Correlation between copy number variation genes and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C12F7KCS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon Adenocarcinoma (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/C12F7KCS
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 68 peak regions and 10 molecular subtypes across 413 patients, 150 significant findings detected with Q value < 0.25.

  • Amp Peak 1(2q33.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 4(6p21.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 8(8q24.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 17(19p13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 19(20p12.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 20(20p11.23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 21(20p11.21) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 22(20q11.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 23(20q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 24(20q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 2(1p33) cnvs correlated to 'CN_CNMF'.

  • Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 4(1q43) cnvs correlated to 'CN_CNMF'.

  • Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 9(4p16.2) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 11(4q35.1) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 13(5q21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 14(5q23.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 18(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 19(8p22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • Del Peak 20(8p11.22) cnvs correlated to 'CN_CNMF'.

  • Del Peak 21(8p11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 27(12p13.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 28(13q14.13) cnvs correlated to 'CN_CNMF'.

  • Del Peak 29(14q32.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 30(15q11.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 31(15q21.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 32(15q22.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 35(17p12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 37(18p11.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 38(18q12.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 39(18q21.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 40(18q22.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 42(20p12.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 44(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 150 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
Amp Peak 22(20q11 21) 0 (0%) 117 1.07e-10
(6.69e-08) 		2.86e-11
(1.8e-08) 		1.54e-43
(1.04e-40) 		2.19e-09
(1.34e-06) 		0.0201
(1.00) 		0.000108
(0.06) 		1.47e-14
