Correlation between copy number variation genes and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C17D2S4F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Lung Squamous Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C17D2S4F
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 10 molecular subtypes across 397 patients, 117 significant findings detected with Q value < 0.25.

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

  • Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CNMF',  '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 13(7q21.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 19(12p13.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 23(15q26.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Amp Peak 24(17q25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 25(18p11.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 28(19q13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 29(20p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 31(22q11.21) 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', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 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', and 'MRNASEQ_CHIERARCHICAL'.

  • 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' and 'METHLYATION_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',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • Del Peak 17(6q22.31) cnvs correlated to 'MRNASEQ_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(9q21.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(10p15.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 26(10p15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 27(10q23.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 28(11p15.5) cnvs correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • Del Peak 34(14q11.2) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 40(17q11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 44(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 46(21q22.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 48(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • Del Peak 49(Xp22.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 50(Xp21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 51(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 52(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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 117 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
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
Del Peak 1(1p36 22) 0 (0%) 225 1.43e-06
(0.00115) 		1.78e-08
(1.47e-05) 		1.61e-28
(1.36e-25) 		2.1e-14
(1.76e-11) 		0.412
(1.00) 		0.0262
(1.00) 		8.67e-14
(7.25e-11) 		9.45e-15
(7.92e-12) 		0.000838
(0.586) 		1.83e-05
(0.0143)
Del Peak 24(9q21 11) 0 (0%) 206 0.000177
(0.132) 		4.92e-05
(0.0376) 		5.97e-11
(4.96e-08) 		1.14e-06
(0.000923) 		0.653
(1.00) 		0.239
(1.00) 		4.4e-09
(3.64e-06) 		1.63e-09
(1.35e-06) 		0.000958
(0.664) 		0.000184
(0.137)
Amp Peak 6(3q26 33) 0 (0%) 33 0.000427
(0.306) 		1.71e-05
(0.0134) 		7.05e-12
(5.86e-09) 		6.69e-07
(0.000541) 		0.193
(1.00) 		0.0776
(1.00) 		1.26e-06
(0.00101) 		5.04e-05
(0.0384) 		0.148
(1.00) 		3.07e-06
(0.00245)
Del Peak 5(2q36 2) 0 (0%) 265 0.000236
(0.174) 		4.76e-05
(0.0364) 		1.7e-12
(1.41e-09) 		2.14e-06
(0.00172) 		0.177
(1.00) 		0.126
(1.00) 		6.61e-07
(0.000535) 		2.98e-08
(2.45e-05) 		0.885
(1.00) 		0.163
(1.00)
Amp Peak 3(2p16 1) 0 (0%) 181 0.000305
(0.222) 		0.00165
(1.00) 		3.18e-13
(2.66e-10) 		5.83e-05
(0.0443) 		0.95
(1.00) 		0.643
(1.00) 		1.88e-05
(0.0146) 		7.55e-05
(0.0573) 		0.887
(1.00) 		0.0171
(1.00)
Del Peak 2(1p13 2) 0 (0%) 225 0.000237
(0.175) 		0.00055
(0.391) 		1.23e-15
(1.03e-12) 		5.74e-09
(4.73e-06) 		0.119
(1.00) 		0.0712
(1.00) 		5.56e-07
(0.000451) 		1.96e-07
(0.00016) 		0.127
(1.00) 		0.000788
(0.553)
Del Peak 40(17q11 2) 0 (0%) 301 1.26e-05
(0.00991) 		6.44e-05
(0.049) 		3.04e-08
(2.5e-05) 		0.0177
(1.00) 		0.495
(1.00) 		0.378
(1.00) 		1.48e-06
(0.00119) 		4.83e-08
(3.95e-05) 		0.143
(1.00) 		0.0373
(1.00)
Amp Peak 4(2q31 2) 0 (0%) 265 0.0207
(1.00) 		0.000948
(0.659) 		6.52e-06
(0.00517) 		1.99e-07
(0.000162) 		0.724
(1.00) 		0.887
(1.00) 		0.000194
(0.144) 		0.000248
(0.182) 		0.37
