(1.00) 		0.0579
(1.00) 		0.246
(1.00)
Del Peak 3(1q43) 0 (0%) 254 0.0604
(1.00) 		0.228
(1.00) 		0.101
(1.00) 		0.567
(1.00) 		0.894
(1.00) 		0.186
(1.00) 		0.559
(1.00) 		0.666
(1.00) 		0.638
(1.00) 		0.557
(1.00)
Del Peak 10(6p25 3) 0 (0%) 241 0.0551
(1.00) 		0.359
(1.00) 		0.161
(1.00) 		0.808
(1.00) 		0.429
(1.00) 		0.24
(1.00) 		0.574
(1.00) 		0.705
(1.00) 		0.164
(1.00) 		0.109
(1.00)
Del Peak 22(17q25 3) 0 (0%) 252 0.00155
(0.645) 		0.216
(1.00) 		0.247
(1.00) 		0.161
(1.00) 		0.778
(1.00) 		0.161
(1.00) 		0.204
(1.00) 		0.153
(1.00) 		0.716
(1.00) 		0.341
(1.00)
Del Peak 23(18p11 32) 0 (0%) 227 0.321
(1.00) 		0.316
(1.00) 		0.0604
(1.00) 		0.125
(1.00) 		0.43
(1.00) 		0.0609
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.785
(1.00) 		0.682
(1.00) 		0.689
(1.00)
Del Peak 24(18q23) 0 (0%) 226 0.321
(1.00) 		0.316
(1.00) 		0.134
(1.00) 		0.0651
(1.00) 		0.46
(1.00) 		0.115
(1.00) 		0.383
(1.00) 		0.822
(1.00) 		0.672
(1.00) 		0.421
(1.00) 		0.516
(1.00) 		0.247
(1.00)
'Amp Peak 1(1q22)' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.11

Table S1.  Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 1(1Q22) CNV 5 9 11 2
AMP PEAK 1(1Q22) WILD-TYPE 47 48 43 104

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'CN_CNMF'

P value = 2.14e-07 (Fisher's exact test), Q value = 0.00011

Table S2.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 2(1Q32.1) CNV 2 15 9 1
AMP PEAK 2(1Q32.1) WILD-TYPE 50 42 45 105

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'METHLYATION_CNMF'

P value = 2.28e-06 (Fisher's exact test), Q value = 0.0011

Table S3.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 2(1Q32.1) CNV 9 15 2 1
AMP PEAK 2(1Q32.1) WILD-TYPE 113 27 64 33

Figure S3.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(1q32.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.041

Table S4.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
AMP PEAK 2(1Q32.1) CNV 7 9 11
AMP PEAK 2(1Q32.1) WILD-TYPE 7 136 98

Figure S4.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1q32.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.013

Table S5.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
AMP PEAK 2(1Q32.1) CNV 13 4 10
AMP PEAK 2(1Q32.1) WILD-TYPE 29 101 111

Figure S5.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 6(7p11.2)' versus 'CN_CNMF'

P value = 2.06e-29 (Fisher's exact test), Q value = 1.1e-26

Table S6.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 6(7P11.2) CNV 4 50 12 7
AMP PEAK 6(7P11.2) WILD-TYPE 48 7 42 99

Figure S6.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7p11.2)' versus 'METHLYATION_CNMF'

P value = 4.41e-16 (Fisher's exact test), Q value = 2.4e-13

Table S7.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 6(7P11.2) CNV 22 35 8 6
AMP PEAK 6(7P11.2) WILD-TYPE 100 7 58 28

Figure S7.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(7p11.2)' versus 'RPPA_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.052

Table S8.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
AMP PEAK 6(7P11.2) CNV 13 30 12 12
AMP PEAK 6(7P11.2) WILD-TYPE 39 32 56 62

Figure S8.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 6(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0093

Table S9.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
AMP PEAK 6(7P11.2) CNV 42 15 16
AMP PEAK 6(7P11.2) WILD-TYPE 52 63 81

Figure S9.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.43e-06 (Fisher's exact test), Q value = 0.0031

Table S10.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
AMP PEAK 6(7P11.2) CNV 11 43 18
AMP PEAK 6(7P11.2) WILD-TYPE 3 102 91

Figure S10.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-07 (Chi-square test), Q value = 0.00023

