Correlation between copy number variation genes and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1XW4H4X
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/C1XW4H4X
Overview
Introduction

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

Summary

Testing the association between copy number variation of 70 peak regions and 10 molecular subtypes across 561 patients, 118 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p36.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 5(3q26.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 7(4q12) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • Amp Peak 8(7p11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 9(7q11.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Amp Peak 10(7q21.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Amp Peak 11(7q31.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 12(7q36.1) cnvs correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Amp Peak 13(8q24.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Amp Peak 15(12p13.32) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 16(12q14.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 17(12q15) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 21(17q25.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 22(19p13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • Amp Peak 23(19q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • Del Peak 7(2q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 8(2q37.1) cnvs correlated to 'MIR_CHIERARCHICAL'.

  • Del Peak 9(3p21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(3q13.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 11(3q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 14(4q34.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 15(5q35.2) cnvs correlated to 'MRNA_CNMF',  'MIR_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 16(6q22.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 17(6q26) cnvs correlated to 'CN_CNMF'.

  • Del Peak 19(9p21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 21(10p15.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 22(10p13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CNMF'.

  • Del Peak 23(10p11.23) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 24(10q23.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 25(10q26.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 26(11p15.5) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • Del Peak 27(11p11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

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

  • Del Peak 30(12q12) cnvs correlated to 'CN_CNMF'.

  • Del Peak 31(12q15) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 32(13q14.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • Del Peak 33(14q13.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • Del Peak 34(14q24.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • Del Peak 35(14q31.3) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • Del Peak 36(15q14) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 39(17p13.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 40(17p13.1) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 43(19q13.41) cnvs correlated to 'MRNA_CHIERARCHICAL'.

  • Del Peak 44(21q22.3) cnvs correlated to 'MIR_CNMF'.