(1.00) 		0.511
(1.00)
Del Peak 26(10p15 1) 0 (0%) 229 0.0722
(1.00) 		0.484
(1.00) 		0.000162
(0.121) 		4.03e-06
(0.00321) 		0.469
(1.00) 		0.353
(1.00) 		0.000161
(0.121) 		0.00143
(0.974) 		0.0107
(1.00) 		9.09e-06
(0.00719)
Del Peak 27(10q23 31) 0 (0%) 194 0.0392
(1.00) 		0.00386
(1.00) 		2.17e-05
(0.0168) 		2.08e-06
(0.00167) 		0.36
(1.00) 		0.39
(1.00) 		8.54e-06
(0.00677) 		7.23e-07
(0.000584) 		0.219
(1.00) 		0.0644
(1.00)
Amp Peak 2(1q21 2) 0 (0%) 192 0.0419
(1.00) 		0.00618
(1.00) 		1.98e-07
(0.000162) 		0.00113
(0.777) 		0.16
(1.00) 		0.0492
(1.00) 		1.87e-05
(0.0146) 		4.11e-05
(0.0316) 		0.0393
(1.00) 		0.00181
(1.00)
Amp Peak 13(7q21 2) 0 (0%) 188 0.101
(1.00) 		0.25
(1.00) 		5.34e-10
(4.43e-07) 		1.27e-05
(0.00999) 		0.0573
(1.00) 		0.389
(1.00) 		0.000661
(0.468) 		0.000185
(0.138) 		0.0358
(1.00) 		0.0527
(1.00)
Amp Peak 23(15q26 3) 0 (0%) 258 0.151
(1.00) 		0.021
(1.00) 		1.56e-05
(0.0122) 		9.39e-06
(0.00741) 		0.354
(1.00) 		0.0183
(1.00) 		0.000334
(0.242) 		0.00253
(1.00) 		0.0159
(1.00) 		0.00123
(0.838)
Amp Peak 24(17q25 1) 0 (0%) 206 0.0177
(1.00) 		0.0608
(1.00) 		6.01e-07
(0.000487) 		2.17e-05
(0.0168) 		0.267
(1.00) 		0.292
(1.00) 		0.0039
(1.00) 		0.000165
(0.123) 		0.796
(1.00) 		0.0783
(1.00)
Amp Peak 26(18q11 2) 0 (0%) 271 0.000456
(0.327) 		0.00227
(1.00) 		1.37e-05
(0.0107) 		0.000342
(0.248) 		0.272
(1.00) 		0.74
(1.00) 		0.000841
(0.587) 		5.04e-06
(0.00401) 		0.402
(1.00) 		0.00539
(1.00)
Del Peak 13(4q35 2) 0 (0%) 144 0.1
(1.00) 		0.206
(1.00) 		2.84e-06
(0.00227) 		0.000124
(0.0933) 		0.455
(1.00) 		0.47
(1.00) 		0.000143
(0.108) 		0.0105
(1.00) 		0.44
(1.00) 		0.0957
(1.00)
Del Peak 25(10p15 3) 0 (0%) 219 0.373
(1.00) 		0.442
(1.00) 		4.8e-05
(0.0368) 		9.6e-05
(0.0727) 		0.329
(1.00) 		0.443
(1.00) 		0.00156
(1.00) 		0.000554
(0.393) 		0.0549
(1.00) 		4.45e-05
(0.0342)
Amp Peak 25(18p11 32) 0 (0%) 260 0.0958
(1.00) 		0.00981
(1.00) 		2.48e-05
(0.0192) 		0.000126
(0.0949) 		0.231
(1.00) 		0.451
(1.00) 		0.131
(1.00) 		0.0402
(1.00) 		0.898
(1.00) 		0.0209
(1.00)
Amp Peak 29(20p12 2) 0 (0%) 186 0.000987
(0.68) 		0.0043
(1.00) 		8.92e-08
(7.3e-05) 		0.000161
(0.121) 		0.967
(1.00) 		0.221
(1.00) 		0.0408
(1.00) 		0.00273
(1.00) 		0.259
(1.00) 		0.0945
(1.00)
Del Peak 10(4p15 2) 0 (0%) 158 0.000807
(0.566) 		0.00171
(1.00) 		6.52e-06
(0.00517) 		0.000341
(0.247) 		0.662
(1.00) 		0.0343
(1.00) 		0.0138
(1.00) 		0.00689
(1.00) 		0.302
(1.00) 		0.864
(1.00)
Del Peak 14(5q11 2) 0 (0%) 107 0.842
(1.00) 		0.303
(1.00) 		2.03e-12
(1.69e-09) 		0.000192
(0.143) 		0.959
(1.00) 		0.244
(1.00) 		0.0104
(1.00) 		0.0858
(1.00) 		0.987
(1.00) 		0.00113
(0.777)
Del Peak 15(5q31 1) 0 (0%) 89 0.332
(1.00) 		0.228
(1.00) 		5.7e-09
(4.71e-06) 		3e-05
(0.0232) 		0.272
(1.00) 		0.166
(1.00) 		0.0582
(1.00) 		0.0639
(1.00) 		0.684
(1.00) 		0.00713
(1.00)
Del Peak 28(11p15 5) 0 (0%) 214 0.000689
(0.486) 		0.0528
(1.00) 		1.28e-06
(0.00103) 		0.0352
(1.00) 		0.000764
(0.538) 		2.02e-05
(0.0157) 		0.00293
(1.00) 		0.031
(1.00) 		0.00193
(1.00) 		0.0459
(1.00)
Del Peak 43(19p13 3) 0 (0%) 224 0.334
(1.00) 		0.0231
(1.00) 		1.38e-05
(0.0108) 		0.145
(1.00) 		0.0588
(1.00) 		0.251
(1.00) 		0.284
(1.00) 		0.0283
(1.00) 		0.000224
(0.166) 		0.00297
(1.00)
Del Peak 44(19q13 33) 0 (0%) 291 0.617
(1.00) 		0.0694
(1.00) 		0.000167
(0.125) 		0.000187
(0.139) 		0.244
(1.00) 		0.719
(1.00) 		0.0819
(1.00) 		0.0398
(1.00) 		0.0341
(1.00) 		0.334
(1.00)
Del Peak 48(22q13 32) 0 (0%) 302 0.000281
(0.205) 		8.68e-05
(0.0658) 		0.0172
(1.00) 		0.351
(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)
Del Peak 50(Xp21 1) 0 (0%) 270 0.354
(1.00) 		0.148
(1.00) 		5.39e-05
(0.0411) 		0.00024
(0.177) 		0.344
(1.00) 		0.681
(1.00) 		0.137
(1.00) 		0.00706
(1.00) 		0.538
(1.00) 		0.163
(1.00)
Del Peak 51(Xp11 3) 0 (0%) 272 0.062
(1.00) 		0.175
(1.00) 		9.19e-06
(0.00726) 		4.09e-05
(0.0315) 		0.0923
(1.00) 		0.124
(1.00) 		0.0631
(1.00) 		0.00391
(1.00) 		0.131
(1.00) 		0.138
(1.00)
Del Peak 52(Xq22 3) 0 (0%) 302 0.00853
(1.00) 		0.105
(1.00) 		1.91e-05
(0.0148) 		0.000249
(0.183) 		0.663
(1.00) 		0.92
(1.00) 		0.0422
(1.00) 		0.438
(1.00) 		0.276
(1.00) 		0.797
(1.00)
Amp Peak 8(5p15 33) 0 (0%) 83 0.853
(1.00) 		0.867
(1.00) 		1.07e-05
(0.00841) 		0.0129
(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)
