Correlation between copy number variation genes and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1BC3WKG
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/C1BC3WKG
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 84 peak regions and 12 molecular subtypes across 416 patients, 122 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 4(2q31.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 6(3q26.33) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 8(5p15.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(5p12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 12(7q21.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 15(9p24.1) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 22(15q26.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 23(17q25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 24(18p11.32) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 25(18q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 27(19q13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 28(20p12.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 29(20q11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.22) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 2(1p13.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 5(2q36.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 7(3p13) cnvs correlated to 'CN_CNMF'.

  • Del Peak 8(3p12.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 12(4q32.3) cnvs correlated to 'CN_CNMF'.

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

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

  • Del Peak 15(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 17(6q22.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 18(6q26) cnvs correlated to 'CN_CNMF'.

  • Del Peak 19(7q11.22) cnvs correlated to 'CN_CNMF'.

  • Del Peak 22(9p23) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(9p21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 24(9p21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 25(9q21.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 26(10p15.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 27(10p15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 28(10q23.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 29(11p15.5) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • Del Peak 35(14q11.2) cnvs correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 40(17p11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 41(17q11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 42(17q25.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 44(19p13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 45(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 46(19q13.43) cnvs correlated to 'CN_CNMF'.

  • Del Peak 48(21q22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 50(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 51(Xp22.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 52(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 53(Xq22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 84 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 122 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Del Peak 1(1p36 22) 0 (0%) 236 1.49e-06
(0.00144) 		6.89e-08
(6.77e-05) 		1.69e-26
(1.7e-23) 		4.55e-15
(4.58e-12) 		0.412
(1.00) 		0.0262
(1.00) 		8.67e-14
(8.69e-11) 		9.45e-15
(9.48e-12) 		0.000838
(0.721) 		1.83e-05
(0.0172) 		9.29e-06
(0.00877) 		0.00595
(1.00)
Del Peak 25(9q21 11) 0 (0%) 217 8.38e-05
(0.077) 		1.96e-05
(0.0183) 		6.02e-10
(5.99e-07) 		1.64e-06
(0.00158) 		0.653
(1.00) 		0.239
(1.00) 		4.4e-09
(4.37e-06) 		1.63e-09
(1.62e-06) 		0.000958
(0.818) 		0.000184
(0.166) 		0.0172
(1.00) 		0.000158
(0.143)
Del Peak 2(1p13 1) 0 (0%) 239 0.000956
(0.818) 		6.31e-05
(0.0582) 		4.33e-16
(4.36e-13) 		5.81e-07
(0.000567) 		0.0391
(1.00) 		0.0673
(1.00) 		2.33e-06
(0.00224) 		6.91e-07
(0.000671) 		0.0473
(1.00) 		0.00022
(0.197) 		1.59e-05
(0.0149) 		0.0267
(1.00)
Del Peak 5(2q36 2) 0 (0%) 280 0.000141
(0.128) 		4.34e-05
(0.0401) 		6.14e-13
(6.15e-10) 		1.12e-06
(0.00109) 		0.177
(1.00) 		0.126
(1.00) 		6.61e-07
(0.000642) 		2.98e-08
(2.95e-05) 		0.885
(1.00) 		0.163
(1.00) 		3.47e-05
(0.0322) 		0.272
(1.00)
Amp Peak 6(3q26 33) 0 (0%) 35 0.00118
(0.996) 		3.91e-06
(0.00373) 		3.55e-15
(3.57e-12) 		2.84e-06
(0.00273) 		0.141
(1.00) 		0.0852
(1.00) 		1.32e-06
(0.00128) 		9.29e-05
(0.085) 		0.218
(1.00) 		4.12e-06
(0.00393) 		0.0693
(1.00) 		0.00343
(1.00)
Amp Peak 3(2p16 1) 0 (0%) 191 0.00212
(1.00) 		0.000275
(0.244) 		6.52e-14
(6.53e-11) 		6.98e-06
(0.00662) 		0.95
(1.00) 		0.643
(1.00) 		1.88e-05
(0.0176) 		7.55e-05
(0.0695) 		0.887
(1.00) 		0.0171
(1.00) 		0.0183
(1.00) 		0.477
(1.00)
Del Peak 41(17q11 2) 0 (0%) 316 3.03e-05
(0.0281) 		0.000101
(0.0923) 		2.73e-09
(2.71e-06) 		0.0107
(1.00) 		0.495
(1.00) 		0.378
(1.00) 		1.48e-06
(0.00143) 		4.83e-08
(4.75e-05) 		0.143
(1.00) 		0.0373
(1.00) 		0.112
(1.00) 		0.795
(1.00)
Amp Peak 4(2q31 2) 0 (0%) 277 0.0154
(1.00) 		0.0275
(1.00) 		6.32e-07
(0.000615) 		3.95e-07
(0.000386) 		0.724
(1.00) 		0.887
(1.00) 		0.000194
(0.174) 		0.000248
(0.221) 		0.37
(1.00) 		0.511
(1.00) 		0.0772
(1.00) 		0.309
(1.00)
Del Peak 27(10p15 1) 0 (0%) 243 0.109
(1.00) 		0.633
(1.00) 		0.000162
(0.146) 		2.68e-05
(0.0249) 		0.469
(1.00) 		0.353
(1.00) 		0.000161
(0.145) 		0.00143
(1.00) 		0.0107
(1.00) 		9.09e-06
(0.00859) 		0.00157
(1.00) 		0.0151
(1.00)
Del Peak 28(10q23 31) 0 (0%) 200 0.0148
(1.00) 		0.0131