  • Del Peak 46(Xp22.2) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 118 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 8(7p11 2) 0 (0%) 69 2.56e-11
(1.74e-08) 		7.75e-10
(5.23e-07) 		3.08e-07
(2e-04) 		1.66e-12
(1.13e-09) 		1.53e-20
(1.07e-17) 		1.32e-06
(0.000844) 		8.62e-06
(0.00534) 		5.85e-05
(0.0353) 		1.11e-05
(0.00685) 		0.000357
(0.208)
Amp Peak 9(7q11 21) 0 (0%) 111 8.12e-06
(0.00505) 		2.59e-06
(0.00163) 		4.53e-06
(0.00285) 		2.54e-09
(1.7e-06) 		2.04e-09
(1.37e-06) 		0.00585
(1.00) 		0.00417
(1.00) 		0.336
(1.00) 		0.004
(1.00) 		0.00143
(0.8)
Del Peak 22(10p13) 0 (0%) 103 6.24e-07
(0.000403) 		1.44e-05
(0.00885) 		0.00126
(0.714) 		1.15e-07
(7.58e-05) 		3.98e-15
(2.74e-12) 		0.035
(1.00) 		0.000132
(0.0789) 		0.00458
(1.00) 		0.0885
(1.00) 		0.41
(1.00)
Del Peak 23(10p11 23) 0 (0%) 99 9.69e-10
(6.52e-07) 		1.86e-07
(0.000122) 		0.000199
(0.118) 		9.32e-09
(6.21e-06) 		3.97e-16
(2.75e-13) 		0.027
(1.00) 		0.000786
(0.45) 		0.0175
(1.00) 		0.0443
(1.00) 		0.084
(1.00)
Del Peak 26(11p15 5) 0 (0%) 435 1.59e-09
(1.07e-06) 		2.26e-07
(0.000147) 		0.256
(1.00) 		1.76e-06
(0.00112) 		7.17e-15
(4.93e-12) 		0.000309
(0.181) 		0.268
(1.00) 		0.0938
(1.00) 		0.00119
(0.677) 		0.263
(1.00)
Del Peak 36(15q14) 0 (0%) 413 7.11e-06
(0.00445) 		3.39e-08
(2.25e-05) 		0.012
(1.00) 		2.14e-06
(0.00136) 		3.91e-07
(0.000253) 		0.00231
(1.00) 		0.0699
(1.00) 		0.0241
(1.00) 		0.000352
(0.205) 		0.158
(1.00)
Amp Peak 10(7q21 2) 0 (0%) 95 1.44e-05
(0.00887) 		0.000314
(0.183) 		0.0101
(1.00) 		2.22e-06
(0.00141) 		1.23e-10
(8.37e-08) 		0.00363
(1.00) 		0.0179
(1.00) 		0.0964
(1.00) 		0.0618
(1.00) 		0.00474
(1.00)
Amp Peak 13(8q24 21) 0 (0%) 497 2e-07
(0.000131) 		0.00011
(0.0662) 		0.0368
(1.00) 		5.61e-05
(0.0339) 		3.99e-06
(0.00251) 		0.0699
(1.00) 		0.104
(1.00) 		0.00574
(1.00) 		0.131
(1.00) 		0.345
(1.00)
Amp Peak 22(19p13 2) 0 (0%) 322 6.24e-13
(4.27e-10) 		5.7e-07
(0.000369) 		0.25
(1.00) 		0.00455
(1.00) 		8.93e-20
(6.2e-17) 		0.017
(1.00) 		0.0116
(1.00) 		1.32e-05
(0.00815) 		0.164
(1.00) 		0.0199
(1.00)
Amp Peak 23(19q12) 0 (0%) 358 2.83e-11
(1.92e-08) 		1.78e-09
(1.2e-06) 		0.262
(1.00) 		0.00206
(1.00) 		3.21e-15
(2.22e-12) 		0.0553
(1.00) 		0.0174
(1.00) 		0.000213
(0.125) 		0.0823
(1.00) 		0.0438
(1.00)
Del Peak 15(5q35 2) 0 (0%) 507 1.58e-05
(0.00968) 		0.00244
(1.00) 		0.000142
(0.0849) 		1.46e-06
(0.00093) 		6.24e-05
(0.0376) 		0.00338
(1.00) 		0.944
(1.00) 		0.295
(1.00) 		0.208
(1.00) 		0.841
(1.00)
Del Peak 21(10p15 3) 0 (0%) 105 4.05e-06
(0.00255) 		0.000151
(0.0901) 		0.00631
(1.00) 		1.66e-07
(0.000109) 		5.18e-14
(3.55e-11) 		0.035
(1.00) 		0.00523
(1.00) 		0.0278
(1.00) 		0.0147
(1.00) 		0.41
(1.00)
Del Peak 24(10q23 31) 0 (0%) 63 1.05e-06
(0.000673) 		3.85e-05
(0.0235) 		0.00337
(1.00) 		3.85e-05
(0.0235) 		4.77e-16
(3.3e-13) 		0.196
(1.00) 		0.0105
(1.00) 		0.131
(1.00) 		0.369
(1.00) 		0.16
(1.00)
Del Peak 25(10q26 3) 0 (0%) 62 2.52e-07
(0.000164) 		4.75e-06
(0.00298) 		0.0514
(1.00) 		3.31e-05
(0.0202) 		1.73e-13
(1.18e-10) 		0.0145
(1.00) 		0.117
(1.00) 		0.0761
(1.00) 		0.25
(1.00) 		0.378
(1.00)
Del Peak 27(11p11 2) 0 (0%) 461 2.01e-07
(0.000131) 		0.00016
(0.0951) 		0.941
(1.00) 		1.27e-05
(0.00788) 		6.78e-13
(4.63e-10) 		0.000701
(0.403) 		0.825
(1.00) 		0.576
(1.00) 		0.051
(1.00) 		0.706
(1.00)
Amp Peak 12(7q36 1) 0 (0%) 98 5.21e-05
(0.0316) 		0.00155
(0.868) 		0.0567
(1.00) 		3.8e-06
(0.0024) 		1.66e-05
(0.0102) 		0.00363
(1.00) 		0.227
(1.00) 		0.249
(1.00) 		0.0292
(1.00) 		0.00467
(1.00)
Del Peak 19(9p21 3) 0 (0%) 155 8.3e-06
(0.00515) 		1.52e-07
(1e-04) 		0.572
(1.00) 		0.00351
(1.00) 		1.24e-10
(8.37e-08) 		0.0417
(1.00) 		0.0878
(1.00) 		0.0182
(1.00) 		0.0274
(1.00) 		0.00319
(1.00)
Del Peak 31(12q15) 0 (0%) 484 0.000128
(0.0766) 		6.15e-05
(0.0371) 		0.35
(1.00) 		0.0448
(1.00) 		6.36e-07
(0.000409) 		0.514
(1.00) 		0.527
(1.00) 		0.724
(1.00) 		0.585
(1.00) 		0.943
(1.00)
Del Peak 32(13q14 2) 0 (0%) 325 1.56e-07
(0.000102) 		3.87e-05
(0.0235) 		0.135
(1.00) 		0.184
(1.00) 		3.48e-16
(2.42e-13) 		0.0328
(1.00) 		0.794
(1.00) 		0.107
(1.00) 		0.0921
(1.00) 		0.193
(1.00)
Amp Peak 7(4q12) 0 (0%) 457 0.000491
(0.285) 		1.44e-05
(0.00885) 		0.472
(1.00) 		0.0648
(1.00) 		1.2e-07
(7.89e-05) 		0.384
(1.00) 		0.272
(1.00) 		0.664
(1.00) 		0.0487
(1.00) 		0.403
(1.00)
Del Peak 28(11q14 1) 0 (0%) 467 1.29e-06
(0.000826) 		0.0155
(1.00) 		0.937
(1.00) 		0.00299
(1.00) 		5.38e-16
(3.72e-13) 		0.259
(1.00) 		0.552
(1.00) 		0.5
(1.00) 		0.0908
(1.00) 		0.793
(1.00)
Del Peak 33(14q13 1) 0 (0%) 387 7.74e-06
(0.00482) 		0.0092
(1.00) 		0.577
(1.00) 		0.234
(1.00) 		2.64e-29
(1.84e-26) 		0.108
(1.00) 		0.577
(1.00) 		0.367
(1.00) 		0.291
(1.00) 		0.742
(1.00)
Del Peak 34(14q24 2) 0 (0%) 392 1.26e-07
(8.29e-05) 		0.000602
(0.348) 		0.0408
(1.00) 		0.915
(1.00) 		1.24e-38
(8.66e-36) 		0.0503
(1.00) 		0.457
(1.00) 		0.275
(1.00) 		0.0497
(1.00) 		0.142
(1.00)
Del Peak 35(14q31 3) 0 (0%) 406 5.12e-09
(3.42e-06) 		0.00191
(1.00) 		0.292
(1.00) 		0.88
(1.00) 		1.31e-40
(9.15e-38) 		0.00996
(1.00) 		0.515
(1.00) 		0.108
(1.00) 		0.222
(1.00) 		0.0846
(1.00)
Del Peak 41(17q11 2) 0 (0%) 491 7.34e-06
(0.00458) 		0.00135
(0.761) 		0.00107
(0.607) 		0.0209
(1.00) 		1.05e-06
(0.000675) 		0.496
(1.00) 		0.00594
(1.00) 		0.00512
(1.00) 		0.539
(1.00) 		0.104
(1.00)
Amp Peak 1(1p36 21) 0 (0%) 473 0.562
(1.00) 		0.588
(1.00) 		0.203
(1.00) 		0.0216
(1.00) 		4.4e-08
(2.92e-05) 		0.473
(1.00) 		0.048
(1.00) 		0.0531
(1.00) 		0.0967
(1.00) 		0.0808
(1.00)
Amp Peak 2(1q32 1) 0 (0%) 409 0.913
(1.00) 		0.354
(1.00) 		0.253
(1.00) 		0.177
(1.00) 		4.62e-08
(3.06e-05) 		0.623
(1.00) 		0.84
(1.00) 		0.335
(1.00) 		0.475
(1.00) 		0.095
(1.00)
Amp Peak 3(1q44) 0 (0%) 466 0.275
(1.00) 		0.453
(1.00) 		0.364
(1.00) 		0.399
(1.00) 		2.53e-08
(1.68e-05) 		0.931
(1.00) 		0.426
(1.00) 		0.177
(1.00) 		0.775
(1.00) 		0.439
(1.00)
Amp Peak 5(3q26 33) 0 (0%) 453 0.018
(1.00) 		0.0668
(1.00) 		0.978
(1.00) 		0.519
(1.00) 		1.15e-06
(0.000737) 		0.00452
(1.00) 		0.0685
(1.00) 		0.358
(1.00) 		0.546
(1.00) 		0.321
(1.00)
Amp Peak 11(7q31 2) 0 (0%) 103 0.00103
(0.589) 		0.000736
(0.422) 		0.00185
(1.00) 		0.000489
(0.284) 		2.55e-07
(0.000166) 		0.0107
(1.00) 		0.103
(1.00) 		0.183
(1.00) 		0.256
(1.00) 		0.00355
(1.00)
Amp Peak 15(12p13 32) 0 (0%) 480 0.606
(1.00) 		0.781
(1.00) 		0.544
(1.00) 		0.881
(1.00) 		4.93e-05
(0.0299) 		0.278
(1.00) 		0.411
(1.00) 		0.553
(1.00) 		0.442
(1.00) 		0.151
(1.00)
Amp Peak 16(12q14 1) 0 (0%) 430 0.077
(1.00) 		0.116
(1.00) 		0.181
(1.00) 		0.126
(1.00) 		2.51e-09
(1.68e-06) 		0.525
(1.00) 		0.0452
(1.00) 		0.338
(1.00) 		0.0335
(1.00) 		0.0543
(1.00)
Amp Peak 17(12q15) 0 (0%) 469 0.655
(1.00) 		0.5
(1.00) 		0.569
(1.00) 		0.312
(1.00) 		1.15e-06
(0.000737) 		0.563
(1.00) 		0.273
(1.00) 		0.649
(1.00) 		0.333
(1.00) 		0.349
(1.00)