Amp Peak 9(5p12) 0 (0%) 136 0.919
(1.00) 		0.514
(1.00) 		7.58e-10
(6.28e-07) 		0.00874
(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)
Amp Peak 19(12p13 33) 0 (0%) 199 0.0102
(1.00) 		0.0571
(1.00) 		1.23e-05
(0.00965) 		0.000492
(0.352) 		0.313
(1.00) 		0.729
(1.00) 		0.000418
(0.301) 		0.0103
(1.00) 		0.837
(1.00) 		0.218
(1.00)
Amp Peak 27(19q12) 0 (0%) 230 0.455
(1.00) 		0.249
(1.00) 		4.07e-06
(0.00324) 		0.182
(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)
Amp Peak 28(19q13 2) 0 (0%) 227 0.715
(1.00) 		1
(1.00) 		0.000195
(0.144) 		0.0708
(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)
Amp Peak 31(22q11 21) 0 (0%) 198 0.111
(1.00) 		0.123
(1.00) 		0.000296
(0.216) 		0.000477
(0.342) 		0.888
(1.00) 		0.349
(1.00) 		0.0122
(1.00) 		0.0463
(1.00) 		0.751
(1.00) 		0.027
(1.00)
Del Peak 4(2q22 1) 0 (0%) 292 0.255
(1.00) 		0.318
(1.00) 		0.000271
(0.198) 		0.0198
(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)
Del Peak 7(3p13) 0 (0%) 57 0.419
(1.00) 		0.549
(1.00) 		2.67e-06
(0.00214) 		0.000858
(0.598) 		0.882
(1.00) 		0.0379
(1.00) 		0.0756
(1.00) 		0.0171
(1.00) 		0.432
(1.00) 		0.00134
(0.915)
Del Peak 8(3p12 3) 0 (0%) 65 0.258
(1.00) 		0.342
(1.00) 		3.03e-05
(0.0233) 		0.00259
(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)
Del Peak 11(4q22 1) 0 (0%) 180 0.00685
(1.00) 		0.0579
(1.00) 		0.000102
(0.0771) 		0.00829
(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)
Del Peak 12(4q32 3) 0 (0%) 149 0.00967
(1.00) 		0.0253
(1.00) 		3.5e-07
(0.000285) 		0.000596
(0.422) 		0.101
(1.00) 		0.523
(1.00) 		0.0012
(0.819) 		0.00455
(1.00) 		0.663
(1.00) 		0.242
(1.00)
Del Peak 16(6p25 3) 0 (0%) 297 0.22
(1.00) 		0.11
(1.00) 		0.00878
(1.00) 		0.00143
(0.971) 		0.393
(1.00) 		0.013
(1.00) 		0.00219
(1.00) 		0.000305
(0.222) 		0.179
(1.00) 		0.0797
(1.00)
Del Peak 17(6q22 31) 0 (0%) 302 0.0192
(1.00) 		0.00224
(1.00) 		0.00513
(1.00) 		0.000818
(0.573) 		0.629
(1.00) 		0.354
(1.00) 		0.000249
(0.183) 		0.000587
(0.416) 		0.374
(1.00) 		0.218
(1.00)
Del Peak 19(7q11 22) 0 (0%) 360 0.908
(1.00) 		0.405
(1.00) 		4.4e-05
(0.0338) 		0.829
(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)
Del Peak 22(9p23) 0 (0%) 139 0.00561
(1.00) 		0.00291
(1.00) 		1.97e-10
(1.64e-07) 		0.104
(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)
Del Peak 23(9p21 3) 0 (0%) 95 0.372
(1.00) 		0.172
(1.00) 		4.99e-07
(0.000406) 		0.409
(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)
Del Peak 34(14q11 2) 0 (0%) 257 0.0546
(1.00) 		0.293
(1.00) 		0.163
(1.00) 		0.437
(1.00) 		0.206
(1.00) 		0.159
(1.00) 		0.000386
(0.278) 		9.8e-05
(0.0741) 		0.183
(1.00) 		0.493
(1.00)
Del Peak 46(21q22 3) 0 (0%) 173 0.957
(1.00) 		0.193
(1.00) 		2.13e-08
(1.75e-05) 		0.00206
(1.00) 		0.396
(1.00) 		0.0991
(1.00) 		0.13
(1.00) 		0.0131
(1.00) 		0.0589
(1.00) 		0.161
(1.00)
Del Peak 49(Xp22 2) 0 (0%) 271 0.599
(1.00) 		0.351
(1.00) 		0.000249
(0.183) 		0.0101
(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)
Amp Peak 1(1p34 2) 0 (0%) 334 0.028
(1.00) 		0.481
(1.00) 		0.000892
(0.621) 		0.644
(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)
Amp Peak 5(3p11 1) 0 (0%) 317 0.0748
(1.00) 		0.844
(1.00) 		0.744
(1.00) 		0.957
(1.00) 		0.214
(1.00) 		0.0013
(0.887) 		0.239
(1.00) 		0.541
(1.00) 		0.845
(1.00) 		0.602
(1.00)
Amp Peak 7(4q12) 0 (0%) 304 0.679
(1.00) 		0.759
(1.00) 		0.000353
(0.255) 		0.124
(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)
Amp Peak 10(6p12 1) 0 (0%) 267 0.557
(1.00) 		0.383
(1.00) 		0.0018
(1.00) 		0.168
(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)
Amp Peak 11(6q12) 0 (0%) 280 1
(1.00) 		0.873
(1.00) 		0.00114
(0.781) 		0.0454
(1.00) 		0.348
(1.00) 		0.408
(1.00) 		0.19
(1.00) 		0.42
(1.00) 		0.198
(1.00) 		0.0784
(1.00)
Amp Peak 12(7p11 2) 0 (0%) 204 0.186
(1.00) 		0.0939
(1.00) 		0.00097
(0.669) 		0.00366
(1.00) 		0.687
(1.00) 		0.801
(1.00) 		0.0273
(1.00) 		0.000542
(0.386) 		0.634
(1.00) 		0.0644
(1.00)
Amp Peak 14(8p11 23) 0 (0%) 213 0.00812
(1.00) 		0.168
(1.00) 		0.0254
(1.00) 		0.0352
(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)
Amp Peak 15(8q24 21) 0 (0%) 117 0.871
(1.00) 		0.644
(1.00) 		0.554
(1.00) 		0.969
(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)