(1.00) 		1.64e-05
(0.0154) 		6.74e-06
(0.0064) 		0.36
(1.00) 		0.39
(1.00) 		8.54e-06
(0.00808) 		7.23e-07
(0.000701) 		0.219
(1.00) 		0.0644
(1.00) 		0.116
(1.00) 		0.543
(1.00)
Amp Peak 2(1q21 2) 0 (0%) 203 0.0448
(1.00) 		0.0304
(1.00) 		1.8e-08
(1.78e-05) 		0.0043
(1.00) 		0.16
(1.00) 		0.0492
(1.00) 		1.87e-05
(0.0175) 		4.11e-05
(0.0381) 		0.0393
(1.00) 		0.00181
(1.00) 		0.00803
(1.00) 		0.273
(1.00)
Amp Peak 12(7q21 2) 0 (0%) 198 0.175
(1.00) 		0.116
(1.00) 		1.34e-11
(1.34e-08) 		4.52e-06
(0.00431) 		0.0573
(1.00) 		0.389
(1.00) 		0.000661
(0.573) 		0.000185
(0.167) 		0.0358
(1.00) 		0.0527
(1.00) 		0.0112
(1.00) 		0.0121
(1.00)
Amp Peak 23(17q25 1) 0 (0%) 219 0.0133
(1.00) 		0.0338
(1.00) 		7.84e-09
(7.77e-06) 		5.4e-05
(0.0498) 		0.479
(1.00) 		0.249
(1.00) 		0.00285
(1.00) 		9.13e-05
(0.0837) 		0.772
(1.00) 		0.0601
(1.00) 		0.0455
(1.00) 		0.154
(1.00)
Del Peak 29(11p15 5) 0 (0%) 226 0.000261
(0.231) 		0.0341
(1.00) 		4.67e-06
(0.00445) 		0.023
(1.00) 		0.000764
(0.659) 		2.02e-05
(0.0189) 		0.00293
(1.00) 		0.031
(1.00) 		0.00193
(1.00) 		0.0459
(1.00) 		0.0485
(1.00) 		0.307
(1.00)
Amp Peak 22(15q26 3) 0 (0%) 273 0.253
(1.00) 		0.0414
(1.00) 		1.93e-06
(0.00186) 		1.56e-05
(0.0147) 		0.354
(1.00) 		0.0183
(1.00) 		0.000334
(0.294) 		0.00253
(1.00) 		0.0159
(1.00) 		0.00123
(1.00) 		0.00291
(1.00) 		0.0151
(1.00)
Amp Peak 25(18q11 2) 0 (0%) 286 0.000339
(0.299) 		0.0146
(1.00) 		1.06e-07
(0.000104) 		0.000618
(0.537) 		0.272
(1.00) 		0.74
(1.00) 		0.000841
(0.723) 		5.04e-06
(0.00479) 		0.402
(1.00) 		0.00539
(1.00) 		0.00133
(1.00) 		0.0819
(1.00)
Del Peak 13(4q35 2) 0 (0%) 146 0.0987
(1.00) 		0.396
(1.00) 		1.83e-07
(0.00018) 		0.000424
(0.371) 		0.455
(1.00) 		0.47
(1.00) 		0.000143
(0.13) 		0.0105
(1.00) 		0.44
(1.00) 		0.0957
(1.00) 		0.00104
(0.887) 		0.288
(1.00)
Del Peak 15(5q31 1) 0 (0%) 94 0.273
(1.00) 		0.47
(1.00) 		1.56e-10
(1.56e-07) 		8.05e-05
(0.074) 		0.272
(1.00) 		0.166
(1.00) 		0.0582
(1.00) 		0.0639
(1.00) 		0.684
(1.00) 		0.00713
(1.00) 		0.12
(1.00) 		0.115
(1.00)
Del Peak 17(6q22 31) 0 (0%) 314 0.0278
(1.00) 		0.0123
(1.00) 		9.32e-05
(0.0852) 		0.00145
(1.00) 		0.629
(1.00) 		0.354
(1.00) 		0.000249
(0.222) 		0.000587
(0.51) 		0.374
(1.00) 		0.218
(1.00) 		0.596
(1.00) 		0.0427
(1.00)
Del Peak 26(10p15 3) 0 (0%) 231 0.318
(1.00) 		0.493
(1.00) 		4.61e-05
(0.0426) 		0.000476
(0.416) 		0.329
(1.00) 		0.443
(1.00) 		0.00156
(1.00) 		0.000554
(0.482) 		0.0549
(1.00) 		4.45e-05
(0.0412) 		0.00213
(1.00) 		0.0295
(1.00)
Del Peak 35(14q11 2) 0 (0%) 273 0.0724
(1.00) 		0.237
(1.00) 		0.0692
(1.00) 		0.438
(1.00) 		0.206
(1.00) 		0.159
(1.00) 		0.000386
(0.339) 		9.8e-05
(0.0894) 		0.183
(1.00) 		0.493
(1.00) 		0.0223
(1.00) 		0.000203
(0.182)
Del Peak 44(19p13 3) 0 (0%) 236 0.206
(1.00) 		0.00433
(1.00) 		2.55e-05
(0.0237) 		0.209
(1.00) 		0.0588
(1.00) 		0.251
(1.00) 		0.284
(1.00) 		0.0283
(1.00) 		0.000224
(0.2) 		0.00297
(1.00) 		0.237
(1.00) 		0.0314
(1.00)
Del Peak 45(19q13 33) 0 (0%) 307 0.525
(1.00) 		0.212
(1.00) 		1.01e-06
(0.000979) 		9.24e-05
(0.0846) 		0.244
(1.00) 		0.719
(1.00) 		0.0819
(1.00) 		0.0398
(1.00) 		0.0341
(1.00) 		0.334
(1.00) 		0.148
(1.00) 		0.65
(1.00)
Del Peak 48(21q22 3) 0 (0%) 184 0.876
(1.00) 		0.189
(1.00) 		1.82e-08
(1.8e-05) 		0.000126
(0.114) 		0.396
(1.00) 		0.0991
(1.00) 		0.13
(1.00) 		0.0131
(1.00) 		0.0589
(1.00) 		0.161
(1.00) 		0.0433
(1.00) 		0.851
(1.00)
Del Peak 50(22q13 32) 0 (0%) 319 0.00022
(0.197) 		0.00221
(1.00) 		0.19
(1.00) 		0.414
(1.00) 		0.543
(1.00) 		0.0759
(1.00) 		0.119
(1.00) 		0.1
(1.00) 		0.0185
(1.00) 		0.0144
(1.00) 		0.0194
(1.00) 		0.000155
(0.141)
Del Peak 52(Xp11 3) 0 (0%) 287 0.11
(1.00) 		0.414
(1.00) 		2.49e-06
(0.00239) 		1.46e-05
(0.0137) 		0.0923
(1.00) 		0.124
(1.00) 		0.0631
(1.00) 		0.00391
(1.00) 		0.131
(1.00) 		0.138
(1.00) 		0.00181
(1.00) 		0.125
(1.00)
Del Peak 53(Xq22 3) 0 (0%) 316 0.00842
(1.00) 		0.015
(1.00) 		3.76e-08
(3.71e-05) 		0.000179
(0.161) 		0.663
(1.00) 		0.92
(1.00) 		0.0422
(1.00) 		0.438
(1.00) 		0.276
(1.00) 		0.797
(1.00) 		0.0408
(1.00) 		0.331
(1.00)
Amp Peak 1(1p34 2) 0 (0%) 349 0.0264
(1.00) 		0.231
(1.00) 		2.57e-07
(0.000252) 		0.273
(1.00) 		0.363
(1.00) 		0.619
(1.00) 		0.0242
(1.00) 		0.0572
(1.00) 		0.088
(1.00) 		0.669
(1.00) 		0.341
(1.00) 		0.0594
(1.00)
Amp Peak 8(5p15 33) 0 (0%) 87 0.852
(1.00) 		0.983
(1.00) 		3.61e-06
(0.00345) 		0.00694
(1.00) 		0.405
(1.00) 		0.502
(1.00) 		0.262
(1.00) 		0.487
(1.00) 		0.45
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.902
(1.00)
Amp Peak 9(5p12) 0 (0%) 145 0.961
(1.00) 		0.857
(1.00) 		6.93e-09
(6.86e-06) 		0.0036
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.225
(1.00) 		0.21
(1.00) 		0.792
(1.00) 		0.236
(1.00) 		0.104
(1.00) 		0.0258
(1.00)
Amp Peak 15(9p24 1) 0 (0%) 342 0.188
(1.00) 		0.0431
(1.00) 		0.000198
(0.178) 		0.278
(1.00) 		0.0017
(1.00) 		0.00501
(1.00) 		0.00699
(1.00) 		0.000767
(0.661) 		0.117
(1.00) 		0.0167
(1.00) 		0.429
(1.00) 		0.197
(1.00)
Amp Peak 18(12p13 33) 0 (0%) 210 0.0263
(1.00) 		0.0936
(1.00) 		3.83e-06
(0.00366) 		0.00104
(0.886) 		0.313
(1.00) 		0.729
(1.00) 		0.000418
(0.368) 		0.0103
(1.00) 		0.837
(1.00) 		0.218
(1.00) 		0.0123
(1.00) 		0.37
(1.00)
Amp Peak 24(18p11 32) 0 (0%) 272 0.0831
(1.00) 		0.021
(1.00) 		2.88e-06
(0.00276) 		0.00072
(0.622) 		0.231
(1.00) 		0.451
(1.00) 		0.131
(1.00) 		0.0402
(1.00) 		0.898
(1.00) 		0.0209
(1.00) 		0.0353
(1.00) 		0.69
(1.00)
Amp Peak 26(19q12) 0 (0%) 243 0.438
(1.00) 		0.693
(1.00) 		4.94e-06
(0.0047) 		0.189