Amp Peak 21(17q25 1) 0 (0%) 484 0.026
(1.00) 		0.292
(1.00) 		0.41
(1.00) 		0.367
(1.00) 		0.000122
(0.073) 		0.937
(1.00) 		0.13
(1.00) 		0.292
(1.00) 		1
(1.00) 		0.417
(1.00)
Del Peak 7(2q22 1) 0 (0%) 517 0.00239
(1.00) 		0.0314
(1.00) 		0.453
(1.00) 		0.0264
(1.00) 		1.69e-06
(0.00108) 		0.00338
(1.00) 		0.478
(1.00) 		0.86
(1.00) 		0.181
(1.00) 		0.21
(1.00)
Del Peak 8(2q37 1) 0 (0%) 505 0.0708
(1.00) 		0.00906
(1.00) 		0.242
(1.00) 		0.000184
(0.109) 		0.0065
(1.00) 		0.0265
(1.00) 		0.647
(1.00) 		0.72
(1.00) 		0.181
(1.00) 		0.687
(1.00)
Del Peak 9(3p21 1) 0 (0%) 509 0.243
(1.00) 		0.521
(1.00) 		0.895
(1.00) 		0.0786
(1.00) 		0.000201
(0.118) 		0.252
(1.00) 		0.134
(1.00) 		0.855
(1.00) 		0.461
(1.00) 		0.0959
(1.00)
Del Peak 10(3q13 31) 0 (0%) 506 0.514
(1.00) 		0.863
(1.00) 		0.977
(1.00) 		0.305
(1.00) 		7.21e-06
(0.0045) 		0.405
(1.00) 		0.87
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.0547
(1.00)
Del Peak 11(3q22 1) 0 (0%) 506 0.792
(1.00) 		0.232
(1.00) 		0.627
(1.00) 		0.596
(1.00) 		0.000293
(0.172) 		0.198
(1.00) 		0.859
(1.00) 		0.892
(1.00) 		1
(1.00) 		0.103
(1.00)
Del Peak 14(4q34 3) 0 (0%) 471 0.00463
(1.00) 		0.00535
(1.00) 		0.16
(1.00) 		0.0342
(1.00) 		0.000189
(0.112) 		0.152
(1.00) 		0.0967
(1.00) 		0.283
(1.00) 		0.125
(1.00) 		0.96
(1.00)
Del Peak 16(6q22 31) 0 (0%) 407 0.648
(1.00) 		0.912
(1.00) 		0.599
(1.00) 		0.029
(1.00) 		1.28e-11
(8.7e-09) 		0.311
(1.00) 		0.204
(1.00) 		0.192
(1.00) 		0.796
(1.00) 		0.426
(1.00)
Del Peak 17(6q26) 0 (0%) 387 0.753
(1.00) 		0.07
(1.00) 		0.878
(1.00) 		0.0806
(1.00) 		6.21e-07
(0.000401) 		0.617
(1.00) 		0.0166
(1.00) 		0.0111
(1.00) 		0.761
(1.00) 		0.292
(1.00)
Del Peak 30(12q12) 0 (0%) 485 0.00874
(1.00) 		0.000734
(0.421) 		0.295
(1.00) 		0.0153
(1.00) 		0.0002
(0.118) 		0.299
(1.00) 		0.137
(1.00) 		0.489
(1.00) 		0.941
(1.00) 		0.868
(1.00)
Del Peak 39(17p13 2) 0 (0%) 477 0.00304
(1.00) 		0.71
(1.00) 		0.89
(1.00) 		0.717
(1.00) 		4.96e-10
(3.35e-07) 		0.376
(1.00) 		0.632
(1.00) 		0.487
(1.00) 		0.587
(1.00) 		0.261
(1.00)
Del Peak 40(17p13 1) 0 (0%) 467 0.000432
(0.251) 		0.34
(1.00) 		0.894
(1.00) 		0.749
(1.00) 		4.73e-15
(3.25e-12) 		0.133
(1.00) 		0.709
(1.00) 		0.447
(1.00) 		0.645
(1.00) 		0.295
(1.00)
Del Peak 43(19q13 41) 0 (0%) 462 0.00266
(1.00) 		0.000155
(0.0922) 		0.0027
(1.00) 		0.00241
(1.00) 		0.0013
(0.733) 		0.778
(1.00) 		0.0401
(1.00) 		0.574
(1.00) 		0.02
(1.00) 		0.0941
(1.00)
Del Peak 44(21q22 3) 0 (0%) 502 0.00149
(0.833) 		0.0627
(1.00) 		8.73e-05
(0.0525) 		0.000609
(0.351) 		0.0738
(1.00) 		0.0685
(1.00) 		0.39
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.119
(1.00)
Del Peak 46(Xp22 2) 0 (0%) 438 0.00402
(1.00) 		0.0359
(1.00) 		0.101
(1.00) 		0.216
(1.00) 		8.52e-10
(5.74e-07) 		0.00951
(1.00) 		0.605
(1.00) 		0.253
(1.00) 		0.337
(1.00) 		0.644
(1.00)
Amp Peak 4(2p24 3) 0 (0%) 516 0.0427
(1.00) 		0.0134
(1.00) 		0.772
(1.00) 		0.377
(1.00) 		0.000516
(0.298) 		0.0574
(1.00) 		0.209
(1.00) 		0.112
(1.00) 		0.93
(1.00) 		1
(1.00)
Amp Peak 6(4p16 3) 0 (0%) 515 0.392
(1.00) 		0.296
(1.00) 		0.809
(1.00) 		0.173
(1.00) 		0.465
(1.00) 		0.529
(1.00) 		0.636
(1.00) 		0.53
(1.00) 		0.941
(1.00) 		0.759
(1.00)
Amp Peak 14(11p13) 0 (0%) 535 0.693
(1.00) 		0.858
(1.00) 		0.337
(1.00) 		0.439
(1.00) 		0.468
(1.00) 		0.181
(1.00) 		0.265
(1.00) 		0.112
(1.00) 		0.602
(1.00) 		1
(1.00)
Amp Peak 18(13q34) 0 (0%) 531 0.193
(1.00) 		0.429
(1.00) 		0.165
(1.00) 		0.16
(1.00) 		0.00606
(1.00) 		0.0677
(1.00) 		0.186
(1.00) 		0.368
(1.00) 		1
(1.00)
Amp Peak 19(14q32 33) 0 (0%) 528 0.38
(1.00) 		0.71
(1.00) 		0.0111
(1.00) 		0.835
(1.00) 		0.899
(1.00) 		0.903
(1.00) 		0.0394
(1.00) 		0.275
(1.00) 		0.0429
(1.00) 		0.884
(1.00)
Amp Peak 20(17p13 2) 0 (0%) 516 0.0025
(1.00) 		0.0223
(1.00) 		0.0712
(1.00) 		0.169
(1.00) 		0.00741
(1.00) 		0.865
(1.00) 		0.0545
(1.00) 		0.63
(1.00) 		0.615
(1.00) 		0.281
(1.00)
Amp Peak 24(21q21 1) 0 (0%) 495 0.00298
(1.00) 		0.0068
(1.00) 		0.0838
(1.00) 		0.0589
(1.00) 		0.00142
(0.8) 		0.879
(1.00) 		0.669
(1.00) 		0.83
(1.00) 		0.0967
(1.00) 		0.0663
(1.00)
Del Peak 1(1p36 32) 0 (0%) 462 0.809
(1.00) 		0.0378
(1.00) 		0.505
(1.00) 		0.243
(1.00) 		0.619
(1.00) 		0.339
(1.00) 		0.545
(1.00) 		0.561
(1.00) 		0.252
(1.00) 		0.0437
(1.00)
Del Peak 2(1p36 23) 0 (0%) 426 0.164
(1.00) 		0.0495
(1.00) 		0.317
(1.00) 		0.298
(1.00) 		0.000912
(0.52) 		0.306
(1.00) 		0.279
(1.00) 		0.725
(1.00) 		0.0632
(1.00) 		0.103
(1.00)
Del Peak 3(1p32 3) 0 (0%) 502 0.306
(1.00) 		0.542
(1.00) 		0.982
(1.00) 		0.856
(1.00) 		0.143
(1.00) 		0.822
(1.00) 		0.706
(1.00) 		0.63
(1.00) 		0.803
(1.00) 		0.159
(1.00)
Del Peak 4(1p22 1) 0 (0%) 514 0.865
(1.00) 		0.875
(1.00) 		0.736
(1.00) 		0.188
(1.00) 		0.159
(1.00) 		0.579
(1.00) 		0.888
(1.00) 		0.372
(1.00) 		1
(1.00) 		0.015
(1.00)
Del Peak 5(1q42 11) 0 (0%) 514 0.285
(1.00) 		0.892
(1.00) 		0.418
(1.00) 		0.472
(1.00) 		0.501
(1.00) 		0.412
(1.00) 		0.161
(1.00) 		0.00286
(1.00) 		0.686
(1.00) 		0.647
(1.00)
Del Peak 6(1q44) 0 (0%) 529 0.704
(1.00) 		0.462
(1.00) 		0.669
(1.00) 		0.112
(1.00) 		0.611
(1.00) 		0.187
(1.00) 		0.799
(1.00) 		0.335
(1.00) 		0.539
(1.00) 		0.904
(1.00)
Del Peak 12(3q29) 0 (0%) 498 0.0901
(1.00) 		0.222
(1.00) 		0.575
(1.00) 		0.891
(1.00) 		0.00606
(1.00) 		0.259
(1.00) 		0.379
(1.00) 		0.684
(1.00) 		0.954
(1.00) 		0.731
(1.00)
Del Peak 13(4p16 3) 0 (0%) 484 0.0567
(1.00) 		0.00643
(1.00) 		0.572
(1.00) 		0.0997
(1.00) 		0.0926
(1.00) 		1
(1.00) 		0.832
(1.00) 		0.71
(1.00) 		0.872
(1.00) 		0.818
(1.00)
Del Peak 18(8p23 2) 0 (0%) 495 0.475
(1.00) 		0.659
(1.00) 		0.229
(1.00) 		0.498
(1.00) 		0.065
(1.00) 		0.892
(1.00) 		0.951
(1.00) 		0.946
(1.00) 		0.62
(1.00) 		0.159
(1.00)
Del Peak 20(9q34 2) 0 (0%) 490 0.164
(1.00) 		0.0442
(1.00) 		0.797
(1.00) 		0.261
(1.00) 		0.312
(1.00) 		0.652
(1.00) 		0.113
(1.00) 		0.241
(1.00) 		0.442
(1.00) 		0.0569
(1.00)
Del Peak 29(12p13 1) 0 (0%) 487 0.0266
(1.00) 		0.00333
(1.00) 		0.182
(1.00) 		0.104
(1.00) 		0.106
(1.00) 		0.669
(1.00) 		0.875
(1.00) 		0.522
(1.00) 		0.944
(1.00) 		0.566
(1.00)
Del Peak 37(16p12 2) 0 (0%) 472 0.408
(1.00) 		0.501
(1.00) 		0.0455
(1.00) 		0.737
(1.00) 		0.104
(1.00) 		0.243
(1.00) 		0.405
(1.00) 		0.535
(1.00) 		0.443
(1.00) 		0.422
(1.00)
Del Peak 38(16q23 3) 0 (0%) 466 0.0176
(1.00) 		0.524
(1.00) 		0.727
(1.00) 		0.828
(1.00) 		0.00533
(1.00) 		0.752
(1.00) 		0.0385
(1.00) 		0.0802
(1.00) 		0.528
(1.00) 		0.468
(1.00)
Del Peak 42(18q22 3) 0 (0%) 482 0.254
(1.00) 		0.131
(1.00) 		0.466
(1.00) 		0.461
(1.00) 		0.00217
(1.00) 		0.0928
(1.00) 		0.0315
(1.00) 		0.00134
(0.754) 		0.159
(1.00) 		0.697
(1.00)
Del Peak 45(22q13 32) 0 (0%) 353 0.804
(1.00) 		0.191
(1.00) 		0.0181
(1.00) 		0.187
(1.00) 		0.000823
(0.47) 		0.774
(1.00) 		0.915
(1.00) 		0.941
(1.00) 		0.0721
(1.00) 		0.923
(1.00)
'Amp Peak 1(1p36.21)' versus 'CN_CNMF'