Table S11.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
AMP PEAK 6(7P11.2) CNV 7 28 11 11 2 11 2 0
AMP PEAK 6(7P11.2) WILD-TYPE 37 20 24 60 25 20 2 8

Figure S11.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.1e-12 (Fisher's exact test), Q value = 1.6e-09

Table S12.  Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
AMP PEAK 6(7P11.2) CNV 31 24 17
AMP PEAK 6(7P11.2) WILD-TYPE 11 81 104

Figure S12.  Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 7(7q32.3)' versus 'CN_CNMF'

P value = 5.19e-23 (Fisher's exact test), Q value = 2.8e-20

Table S13.  Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 7(7Q32.3) CNV 13 53 17 17
AMP PEAK 7(7Q32.3) WILD-TYPE 39 4 37 89

Figure S13.  Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(7q32.3)' versus 'METHLYATION_CNMF'

P value = 2.11e-08 (Fisher's exact test), Q value = 1.1e-05

Table S14.  Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 7(7Q32.3) CNV 45 32 15 6
AMP PEAK 7(7Q32.3) WILD-TYPE 77 10 51 28

Figure S14.  Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(7q32.3)' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.12

Table S15.  Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
AMP PEAK 7(7Q32.3) CNV 50 25 25
AMP PEAK 7(7Q32.3) WILD-TYPE 44 53 72

Figure S15.  Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(7q32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0049

Table S16.  Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
AMP PEAK 7(7Q32.3) CNV 29 37 33
AMP PEAK 7(7Q32.3) WILD-TYPE 13 68 88

Figure S16.  Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 8(8q24.12)' versus 'CN_CNMF'

P value = 2.32e-12 (Fisher's exact test), Q value = 1.2e-09

Table S17.  Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 8(8Q24.12) CNV 17 11 25 2
AMP PEAK 8(8Q24.12) WILD-TYPE 35 46 29 104

Figure S17.  Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(8q24.12)' versus 'METHLYATION_CNMF'

P value = 5.52e-09 (Fisher's exact test), Q value = 2.8e-06

Table S18.  Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 8(8Q24.12) CNV 46 4 3 2
AMP PEAK 8(8Q24.12) WILD-TYPE 76 38 63 32

Figure S18.  Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(8q24.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.12

Table S19.  Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
AMP PEAK 8(8Q24.12) CNV 17 6 10 9 1 8 3 1
AMP PEAK 8(8Q24.12) WILD-TYPE 27 42 25 62 26 23 1 7

Figure S19.  Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 9(10p15.3)' versus 'CN_CNMF'

P value = 1e-09 (Fisher's exact test), Q value = 5.3e-07

Table S20.  Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 9(10P15.3) CNV 19 5 15 2
AMP PEAK 9(10P15.3) WILD-TYPE 33 52 39 104

Figure S20.  Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(10p15.3)' versus 'METHLYATION_CNMF'

P value = 2.97e-09 (Fisher's exact test), Q value = 1.5e-06

Table S21.  Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 9(10P15.3) CNV 36 1 0 4
AMP PEAK 9(10P15.3) WILD-TYPE 86 41 66 30

Figure S21.  Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(10p15.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000284 (Chi-square test), Q value = 0.13

Table S22.  Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
AMP PEAK 9(10P15.3) CNV 12 3 10 7 2 3 3 1
AMP PEAK 9(10P15.3) WILD-TYPE 32 45 25 64 25 28 1 7

Figure S22.  Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 11(12p13.32)' versus 'CN_CNMF'

P value = 1.69e-10 (Fisher's exact test), Q value = 8.9e-08

Table S23.  Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 11(12P13.32) CNV 20 8 14 1
AMP PEAK 11(12P13.32) WILD-TYPE 32 49 40 105

Figure S23.  Get High-res Image Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(12p13.32)' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.024

Table S24.  Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 11(12P13.32) CNV 33 5 2 3
AMP PEAK 11(12P13.32) WILD-TYPE 89 37 64 31

Figure S24.  Get High-res Image Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(12p12.1)' versus 'CN_CNMF'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0023

Table S25.  Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 12(12P12.1) CNV 12 5 10 1
AMP PEAK 12(12P12.1) WILD-TYPE 40 52 44 105

Figure S25.  Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(12p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000392 (Fisher's exact test), Q value = 0.17