(1.00) 		0.231
(1.00) 		0.0287
(1.00) 		0.00823
(1.00) 		0.13
(1.00) 		0.913
(1.00) 		0.37
(1.00) 		0.0616
(1.00) 		0.51
(1.00)
Amp Peak 27(19q13 2) 0 (0%) 239 0.678
(1.00) 		0.86
(1.00) 		0.00025
(0.222) 		0.101
(1.00) 		0.356
(1.00) 		0.117
(1.00) 		0.106
(1.00) 		0.085
(1.00) 		0.77
(1.00) 		0.246
(1.00) 		0.302
(1.00) 		0.574
(1.00)
Amp Peak 28(20p12 2) 0 (0%) 193 0.00106
(0.898) 		0.0142
(1.00) 		6.62e-09
(6.57e-06) 		0.000419
(0.368) 		0.967
(1.00) 		0.221
(1.00) 		0.0408
(1.00) 		0.00273
(1.00) 		0.259
(1.00) 		0.0945
(1.00) 		0.172
(1.00) 		0.551
(1.00)
Amp Peak 29(20q11 21) 0 (0%) 175 0.86
(1.00) 		0.948
(1.00) 		0.000192
(0.173) 		0.0234
(1.00) 		0.669
(1.00) 		0.588
(1.00) 		0.585
(1.00) 		0.757
(1.00) 		0.941
(1.00) 		0.373
(1.00) 		0.228
(1.00) 		0.937
(1.00)
Del Peak 4(2q22 1) 0 (0%) 309 0.208
(1.00) 		0.245
(1.00) 		0.000112
(0.102) 		0.0327
(1.00) 		0.667
(1.00) 		0.0777
(1.00) 		0.0219
(1.00) 		0.0165
(1.00) 		0.512
(1.00) 		0.226
(1.00) 		0.000892
(0.765) 		0.779
(1.00)
Del Peak 7(3p13) 0 (0%) 61 0.304
(1.00) 		0.987
(1.00) 		6.21e-07
(0.000605) 		0.000609
(0.529) 		0.882
(1.00) 		0.0379
(1.00) 		0.0756
(1.00) 		0.0171
(1.00) 		0.432
(1.00) 		0.00134
(1.00) 		0.1
(1.00) 		0.0425
(1.00)
Del Peak 8(3p12 3) 0 (0%) 70 0.164
(1.00) 		0.954
(1.00) 		1.47e-05
(0.0138) 		0.0019
(1.00) 		1
(1.00) 		0.092
(1.00) 		0.12
(1.00) 		0.0235
(1.00) 		0.701
(1.00) 		0.00577
(1.00) 		0.116
(1.00) 		0.246
(1.00)
Del Peak 10(4p15 2) 0 (0%) 165 0.000325
(0.287) 		0.00153
(1.00) 		4.09e-07
(4e-04) 		0.00088
(0.755) 		0.662
(1.00) 		0.0343
(1.00) 		0.0138
(1.00) 		0.00689
(1.00) 		0.302
(1.00) 		0.864
(1.00) 		0.00495
(1.00) 		0.412
(1.00)
Del Peak 11(4q22 1) 0 (0%) 188 0.00688
(1.00) 		0.0456
(1.00) 		1.43e-06
(0.00138) 		0.0173
(1.00) 		0.123
(1.00) 		0.381
(1.00) 		0.00473
(1.00) 		0.00722
(1.00) 		0.35
(1.00) 		0.168
(1.00) 		0.00308
(1.00) 		0.571
(1.00)
Del Peak 12(4q32 3) 0 (0%) 152 0.0113
(1.00) 		0.0203
(1.00) 		3.01e-08
(2.96e-05) 		0.00238
(1.00) 		0.101
(1.00) 		0.523
(1.00) 		0.0012
(1.00) 		0.00455
(1.00) 		0.663
(1.00) 		0.242
(1.00) 		0.0101
(1.00) 		0.317
(1.00)
Del Peak 14(5q11 2) 0 (0%) 111 0.706
(1.00) 		0.656
(1.00) 		2.04e-12
(2.04e-09) 		0.000313
(0.277) 		0.959
(1.00) 		0.244
(1.00) 		0.0104
(1.00) 		0.0858
(1.00) 		0.987
(1.00) 		0.00113
(0.958) 		0.232
(1.00) 		0.139
(1.00)
Del Peak 18(6q26) 0 (0%) 306 0.0421
(1.00) 		0.0154
(1.00) 		0.000219
(0.196) 		0.00116
(0.982) 		0.921
(1.00) 		0.69
(1.00) 		0.00204
(1.00) 		0.00223
(1.00) 		0.184
(1.00) 		0.085
(1.00) 		0.138
(1.00) 		0.23
(1.00)
Del Peak 19(7q11 22) 0 (0%) 377 0.802
(1.00) 		0.106
(1.00) 		6.68e-05
(0.0615) 		0.687
(1.00) 		0.958
(1.00) 		0.75
(1.00) 		0.0465
(1.00) 		0.0493
(1.00) 		0.61
(1.00) 		0.358
(1.00) 		0.4
(1.00) 		0.886
(1.00)
Del Peak 22(9p23) 0 (0%) 143 0.0103
(1.00) 		0.00676
(1.00) 		2.72e-10
(2.71e-07) 		0.0448
(1.00) 		0.146
(1.00) 		0.208
(1.00) 		0.00281
(1.00) 		0.0746
(1.00) 		0.0991
(1.00) 		0.0328
(1.00) 		0.125
(1.00) 		0.043
(1.00)
Del Peak 23(9p21 3) 0 (0%) 98 0.326
(1.00) 		0.311
(1.00) 		1.46e-07
(0.000143) 		0.325
(1.00) 		0.695
(1.00) 		0.388
(1.00) 		0.0535
(1.00) 		0.472
(1.00) 		0.351
(1.00) 		0.421
(1.00) 		0.337
(1.00) 		0.241
(1.00)
Del Peak 24(9p21 1) 0 (0%) 148 0.121
(1.00) 		0.0364
(1.00) 		8.75e-08
(8.59e-05) 		0.1
(1.00) 		0.673
(1.00) 		0.391
(1.00) 		0.0177
(1.00) 		0.204
(1.00) 		0.0873
(1.00) 		0.0938
(1.00) 		0.653
(1.00) 		0.16
(1.00)
Del Peak 40(17p11 2) 0 (0%) 202 0.217
(1.00) 		0.0324
(1.00) 		0.000167
(0.15) 		0.102
(1.00) 		0.15
(1.00) 		0.0182
(1.00) 		0.0446
(1.00) 		0.0798
(1.00) 		0.183
(1.00) 		0.165
(1.00) 		0.32
(1.00) 		0.0761
(1.00)
Del Peak 42(17q25 3) 0 (0%) 333 0.0046
(1.00) 		0.015
(1.00) 		1.43e-05
(0.0135) 		0.0983
(1.00) 		0.622
(1.00) 		0.994
(1.00) 		0.146
(1.00) 		0.00187
(1.00) 		0.529
(1.00) 		0.223
(1.00) 		0.348
(1.00) 		0.814
(1.00)
Del Peak 46(19q13 43) 0 (0%) 309 0.619
(1.00) 		0.491
(1.00) 		8.08e-06
(0.00765) 		0.000848
(0.728) 		0.446
(1.00) 		0.543
(1.00) 		0.0902
(1.00) 		0.02
(1.00) 		0.077
(1.00) 		0.437
(1.00) 		0.477
(1.00) 		0.607
(1.00)
Del Peak 51(Xp22 2) 0 (0%) 285 0.636
(1.00) 		0.51
(1.00) 		3.12e-05
(0.0289) 		0.0174
(1.00) 		0.277
(1.00) 		0.783
(1.00) 		0.236
(1.00) 		0.103
(1.00) 		0.179
(1.00) 		0.235
(1.00) 		0.0509
(1.00) 		0.241
(1.00)
Amp Peak 5(3p11 1) 0 (0%) 332 0.104
(1.00) 		0.836
(1.00) 		0.863
(1.00) 		0.788
(1.00) 		0.214
(1.00) 		0.0013
(1.00) 		0.239
(1.00) 		0.541
(1.00) 		0.845
(1.00) 		0.602
(1.00) 		0.339
(1.00) 		0.0999
(1.00)
Amp Peak 7(4q12) 0 (0%) 318 0.809
(1.00) 		0.2
(1.00) 		0.00214
(1.00) 		0.118
(1.00) 		0.356
(1.00) 		0.131
(1.00) 		0.221
(1.00) 		0.106
(1.00) 		0.178
(1.00) 		0.393
(1.00) 		0.069
(1.00) 		0.149
(1.00)
Amp Peak 10(6p12 1) 0 (0%) 281 0.551
(1.00) 		0.737
(1.00) 		0.000939
(0.804) 		0.385
(1.00) 		0.962
(1.00) 		0.3
(1.00) 		0.106
(1.00) 		0.522
(1.00) 		0.27
(1.00) 		0.267
(1.00) 		0.0885
(1.00) 		0.0596
(1.00)
Amp Peak 11(7p11 2) 0 (0%) 214 0.164
(1.00) 		0.0996
(1.00) 		0.000543
(0.474) 		0.00576
(1.00) 		0.687
(1.00) 		0.801
(1.00) 		0.0273
(1.00) 		0.000542
(0.474) 		0.634
(1.00) 		0.0644
(1.00) 		0.276
(1.00) 		0.164
(1.00)
Amp Peak 13(8p11 23) 0 (0%) 223 0.0137
(1.00) 		0.467
(1.00) 		0.157
(1.00) 		0.0813
(1.00) 		0.192
(1.00) 		0.0988
(1.00) 		0.363
(1.00) 		0.537
(1.00) 		0.135
(1.00) 		0.371
(1.00) 		0.862
(1.00) 		0.664
(1.00)
Amp Peak 14(8q24 21) 0 (0%) 125 0.919
(1.00) 		0.788
(1.00) 		0.226
(1.00) 		0.91
(1.00) 		0.917
(1.00) 		0.708
(1.00) 		0.995