P value = 4.4e-08 (Fisher's exact test), Q value = 2.9e-05

Table S1.  Gene #1: 'Amp Peak 1(1p36.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 1(1P36.21) CNV 49 19 20
AMP PEAK 1(1P36.21) WILD-TYPE 112 169 192

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p36.21)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 4.62e-08 (Fisher's exact test), Q value = 3.1e-05

Table S2.  Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 2(1Q32.1) CNV 72 37 43
AMP PEAK 2(1Q32.1) WILD-TYPE 89 151 169

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 3(1q44)' versus 'CN_CNMF'

P value = 2.53e-08 (Fisher's exact test), Q value = 1.7e-05

Table S3.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 3(1Q44) CNV 52 22 21
AMP PEAK 3(1Q44) WILD-TYPE 109 166 191

Figure S3.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 5(3q26.33)' versus 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00074

Table S4.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 5(3Q26.33) CNV 53 31 24
AMP PEAK 5(3Q26.33) WILD-TYPE 108 157 188

Figure S4.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 7(4q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0089

Table S5.  Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 7(4Q12) CNV 13 53 32
AMP PEAK 7(4Q12) WILD-TYPE 104 118 188

Figure S5.  Get High-res Image Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 7(4q12)' versus 'CN_CNMF'

P value = 1.2e-07 (Fisher's exact test), Q value = 7.9e-05

Table S6.  Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 7(4Q12) CNV 53 30 21
AMP PEAK 7(4Q12) WILD-TYPE 108 158 191

Figure S6.  Get High-res Image Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNA_CNMF'

P value = 2.56e-11 (Fisher's exact test), Q value = 1.7e-08

Table S7.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 8(7P11.2) CNV 139 67 147 89
AMP PEAK 8(7P11.2) WILD-TYPE 8 29 5 24

Figure S7.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 7.75e-10 (Fisher's exact test), Q value = 5.2e-07

Table S8.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 8(7P11.2) CNV 112 125 205
AMP PEAK 8(7P11.2) WILD-TYPE 5 46 15

Figure S8.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'MIR_CNMF'

P value = 3.08e-07 (Fisher's exact test), Q value = 2e-04

Table S9.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 155 73 104
AMP PEAK 8(7P11.2) CNV 136 122 59 95
AMP PEAK 8(7P11.2) WILD-TYPE 3 33 14 9