(9.62e-12) 		3.85e-12
(2.47e-09) 		0.443
(1.00) 		1
(1.00)
Amp Peak 23(20q12) 0 (0%) 116 9.28e-12
(5.91e-09) 		1.82e-11
(1.15e-08) 		6.28e-43
(4.24e-40) 		1.58e-08
(9.58e-06) 		0.00771
(1.00) 		2.18e-05
(0.0125) 		5.48e-14
(3.59e-11) 		1.34e-11
(8.53e-09) 		0.406
(1.00) 		0.948
(1.00)
Amp Peak 24(20q13 32) 0 (0%) 113 2.87e-10
(1.79e-07) 		6.27e-12
(4e-09) 		3.18e-43
(2.15e-40) 		1.58e-08
(9.58e-06) 		0.00832
(1.00) 		1.3e-05
(0.00749) 		5.48e-14
(3.59e-11) 		1.34e-11
(8.53e-09) 		0.414
(1.00) 		0.96
(1.00)
Del Peak 35(17p12) 0 (0%) 184 6.12e-08
(3.66e-05) 		1.6e-06
(0.000933) 		2.81e-35
(1.89e-32) 		1.8e-09
(1.11e-06) 		0.0465
(1.00) 		7.42e-05
(0.0416) 		1.06e-10
(6.61e-08) 		3.2e-08
(1.92e-05) 		0.363
(1.00) 		0.729
(1.00)
Del Peak 38(18q12 2) 0 (0%) 166 8.37e-11
(5.25e-08) 		1.08e-09
(6.69e-07) 		1.87e-45
(1.27e-42) 		8.98e-16
(5.9e-13) 		0.0214
(1.00) 		0.000421
(0.226) 		7.66e-16
(5.04e-13) 		1.07e-08
(6.52e-06) 		0.449
(1.00) 		0.865
(1.00)
Del Peak 39(18q21 2) 0 (0%) 153 3.06e-10
(1.91e-07) 		6.85e-10
(4.25e-07) 		1.51e-45
(1.03e-42) 		3.29e-12
(2.11e-09) 		0.0109
(1.00) 		0.000225
(0.122) 		8.74e-13
(5.66e-10) 		7.14e-07
(0.000421) 		0.0517
(1.00) 		0.901
(1.00)
Del Peak 40(18q22 1) 0 (0%) 153 6.92e-11
(4.35e-08) 		3.65e-09
(2.23e-06) 		1.58e-47
(1.07e-44) 		2.02e-12
(1.3e-09) 		0.0178
(1.00) 		0.000224
(0.122) 		4.05e-12
(2.59e-09) 		2.76e-07
(0.000164) 		0.0746
(1.00) 		0.912
(1.00)
Amp Peak 11(13q12 13) 0 (0%) 163 7.21e-08
(4.31e-05) 		5.27e-06
(0.00307) 		5.04e-36
(3.39e-33) 		0.00027
(0.146) 		0.0709
(1.00) 		0.0124
(1.00) 		1.27e-06
(0.000745) 		0.000196
(0.107) 		0.459
(1.00) 		0.798
(1.00)
Del Peak 37(18p11 31) 0 (0%) 193 1.51e-12
(9.71e-10) 		3.65e-09
(2.23e-06) 		1.93e-42
(1.3e-39) 		3.11e-13
(2.02e-10) 		0.0023
(1.00) 		0.00104
(0.527) 		3.11e-17
(2.06e-14) 		8.19e-10
(5.07e-07) 		0.48
(1.00) 		0.841
(1.00)
Amp Peak 12(13q22 1) 0 (0%) 159 6.34e-05
(0.0358) 		5.43e-05
(0.0307) 		7.2e-33
(4.83e-30) 		0.00051
(0.27) 		0.152
(1.00) 		0.0444
(1.00) 		1.15e-06
(0.000674) 		7.67e-05
(0.0429) 		0.272
(1.00) 		0.977
(1.00)
Amp Peak 13(16p11 2) 0 (0%) 297 0.000447
(0.237) 		0.000375
(0.202) 		8.55e-19
(5.67e-16) 		0.0212
(1.00) 		0.373
(1.00) 		0.033
(1.00) 		0.000429
(0.229) 		0.00838
(1.00) 		0.771
(1.00) 		0.809
(1.00)
Amp Peak 21(20p11 21) 0 (0%) 183 0.000692
(0.359) 		4.27e-05
(0.0243) 		4e-23
(2.67e-20) 		0.00113
(0.572) 		0.0624
(1.00) 		0.0394
(1.00) 		2.41e-07
(0.000143) 		1.39e-06
(0.000812) 		0.174
(1.00) 		0.509
(1.00)
Del Peak 11(4q35 1) 0 (0%) 276 0.000128
(0.0703) 		0.00928
(1.00) 		1.05e-13
(6.82e-11) 		7.69e-05
(0.043) 		0.173
(1.00) 		0.146
(1.00) 		0.000239
(0.129) 		0.000527
(0.278) 		0.416
(1.00) 		0.235
(1.00)
Del Peak 19(8p22) 0 (0%) 228 0.00115
(0.579) 		0.000958