Amp Peak 16(9p24 1) 0 (0%) 324 0.375
(1.00) 		0.0295
(1.00) 		0.000354
(0.255) 		0.177
(1.00) 		0.0017
(1.00) 		0.00501
(1.00) 		0.00699
(1.00) 		0.000767
(0.539) 		0.117
(1.00) 		0.0167
(1.00)
Amp Peak 17(9p13 3) 0 (0%) 288 0.17
(1.00) 		0.373
(1.00) 		0.043
(1.00) 		0.0387
(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)
Amp Peak 18(11q13 3) 0 (0%) 254 0.0697
(1.00) 		0.0306
(1.00) 		0.00486
(1.00) 		0.000518
(0.37) 		0.19
(1.00) 		0.0358
(1.00) 		0.0123
(1.00) 		0.124
(1.00) 		0.0454
(1.00) 		0.00669
(1.00)
Amp Peak 20(12q15) 0 (0%) 253 0.312
(1.00) 		0.527
(1.00) 		0.00531
(1.00) 		0.00136
(0.927) 		0.764
(1.00) 		0.524
(1.00) 		0.0588
(1.00) 		0.0807
(1.00) 		1
(1.00) 		0.437
(1.00)
Amp Peak 21(13q34) 0 (0%) 326 0.964
(1.00) 		0.0489
(1.00) 		0.0384
(1.00) 		0.182
(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)
Amp Peak 22(14q13 3) 0 (0%) 276 0.345
(1.00) 		0.246
(1.00) 		0.127
(1.00) 		0.0969
(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)
Amp Peak 30(20q11 21) 0 (0%) 168 0.991
(1.00) 		0.844
(1.00) 		0.00052
(0.371) 		0.0132
(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)
Amp Peak 32(Xq28) 0 (0%) 291 0.633
(1.00) 		0.636
(1.00) 		0.039
(1.00) 		0.0815
(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)
Del Peak 3(2p25 3) 0 (0%) 360 0.0461
(1.00) 		0.179
(1.00) 		0.0773
(1.00) 		0.37
(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)
Del Peak 6(3p25 3) 0 (0%) 84 0.54
(1.00) 		0.176
(1.00) 		0.0278
(1.00) 		0.00221
(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)
Del Peak 9(3q11 1) 0 (0%) 338 0.759
(1.00) 		0.478
(1.00) 		0.117
(1.00) 		0.0538
(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)
Del Peak 18(6q26) 0 (0%) 294 0.0659
(1.00) 		0.00298
(1.00) 		0.00234
(1.00) 		0.000727
(0.512) 		0.921
(1.00) 		0.69
(1.00) 		0.00204
(1.00) 		0.00223
(1.00) 		0.184
(1.00) 		0.085
(1.00)
Del Peak 20(7q36 3) 0 (0%) 316 0.187
(1.00) 		0.112
(1.00) 		0.00095
(0.659) 		0.274
(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)
Del Peak 21(8p23 2) 0 (0%) 130 0.864
(1.00) 		0.459
(1.00) 		0.000961
(0.665) 		0.173
(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)
Del Peak 29(11q22 1) 0 (0%) 279 0.493
(1.00) 		0.288
(1.00) 		0.0053
(1.00) 		0.0314
(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)
Del Peak 30(11q25) 0 (0%) 254 0.798
(1.00) 		0.429
(1.00) 		0.0746
(1.00) 		0.333
(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)
Del Peak 31(12q24 31) 0 (0%) 334 0.965
(1.00) 		0.332
(1.00) 		0.426
(1.00) 		0.435
(1.00) 		0.323
(1.00) 		0.207
(1.00) 		0.849
(1.00) 		0.808
(1.00) 		0.0766
(1.00) 		0.362
(1.00)
Del Peak 32(13q12 11) 0 (0%) 137 0.0547
(1.00) 		0.611
(1.00) 		0.0344
(1.00) 		0.164
(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)
Del Peak 33(13q14 2) 0 (0%) 126 0.0512
(1.00) 		0.0962
(1.00) 		0.00096
(0.665) 		0.053
(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)
Del Peak 35(15q12) 0 (0%) 266 0.725
(1.00) 		0.228
(1.00) 		0.45
(1.00) 		0.347
(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)
Del Peak 36(15q21 1) 0 (0%) 273 0.643
(1.00) 		0.242
(1.00) 		0.298
(1.00) 		0.969
(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)
Del Peak 37(16p13 3) 0 (0%) 249 0.239
(1.00) 		0.245
(1.00) 		0.00525
(1.00) 		0.197
(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)
Del Peak 38(16q23 1) 0 (0%) 231 0.942
(1.00) 		0.659
(1.00) 		0.0863
(1.00) 		0.271
(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)
Del Peak 39(17p11 2) 0 (0%) 195 0.194
(1.00) 		0.401
(1.00) 		0.00185
(1.00) 		0.161
(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)
Del Peak 41(17q25 3) 0 (0%) 321 0.00515
(1.00) 		0.0421
(1.00) 		0.000405
(0.292) 		0.0446
(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)
Del Peak 42(18q23) 0 (0%) 218 0.508
(1.00) 		0.788
(1.00) 		0.502
(1.00) 		0.898
(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)
Del Peak 45(21q21 1) 0 (0%) 208 0.481
(1.00) 		0.135
(1.00) 		0.0117
(1.00) 		0.0293
(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)
Del Peak 47(22q11 21) 0 (0%) 329 0.0904
(1.00) 		0.0093
(1.00) 		0.0672
(1.00) 		0.0841
(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)
'Amp Peak 2(1q21.2)' versus 'CN_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 0.00016