Table S26.  Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
AMP PEAK 12(12P12.1) CNV 2 24 2
AMP PEAK 12(12P12.1) WILD-TYPE 34 117 90

Figure S26.  Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(12p12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.84e-05 (Chi-square test), Q value = 0.032

Table S27.  Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
AMP PEAK 12(12P12.1) CNV 7 6 7 1 2 2 3 0
AMP PEAK 12(12P12.1) WILD-TYPE 37 42 28 70 25 29 1 8

Figure S27.  Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 13(12q14.1)' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.0094

Table S28.  Gene #13: 'Amp Peak 13(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 13(12Q14.1) CNV 1 6 11 1
AMP PEAK 13(12Q14.1) WILD-TYPE 51 51 43 105

Figure S28.  Get High-res Image Gene #13: 'Amp Peak 13(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(13q33.3)' versus 'CN_CNMF'

P value = 0.000431 (Fisher's exact test), Q value = 0.19

Table S29.  Gene #14: 'Amp Peak 14(13q33.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 14(13Q33.3) CNV 5 3 7 0
AMP PEAK 14(13Q33.3) WILD-TYPE 47 54 47 106

Figure S29.  Get High-res Image Gene #14: 'Amp Peak 14(13q33.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q25.1)' versus 'CN_CNMF'

P value = 7.64e-06 (Fisher's exact test), Q value = 0.0037

Table S30.  Gene #15: 'Amp Peak 15(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 15(17Q25.1) CNV 1 1 12 2
AMP PEAK 15(17Q25.1) WILD-TYPE 51 56 42 104

Figure S30.  Get High-res Image Gene #15: 'Amp Peak 15(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(18q23)' versus 'RPPA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.06

Table S31.  Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
AMP PEAK 16(18Q23) CNV 3 8 0 0
AMP PEAK 16(18Q23) WILD-TYPE 49 54 68 74

Figure S31.  Get High-res Image Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 16(18q23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Chi-square test), Q value = 0.12

Table S32.  Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
AMP PEAK 16(18Q23) CNV 1 3 4 1 0 1 2 0
AMP PEAK 16(18Q23) WILD-TYPE 43 45 31 70 27 30 2 8

Figure S32.  Get High-res Image Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 17(19p13.3)' versus 'CN_CNMF'

P value = 9.09e-05 (Fisher's exact test), Q value = 0.042

Table S33.  Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 17(19P13.3) CNV 2 17 8 33
AMP PEAK 17(19P13.3) WILD-TYPE 50 40 46 73

Figure S33.  Get High-res Image Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(19p13.3)' versus 'METHLYATION_CNMF'

P value = 1.07e-08 (Fisher's exact test), Q value = 5.5e-06

Table S34.  Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 17(19P13.3) CNV 10 14 29 3
AMP PEAK 17(19P13.3) WILD-TYPE 112 28 37 31

Figure S34.  Get High-res Image Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(19q13.2)' versus 'CN_CNMF'

P value = 7.29e-07 (Fisher's exact test), Q value = 0.00037

Table S35.  Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 18(19Q13.2) CNV 0 14 3 2
AMP PEAK 18(19Q13.2) WILD-TYPE 52 43 51 104

Figure S35.  Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(19q13.2)' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0048

Table S36.  Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 18(19Q13.2) CNV 6 11 0 1
AMP PEAK 18(19Q13.2) WILD-TYPE 116 31 66 33

Figure S36.  Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(19q13.2)' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.056

Table S37.  Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
AMP PEAK 18(19Q13.2) CNV 15 3 1
AMP PEAK 18(19Q13.2) WILD-TYPE 79 75 96

Figure S37.  Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(19q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.25e-06 (Chi-square test), Q value = 0.0026

Table S38.  Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
AMP PEAK 18(19Q13.2) CNV 2 13 1 3 0 0 0 0
AMP PEAK 18(19Q13.2) WILD-TYPE 42 35 34 68 27 31 4 8

Figure S38.  Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 18(19q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.89e-06 (Fisher's exact test), Q value = 0.0029

Table S39.  Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
AMP PEAK 18(19Q13.2) CNV 11 6 2
AMP PEAK 18(19Q13.2) WILD-TYPE 31 99 119

Figure S39.  Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 19(Xp22.33)' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #19: 'Amp Peak 19(Xp22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 19(XP22.33) CNV 7 6 5 0
AMP PEAK 19(XP22.33) WILD-TYPE 45 51 49 106