(1.00) 		0.509
(1.00) 		0.866
(1.00) 		0.497
(1.00) 		0.887
(1.00) 		0.925
(1.00)
Amp Peak 16(9p13 3) 0 (0%) 301 0.23
(1.00) 		0.641
(1.00) 		0.00415
(1.00) 		0.116
(1.00) 		0.0708
(1.00) 		0.00898
(1.00) 		0.0114
(1.00) 		0.00149
(1.00) 		0.823
(1.00) 		0.555
(1.00) 		0.197
(1.00) 		0.628
(1.00)
Amp Peak 17(11q13 3) 0 (0%) 265 0.0582
(1.00) 		0.0872
(1.00) 		0.00348
(1.00) 		0.000474
(0.415) 		0.19
(1.00) 		0.0358
(1.00) 		0.0123
(1.00) 		0.124
(1.00) 		0.0454
(1.00) 		0.00669
(1.00) 		0.00124
(1.00) 		0.403
(1.00)
Amp Peak 19(12q15) 0 (0%) 270 0.235
(1.00) 		0.326
(1.00) 		0.00174
(1.00) 		0.00255
(1.00) 		0.764
(1.00) 		0.524
(1.00) 		0.0588
(1.00) 		0.0807
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.0316
(1.00) 		0.593
(1.00)
Amp Peak 20(13q34) 0 (0%) 342 0.981
(1.00) 		0.0207
(1.00) 		0.138
(1.00) 		0.533
(1.00) 		0.87
(1.00) 		0.0834
(1.00) 		0.578
(1.00) 		0.809
(1.00) 		0.155
(1.00) 		0.381
(1.00) 		0.222
(1.00) 		0.794
(1.00)
Amp Peak 21(14q13 3) 0 (0%) 286 0.316
(1.00) 		0.194
(1.00) 		0.108
(1.00) 		0.147
(1.00) 		0.57
(1.00) 		0.00826
(1.00) 		0.0675
(1.00) 		0.0164
(1.00) 		0.0032
(1.00) 		0.532
(1.00) 		0.204
(1.00) 		0.00575
(1.00)
Amp Peak 30(22q11 21) 0 (0%) 210 0.141
(1.00) 		0.204
(1.00) 		0.00184
(1.00) 		0.000296
(0.262) 		0.888
(1.00) 		0.349
(1.00) 		0.0104
(1.00) 		0.0345
(1.00) 		0.751
(1.00) 		0.027
(1.00) 		0.666
(1.00) 		0.852
(1.00)
Amp Peak 31(Xq28) 0 (0%) 307 0.793
(1.00) 		0.71
(1.00) 		0.0894
(1.00) 		0.215
(1.00) 		0.0701
(1.00) 		0.069
(1.00) 		0.109
(1.00) 		0.0781
(1.00) 		0.518
(1.00) 		0.303
(1.00) 		0.073
(1.00) 		0.128
(1.00)
Del Peak 3(2p25 3) 0 (0%) 377 0.0858
(1.00) 		0.0152
(1.00) 		0.394
(1.00) 		0.424
(1.00) 		0.11
(1.00) 		0.838
(1.00) 		0.319
(1.00) 		0.128
(1.00) 		0.0533
(1.00) 		0.0247
(1.00) 		0.123
(1.00) 		0.311
(1.00)
Del Peak 6(3p25 3) 0 (0%) 88 0.674
(1.00) 		0.63
(1.00) 		0.0138
(1.00) 		0.00194
(1.00) 		0.637
(1.00) 		0.18
(1.00) 		0.078
(1.00) 		0.0433
(1.00) 		0.602
(1.00) 		0.0597
(1.00) 		0.533
(1.00) 		0.302
(1.00)
Del Peak 9(3q11 1) 0 (0%) 355 0.762
(1.00) 		0.625
(1.00) 		0.122
(1.00) 		0.259
(1.00) 		0.765
(1.00) 		0.282
(1.00) 		0.885
(1.00) 		0.803
(1.00) 		0.289
(1.00) 		0.887
(1.00) 		0.938
(1.00) 		0.385
(1.00)
Del Peak 16(6p25 3) 0 (0%) 313 0.319
(1.00) 		0.0462
(1.00) 		0.0212
(1.00) 		0.000974
(0.831) 		0.393
(1.00) 		0.013
(1.00) 		0.00219
(1.00) 		0.000305
(0.27) 		0.179
(1.00) 		0.0797
(1.00) 		0.438
(1.00) 		0.0956
(1.00)
Del Peak 20(7q36 3) 0 (0%) 332 0.17
(1.00) 		0.131
(1.00) 		0.000708
(0.612) 		0.178
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.00254
(1.00) 		0.0054
(1.00) 		0.028
(1.00) 		0.166
(1.00) 		0.0247
(1.00) 		0.0251
(1.00)
Del Peak 21(8p23 2) 0 (0%) 134 0.667
(1.00) 		0.847
(1.00) 		0.000531
(0.464) 		0.206
(1.00) 		0.345
(1.00) 		0.141
(1.00) 		0.494
(1.00) 		0.0421
(1.00) 		0.68
(1.00) 		0.0705
(1.00) 		0.117
(1.00) 		0.469
(1.00)
Del Peak 30(11q22 1) 0 (0%) 290 0.708
(1.00) 		0.379
(1.00) 		0.00114
(0.966) 		0.0101
(1.00) 		0.103
(1.00) 		0.995
(1.00) 		0.13
(1.00) 		0.263
(1.00) 		0.382
(1.00) 		0.849
(1.00) 		0.727
(1.00) 		0.411
(1.00)
Del Peak 31(11q25) 0 (0%) 264 0.874
(1.00) 		0.578
(1.00) 		0.00925
(1.00) 		0.273
(1.00) 		0.113
(1.00) 		0.908
(1.00) 		0.134
(1.00) 		0.104
(1.00) 		0.49
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.684
(1.00)
Del Peak 32(12q24 32) 0 (0%) 344 0.467
(1.00) 		0.266
(1.00) 		0.717
(1.00) 		0.954
(1.00) 		0.396
(1.00) 		0.597
(1.00) 		0.944
(1.00) 		0.895
(1.00) 		0.472
(1.00) 		0.803
(1.00) 		0.971
(1.00) 		0.464
(1.00)
Del Peak 33(13q12 11) 0 (0%) 143 0.104
(1.00) 		0.463
(1.00) 		0.0231
(1.00) 		0.18
(1.00) 		0.907
(1.00) 		0.268
(1.00) 		0.73
(1.00) 		0.286
(1.00) 		0.812
(1.00) 		0.681
(1.00) 		0.964
(1.00) 		0.0516
(1.00)
Del Peak 34(13q14 2) 0 (0%) 134 0.0997
(1.00) 		0.321
(1.00) 		0.00111
(0.939) 		0.0629
(1.00) 		0.707
(1.00) 		0.682
(1.00) 		0.108
(1.00) 		0.121
(1.00) 		0.893
(1.00) 		0.672
(1.00) 		0.392
(1.00) 		0.0294
(1.00)
Del Peak 36(15q12) 0 (0%) 280 0.47
(1.00) 		0.469
(1.00) 		0.468
(1.00) 		0.142
(1.00) 		0.0717
(1.00) 		0.00798
(1.00) 		0.215
(1.00) 		0.149
(1.00) 		0.024
(1.00) 		0.189
(1.00) 		0.102
(1.00) 		0.357
(1.00)
Del Peak 37(15q21 1) 0 (0%) 287 0.382
(1.00) 		0.415
(1.00) 		0.498
(1.00) 		0.71
(1.00) 		0.138
(1.00) 		0.00763
(1.00) 		0.299
(1.00) 		0.104
(1.00) 		0.0265
(1.00) 		0.199
(1.00) 		0.00528
(1.00) 		0.286
(1.00)
Del Peak 38(16p13 3) 0 (0%) 263 0.348
(1.00) 		0.339
(1.00) 		0.00958
(1.00) 		0.145
(1.00) 		0.149
(1.00) 		0.606
(1.00) 		0.371
(1.00) 		0.268
(1.00) 		0.427
(1.00) 		0.401
(1.00) 		0.438
(1.00) 		0.0287
(1.00)
Del Peak 39(16q23 1) 0 (0%) 243 0.874
(1.00) 		0.336
(1.00) 		0.218
(1.00) 		0.145
(1.00) 		0.354
(1.00) 		0.761
(1.00) 		0.198
(1.00) 		0.203
(1.00) 		0.931
(1.00) 		0.56
(1.00) 		0.0464
(1.00) 		0.393
(1.00)
Del Peak 43(18q23) 0 (0%) 230 0.454
(1.00) 		0.217
(1.00) 		0.0441
(1.00) 		0.961
(1.00) 		0.801
(1.00) 		0.397
(1.00) 		0.524
(1.00) 		0.0228
(1.00) 		0.942
(1.00) 		0.444
(1.00) 		0.937
(1.00) 		0.332
(1.00)
Del Peak 47(21q21 1) 0 (0%) 218 0.571
(1.00) 		0.395
(1.00) 		0.000633
(0.548) 		0.00268
(1.00) 		0.585
(1.00) 		0.89
(1.00) 		0.373
(1.00) 		0.533
(1.00) 		0.0379
(1.00) 		0.0275
(1.00) 		0.0195
(1.00) 		0.048
(1.00)
Del Peak 49(22q11 21) 0 (0%) 346 0.0298
(1.00) 		0.16
(1.00) 		0.173
(1.00) 		0.123
(1.00) 		0.145
(1.00) 		0.129
(1.00) 		0.645
(1.00) 		0.329
(1.00) 		0.0583
(1.00) 		0.0974
(1.00) 		0.304
(1.00) 		0.383
(1.00)
'Amp Peak 1(1p34.2)' versus 'CN_CNMF'