Table S1.  Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 2(1Q21.2) CNV 57 92 56
AMP PEAK 2(1Q21.2) WILD-TYPE 86 37 69

Figure S1.  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 = 0.015

Table S2.  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 S2.  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 = 0.032

Table S3.  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 S3.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000305 (Fisher's exact test), Q value = 0.22

Table S4.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
AMP PEAK 3(2P16.1) CNV 19 40 12 15
AMP PEAK 3(2P16.1) WILD-TYPE 24 10 18 16

Figure S4.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 3.18e-13 (Fisher's exact test), Q value = 2.7e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 3(2P16.1) CNV 49 102 65
AMP PEAK 3(2P16.1) WILD-TYPE 94 27 60

Figure S5.  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 = 5.83e-05 (Fisher's exact test), Q value = 0.044

Table S6.  Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 3(2P16.1) CNV 43 61 31
AMP PEAK 3(2P16.1) WILD-TYPE 55 22 38

Figure S6.  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 = 0.015

Table S7.  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 S7.  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 = 0.057

Table S8.  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 S8.  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 = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S9.  Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 4(2Q31.2) CNV 30 63 39
AMP PEAK 4(2Q31.2) WILD-TYPE 113 66 86

Figure S9.  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 = 1.99e-07 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 4(2Q31.2) CNV 23 48 14
AMP PEAK 4(2Q31.2) WILD-TYPE 75 35 55

Figure S10.  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 = 0.14

Table S11.  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 S11.  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 = 0.18

Table S12.  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 S12.  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 = 1.71e-05 (Fisher's exact test), Q value = 0.013

Table S13.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
AMP PEAK 6(3Q26.33) CNV 19 54 67
AMP PEAK 6(3Q26.33) WILD-TYPE 9 0 5

Figure S13.  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 = 7.05e-12 (Fisher's exact test), Q value = 5.9e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 6(3Q26.33) CNV 113 129 122
AMP PEAK 6(3Q26.33) WILD-TYPE 30 0 3

Figure S14.  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 = 6.69e-07 (Fisher's exact test), Q value = 0.00054

Table S15.  Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 6(3Q26.33) CNV 79 83 67
AMP PEAK 6(3Q26.33) WILD-TYPE 19 0 2

Figure S15.  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 = 1.26e-06 (Fisher's exact test), Q value = 0.001

Table S16.  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 73 102 100 42
AMP PEAK 6(3Q26.33) WILD-TYPE 4 0 11 13

Figure S16.  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 = 5.04e-05 (Fisher's exact test), Q value = 0.038

Table S17.  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 63 147
AMP PEAK 6(3Q26.33) WILD-TYPE 0 7 21

Figure S17.  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 = 3.07e-06 (Fisher's exact test), Q value = 0.0024

Table S18.  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 111 155 73
AMP PEAK 6(3Q26.33) WILD-TYPE 2 26 0

Figure S18.  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 = 1.07e-05 (Fisher's exact test), Q value = 0.0084

Table S19.  Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 8(5P15.33) CNV 99 100 115
AMP PEAK 8(5P15.33) WILD-TYPE 44 29 10

Figure S19.  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 = 7.58e-10 (Fisher's exact test), Q value = 6.3e-07

Table S20.  Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 9(5P12) CNV 70 84 107
AMP PEAK 9(5P12) WILD-TYPE 73 45 18

Figure S20.  Get High-res Image Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(7q21.2)' versus 'CN_CNMF'

P value = 5.34e-10 (Fisher's exact test), Q value = 4.4e-07

Table S21.  Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 13(7Q21.2) CNV 51 96 62
AMP PEAK 13(7Q21.2) WILD-TYPE 92 33 63

Figure S21.  Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(7q21.2)' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.01

Table S22.  Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 13(7Q21.2) CNV 35 58 30
AMP PEAK 13(7Q21.2) WILD-TYPE 63 25 39

Figure S22.  Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(7q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000185 (Fisher's exact test), Q value = 0.14

Table S23.  Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 13(7Q21.2) CNV 74 33 75
AMP PEAK 13(7Q21.2) WILD-TYPE 33 37 93

Figure S23.  Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(12p13.33)' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0097

Table S24.  Gene #19: 'Amp Peak 19(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 19(12P13.33) CNV 51 83 64
AMP PEAK 19(12P13.33) WILD-TYPE 92 46 61

Figure S24.  Get High-res Image Gene #19: 'Amp Peak 19(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(15q26.3)' versus 'CN_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.012

Table S25.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 23(15Q26.3) CNV 30 61 48
AMP PEAK 23(15Q26.3) WILD-TYPE 113 68 77

Figure S25.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(15q26.3)' versus 'METHLYATION_CNMF'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0074

Table S26.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 23(15Q26.3) CNV 16 40 27
AMP PEAK 23(15Q26.3) WILD-TYPE 82 43 42

Figure S26.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.24

Table S27.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
AMP PEAK 23(15Q26.3) CNV 17 52 33 17
AMP PEAK 23(15Q26.3) WILD-TYPE 60 50 78 38

Figure S27.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q25.1)' versus 'CN_CNMF'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00049

Table S28.  Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 24(17Q25.1) CNV 46 83 62
AMP PEAK 24(17Q25.1) WILD-TYPE 97 46 63

Figure S28.  Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q25.1)' versus 'METHLYATION_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017

Table S29.  Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 24(17Q25.1) CNV 34 55 25
AMP PEAK 24(17Q25.1) WILD-TYPE 64 28 44

Figure S29.  Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 24(17Q25.1) CNV 67 32 62
AMP PEAK 24(17Q25.1) WILD-TYPE 40 38 106

Figure S30.  Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(18p11.32)' versus 'CN_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.019

Table S31.  Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 25(18P11.32) CNV 32 63 42
AMP PEAK 25(18P11.32) WILD-TYPE 111 66 83

Figure S31.  Get High-res Image Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(18p11.32)' versus 'METHLYATION_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.095

Table S32.  Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 25(18P11.32) CNV 18 38 28
AMP PEAK 25(18P11.32) WILD-TYPE 80 45 41