Figure S40.  Get High-res Image Gene #19: 'Amp Peak 19(Xp22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(Xp11.22)' versus 'CN_CNMF'

P value = 1.84e-09 (Fisher's exact test), Q value = 9.6e-07

Table S41.  Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
AMP PEAK 20(XP11.22) CNV 19 4 13 2
AMP PEAK 20(XP11.22) WILD-TYPE 33 53 41 104

Figure S41.  Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(Xp11.22)' versus 'METHLYATION_CNMF'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00076

Table S42.  Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
AMP PEAK 20(XP11.22) CNV 32 4 1 1
AMP PEAK 20(XP11.22) WILD-TYPE 90 38 65 33

Figure S42.  Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(Xp11.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000355 (Fisher's exact test), Q value = 0.16

Table S43.  Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
AMP PEAK 20(XP11.22) CNV 1 31 6
AMP PEAK 20(XP11.22) WILD-TYPE 35 110 86

Figure S43.  Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MRNA_CNMF'

P value = 0.000549 (Fisher's exact test), Q value = 0.24

Table S44.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 1(1P36.31) CNV 0 8 2
DEL PEAK 1(1P36.31) WILD-TYPE 9 2 6

Figure S44.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNA_CHIERARCHICAL'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.027

Table S45.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
DEL PEAK 1(1P36.31) CNV 7 2 0 1
DEL PEAK 1(1P36.31) WILD-TYPE 0 4 10 3

Figure S45.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'CN_CNMF'

P value = 8.49e-14 (Fisher's exact test), Q value = 4.5e-11

Table S46.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 1(1P36.31) CNV 5 9 15 67
DEL PEAK 1(1P36.31) WILD-TYPE 47 48 39 39

Figure S46.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.31)' versus 'METHLYATION_CNMF'

P value = 4.92e-43 (Fisher's exact test), Q value = 2.7e-40

Table S47.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 1(1P36.31) CNV 8 9 66 9
DEL PEAK 1(1P36.31) WILD-TYPE 114 33 0 25

Figure S47.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CNMF'

P value = 7.9e-06 (Fisher's exact test), Q value = 0.0038

Table S48.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
DEL PEAK 1(1P36.31) CNV 16 34 46
DEL PEAK 1(1P36.31) WILD-TYPE 78 44 51

Figure S48.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.23e-23 (Fisher's exact test), Q value = 1.8e-20

Table S49.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
DEL PEAK 1(1P36.31) CNV 36 21 39
DEL PEAK 1(1P36.31) WILD-TYPE 0 120 53

Figure S49.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CNMF'

P value = 8.86e-06 (Chi-square test), Q value = 0.0043

Table S50.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
DEL PEAK 1(1P36.31) CNV 11 10 40 12 23
DEL PEAK 1(1P36.31) WILD-TYPE 51 38 49 4 30

Figure S50.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.13

Table S51.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
DEL PEAK 1(1P36.31) CNV 2 40 54
DEL PEAK 1(1P36.31) WILD-TYPE 12 105 55

Figure S51.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.15e-08 (Chi-square test), Q value = 5.9e-06

Table S52.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
DEL PEAK 1(1P36.31) CNV 2 14 8 33 21 14 0 4
DEL PEAK 1(1P36.31) WILD-TYPE 42 34 27 38 6 17 4 4

Figure S52.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.048

Table S53.  Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
DEL PEAK 1(1P36.31) CNV 9 27 60
DEL PEAK 1(1P36.31) WILD-TYPE 33 78 61

Figure S53.  Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.078

Table S54.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
DEL PEAK 2(1P32.3) CNV 7 2 1 0
DEL PEAK 2(1P32.3) WILD-TYPE 0 4 9 4

Figure S54.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'CN_CNMF'

P value = 2.21e-17 (Fisher's exact test), Q value = 1.2e-14

Table S55.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 2(1P32.3) CNV 4 5 12 67
DEL PEAK 2(1P32.3) WILD-TYPE 48 52 42 39

Figure S55.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p32.3)' versus 'METHLYATION_CNMF'

P value = 2.3e-48 (Fisher's exact test), Q value = 1.3e-45

Table S56.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 2(1P32.3) CNV 4 6 66 9
DEL PEAK 2(1P32.3) WILD-TYPE 118 36 0 25