P value = 2.57e-07 (Fisher's exact test), Q value = 0.00025

Table S1.  Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 1(1P34.2) CNV 18 7 42
AMP PEAK 1(1P34.2) WILD-TYPE 132 117 100

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.8e-08 (Fisher's exact test), Q value = 1.8e-05

Table S2.  Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 2(1Q21.2) CNV 63 91 59
AMP PEAK 2(1Q21.2) WILD-TYPE 87 33 83

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.87e-05 (Fisher's exact test), Q value = 0.018

Table S3.  Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
AMP PEAK 2(1Q21.2) CNV 27 72 55 25
AMP PEAK 2(1Q21.2) WILD-TYPE 50 30 56 30

Figure S3.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.11e-05 (Fisher's exact test), Q value = 0.038

Table S4.  Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 2(1Q21.2) CNV 74 35 70
AMP PEAK 2(1Q21.2) WILD-TYPE 33 35 98

Figure S4.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(2p16.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000275 (Fisher's exact test), Q value = 0.24

Table S5.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
AMP PEAK 3(2P16.1) CNV 7 42 15 22
AMP PEAK 3(2P16.1) WILD-TYPE 15 14 8 31

Figure S5.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 3(2p16.1)' versus 'CN_CNMF'

P value = 6.52e-14 (Fisher's exact test), Q value = 6.5e-11

Table S6.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 3(2P16.1) CNV 55 101 69
AMP PEAK 3(2P16.1) WILD-TYPE 95 23 73

Figure S6.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(2p16.1)' versus 'METHLYATION_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0066

Table S7.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
AMP PEAK 3(2P16.1) CNV 43 62 30
AMP PEAK 3(2P16.1) WILD-TYPE 53 20 42

Figure S7.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(2p16.1)' versus 'MRNASEQ_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.018

Table S8.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
AMP PEAK 3(2P16.1) CNV 29 71 64 21
AMP PEAK 3(2P16.1) WILD-TYPE 48 31 47 34

Figure S8.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(2p16.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.55e-05 (Fisher's exact test), Q value = 0.069

Table S9.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 3(2P16.1) CNV 75 37 73
AMP PEAK 3(2P16.1) WILD-TYPE 32 33 95

Figure S9.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(2q31.2)' versus 'CN_CNMF'

P value = 6.32e-07 (Fisher's exact test), Q value = 0.00061

Table S10.  Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 4(2Q31.2) CNV 32 64 43
AMP PEAK 4(2Q31.2) WILD-TYPE 118 60 99

Figure S10.  Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(2q31.2)' versus 'METHLYATION_CNMF'

P value = 3.95e-07 (Fisher's exact test), Q value = 0.00039

Table S11.  Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
AMP PEAK 4(2Q31.2) CNV 24 47 14
AMP PEAK 4(2Q31.2) WILD-TYPE 72 35 58

Figure S11.  Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 4(2q31.2)' versus 'MRNASEQ_CNMF'

P value = 0.000194 (Fisher's exact test), Q value = 0.17

Table S12.  Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
AMP PEAK 4(2Q31.2) CNV 20 53 31 14
AMP PEAK 4(2Q31.2) WILD-TYPE 57 49 80 41

Figure S12.  Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 4(2q31.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.22

Table S13.  Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 4(2Q31.2) CNV 53 22 43
AMP PEAK 4(2Q31.2) WILD-TYPE 54 48 125

Figure S13.  Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(3q26.33)' versus 'MRNA_CHIERARCHICAL'

P value = 3.91e-06 (Fisher's exact test), Q value = 0.0037

Table S14.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
AMP PEAK 6(3Q26.33) CNV 14 56 20 51
AMP PEAK 6(3Q26.33) WILD-TYPE 8 0 3 2

Figure S14.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 6(3q26.33)' versus 'CN_CNMF'

P value = 3.55e-15 (Fisher's exact test), Q value = 3.6e-12

Table S15.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 6(3Q26.33) CNV 116 124 141
AMP PEAK 6(3Q26.33) WILD-TYPE 34 0 1

Figure S15.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(3q26.33)' versus 'METHLYATION_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0027

Table S16.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
AMP PEAK 6(3Q26.33) CNV 78 82 69
AMP PEAK 6(3Q26.33) WILD-TYPE 18 0 3

Figure S16.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(3q26.33)' versus 'MRNASEQ_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.0013

Table S17.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
AMP PEAK 6(3Q26.33) CNV 73 102 101 42
AMP PEAK 6(3Q26.33) WILD-TYPE 4 0 10 13

Figure S17.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(3q26.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.29e-05 (Fisher's exact test), Q value = 0.085

Table S18.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 6(3Q26.33) CNV 107 63 148
AMP PEAK 6(3Q26.33) WILD-TYPE 0 7 20

Figure S18.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(3q26.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.12e-06 (Fisher's exact test), Q value = 0.0039

Table S19.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
AMP PEAK 6(3Q26.33) CNV 111 156 73
AMP PEAK 6(3Q26.33) WILD-TYPE 2 25 0

Figure S19.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(5p15.33)' versus 'CN_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0035

Table S20.  Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 8(5P15.33) CNV 103 96 130
AMP PEAK 8(5P15.33) WILD-TYPE 47 28 12

Figure S20.  Get High-res Image Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(5p12)' versus 'CN_CNMF'

P value = 6.93e-09 (Fisher's exact test), Q value = 6.9e-06

Table S21.  Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 9(5P12) CNV 73 81 117
AMP PEAK 9(5P12) WILD-TYPE 77 43 25

Figure S21.  Get High-res Image Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q21.2)' versus 'CN_CNMF'

P value = 1.34e-11 (Fisher's exact test), Q value = 1.3e-08

Table S22.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 12(7Q21.2) CNV 52 95 71
AMP PEAK 12(7Q21.2) WILD-TYPE 98 29 71

Figure S22.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q21.2)' versus 'METHLYATION_CNMF'

P value = 4.52e-06 (Fisher's exact test), Q value = 0.0043

Table S23.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
AMP PEAK 12(7Q21.2) CNV 33 58 32
AMP PEAK 12(7Q21.2) WILD-TYPE 63 24 40

Figure S23.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(7q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000185 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 12(7Q21.2) CNV 74 33 75
AMP PEAK 12(7Q21.2) WILD-TYPE 33 37 93