Figure S9.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

'Amp Peak 8(7p11.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.66e-12 (Fisher's exact test), Q value = 1.1e-09

Table S10.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
AMP PEAK 8(7P11.2) CNV 173 146 93
AMP PEAK 8(7P11.2) WILD-TYPE 8 9 42

Figure S10.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'CN_CNMF'

P value = 1.53e-20 (Fisher's exact test), Q value = 1.1e-17

Table S11.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 8(7P11.2) CNV 149 132 211
AMP PEAK 8(7P11.2) WILD-TYPE 12 56 1

Figure S11.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00084

Table S12.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 27 16 27
AMP PEAK 8(7P11.2) CNV 38 27 16 16
AMP PEAK 8(7P11.2) WILD-TYPE 1 0 0 11

Figure S12.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 8(7p11.2)' versus 'RPPA_CNMF'

P value = 8.62e-06 (Fisher's exact test), Q value = 0.0053

Table S13.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
AMP PEAK 8(7P11.2) CNV 49 42 44 44
AMP PEAK 8(7P11.2) WILD-TYPE 5 16 0 1

Figure S13.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #7: 'RPPA_CNMF'

'Amp Peak 8(7p11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.035

Table S14.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
AMP PEAK 8(7P11.2) CNV 64 31 84
AMP PEAK 8(7P11.2) WILD-TYPE 0 2 20

Figure S14.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0068

Table S15.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
AMP PEAK 8(7P11.2) CNV 31 66 34
AMP PEAK 8(7P11.2) WILD-TYPE 13 1 2

Figure S15.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.21

Table S16.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 21 60
AMP PEAK 8(7P11.2) CNV 64 21 46
AMP PEAK 8(7P11.2) WILD-TYPE 2 0 14

Figure S16.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'MRNA_CNMF'

P value = 8.12e-06 (Fisher's exact test), Q value = 0.005

Table S17.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 9(7Q11.21) CNV 133 63 124 82
AMP PEAK 9(7Q11.21) WILD-TYPE 14 33 28 31

Figure S17.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(7q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.59e-06 (Fisher's exact test), Q value = 0.0016

Table S18.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 9(7Q11.21) CNV 95 114 193
AMP PEAK 9(7Q11.21) WILD-TYPE 22 57 27

Figure S18.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'MIR_CNMF'

P value = 4.53e-06 (Fisher's exact test), Q value = 0.0028

Table S19.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 155 73 104
AMP PEAK 9(7Q11.21) CNV 126 111 49 90
AMP PEAK 9(7Q11.21) WILD-TYPE 13 44 24 14

Figure S19.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

'Amp Peak 9(7q11.21)' versus 'MIR_CHIERARCHICAL'

P value = 2.54e-09 (Fisher's exact test), Q value = 1.7e-06

Table S20.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
AMP PEAK 9(7Q11.21) CNV 157 137 82
AMP PEAK 9(7Q11.21) WILD-TYPE 24 18 53

Figure S20.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'CN_CNMF'

P value = 2.04e-09 (Fisher's exact test), Q value = 1.4e-06

Table S21.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 9(7Q11.21) CNV 144 122 184
AMP PEAK 9(7Q11.21) WILD-TYPE 17 66 28

Figure S21.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 10(7q21.2)' versus 'MRNA_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0089

Table S22.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 10(7Q21.2) CNV 131 63 134 90
AMP PEAK 10(7Q21.2) WILD-TYPE 16 33 18 23

Figure S22.  Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 10(7q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000314 (Fisher's exact test), Q value = 0.18

Table S23.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 10(7Q21.2) CNV 101 124 193
AMP PEAK 10(7Q21.2) WILD-TYPE 16 47 27

Figure S23.  Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 10(7q21.2)' versus 'MIR_CHIERARCHICAL'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.0014

Table S24.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
AMP PEAK 10(7Q21.2) CNV 162 133 91
AMP PEAK 10(7Q21.2) WILD-TYPE 19 22 44

Figure S24.  Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 10(7q21.2)' versus 'CN_CNMF'

P value = 1.23e-10 (Fisher's exact test), Q value = 8.4e-08

Table S25.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 10(7Q21.2) CNV 145 127 194
AMP PEAK 10(7Q21.2) WILD-TYPE 16 61 18

Figure S25.  Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 11(7q31.2)' versus 'CN_CNMF'

P value = 2.55e-07 (Fisher's exact test), Q value = 0.00017

Table S26.  Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 11(7Q31.2) CNV 141 129 188
AMP PEAK 11(7Q31.2) WILD-TYPE 20 59 24

Figure S26.  Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 12(7q36.1)' versus 'MRNA_CNMF'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.032

Table S27.  Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 12(7Q36.1) CNV 131 63 131 91
AMP PEAK 12(7Q36.1) WILD-TYPE 16 33 21 22

Figure S27.  Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(7q36.1)' versus 'MIR_CHIERARCHICAL'

P value = 3.8e-06 (Fisher's exact test), Q value = 0.0024

Table S28.  Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
AMP PEAK 12(7Q36.1) CNV 162 131 91
AMP PEAK 12(7Q36.1) WILD-TYPE 19 24 44

Figure S28.  Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 12(7q36.1)' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.01

Table S29.  Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 12(7Q36.1) CNV 139 135 189
AMP PEAK 12(7Q36.1) WILD-TYPE 22 53 23

Figure S29.  Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2e-07 (Fisher's exact test), Q value = 0.00013

Table S30.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 13(8Q24.21) CNV 8 24 6 19
AMP PEAK 13(8Q24.21) WILD-TYPE 139 72 146 94

Figure S30.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 0.00011 (Fisher's exact test), Q value = 0.066

Table S31.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 13(8Q24.21) CNV 7 34 16
AMP PEAK 13(8Q24.21) WILD-TYPE 110 137 204

Figure S31.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.61e-05 (Fisher's exact test), Q value = 0.034

Table S32.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
AMP PEAK 13(8Q24.21) CNV 12 12 30
AMP PEAK 13(8Q24.21) WILD-TYPE 169 143 105

Figure S32.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

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

P value = 3.99e-06 (Fisher's exact test), Q value = 0.0025

Table S33.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 13(8Q24.21) CNV 31 25 8
AMP PEAK 13(8Q24.21) WILD-TYPE 130 163 204

Figure S33.  Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 15(12p13.32)' versus 'CN_CNMF'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.03

Table S34.  Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 15(12P13.32) CNV 40 23 18
AMP PEAK 15(12P13.32) WILD-TYPE 121 165 194

Figure S34.  Get High-res Image Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 16(12q14.1)' versus 'CN_CNMF'

P value = 2.51e-09 (Fisher's exact test), Q value = 1.7e-06

Table S35.  Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 16(12Q14.1) CNV 67 28 36
AMP PEAK 16(12Q14.1) WILD-TYPE 94 160 176

Figure S35.  Get High-res Image Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 17(12q15)' versus 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00074

Table S36.  Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 17(12Q15) CNV 48 20 24
AMP PEAK 17(12Q15) WILD-TYPE 113 168 188

Figure S36.  Get High-res Image Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 21(17q25.1)' versus 'CN_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.073