Figure S56.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p32.3)' versus 'RPPA_CNMF'

P value = 0.000477 (Fisher's exact test), Q value = 0.21

Table S57.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 2(1P32.3) CNV 8 16 28 35
DEL PEAK 2(1P32.3) WILD-TYPE 44 46 40 39

Figure S57.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CNMF'

P value = 2.73e-09 (Fisher's exact test), Q value = 1.4e-06

Table S58.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
DEL PEAK 2(1P32.3) CNV 9 34 45
DEL PEAK 2(1P32.3) WILD-TYPE 85 44 52

Figure S58.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-27 (Fisher's exact test), Q value = 1.7e-24

Table S59.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
DEL PEAK 2(1P32.3) CNV 36 14 38
DEL PEAK 2(1P32.3) WILD-TYPE 0 127 54

Figure S59.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CNMF'

P value = 5.78e-08 (Chi-square test), Q value = 2.9e-05

Table S60.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
DEL PEAK 2(1P32.3) CNV 11 4 40 12 21
DEL PEAK 2(1P32.3) WILD-TYPE 51 44 49 4 32

Figure S60.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.015

Table S61.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
DEL PEAK 2(1P32.3) CNV 1 35 52
DEL PEAK 2(1P32.3) WILD-TYPE 13 110 57

Figure S61.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.54e-09 (Chi-square test), Q value = 8.1e-07

Table S62.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
DEL PEAK 2(1P32.3) CNV 2 9 8 32 21 12 0 4
DEL PEAK 2(1P32.3) WILD-TYPE 42 39 27 39 6 19 4 4

Figure S62.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00054

Table S63.  Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
DEL PEAK 2(1P32.3) CNV 5 24 59
DEL PEAK 2(1P32.3) WILD-TYPE 37 81 62

Figure S63.  Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(2p25.3)' versus 'CN_CNMF'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.00097

Table S64.  Gene #24: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 4(2P25.3) CNV 9 2 12 1
DEL PEAK 4(2P25.3) WILD-TYPE 43 55 42 105

Figure S64.  Get High-res Image Gene #24: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.1)' versus 'CN_CNMF'

P value = 9.7e-07 (Fisher's exact test), Q value = 0.00048

Table S65.  Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 5(2Q37.1) CNV 14 9 9 1
DEL PEAK 5(2Q37.1) WILD-TYPE 38 48 45 105

Figure S65.  Get High-res Image Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.1)' versus 'METHLYATION_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0092

Table S66.  Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 5(2Q37.1) CNV 28 2 1 2
DEL PEAK 5(2Q37.1) WILD-TYPE 94 40 65 32

Figure S66.  Get High-res Image Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'CN_CNMF'

P value = 6.07e-06 (Fisher's exact test), Q value = 0.003

Table S67.  Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 6(2Q37.3) CNV 15 10 12 3
DEL PEAK 6(2Q37.3) WILD-TYPE 37 47 42 103

Figure S67.  Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(2q37.3)' versus 'METHLYATION_CNMF'

P value = 1.8e-07 (Fisher's exact test), Q value = 9.1e-05

Table S68.  Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 6(2Q37.3) CNV 35 1 2 2
DEL PEAK 6(2Q37.3) WILD-TYPE 87 41 64 32

Figure S68.  Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.052

Table S69.  Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
DEL PEAK 6(2Q37.3) CNV 3 28 9
DEL PEAK 6(2Q37.3) WILD-TYPE 39 77 112

Figure S69.  Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p21.1)' versus 'CN_CNMF'

P value = 5.04e-07 (Fisher's exact test), Q value = 0.00025

Table S70.  Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 7(3P21.1) CNV 8 4 15 1
DEL PEAK 7(3P21.1) WILD-TYPE 44 53 39 105

Figure S70.  Get High-res Image Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p21.1)' versus 'RPPA_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.21

Table S71.  Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 7(3P21.1) CNV 4 16 3 4
DEL PEAK 7(3P21.1) WILD-TYPE 48 46 65 70

Figure S71.  Get High-res Image Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 8(4q35.2)' versus 'CN_CNMF'

P value = 9.34e-09 (Fisher's exact test), Q value = 4.8e-06

Table S72.  Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 8(4Q35.2) CNV 16 4 32 24
DEL PEAK 8(4Q35.2) WILD-TYPE 36 53 22 82