Figure S24.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(9p24.1)' versus 'CN_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.18

Table S25.  Gene #15: 'Amp Peak 15(9p24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 15(9P24.1) CNV 28 34 12
AMP PEAK 15(9P24.1) WILD-TYPE 122 90 130

Figure S25.  Get High-res Image Gene #15: 'Amp Peak 15(9p24.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.83e-06 (Fisher's exact test), Q value = 0.0037

Table S26.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 18(12P13.33) CNV 54 82 70
AMP PEAK 18(12P13.33) WILD-TYPE 96 42 72

Figure S26.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'CN_CNMF'

P value = 1.93e-06 (Fisher's exact test), Q value = 0.0019

Table S27.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 22(15Q26.3) CNV 31 62 50
AMP PEAK 22(15Q26.3) WILD-TYPE 119 62 92

Figure S27.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'METHLYATION_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.015

Table S28.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
AMP PEAK 22(15Q26.3) CNV 16 40 27
AMP PEAK 22(15Q26.3) WILD-TYPE 80 42 45

Figure S28.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(17q25.1)' versus 'CN_CNMF'

P value = 7.84e-09 (Fisher's exact test), Q value = 7.8e-06

Table S29.  Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 23(17Q25.1) CNV 48 85 64
AMP PEAK 23(17Q25.1) WILD-TYPE 102 39 78

Figure S29.  Get High-res Image Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(17q25.1)' versus 'METHLYATION_CNMF'

P value = 5.4e-05 (Fisher's exact test), Q value = 0.05

Table S30.  Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
AMP PEAK 23(17Q25.1) CNV 32 53 27
AMP PEAK 23(17Q25.1) WILD-TYPE 64 29 45

Figure S30.  Get High-res Image Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.13e-05 (Fisher's exact test), Q value = 0.084

Table S31.  Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 23(17Q25.1) CNV 66 32 59
AMP PEAK 23(17Q25.1) WILD-TYPE 41 38 109

Figure S31.  Get High-res Image Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(18p11.32)' versus 'CN_CNMF'

P value = 2.88e-06 (Fisher's exact test), Q value = 0.0028

Table S32.  Gene #24: 'Amp Peak 24(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 24(18P11.32) CNV 36 65 43
AMP PEAK 24(18P11.32) WILD-TYPE 114 59 99

Figure S32.  Get High-res Image Gene #24: 'Amp Peak 24(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(18q11.2)' versus 'CN_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 1e-04

Table S33.  Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 25(18Q11.2) CNV 26 61 43
AMP PEAK 25(18Q11.2) WILD-TYPE 124 63 99

Figure S33.  Get High-res Image Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-06 (Fisher's exact test), Q value = 0.0048

Table S34.  Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 25(18Q11.2) CNV 46 31 32
AMP PEAK 25(18Q11.2) WILD-TYPE 61 39 136

Figure S34.  Get High-res Image Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(19q12)' versus 'CN_CNMF'

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0047

Table S35.  Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 26(19Q12) CNV 47 74 52
AMP PEAK 26(19Q12) WILD-TYPE 103 50 90

Figure S35.  Get High-res Image Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(19q13.2)' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.22

Table S36.  Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 27(19Q13.2) CNV 50 71 56
AMP PEAK 27(19Q13.2) WILD-TYPE 100 53 86

Figure S36.  Get High-res Image Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(20p12.2)' versus 'CN_CNMF'

P value = 6.62e-09 (Fisher's exact test), Q value = 6.6e-06

Table S37.  Gene #28: 'Amp Peak 28(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 28(20P12.2) CNV 55 91 77
AMP PEAK 28(20P12.2) WILD-TYPE 95 33 65

Figure S37.  Get High-res Image Gene #28: 'Amp Peak 28(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20q11.21)' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.17

Table S38.  Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
AMP PEAK 29(20Q11.21) CNV 67 83 91
AMP PEAK 29(20Q11.21) WILD-TYPE 83 41 51

Figure S38.  Get High-res Image Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNA_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0014

Table S39.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 1(1P36.22) CNV 9 38 14 8
DEL PEAK 1(1P36.22) WILD-TYPE 33 14 18 20

Figure S39.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNA_CHIERARCHICAL'

P value = 6.89e-08 (Fisher's exact test), Q value = 6.8e-05

Table S40.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 1(1P36.22) CNV 8 42 8 11
DEL PEAK 1(1P36.22) WILD-TYPE 14 14 15 42

Figure S40.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.22)' versus 'CN_CNMF'

P value = 1.69e-26 (Fisher's exact test), Q value = 1.7e-23

Table S41.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 1(1P36.22) CNV 40 103 37
DEL PEAK 1(1P36.22) WILD-TYPE 110 21 105

Figure S41.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.22)' versus 'METHLYATION_CNMF'

P value = 4.55e-15 (Fisher's exact test), Q value = 4.6e-12

Table S42.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 1(1P36.22) CNV 16 61 23
DEL PEAK 1(1P36.22) WILD-TYPE 80 21 49

Figure S42.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNASEQ_CNMF'

P value = 8.67e-14 (Fisher's exact test), Q value = 8.7e-11

Table S43.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 1(1P36.22) CNV 19 77 35 18
DEL PEAK 1(1P36.22) WILD-TYPE 58 25 76 37

Figure S43.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.45e-15 (Fisher's exact test), Q value = 9.5e-12

Table S44.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 1(1P36.22) CNV 80 18 51
DEL PEAK 1(1P36.22) WILD-TYPE 27 52 117

Figure S44.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.017

Table S45.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 1(1P36.22) CNV 42 66 49
DEL PEAK 1(1P36.22) WILD-TYPE 71 115 24

Figure S45.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.29e-06 (Fisher's exact test), Q value = 0.0088

Table S46.  Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 41
DEL PEAK 1(1P36.22) CNV 44 20 30
DEL PEAK 1(1P36.22) WILD-TYPE 74 52 11

Figure S46.  Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 6.31e-05 (Fisher's exact test), Q value = 0.058

Table S47.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 2(1P13.1) CNV 9 37 12 12
DEL PEAK 2(1P13.1) WILD-TYPE 13 19 11 41

Figure S47.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 4.33e-16 (Fisher's exact test), Q value = 4.4e-13

Table S48.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 2(1P13.1) CNV 36 90 51
DEL PEAK 2(1P13.1) WILD-TYPE 114 34 91

Figure S48.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00057

Table S49.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 2(1P13.1) CNV 21 50 27
DEL PEAK 2(1P13.1) WILD-TYPE 75 32 45

Figure S49.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.33e-06 (Fisher's exact test), Q value = 0.0022

Table S50.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 2(1P13.1) CNV 26 66 38 17
DEL PEAK 2(1P13.1) WILD-TYPE 51 36 73 38

Figure S50.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 6.91e-07 (Fisher's exact test), Q value = 0.00067

Table S51.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 2(1P13.1) CNV 68 26 53
DEL PEAK 2(1P13.1) WILD-TYPE 39 44 115

Figure S51.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.00022 (Fisher's exact test), Q value = 0.2

Table S52.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 2(1P13.1) CNV 40 67 46
DEL PEAK 2(1P13.1) WILD-TYPE 73 114 27

Figure S52.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.59e-05 (Fisher's exact test), Q value = 0.015

Table S53.  Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 41
DEL PEAK 2(1P13.1) CNV 45 17 28
DEL PEAK 2(1P13.1) WILD-TYPE 73 55 13

Figure S53.  Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 4(2q22.1)' versus 'CN_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.1

Table S54.  Gene #35: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 4(2Q22.1) CNV 23 47 37
DEL PEAK 4(2Q22.1) WILD-TYPE 127 77 105

Figure S54.  Get High-res Image Gene #35: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNA_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.13

Table S55.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 5(2Q36.2) CNV 8 28 4 10
DEL PEAK 5(2Q36.2) WILD-TYPE 34 24 28 18

Figure S55.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.34e-05 (Fisher's exact test), Q value = 0.04

Table S56.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 5(2Q36.2) CNV 4 31 7 8
DEL PEAK 5(2Q36.2) WILD-TYPE 18 25 16 45

Figure S56.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(2q36.2)' versus 'CN_CNMF'

P value = 6.14e-13 (Fisher's exact test), Q value = 6.1e-10

Table S57.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 5(2Q36.2) CNV 26 73 37
DEL PEAK 5(2Q36.2) WILD-TYPE 124 51 105