Table S37.  Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 21(17Q25.1) CNV 38 21 18
AMP PEAK 21(17Q25.1) WILD-TYPE 123 167 194

Figure S37.  Get High-res Image Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(19p13.2)' versus 'MRNA_CNMF'

P value = 6.24e-13 (Fisher's exact test), Q value = 4.3e-10

Table S38.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 22(19P13.2) CNV 56 36 101 24
AMP PEAK 22(19P13.2) WILD-TYPE 91 60 51 89

Figure S38.  Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(19p13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 5.7e-07 (Fisher's exact test), Q value = 0.00037

Table S39.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 22(19P13.2) CNV 72 51 94
AMP PEAK 22(19P13.2) WILD-TYPE 45 120 126

Figure S39.  Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(19p13.2)' versus 'CN_CNMF'

P value = 8.93e-20 (Fisher's exact test), Q value = 6.2e-17

Table S40.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 22(19P13.2) CNV 48 48 143
AMP PEAK 22(19P13.2) WILD-TYPE 113 140 69

Figure S40.  Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(19p13.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0081

Table S41.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
AMP PEAK 22(19P13.2) CNV 42 8 34
AMP PEAK 22(19P13.2) WILD-TYPE 22 25 70

Figure S41.  Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(19q12)' versus 'MRNA_CNMF'

P value = 2.83e-11 (Fisher's exact test), Q value = 1.9e-08

Table S42.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 23(19Q12) CNV 55 28 84 16
AMP PEAK 23(19Q12) WILD-TYPE 92 68 68 97

Figure S42.  Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.78e-09 (Fisher's exact test), Q value = 1.2e-06

Table S43.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
AMP PEAK 23(19Q12) CNV 62 32 89
AMP PEAK 23(19Q12) WILD-TYPE 55 139 131

Figure S43.  Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(19q12)' versus 'CN_CNMF'

P value = 3.21e-15 (Fisher's exact test), Q value = 2.2e-12

Table S44.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
AMP PEAK 23(19Q12) CNV 38 43 122
AMP PEAK 23(19Q12) WILD-TYPE 123 145 90

Figure S44.  Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 23(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000213 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
AMP PEAK 23(19Q12) CNV 35 7 27
AMP PEAK 23(19Q12) WILD-TYPE 29 26 77

Figure S45.  Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Del Peak 7(2q22.1)' versus 'CN_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.0011

Table S46.  Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 7(2Q22.1) CNV 26 14 4
DEL PEAK 7(2Q22.1) WILD-TYPE 135 174 208

Figure S46.  Get High-res Image Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 8(2q37.1)' versus 'MIR_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.11

Table S47.  Gene #32: 'Del Peak 8(2q37.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 8(2Q37.1) CNV 13 9 27
DEL PEAK 8(2Q37.1) WILD-TYPE 168 146 108

Figure S47.  Get High-res Image Gene #32: 'Del Peak 8(2q37.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 9(3p21.1)' versus 'CN_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.12

Table S48.  Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 9(3P21.1) CNV 23 22 7
DEL PEAK 9(3P21.1) WILD-TYPE 138 166 205

Figure S48.  Get High-res Image Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 10(3q13.31)' versus 'CN_CNMF'

P value = 7.21e-06 (Fisher's exact test), Q value = 0.0045

Table S49.  Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 10(3Q13.31) CNV 27 22 6
DEL PEAK 10(3Q13.31) WILD-TYPE 134 166 206

Figure S49.  Get High-res Image Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 11(3q22.1)' versus 'CN_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.17

Table S50.  Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 11(3Q22.1) CNV 24 23 8
DEL PEAK 11(3Q22.1) WILD-TYPE 137 165 204

Figure S50.  Get High-res Image Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 14(4q34.3)' versus 'CN_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 14(4Q34.3) CNV 41 29 20
DEL PEAK 14(4Q34.3) WILD-TYPE 120 159 192

Figure S51.  Get High-res Image Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 15(5q35.2)' versus 'MRNA_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0097

Table S52.  Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 15(5Q35.2) CNV 8 22 7 15
DEL PEAK 15(5Q35.2) WILD-TYPE 139 74 145 98

Figure S52.  Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(5q35.2)' versus 'MIR_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.085

Table S53.  Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 155 73 104
DEL PEAK 15(5Q35.2) CNV 4 26 11 7
DEL PEAK 15(5Q35.2) WILD-TYPE 135 129 62 97

Figure S53.  Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 15(5q35.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00093

Table S54.  Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 15(5Q35.2) CNV 14 5 29
DEL PEAK 15(5Q35.2) WILD-TYPE 167 150 106

Figure S54.  Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 15(5q35.2)' versus 'CN_CNMF'

P value = 6.24e-05 (Fisher's exact test), Q value = 0.038

Table S55.  Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 15(5Q35.2) CNV 18 29 7
DEL PEAK 15(5Q35.2) WILD-TYPE 143 159 205

Figure S55.  Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 16(6q22.31)' versus 'CN_CNMF'

P value = 1.28e-11 (Fisher's exact test), Q value = 8.7e-09

Table S56.  Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 16(6Q22.31) CNV 79 34 41
DEL PEAK 16(6Q22.31) WILD-TYPE 82 154 171

Figure S56.  Get High-res Image Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 17(6q26)' versus 'CN_CNMF'

P value = 6.21e-07 (Fisher's exact test), Q value = 4e-04

Table S57.  Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 17(6Q26) CNV 76 40 58
DEL PEAK 17(6Q26) WILD-TYPE 85 148 154

Figure S57.  Get High-res Image Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 19(9p21.3)' versus 'MRNA_CNMF'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0052

Table S58.  Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 19(9P21.3) CNV 100 62 133 75
DEL PEAK 19(9P21.3) WILD-TYPE 47 34 19 38

Figure S58.  Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.52e-07 (Fisher's exact test), Q value = 1e-04

Table S59.  Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 19(9P21.3) CNV 107 112 151
DEL PEAK 19(9P21.3) WILD-TYPE 10 59 69

Figure S59.  Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(9p21.3)' versus 'CN_CNMF'

P value = 1.24e-10 (Fisher's exact test), Q value = 8.4e-08

Table S60.  Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 19(9P21.3) CNV 108 112 186
DEL PEAK 19(9P21.3) WILD-TYPE 53 76 26

Figure S60.  Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 21(10p15.3)' versus 'MRNA_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0025

Table S61.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 21(10P15.3) CNV 129 63 134 82
DEL PEAK 21(10P15.3) WILD-TYPE 18 33 18 31

Figure S61.  Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 21(10p15.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.09

Table S62.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 21(10P15.3) CNV 104 120 184
DEL PEAK 21(10P15.3) WILD-TYPE 13 51 36

Figure S62.  Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 21(10p15.3)' versus 'MIR_CHIERARCHICAL'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00011

Table S63.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 21(10P15.3) CNV 157 136 86
DEL PEAK 21(10P15.3) WILD-TYPE 24 19 49

Figure S63.  Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 21(10p15.3)' versus 'CN_CNMF'

P value = 5.18e-14 (Fisher's exact test), Q value = 3.6e-11

Table S64.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 21(10P15.3) CNV 137 120 199
DEL PEAK 21(10P15.3) WILD-TYPE 24 68 13

Figure S64.  Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(10p13)' versus 'MRNA_CNMF'