Figure S32.  Get High-res Image Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(18q11.2)' versus 'CN_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.011

Table S33.  Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 26(18Q11.2) CNV 26 57 43
AMP PEAK 26(18Q11.2) WILD-TYPE 117 72 82

Figure S33.  Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(18q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.25

Table S34.  Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 26(18Q11.2) CNV 17 37 21
AMP PEAK 26(18Q11.2) WILD-TYPE 81 46 48

Figure S34.  Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-06 (Fisher's exact test), Q value = 0.004

Table S35.  Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
AMP PEAK 26(18Q11.2) CNV 46 31 32
AMP PEAK 26(18Q11.2) WILD-TYPE 61 39 136

Figure S35.  Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'CN_CNMF'

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0032

Table S36.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 27(19Q12) CNV 45 77 45
AMP PEAK 27(19Q12) WILD-TYPE 98 52 80

Figure S36.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(19q13.2)' versus 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.14

Table S37.  Gene #28: 'Amp Peak 28(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 28(19Q13.2) CNV 48 74 48
AMP PEAK 28(19Q13.2) WILD-TYPE 95 55 77

Figure S37.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20p12.2)' versus 'CN_CNMF'

P value = 8.92e-08 (Fisher's exact test), Q value = 7.3e-05

Table S38.  Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 29(20P12.2) CNV 53 92 66
AMP PEAK 29(20P12.2) WILD-TYPE 90 37 59

Figure S38.  Get High-res Image Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20p12.2)' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 29(20P12.2) CNV 42 60 33
AMP PEAK 29(20P12.2) WILD-TYPE 56 23 36

Figure S39.  Get High-res Image Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 31(22q11.21)' versus 'CN_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.22

Table S40.  Gene #31: 'Amp Peak 31(22q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 31(22Q11.21) CNV 54 80 65
AMP PEAK 31(22Q11.21) WILD-TYPE 89 49 60

Figure S40.  Get High-res Image Gene #31: 'Amp Peak 31(22q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0011

Table S41.  Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 1(1P36.22) CNV 9 37 13 10
DEL PEAK 1(1P36.22) WILD-TYPE 34 13 17 21

Figure S41.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.78e-08 (Fisher's exact test), Q value = 1.5e-05

Table S42.  Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 1(1P36.22) CNV 11 41 17
DEL PEAK 1(1P36.22) WILD-TYPE 17 13 55

Figure S42.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.61e-28 (Fisher's exact test), Q value = 1.4e-25

Table S43.  Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 1(1P36.22) CNV 34 107 31
DEL PEAK 1(1P36.22) WILD-TYPE 109 22 94

Figure S43.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.1e-14 (Fisher's exact test), Q value = 1.8e-11

Table S44.  Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 1(1P36.22) CNV 17 61 22
DEL PEAK 1(1P36.22) WILD-TYPE 81 22 47

Figure S44.  Get High-res Image Gene #33: '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 = 7.2e-11

Table S45.  Gene #33: '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 S45.  Get High-res Image Gene #33: '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 = 7.9e-12

Table S46.  Gene #33: '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 S46.  Get High-res Image Gene #33: '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 = 0.014

Table S47.  Gene #33: '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 S47.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000237 (Fisher's exact test), Q value = 0.17

Table S48.  Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 2(1P13.2) CNV 17 35 8 10
DEL PEAK 2(1P13.2) WILD-TYPE 26 15 22 21

Figure S48.  Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.23e-15 (Fisher's exact test), Q value = 1e-12

Table S49.  Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 2(1P13.2) CNV 35 93 44
DEL PEAK 2(1P13.2) WILD-TYPE 108 36 81

Figure S49.  Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.74e-09 (Fisher's exact test), Q value = 4.7e-06

Table S50.  Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 2(1P13.2) CNV 20 54 28
DEL PEAK 2(1P13.2) WILD-TYPE 78 29 41

Figure S50.  Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.56e-07 (Fisher's exact test), Q value = 0.00045

Table S51.  Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 2(1P13.2) CNV 27 68 38 17
DEL PEAK 2(1P13.2) WILD-TYPE 50 34 73 38

Figure S51.  Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.96e-07 (Fisher's exact test), Q value = 0.00016

Table S52.  Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 2(1P13.2) CNV 70 26 54
DEL PEAK 2(1P13.2) WILD-TYPE 37 44 114

Figure S52.  Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000271 (Fisher's exact test), Q value = 0.2

Table S53.  Gene #36: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 4(2Q22.1) CNV 22 47 36
DEL PEAK 4(2Q22.1) WILD-TYPE 121 82 89

Figure S53.  Get High-res Image Gene #36: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000236 (Fisher's exact test), Q value = 0.17

Table S54.  Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 5(2Q36.2) CNV 9 26 3 12
DEL PEAK 5(2Q36.2) WILD-TYPE 34 24 27 19

Figure S54.  Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 4.76e-05 (Fisher's exact test), Q value = 0.036

Table S55.  Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 5(2Q36.2) CNV 5 30 15
DEL PEAK 5(2Q36.2) WILD-TYPE 23 24 57

Figure S55.  Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.7e-12 (Fisher's exact test), Q value = 1.4e-09

Table S56.  Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 5(2Q36.2) CNV 23 74 35
DEL PEAK 5(2Q36.2) WILD-TYPE 120 55 90

Figure S56.  Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0017

Table S57.  Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 5(2Q36.2) CNV 17 44 25
DEL PEAK 5(2Q36.2) WILD-TYPE 81 39 44

Figure S57.  Get High-res Image Gene #37: '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 = 0.00054

Table S58.  Gene #37: '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 S58.  Get High-res Image Gene #37: '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 = 2.5e-05

Table S59.  Gene #37: '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 S59.  Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0021

Table S60.  Gene #39: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 7(3P13) CNV 105 119 116
DEL PEAK 7(3P13) WILD-TYPE 38 10 9

Figure S60.  Get High-res Image Gene #39: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.023

Table S61.  Gene #40: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 8(3P12.3) CNV 103 116 113
DEL PEAK 8(3P12.3) WILD-TYPE 40 13 12