Figure S57.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q36.2)' versus 'METHLYATION_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.0011

Table S58.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 5(2Q36.2) CNV 17 45 24
DEL PEAK 5(2Q36.2) WILD-TYPE 79 37 48

Figure S58.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNASEQ_CNMF'

P value = 6.61e-07 (Fisher's exact test), Q value = 0.00064

Table S59.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 5(2Q36.2) CNV 27 53 30 6
DEL PEAK 5(2Q36.2) WILD-TYPE 50 49 81 49

Figure S59.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.98e-08 (Fisher's exact test), Q value = 2.9e-05

Table S60.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 5(2Q36.2) CNV 60 19 37
DEL PEAK 5(2Q36.2) WILD-TYPE 47 51 131

Figure S60.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(2q36.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.47e-05 (Fisher's exact test), Q value = 0.032

Table S61.  Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 41
DEL PEAK 5(2Q36.2) CNV 47 10 20
DEL PEAK 5(2Q36.2) WILD-TYPE 71 62 21

Figure S61.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 7(3p13)' versus 'CN_CNMF'

P value = 6.21e-07 (Fisher's exact test), Q value = 0.00061

Table S62.  Gene #38: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 7(3P13) CNV 109 114 132
DEL PEAK 7(3P13) WILD-TYPE 41 10 10

Figure S62.  Get High-res Image Gene #38: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(3p12.3)' versus 'CN_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.014

Table S63.  Gene #39: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 8(3P12.3) CNV 107 111 128
DEL PEAK 8(3P12.3) WILD-TYPE 43 13 14

Figure S63.  Get High-res Image Gene #39: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4p15.2)' versus 'CN_CNMF'

P value = 4.09e-07 (Fisher's exact test), Q value = 4e-04

Table S64.  Gene #41: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 10(4P15.2) CNV 72 98 81
DEL PEAK 10(4P15.2) WILD-TYPE 78 26 61

Figure S64.  Get High-res Image Gene #41: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q22.1)' versus 'CN_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0014

Table S65.  Gene #42: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 11(4Q22.1) CNV 65 91 72
DEL PEAK 11(4Q22.1) WILD-TYPE 85 33 70

Figure S65.  Get High-res Image Gene #42: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(4q32.3)' versus 'CN_CNMF'

P value = 3.01e-08 (Fisher's exact test), Q value = 3e-05

Table S66.  Gene #43: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 12(4Q32.3) CNV 75 103 86
DEL PEAK 12(4Q32.3) WILD-TYPE 75 21 56

Figure S66.  Get High-res Image Gene #43: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00018

Table S67.  Gene #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 13(4Q35.2) CNV 81 104 85
DEL PEAK 13(4Q35.2) WILD-TYPE 69 20 57

Figure S67.  Get High-res Image Gene #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000143 (Fisher's exact test), Q value = 0.13

Table S68.  Gene #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 13(4Q35.2) CNV 40 82 67 30
DEL PEAK 13(4Q35.2) WILD-TYPE 37 20 44 25

Figure S68.  Get High-res Image Gene #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.04e-12 (Fisher's exact test), Q value = 2e-09

Table S69.  Gene #45: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 14(5Q11.2) CNV 78 103 124
DEL PEAK 14(5Q11.2) WILD-TYPE 72 21 18

Figure S69.  Get High-res Image Gene #45: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(5q31.1)' versus 'CN_CNMF'

P value = 1.56e-10 (Fisher's exact test), Q value = 1.6e-07

Table S70.  Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 15(5Q31.1) CNV 88 109 125
DEL PEAK 15(5Q31.1) WILD-TYPE 62 15 17

Figure S70.  Get High-res Image Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(5q31.1)' versus 'METHLYATION_CNMF'

P value = 8.05e-05 (Fisher's exact test), Q value = 0.074

Table S71.  Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 15(5Q31.1) CNV 62 70 65
DEL PEAK 15(5Q31.1) WILD-TYPE 34 12 7

Figure S71.  Get High-res Image Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(6q22.31)' versus 'CN_CNMF'

P value = 9.32e-05 (Fisher's exact test), Q value = 0.085

Table S72.  Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 17(6Q22.31) CNV 26 48 28
DEL PEAK 17(6Q22.31) WILD-TYPE 124 76 114

Figure S72.  Get High-res Image Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(6q22.31)' versus 'MRNASEQ_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.22

Table S73.  Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 17(6Q22.31) CNV 9 38 19 14
DEL PEAK 17(6Q22.31) WILD-TYPE 68 64 92 41

Figure S73.  Get High-res Image Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(6q26)' versus 'CN_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.2

Table S74.  Gene #49: 'Del Peak 18(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 18(6Q26) CNV 32 50 28
DEL PEAK 18(6Q26) WILD-TYPE 118 74 114

Figure S74.  Get High-res Image Gene #49: 'Del Peak 18(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(7q11.22)' versus 'CN_CNMF'

P value = 6.68e-05 (Fisher's exact test), Q value = 0.062

Table S75.  Gene #50: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 19(7Q11.22) CNV 11 3 25
DEL PEAK 19(7Q11.22) WILD-TYPE 139 121 117

Figure S75.  Get High-res Image Gene #50: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p23)' versus 'CN_CNMF'

P value = 2.72e-10 (Fisher's exact test), Q value = 2.7e-07

Table S76.  Gene #53: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 22(9P23) CNV 78 73 122
DEL PEAK 22(9P23) WILD-TYPE 72 51 20

Figure S76.  Get High-res Image Gene #53: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9p21.3)' versus 'CN_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00014

Table S77.  Gene #54: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 23(9P21.3) CNV 96 93 129
DEL PEAK 23(9P21.3) WILD-TYPE 54 31 13

Figure S77.  Get High-res Image Gene #54: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(9p21.1)' versus 'CN_CNMF'

P value = 8.75e-08 (Fisher's exact test), Q value = 8.6e-05

Table S78.  Gene #55: 'Del Peak 24(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 24(9P21.1) CNV 81 70 117
DEL PEAK 24(9P21.1) WILD-TYPE 69 54 25

Figure S78.  Get High-res Image Gene #55: 'Del Peak 24(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNA_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.077

Table S79.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 25(9Q21.11) CNV 28 12 19 15
DEL PEAK 25(9Q21.11) WILD-TYPE 14 40 13 13

Figure S79.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.018

Table S80.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 25(9Q21.11) CNV 14 13 17 30
DEL PEAK 25(9Q21.11) WILD-TYPE 8 43 6 23

Figure S80.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(9q21.11)' versus 'CN_CNMF'

P value = 6.02e-10 (Fisher's exact test), Q value = 6e-07

Table S81.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 25(9Q21.11) CNV 70 34 95
DEL PEAK 25(9Q21.11) WILD-TYPE 80 90 47

Figure S81.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.64e-06 (Fisher's exact test), Q value = 0.0016

Table S82.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 25(9Q21.11) CNV 52 22 48
DEL PEAK 25(9Q21.11) WILD-TYPE 44 60 24

Figure S82.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 4.4e-09 (Fisher's exact test), Q value = 4.4e-06

Table S83.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 25(9Q21.11) CNV 43 23 71 29
DEL PEAK 25(9Q21.11) WILD-TYPE 34 79 40 26

Figure S83.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.6e-06

Table S84.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 25(9Q21.11) CNV 25 45 96
DEL PEAK 25(9Q21.11) WILD-TYPE 82 25 72

Figure S84.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.17

Table S85.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 25(9Q21.11) CNV 65 91 20
DEL PEAK 25(9Q21.11) WILD-TYPE 48 90 53

Figure S85.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(9q21.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 40 108
DEL PEAK 25(9Q21.11) CNV 35 11 68
DEL PEAK 25(9Q21.11) WILD-TYPE 48 29 40

Figure S86.  Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(10p15.3)' versus 'CN_CNMF'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.043

Table S87.  Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 26(10P15.3) CNV 48 73 64
DEL PEAK 26(10P15.3) WILD-TYPE 102 51 78

Figure S87.  Get High-res Image Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10p15.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.041

Table S88.  Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 26(10P15.3) CNV 60 63 46
DEL PEAK 26(10P15.3) WILD-TYPE 53 118 27

Figure S88.  Get High-res Image Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(10p15.1)' versus 'CN_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.15