Figure S72.  Get High-res Image Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4q35.2)' versus 'METHLYATION_CNMF'

P value = 9.66e-07 (Fisher's exact test), Q value = 0.00048

Table S73.  Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 8(4Q35.2) CNV 43 2 28 3
DEL PEAK 8(4Q35.2) WILD-TYPE 79 40 38 31

Figure S73.  Get High-res Image Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(5q35.2)' versus 'CN_CNMF'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.1e-06

Table S74.  Gene #29: 'Del Peak 9(5q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 9(5Q35.2) CNV 13 1 17 3
DEL PEAK 9(5Q35.2) WILD-TYPE 39 56 37 103

Figure S74.  Get High-res Image Gene #29: 'Del Peak 9(5q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q24.3)' versus 'CN_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.061

Table S75.  Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 11(6Q24.3) CNV 6 12 19 8
DEL PEAK 11(6Q24.3) WILD-TYPE 46 45 35 98

Figure S75.  Get High-res Image Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q24.3)' versus 'MIRSEQ_CNMF'

P value = 0.000171 (Chi-square test), Q value = 0.078

Table S76.  Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
DEL PEAK 11(6Q24.3) CNV 22 7 12 1 3
DEL PEAK 11(6Q24.3) WILD-TYPE 40 41 77 15 50

Figure S76.  Get High-res Image Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(9p21.3)' versus 'CN_CNMF'

P value = 3.04e-11 (Fisher's exact test), Q value = 1.6e-08

Table S77.  Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 12(9P21.3) CNV 13 38 30 18
DEL PEAK 12(9P21.3) WILD-TYPE 39 19 24 88

Figure S77.  Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.66e-08 (Fisher's exact test), Q value = 1.4e-05

Table S78.  Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 12(9P21.3) CNV 49 30 13 5
DEL PEAK 12(9P21.3) WILD-TYPE 73 12 53 29

Figure S78.  Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(9p21.3)' versus 'RPPA_CNMF'

P value = 8.67e-06 (Fisher's exact test), Q value = 0.0042

Table S79.  Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 12(9P21.3) CNV 11 38 26 18
DEL PEAK 12(9P21.3) WILD-TYPE 41 24 42 56

Figure S79.  Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 12(9p21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 9.22e-05 (Fisher's exact test), Q value = 0.043

Table S80.  Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 129 119
DEL PEAK 12(9P21.3) CNV 2 63 28
DEL PEAK 12(9P21.3) WILD-TYPE 6 66 91

Figure S80.  Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000199 (Fisher's exact test), Q value = 0.09

Table S81.  Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
DEL PEAK 12(9P21.3) CNV 27 38 34
DEL PEAK 12(9P21.3) WILD-TYPE 15 67 87

Figure S81.  Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'CN_CNMF'

P value = 6.21e-19 (Fisher's exact test), Q value = 3.3e-16

Table S82.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 13(10Q26.3) CNV 14 38 25 4
DEL PEAK 13(10Q26.3) WILD-TYPE 38 19 29 102

Figure S82.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(10q26.3)' versus 'METHLYATION_CNMF'

P value = 1.3e-20 (Fisher's exact test), Q value = 7e-18

Table S83.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 13(10Q26.3) CNV 36 37 3 4
DEL PEAK 13(10Q26.3) WILD-TYPE 86 5 63 30

Figure S83.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(10q26.3)' versus 'RPPA_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 7.9e-05

Table S84.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 13(10Q26.3) CNV 13 36 13 11
DEL PEAK 13(10Q26.3) WILD-TYPE 39 26 55 63

Figure S84.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 13(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000214 (Fisher's exact test), Q value = 0.097

Table S85.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 129 119
DEL PEAK 13(10Q26.3) CNV 2 51 20
DEL PEAK 13(10Q26.3) WILD-TYPE 6 78 99

Figure S85.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.1e-05

Table S86.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
DEL PEAK 13(10Q26.3) CNV 50 14 17
DEL PEAK 13(10Q26.3) WILD-TYPE 44 64 80

Figure S86.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.92e-09 (Fisher's exact test), Q value = 1.5e-06

Table S87.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
DEL PEAK 13(10Q26.3) CNV 1 64 16
DEL PEAK 13(10Q26.3) WILD-TYPE 35 77 76

Figure S87.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.98e-06 (Fisher's exact test), Q value = 0.0029