Figure S61.  Get High-res Image Gene #40: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S62.  Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 10(4P15.2) CNV 70 99 70
DEL PEAK 10(4P15.2) WILD-TYPE 73 30 55

Figure S62.  Get High-res Image Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000341 (Fisher's exact test), Q value = 0.25

Table S63.  Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 10(4P15.2) CNV 44 61 44
DEL PEAK 10(4P15.2) WILD-TYPE 54 22 25

Figure S63.  Get High-res Image Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000102 (Fisher's exact test), Q value = 0.077

Table S64.  Gene #43: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 11(4Q22.1) CNV 65 90 62
DEL PEAK 11(4Q22.1) WILD-TYPE 78 39 63

Figure S64.  Get High-res Image Gene #43: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00028

Table S65.  Gene #44: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 12(4Q32.3) CNV 72 104 72
DEL PEAK 12(4Q32.3) WILD-TYPE 71 25 53

Figure S65.  Get High-res Image Gene #44: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0023

Table S66.  Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 13(4Q35.2) CNV 76 104 73
DEL PEAK 13(4Q35.2) WILD-TYPE 67 25 52

Figure S66.  Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000124 (Fisher's exact test), Q value = 0.093

Table S67.  Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 13(4Q35.2) CNV 47 65 42
DEL PEAK 13(4Q35.2) WILD-TYPE 51 18 27

Figure S67.  Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000143 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #45: '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 #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.03e-12 (Fisher's exact test), Q value = 1.7e-09

Table S69.  Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 14(5Q11.2) CNV 73 108 109
DEL PEAK 14(5Q11.2) WILD-TYPE 70 21 16

Figure S69.  Get High-res Image Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000192 (Fisher's exact test), Q value = 0.14

Table S70.  Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 14(5Q11.2) CNV 57 69 56
DEL PEAK 14(5Q11.2) WILD-TYPE 41 14 13

Figure S70.  Get High-res Image Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.7e-09 (Fisher's exact test), Q value = 4.7e-06

Table S71.  Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 15(5Q31.1) CNV 86 111 111
DEL PEAK 15(5Q31.1) WILD-TYPE 57 18 14

Figure S71.  Get High-res Image Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S72.  Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 15(5Q31.1) CNV 63 71 63
DEL PEAK 15(5Q31.1) WILD-TYPE 35 12 6

Figure S72.  Get High-res Image Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000305 (Fisher's exact test), Q value = 0.22

Table S73.  Gene #48: 'Del Peak 16(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 16(6P25.3) CNV 43 11 36
DEL PEAK 16(6P25.3) WILD-TYPE 64 59 132

Figure S73.  Get High-res Image Gene #48: 'Del Peak 16(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S74.  Gene #49: '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 S74.  Get High-res Image Gene #49: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.4e-05 (Fisher's exact test), Q value = 0.034

Table S75.  Gene #51: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 19(7Q11.22) CNV 11 3 23
DEL PEAK 19(7Q11.22) WILD-TYPE 132 126 102

Figure S75.  Get High-res Image Gene #51: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.97e-10 (Fisher's exact test), Q value = 1.6e-07

Table S76.  Gene #54: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 22(9P23) CNV 74 75 109
DEL PEAK 22(9P23) WILD-TYPE 69 54 16

Figure S76.  Get High-res Image Gene #54: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00041

Table S77.  Gene #55: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 23(9P21.3) CNV 92 96 114
DEL PEAK 23(9P21.3) WILD-TYPE 51 33 11

Figure S77.  Get High-res Image Gene #55: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNA_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13

Table S78.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 24(9Q21.11) CNV 28 12 19 15
DEL PEAK 24(9Q21.11) WILD-TYPE 15 38 11 16

Figure S78.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.038

Table S79.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 24(9Q21.11) CNV 16 13 45
DEL PEAK 24(9Q21.11) WILD-TYPE 12 41 27

Figure S79.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(9q21.11)' versus 'CN_CNMF'

P value = 5.97e-11 (Fisher's exact test), Q value = 5e-08

Table S80.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 24(9Q21.11) CNV 69 35 87
DEL PEAK 24(9Q21.11) WILD-TYPE 74 94 38

Figure S80.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00092

Table S81.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 24(9Q21.11) CNV 54 22 46
DEL PEAK 24(9Q21.11) WILD-TYPE 44 61 23

Figure S81.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 4.4e-09 (Fisher's exact test), Q value = 3.6e-06

Table S82.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 24(9Q21.11) CNV 43 23 71 29
DEL PEAK 24(9Q21.11) WILD-TYPE 34 79 40 26

Figure S82.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.3e-06

Table S83.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 24(9Q21.11) CNV 25 45 96
DEL PEAK 24(9Q21.11) WILD-TYPE 82 25 72

Figure S83.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.14

Table S84.  Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 24(9Q21.11) CNV 65 91 20
DEL PEAK 24(9Q21.11) WILD-TYPE 48 90 53

Figure S84.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(10p15.3)' versus 'CN_CNMF'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.037

Table S85.  Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 25(10P15.3) CNV 45 75 58
DEL PEAK 25(10P15.3) WILD-TYPE 98 54 67

Figure S85.  Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10p15.3)' versus 'METHLYATION_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.073

Table S86.  Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 25(10P15.3) CNV 34 54 27
DEL PEAK 25(10P15.3) WILD-TYPE 64 29 42

Figure S86.  Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(10p15.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.034

Table S87.  Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 113 181 73
DEL PEAK 25(10P15.3) CNV 60 63 46
DEL PEAK 25(10P15.3) WILD-TYPE 53 118 27

Figure S87.  Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(10p15.1)' versus 'CN_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.12

Table S88.  Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 26(10P15.1) CNV 43 71 54
DEL PEAK 26(10P15.1) WILD-TYPE 100 58 71

Figure S88.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10p15.1)' versus 'METHLYATION_CNMF'