P value = 6.24e-07 (Fisher's exact test), Q value = 4e-04

Table S65.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 22(10P13) CNV 131 65 135 79
DEL PEAK 22(10P13) WILD-TYPE 16 31 17 34

Figure S65.  Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(10p13)' versus 'MRNA_CHIERARCHICAL'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0089

Table S66.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 22(10P13) CNV 104 118 188
DEL PEAK 22(10P13) WILD-TYPE 13 53 32

Figure S66.  Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 22(10p13)' versus 'MIR_CHIERARCHICAL'

P value = 1.15e-07 (Fisher's exact test), Q value = 7.6e-05

Table S67.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 22(10P13) CNV 157 138 87
DEL PEAK 22(10P13) WILD-TYPE 24 17 48

Figure S67.  Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 22(10p13)' versus 'CN_CNMF'

P value = 3.98e-15 (Fisher's exact test), Q value = 2.7e-12

Table S68.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 22(10P13) CNV 137 120 201
DEL PEAK 22(10P13) WILD-TYPE 24 68 11

Figure S68.  Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(10p13)' versus 'RPPA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.079

Table S69.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
DEL PEAK 22(10P13) CNV 50 38 42 37
DEL PEAK 22(10P13) WILD-TYPE 4 20 2 8

Figure S69.  Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #7: 'RPPA_CNMF'

'Del Peak 23(10p11.23)' versus 'MRNA_CNMF'

P value = 9.69e-10 (Fisher's exact test), Q value = 6.5e-07

Table S70.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 23(10P11.23) CNV 130 61 142 83
DEL PEAK 23(10P11.23) WILD-TYPE 17 35 10 30

Figure S70.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 23(10p11.23)' versus 'MRNA_CHIERARCHICAL'

P value = 1.86e-07 (Fisher's exact test), Q value = 0.00012

Table S71.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 23(10P11.23) CNV 110 119 187
DEL PEAK 23(10P11.23) WILD-TYPE 7 52 33

Figure S71.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 23(10p11.23)' versus 'MIR_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.12

Table S72.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 155 73 104
DEL PEAK 23(10P11.23) CNV 129 117 55 86
DEL PEAK 23(10P11.23) WILD-TYPE 10 38 18 18

Figure S72.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 23(10p11.23)' versus 'MIR_CHIERARCHICAL'

P value = 9.32e-09 (Fisher's exact test), Q value = 6.2e-06

Table S73.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 23(10P11.23) CNV 162 138 87
DEL PEAK 23(10P11.23) WILD-TYPE 19 17 48

Figure S73.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 23(10p11.23)' versus 'CN_CNMF'

P value = 3.97e-16 (Fisher's exact test), Q value = 2.8e-13

Table S74.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 23(10P11.23) CNV 138 121 203
DEL PEAK 23(10P11.23) WILD-TYPE 23 67 9

Figure S74.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNA_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00067

Table S75.  Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 24(10Q23.31) CNV 136 75 147 91
DEL PEAK 24(10Q23.31) WILD-TYPE 11 21 5 22

Figure S75.  Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.023

Table S76.  Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 24(10Q23.31) CNV 113 137 199
DEL PEAK 24(10Q23.31) WILD-TYPE 4 34 21

Figure S76.  Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'MIR_CHIERARCHICAL'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.023

Table S77.  Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 24(10Q23.31) CNV 169 144 105
DEL PEAK 24(10Q23.31) WILD-TYPE 12 11 30

Figure S77.  Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'CN_CNMF'

P value = 4.77e-16 (Fisher's exact test), Q value = 3.3e-13

Table S78.  Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 24(10Q23.31) CNV 149 139 210
DEL PEAK 24(10Q23.31) WILD-TYPE 12 49 2

Figure S78.  Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNA_CNMF'

P value = 2.52e-07 (Fisher's exact test), Q value = 0.00016

Table S79.  Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 25(10Q26.3) CNV 136 75 148 91
DEL PEAK 25(10Q26.3) WILD-TYPE 11 21 4 22

Figure S79.  Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.003

Table S80.  Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 25(10Q26.3) CNV 115 138 197
DEL PEAK 25(10Q26.3) WILD-TYPE 2 33 23

Figure S80.  Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(10q26.3)' versus 'MIR_CHIERARCHICAL'

P value = 3.31e-05 (Fisher's exact test), Q value = 0.02

Table S81.  Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 25(10Q26.3) CNV 172 140 106
DEL PEAK 25(10Q26.3) WILD-TYPE 9 15 29

Figure S81.  Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 25(10q26.3)' versus 'CN_CNMF'

P value = 1.73e-13 (Fisher's exact test), Q value = 1.2e-10

Table S82.  Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 25(10Q26.3) CNV 148 142 209
DEL PEAK 25(10Q26.3) WILD-TYPE 13 46 3

Figure S82.  Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNA_CNMF'

P value = 1.59e-09 (Fisher's exact test), Q value = 1.1e-06

Table S83.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 26(11P15.5) CNV 32 42 13 32
DEL PEAK 26(11P15.5) WILD-TYPE 115 54 139 81

Figure S83.  Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 2.26e-07 (Fisher's exact test), Q value = 0.00015

Table S84.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 26(11P15.5) CNV 10 61 48
DEL PEAK 26(11P15.5) WILD-TYPE 107 110 172

Figure S84.  Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'MIR_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0011

Table S85.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 26(11P15.5) CNV 31 28 55
DEL PEAK 26(11P15.5) WILD-TYPE 150 127 80

Figure S85.  Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'CN_CNMF'

P value = 7.17e-15 (Fisher's exact test), Q value = 4.9e-12

Table S86.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 26(11P15.5) CNV 62 51 13
DEL PEAK 26(11P15.5) WILD-TYPE 99 137 199

Figure S86.  Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'METHLYATION_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.18

Table S87.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 27 16 27
DEL PEAK 26(11P15.5) CNV 0 4 1 9
DEL PEAK 26(11P15.5) WILD-TYPE 39 23 15 18

Figure S87.  Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 27(11p11.2)' versus 'MRNA_CNMF'

P value = 2.01e-07 (Fisher's exact test), Q value = 0.00013

Table S88.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 27(11P11.2) CNV 26 34 10 24
DEL PEAK 27(11P11.2) WILD-TYPE 121 62 142 89

Figure S88.  Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(11p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.095

Table S89.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 27(11P11.2) CNV 10 47 37
DEL PEAK 27(11P11.2) WILD-TYPE 107 124 183

Figure S89.  Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(11p11.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0079

Table S90.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 27(11P11.2) CNV 19 28 43
DEL PEAK 27(11P11.2) WILD-TYPE 162 127 92

Figure S90.  Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 27(11p11.2)' versus 'CN_CNMF'

P value = 6.78e-13 (Fisher's exact test), Q value = 4.6e-10

Table S91.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 27(11P11.2) CNV 54 36 10
DEL PEAK 27(11P11.2) WILD-TYPE 107 152 202

Figure S91.  Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.29e-06 (Fisher's exact test), Q value = 0.00083

Table S92.  Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 28(11Q14.1) CNV 29 33 12 14
DEL PEAK 28(11Q14.1) WILD-TYPE 118 63 140 99

Figure S92.  Get High-res Image Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 5.38e-16 (Fisher's exact test), Q value = 3.7e-13