Table S88.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
DEL PEAK 13(10Q26.3) CNV 10 53 18
DEL PEAK 13(10Q26.3) WILD-TYPE 4 92 91

Figure S88.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-09 (Chi-square test), Q value = 2.3e-06

Table S89.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
DEL PEAK 13(10Q26.3) CNV 9 33 5 13 5 12 3 1
DEL PEAK 13(10Q26.3) WILD-TYPE 35 15 30 58 22 19 1 7

Figure S89.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.26e-11 (Fisher's exact test), Q value = 6.7e-09

Table S90.  Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
DEL PEAK 13(10Q26.3) CNV 32 29 20
DEL PEAK 13(10Q26.3) WILD-TYPE 10 76 101

Figure S90.  Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(11p15.5)' versus 'CN_CNMF'

P value = 1.88e-09 (Fisher's exact test), Q value = 9.8e-07

Table S91.  Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 14(11P15.5) CNV 23 8 20 6
DEL PEAK 14(11P15.5) WILD-TYPE 29 49 34 100

Figure S91.  Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(11p15.5)' versus 'METHLYATION_CNMF'

P value = 2.11e-10 (Fisher's exact test), Q value = 1.1e-07

Table S92.  Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 14(11P15.5) CNV 46 6 0 5
DEL PEAK 14(11P15.5) WILD-TYPE 76 36 66 29

Figure S92.  Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.012

Table S93.  Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
DEL PEAK 14(11P15.5) CNV 0 42 15
DEL PEAK 14(11P15.5) WILD-TYPE 36 99 77

Figure S93.  Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(11q25)' versus 'CN_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.11

Table S94.  Gene #35: 'Del Peak 15(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 15(11Q25) CNV 6 4 10 1
DEL PEAK 15(11Q25) WILD-TYPE 46 53 44 105

Figure S94.  Get High-res Image Gene #35: 'Del Peak 15(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(12q12)' versus 'CN_CNMF'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.0026

Table S95.  Gene #36: 'Del Peak 16(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 16(12Q12) CNV 18 4 8 5
DEL PEAK 16(12Q12) WILD-TYPE 34 53 46 101

Figure S95.  Get High-res Image Gene #36: 'Del Peak 16(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(13q14.2)' versus 'CN_CNMF'

P value = 3.93e-30 (Fisher's exact test), Q value = 2.2e-27

Table S96.  Gene #37: 'Del Peak 17(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 17(13Q14.2) CNV 19 8 47 3
DEL PEAK 17(13Q14.2) WILD-TYPE 33 49 7 103

Figure S96.  Get High-res Image Gene #37: 'Del Peak 17(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q21.2)' versus 'CN_CNMF'

P value = 1.52e-29 (Fisher's exact test), Q value = 8.3e-27

Table S97.  Gene #38: 'Del Peak 18(13q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 18(13Q21.2) CNV 20 10 47 3
DEL PEAK 18(13Q21.2) WILD-TYPE 32 47 7 103

Figure S97.  Get High-res Image Gene #38: 'Del Peak 18(13q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(13q22.1)' versus 'CN_CNMF'

P value = 2.75e-25 (Fisher's exact test), Q value = 1.5e-22

Table S98.  Gene #39: 'Del Peak 19(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 19(13Q22.1) CNV 18 9 45 5
DEL PEAK 19(13Q22.1) WILD-TYPE 34 48 9 101

Figure S98.  Get High-res Image Gene #39: 'Del Peak 19(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(13q34)' versus 'CN_CNMF'

P value = 5.37e-17 (Fisher's exact test), Q value = 2.9e-14

Table S99.  Gene #40: 'Del Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 20(13Q34) CNV 15 6 33 3
DEL PEAK 20(13Q34) WILD-TYPE 37 51 21 103

Figure S99.  Get High-res Image Gene #40: 'Del Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(14q24.3)' versus 'CN_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.026

Table S100.  Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 21(14Q24.3) CNV 7 14 25 15
DEL PEAK 21(14Q24.3) WILD-TYPE 45 43 29 91

Figure S100.  Get High-res Image Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 0.000514 (Chi-square test), Q value = 0.22

Table S101.  Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
DEL PEAK 21(14Q24.3) CNV 27 8 15 3 8
DEL PEAK 21(14Q24.3) WILD-TYPE 35 40 74 13 45