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0032

Table S89.  Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 26(10P15.1) CNV 32 55 23
DEL PEAK 26(10P15.1) WILD-TYPE 66 28 46

Figure S89.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S90.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0072

Table S91.  Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S91.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(10q23.31)' versus 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017

Table S92.  Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 27(10Q23.31) CNV 58 87 58
DEL PEAK 27(10Q23.31) WILD-TYPE 85 42 67

Figure S92.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(10q23.31)' versus 'METHLYATION_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0017

Table S93.  Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 27(10Q23.31) CNV 34 60 33
DEL PEAK 27(10Q23.31) WILD-TYPE 64 23 36

Figure S93.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 8.54e-06 (Fisher's exact test), Q value = 0.0068

Table S94.  Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S94.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.23e-07 (Fisher's exact test), Q value = 0.00058

Table S95.  Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 27(10Q23.31) CNV 75 36 63
DEL PEAK 27(10Q23.31) WILD-TYPE 32 34 105

Figure S95.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(11p15.5)' versus 'CN_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.001

Table S96.  Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 28(11P15.5) CNV 49 53 81
DEL PEAK 28(11P15.5) WILD-TYPE 94 76 44

Figure S96.  Get High-res Image Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.016

Table S97.  Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
DEL PEAK 28(11P15.5) CNV 29 17 36 10
DEL PEAK 28(11P15.5) WILD-TYPE 29 30 13 30

Figure S97.  Get High-res Image Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.074

Table S98.  Gene #66: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 34(14Q11.2) CNV 38 39 44
DEL PEAK 34(14Q11.2) WILD-TYPE 69 31 124

Figure S98.  Get High-res Image Gene #66: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(17q11.2)' versus 'MRNA_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0099

Table S99.  Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 40(17Q11.2) CNV 21 3 11 7
DEL PEAK 40(17Q11.2) WILD-TYPE 22 47 19 24

Figure S99.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.049

Table S100.  Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 40(17Q11.2) CNV 9 4 29
DEL PEAK 40(17Q11.2) WILD-TYPE 19 50 43

Figure S100.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q11.2)' versus 'CN_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05

Table S101.  Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 40(17Q11.2) CNV 40 10 46
DEL PEAK 40(17Q11.2) WILD-TYPE 103 119 79

Figure S101.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.0012

Table S102.  Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
DEL PEAK 40(17Q11.2) CNV 24 7 36 19
DEL PEAK 40(17Q11.2) WILD-TYPE 53 95 75 36

Figure S102.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-08 (Fisher's exact test), Q value = 4e-05

Table S103.  Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
DEL PEAK 40(17Q11.2) CNV 7 20 59
DEL PEAK 40(17Q11.2) WILD-TYPE 100 50 109

Figure S103.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(19p13.3)' versus 'CN_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.011

Table S104.  Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 43(19P13.3) CNV 48 49 76
DEL PEAK 43(19P13.3) WILD-TYPE 95 80 49

Figure S104.  Get High-res Image Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.17

Table S105.  Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 133 166 68
DEL PEAK 43(19P13.3) CNV 71 72 16
DEL PEAK 43(19P13.3) WILD-TYPE 62 94 52

Figure S105.  Get High-res Image Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 44(19q13.33)' versus 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.12

Table S106.  Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 44(19Q13.33) CNV 22 48 36
DEL PEAK 44(19Q13.33) WILD-TYPE 121 81 89

Figure S106.  Get High-res Image Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19q13.33)' versus 'METHLYATION_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.14

Table S107.  Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 44(19Q13.33) CNV 12 30 23
DEL PEAK 44(19Q13.33) WILD-TYPE 86 53 46

Figure S107.  Get High-res Image Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(21q22.3)' versus 'CN_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.8e-05

Table S108.  Gene #78: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 46(21Q22.3) CNV 53 91 80
DEL PEAK 46(21Q22.3) WILD-TYPE 90 38 45

Figure S108.  Get High-res Image Gene #78: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.21

Table S109.  Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 48(22Q13.32) CNV 9 7 7 18
DEL PEAK 48(22Q13.32) WILD-TYPE 34 43 23 13

Figure S109.  Get High-res Image Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.066

Table S110.  Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 48(22Q13.32) CNV 17 9 15
DEL PEAK 48(22Q13.32) WILD-TYPE 11 45 57

Figure S110.  Get High-res Image Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 49(Xp22.2)' versus 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S111.  Gene #81: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 49(XP22.2) CNV 28 53 45
DEL PEAK 49(XP22.2) WILD-TYPE 115 76 80

Figure S111.  Get High-res Image Gene #81: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'CN_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.041

Table S112.  Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 50(XP21.1) CNV 27 55 45
DEL PEAK 50(XP21.1) WILD-TYPE 116 74 80

Figure S112.  Get High-res Image Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18

Table S113.  Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 50(XP21.1) CNV 18 36 29
DEL PEAK 50(XP21.1) WILD-TYPE 80 47 40

Figure S113.  Get High-res Image Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 51(Xp11.3)' versus 'CN_CNMF'

P value = 9.19e-06 (Fisher's exact test), Q value = 0.0073

Table S114.  Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 51(XP11.3) CNV 26 58 41
DEL PEAK 51(XP11.3) WILD-TYPE 117 71 84

Figure S114.  Get High-res Image Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 51(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.032

Table S115.  Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 51(XP11.3) CNV 16 38 26
DEL PEAK 51(XP11.3) WILD-TYPE 82 45 43

Figure S115.  Get High-res Image Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 52(Xq22.3)' versus 'CN_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.015

Table S116.  Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 52(XQ22.3) CNV 18 31 46
DEL PEAK 52(XQ22.3) WILD-TYPE 125 98 79

Figure S116.  Get High-res Image Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xq22.3)' versus 'METHLYATION_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S117.  Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 52(XQ22.3) CNV 10 20 25
DEL PEAK 52(XQ22.3) WILD-TYPE 88 63 44

Figure S117.  Get High-res Image Gene #84: 'Del Peak 52(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 = 397

  • Number of copy number variation regions = 84

  • Number of molecular subtypes = 10

  • 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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