Table S93.  Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 28(11Q14.1) CNV 60 24 10
DEL PEAK 28(11Q14.1) WILD-TYPE 101 164 202

Figure S93.  Get High-res Image Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 30(12q12)' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S94.  Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 30(12Q12) CNV 35 26 15
DEL PEAK 30(12Q12) WILD-TYPE 126 162 197

Figure S94.  Get High-res Image Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 31(12q15)' versus 'MRNA_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.077

Table S95.  Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 31(12Q15) CNV 20 21 7 21
DEL PEAK 31(12Q15) WILD-TYPE 127 75 145 92

Figure S95.  Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(12q15)' versus 'MRNA_CHIERARCHICAL'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.037

Table S96.  Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 31(12Q15) CNV 4 35 30
DEL PEAK 31(12Q15) WILD-TYPE 113 136 190

Figure S96.  Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(12q15)' versus 'CN_CNMF'

P value = 6.36e-07 (Fisher's exact test), Q value = 0.00041

Table S97.  Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 31(12Q15) CNV 40 25 12
DEL PEAK 31(12Q15) WILD-TYPE 121 163 200

Figure S97.  Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.56e-07 (Fisher's exact test), Q value = 1e-04

Table S98.  Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 32(13Q14.2) CNV 81 45 36 53
DEL PEAK 32(13Q14.2) WILD-TYPE 66 51 116 60

Figure S98.  Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 3.87e-05 (Fisher's exact test), Q value = 0.024

Table S99.  Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 32(13Q14.2) CNV 29 78 108
DEL PEAK 32(13Q14.2) WILD-TYPE 88 93 112

Figure S99.  Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.48e-16 (Fisher's exact test), Q value = 2.4e-13

Table S100.  Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 32(13Q14.2) CNV 101 90 45
DEL PEAK 32(13Q14.2) WILD-TYPE 60 98 167

Figure S100.  Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 33(14q13.1)' versus 'MRNA_CNMF'

P value = 7.74e-06 (Fisher's exact test), Q value = 0.0048

Table S101.  Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 33(14Q13.1) CNV 55 39 25 44
DEL PEAK 33(14Q13.1) WILD-TYPE 92 57 127 69

Figure S101.  Get High-res Image Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(14q13.1)' versus 'CN_CNMF'

P value = 2.64e-29 (Fisher's exact test), Q value = 1.8e-26

Table S102.  Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 33(14Q13.1) CNV 103 51 20
DEL PEAK 33(14Q13.1) WILD-TYPE 58 137 192

Figure S102.  Get High-res Image Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 34(14q24.2)' versus 'MRNA_CNMF'

P value = 1.26e-07 (Fisher's exact test), Q value = 8.3e-05

Table S103.  Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 34(14Q24.2) CNV 52 42 22 46
DEL PEAK 34(14Q24.2) WILD-TYPE 95 54 130 67

Figure S103.  Get High-res Image Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(14q24.2)' versus 'CN_CNMF'

P value = 1.24e-38 (Fisher's exact test), Q value = 8.7e-36

Table S104.  Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 34(14Q24.2) CNV 107 51 11
DEL PEAK 34(14Q24.2) WILD-TYPE 54 137 201

Figure S104.  Get High-res Image Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 35(14q31.3)' versus 'MRNA_CNMF'

P value = 5.12e-09 (Fisher's exact test), Q value = 3.4e-06

Table S105.  Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 35(14Q31.3) CNV 52 38 16 42
DEL PEAK 35(14Q31.3) WILD-TYPE 95 58 136 71

Figure S105.  Get High-res Image Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(14q31.3)' versus 'CN_CNMF'

P value = 1.31e-40 (Fisher's exact test), Q value = 9.2e-38

Table S106.  Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 35(14Q31.3) CNV 102 47 6
DEL PEAK 35(14Q31.3) WILD-TYPE 59 141 206

Figure S106.  Get High-res Image Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 36(15q14)' versus 'MRNA_CNMF'

P value = 7.11e-06 (Fisher's exact test), Q value = 0.0045

Table S107.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 36(15Q14) CNV 35 38 23 43
DEL PEAK 36(15Q14) WILD-TYPE 112 58 129 70

Figure S107.  Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(15q14)' versus 'MRNA_CHIERARCHICAL'

P value = 3.39e-08 (Fisher's exact test), Q value = 2.3e-05

Table S108.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 36(15Q14) CNV 14 72 53
DEL PEAK 36(15Q14) WILD-TYPE 103 99 167

Figure S108.  Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(15q14)' versus 'MIR_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0014

Table S109.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
DEL PEAK 36(15Q14) CNV 50 23 56
DEL PEAK 36(15Q14) WILD-TYPE 131 132 79

Figure S109.  Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 36(15q14)' versus 'CN_CNMF'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00025

Table S110.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 36(15Q14) CNV 68 43 37
DEL PEAK 36(15Q14) WILD-TYPE 93 145 175

Figure S110.  Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 36(15q14)' versus 'MRNASEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.2

Table S111.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
DEL PEAK 36(15Q14) CNV 24 14 7
DEL PEAK 36(15Q14) WILD-TYPE 20 53 29

Figure S111.  Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Del Peak 39(17p13.2)' versus 'CN_CNMF'

P value = 4.96e-10 (Fisher's exact test), Q value = 3.4e-07

Table S112.  Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 39(17P13.2) CNV 42 34 8
DEL PEAK 39(17P13.2) WILD-TYPE 119 154 204

Figure S112.  Get High-res Image Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 40(17p13.1)' versus 'CN_CNMF'

P value = 4.73e-15 (Fisher's exact test), Q value = 3.3e-12

Table S113.  Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 40(17P13.1) CNV 52 36 6
DEL PEAK 40(17P13.1) WILD-TYPE 109 152 206

Figure S113.  Get High-res Image Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 7.34e-06 (Fisher's exact test), Q value = 0.0046

Table S114.  Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 41(17Q11.2) CNV 35 9 12 5
DEL PEAK 41(17Q11.2) WILD-TYPE 112 87 140 108

Figure S114.  Get High-res Image Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00068

Table S115.  Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 41(17Q11.2) CNV 30 32 8
DEL PEAK 41(17Q11.2) WILD-TYPE 131 156 204

Figure S115.  Get High-res Image Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 43(19q13.41)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.092

Table S116.  Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
DEL PEAK 43(19Q13.41) CNV 12 48 32
DEL PEAK 43(19Q13.41) WILD-TYPE 105 123 188

Figure S116.  Get High-res Image Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(21q22.3)' versus 'MIR_CNMF'

P value = 8.73e-05 (Fisher's exact test), Q value = 0.052

Table S117.  Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 155 73 104
DEL PEAK 44(21Q22.3) CNV 8 32 8 5
DEL PEAK 44(21Q22.3) WILD-TYPE 131 123 65 99

Figure S117.  Get High-res Image Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 46(Xp22.2)' versus 'CN_CNMF'

P value = 8.52e-10 (Fisher's exact test), Q value = 5.7e-07

Table S118.  Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
DEL PEAK 46(XP22.2) CNV 65 29 29
DEL PEAK 46(XP22.2) WILD-TYPE 96 159 183

Figure S118.  Get High-res Image Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 561

  • Number of copy number variation regions = 70

  • 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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