Figure S101.  Get High-res Image Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'CN_CNMF'

P value = 1.55e-15 (Fisher's exact test), Q value = 8.3e-13

Table S102.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 25(19Q13.42) CNV 13 9 39 75
DEL PEAK 25(19Q13.42) WILD-TYPE 39 48 15 31

Figure S102.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(19q13.42)' versus 'METHLYATION_CNMF'

P value = 9.49e-28 (Fisher's exact test), Q value = 5.2e-25

Table S103.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 25(19Q13.42) CNV 53 4 66 10
DEL PEAK 25(19Q13.42) WILD-TYPE 69 38 0 24

Figure S103.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 4e-04

Table S104.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
DEL PEAK 25(19Q13.42) CNV 27 50 59
DEL PEAK 25(19Q13.42) WILD-TYPE 67 28 38

Figure S104.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.06e-15 (Fisher's exact test), Q value = 4.8e-12

Table S105.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
DEL PEAK 25(19Q13.42) CNV 36 47 53
DEL PEAK 25(19Q13.42) WILD-TYPE 0 94 39

Figure S105.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 8.24e-05 (Chi-square test), Q value = 0.038

Table S106.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
DEL PEAK 25(19Q13.42) CNV 27 14 51 15 29
DEL PEAK 25(19Q13.42) WILD-TYPE 35 34 38 1 24

Figure S106.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000298 (Fisher's exact test), Q value = 0.13

Table S107.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
DEL PEAK 25(19Q13.42) CNV 1 69 66
DEL PEAK 25(19Q13.42) WILD-TYPE 13 76 43

Figure S107.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.28e-05 (Chi-square test), Q value = 0.011

Table S108.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
DEL PEAK 25(19Q13.42) CNV 16 13 20 41 24 17 1 4
DEL PEAK 25(19Q13.42) WILD-TYPE 28 35 15 30 3 14 3 4

Figure S108.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.6e-05

Table S109.  Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
DEL PEAK 25(19Q13.42) CNV 5 57 74
DEL PEAK 25(19Q13.42) WILD-TYPE 37 48 47

Figure S109.  Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(22q13.31)' versus 'CN_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 7.4e-07

Table S110.  Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 26(22Q13.31) CNV 11 14 15 0
DEL PEAK 26(22Q13.31) WILD-TYPE 41 43 39 106

Figure S110.  Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(22q13.31)' versus 'METHLYATION_CNMF'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.0014

Table S111.  Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
DEL PEAK 26(22Q13.31) CNV 23 13 0 3
DEL PEAK 26(22Q13.31) WILD-TYPE 99 29 66 31

Figure S111.  Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(22q13.31)' versus 'RPPA_CNMF'

P value = 6.75e-05 (Fisher's exact test), Q value = 0.031

Table S112.  Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 26(22Q13.31) CNV 4 22 8 6
DEL PEAK 26(22Q13.31) WILD-TYPE 48 40 60 68

Figure S112.  Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 6.92e-06 (Fisher's exact test), Q value = 0.0034

Table S113.  Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
DEL PEAK 26(22Q13.31) CNV 28 5 7
DEL PEAK 26(22Q13.31) WILD-TYPE 66 73 90

Figure S113.  Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.77e-05 (Fisher's exact test), Q value = 0.018

Table S114.  Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
DEL PEAK 26(22Q13.31) CNV 0 33 7
DEL PEAK 26(22Q13.31) WILD-TYPE 36 108 85

Figure S114.  Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(Xp22.2)' versus 'CN_CNMF'

P value = 6.73e-09 (Fisher's exact test), Q value = 3.5e-06

Table S115.  Gene #47: 'Del Peak 27(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 27(XP22.2) CNV 14 5 28 11
DEL PEAK 27(XP22.2) WILD-TYPE 38 52 26 95

Figure S115.  Get High-res Image Gene #47: 'Del Peak 27(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(Xq21.1)' versus 'CN_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.028

Table S116.  Gene #48: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
DEL PEAK 28(XQ21.1) CNV 6 3 18 8
DEL PEAK 28(XQ21.1) WILD-TYPE 46 54 36 98

Figure S116.  Get High-res Image Gene #48: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #3: 'CN_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 = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 269

  • Number of copy number variation regions = 48

  • Number of molecular subtypes = 12

  • Exclude regions 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

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

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