Table S89.  Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 27(10P15.1) CNV 46 69 58
DEL PEAK 27(10P15.1) WILD-TYPE 104 55 84

Figure S89.  Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(10p15.1)' versus 'METHLYATION_CNMF'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.025

Table S90.  Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 27(10P15.1) CNV 32 53 25
DEL PEAK 27(10P15.1) WILD-TYPE 64 29 47

Figure S90.  Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.15

Table S91.  Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 27(10P15.1) CNV 26 60 47 14
DEL PEAK 27(10P15.1) WILD-TYPE 51 42 64 41

Figure S91.  Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0086

Table S92.  Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 27(10P15.1) CNV 53 58 47
DEL PEAK 27(10P15.1) WILD-TYPE 60 123 26

Figure S92.  Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(10q23.31)' versus 'CN_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.015

Table S93.  Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 28(10Q23.31) CNV 61 85 70
DEL PEAK 28(10Q23.31) WILD-TYPE 89 39 72

Figure S93.  Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(10q23.31)' versus 'METHLYATION_CNMF'

P value = 6.74e-06 (Fisher's exact test), Q value = 0.0064

Table S94.  Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 28(10Q23.31) CNV 33 58 36
DEL PEAK 28(10Q23.31) WILD-TYPE 63 24 36

Figure S94.  Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 8.54e-06 (Fisher's exact test), Q value = 0.0081

Table S95.  Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 28(10Q23.31) CNV 27 72 51 24
DEL PEAK 28(10Q23.31) WILD-TYPE 50 30 60 31

Figure S95.  Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.23e-07 (Fisher's exact test), Q value = 7e-04

Table S96.  Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 28(10Q23.31) CNV 75 36 63
DEL PEAK 28(10Q23.31) WILD-TYPE 32 34 105

Figure S96.  Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(11p15.5)' versus 'MRNA_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.23

Table S97.  Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 29(11P15.5) CNV 30 20 9 18
DEL PEAK 29(11P15.5) WILD-TYPE 12 32 23 10

Figure S97.  Get High-res Image Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(11p15.5)' versus 'CN_CNMF'

P value = 4.67e-06 (Fisher's exact test), Q value = 0.0045

Table S98.  Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 29(11P15.5) CNV 49 54 87
DEL PEAK 29(11P15.5) WILD-TYPE 101 70 55

Figure S98.  Get High-res Image Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.019

Table S99.  Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
DEL PEAK 29(11P15.5) CNV 29 17 36 10
DEL PEAK 29(11P15.5) WILD-TYPE 29 30 13 30

Figure S99.  Get High-res Image Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.089

Table S100.  Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 35(14Q11.2) CNV 38 39 44
DEL PEAK 35(14Q11.2) WILD-TYPE 69 31 124

Figure S100.  Get High-res Image Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(14q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000203 (Fisher's exact test), Q value = 0.18

Table S101.  Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 40 108
DEL PEAK 35(14Q11.2) CNV 16 21 45
DEL PEAK 35(14Q11.2) WILD-TYPE 67 19 63

Figure S101.  Get High-res Image Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 40(17p11.2)' versus 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.15

Table S102.  Gene #71: 'Del Peak 40(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 40(17P11.2) CNV 68 53 93
DEL PEAK 40(17P11.2) WILD-TYPE 82 71 49

Figure S102.  Get High-res Image Gene #71: 'Del Peak 40(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(17q11.2)' versus 'MRNA_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.028

Table S103.  Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 41(17Q11.2) CNV 21 4 11 6
DEL PEAK 41(17Q11.2) WILD-TYPE 21 48 21 22

Figure S103.  Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 41(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.092

Table S104.  Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 41(17Q11.2) CNV 8 4 9 21
DEL PEAK 41(17Q11.2) WILD-TYPE 14 52 14 32

Figure S104.  Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 41(17q11.2)' versus 'CN_CNMF'

P value = 2.73e-09 (Fisher's exact test), Q value = 2.7e-06

Table S105.  Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 41(17Q11.2) CNV 39 8 53
DEL PEAK 41(17Q11.2) WILD-TYPE 111 116 89

Figure S105.  Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.0014

Table S106.  Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 41(17Q11.2) CNV 24 7 36 19
DEL PEAK 41(17Q11.2) WILD-TYPE 53 95 75 36

Figure S106.  Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-08 (Fisher's exact test), Q value = 4.8e-05

Table S107.  Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 41(17Q11.2) CNV 7 20 59
DEL PEAK 41(17Q11.2) WILD-TYPE 100 50 109

Figure S107.  Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(17q25.3)' versus 'CN_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.014

Table S108.  Gene #73: 'Del Peak 42(17q25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 42(17Q25.3) CNV 27 11 45
DEL PEAK 42(17Q25.3) WILD-TYPE 123 113 97

Figure S108.  Get High-res Image Gene #73: 'Del Peak 42(17q25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19p13.3)' versus 'CN_CNMF'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.024

Table S109.  Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 44(19P13.3) CNV 47 51 82
DEL PEAK 44(19P13.3) WILD-TYPE 103 73 60

Figure S109.  Get High-res Image Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.2

Table S110.  Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 166 68
DEL PEAK 44(19P13.3) CNV 71 72 16
DEL PEAK 44(19P13.3) WILD-TYPE 62 94 52

Figure S110.  Get High-res Image Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 45(19q13.33)' versus 'CN_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00098

Table S111.  Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 45(19Q13.33) CNV 20 51 38
DEL PEAK 45(19Q13.33) WILD-TYPE 130 73 104

Figure S111.  Get High-res Image Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 45(19q13.33)' versus 'METHLYATION_CNMF'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.085

Table S112.  Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 45(19Q13.33) CNV 11 30 24
DEL PEAK 45(19Q13.33) WILD-TYPE 85 52 48

Figure S112.  Get High-res Image Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(19q13.43)' versus 'CN_CNMF'

P value = 8.08e-06 (Fisher's exact test), Q value = 0.0077

Table S113.  Gene #77: 'Del Peak 46(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 46(19Q13.43) CNV 21 49 37
DEL PEAK 46(19Q13.43) WILD-TYPE 129 75 105

Figure S113.  Get High-res Image Gene #77: 'Del Peak 46(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(21q22.3)' versus 'CN_CNMF'

P value = 1.82e-08 (Fisher's exact test), Q value = 1.8e-05

Table S114.  Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 48(21Q22.3) CNV 56 89 87
DEL PEAK 48(21Q22.3) WILD-TYPE 94 35 55

Figure S114.  Get High-res Image Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(21q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.11

Table S115.  Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 48(21Q22.3) CNV 38 58 42
DEL PEAK 48(21Q22.3) WILD-TYPE 58 24 30

Figure S115.  Get High-res Image Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 50(22q13.32)' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.2

Table S116.  Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 50(22Q13.32) CNV 8 8 8 17
DEL PEAK 50(22Q13.32) WILD-TYPE 34 44 24 11

Figure S116.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 50(22q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.14

Table S117.  Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 40 108
DEL PEAK 50(22Q13.32) CNV 13 2 36
DEL PEAK 50(22Q13.32) WILD-TYPE 70 38 72

Figure S117.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 51(Xp22.2)' versus 'CN_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.029

Table S118.  Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 51(XP22.2) CNV 27 48 56
DEL PEAK 51(XP22.2) WILD-TYPE 123 76 86

Figure S118.  Get High-res Image Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xp11.3)' versus 'CN_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.0024

Table S119.  Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 52(XP11.3) CNV 25 54 50
DEL PEAK 52(XP11.3) WILD-TYPE 125 70 92

Figure S119.  Get High-res Image Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.014

Table S120.  Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 52(XP11.3) CNV 15 39 26
DEL PEAK 52(XP11.3) WILD-TYPE 81 43 46

Figure S120.  Get High-res Image Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 53(Xq22.3)' versus 'CN_CNMF'

P value = 3.76e-08 (Fisher's exact test), Q value = 3.7e-05

Table S121.  Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
DEL PEAK 53(XQ22.3) CNV 15 30 55
DEL PEAK 53(XQ22.3) WILD-TYPE 135 94 87

Figure S121.  Get High-res Image Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 53(Xq22.3)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.16

Table S122.  Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
DEL PEAK 53(XQ22.3) CNV 9 21 25
DEL PEAK 53(XQ22.3) WILD-TYPE 87 61 47

Figure S122.  Get High-res Image Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_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 = LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 416

  • Number of copy number variation regions = 84

  • 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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