(0.489) 		2.41e-30
(1.61e-27) 		3.46e-07
(0.000205) 		0.0649
(1.00) 		0.00013
(0.0714) 		2.16e-05
(0.0124) 		0.000656
(0.343) 		0.115
(1.00) 		0.832
(1.00)
Del Peak 29(14q32 11) 0 (0%) 280 2.12e-05
(0.0122) 		0.00011
(0.061) 		1.61e-20
(1.07e-17) 		0.000707
(0.366) 		0.00347
(1.00) 		0.0236
(1.00) 		7.3e-05
(0.041) 		0.00084
(0.431) 		0.319
(1.00) 		0.0612
(1.00)
Del Peak 30(15q11 2) 0 (0%) 253 0.000422
(0.226) 		0.00683
(1.00) 		1.2e-21
(7.98e-19) 		0.00432
(1.00) 		0.0746
(1.00) 		0.07
(1.00) 		2.09e-06
(0.00122) 		0.000117
(0.0647) 		0.877
(1.00) 		0.893
(1.00)
Del Peak 32(15q22 33) 0 (0%) 268 0.000758
(0.391) 		0.00327
(1.00) 		2.48e-21
(1.65e-18) 		0.000435
(0.231) 		0.141
(1.00) 		0.0512
(1.00) 		3.07e-08
(1.84e-05) 		7.55e-06
(0.00437) 		0.949
(1.00) 		0.365
(1.00)
Amp Peak 9(11p15 5) 0 (0%) 327 1.38e-05
(0.00795) 		0.000201
(0.11) 		1.54e-09
(9.48e-07) 		0.000612
(0.321) 		0.00156
(0.777) 		0.00358
(1.00) 		0.00193
(0.959) 		0.00845
(1.00) 		0.117
(1.00) 		0.201
(1.00)
Amp Peak 14(16q12 1) 0 (0%) 311 3.02e-05
(0.0173) 		0.000126
(0.0696) 		1.67e-20
(1.11e-17) 		0.0511
(1.00) 		0.619
(1.00) 		0.081
(1.00) 		0.000642
(0.336) 		0.00254
(1.00) 		0.902
(1.00) 		0.93
(1.00)
Del Peak 1(1p36 11) 0 (0%) 263 6.81e-05
(0.0384) 		0.00576
(1.00) 		6.32e-17
(4.17e-14) 		0.000792
(0.408) 		0.0155
(1.00) 		0.0238
(1.00) 		0.000347
(0.187) 		0.0012
(0.604) 		0.409
(1.00) 		0.0624
(1.00)
Del Peak 9(4p16 2) 0 (0%) 292 0.00194
(0.963) 		0.0107
(1.00) 		1.16e-12
(7.47e-10) 		0.011
(1.00) 		0.442
(1.00) 		0.0866
(1.00) 		0.000237
(0.129) 		0.000107
(0.0594) 		0.376
(1.00) 		0.206
(1.00)
Del Peak 10(4q22 1) 0 (0%) 287 0.000585
(0.308) 		0.00864
(1.00) 		8.5e-12
(5.42e-09) 		0.00207
(1.00) 		0.516
(1.00) 		0.391
(1.00) 		9.23e-05
(0.0515) 		2.81e-05
(0.0161) 		0.21
(1.00) 		0.518
(1.00)
Del Peak 31(15q21 1) 0 (0%) 262 0.013
(1.00) 		0.0411
(1.00) 		8.15e-18
(5.39e-15) 		0.00747
(1.00) 		0.0441
(1.00) 		0.0657
(1.00) 		2.03e-07
(0.000121) 		2.05e-05
(0.0118) 		0.979
(1.00) 		0.621
(1.00)
Amp Peak 15(17q12) 0 (0%) 312 0.0989
(1.00) 		0.0852
(1.00) 		7.53e-07
(0.000443) 		0.0164
(1.00) 		0.582
(1.00) 		0.00276
(1.00) 		4.59e-05
(0.026) 		0.0142
(1.00) 		0.0121
(1.00) 		0.986
(1.00)
Amp Peak 16(17q24 1) 0 (0%) 321 0.0519
(1.00) 		0.00821
(1.00) 		1.61e-08
(9.69e-06) 		0.0123
(1.00) 		0.304
(1.00) 		0.00527
(1.00) 		6.04e-06
(0.00351) 		0.00312
(1.00) 		0.00254
(1.00) 		0.781
(1.00)
Del Peak 18(8p23 3) 0 (0%) 242 0.00276
(1.00) 		0.000603
(0.316) 		6.84e-26
(4.58e-23) 		3.61e-06
(0.00211) 		0.0514
(1.00) 		0.00096
(0.489) 		0.000672
(0.35) 		0.00231
(1.00) 		0.154
(1.00) 		0.848
(1.00)
Del Peak 42(20p12 1) 0 (0%) 334 0.0656
(1.00) 		0.173
(1.00) 		1.38e-13
(8.97e-11) 		0.00404
(1.00) 		0.323
(1.00) 		0.278
(1.00) 		0.00015
(0.082) 		0.00674
(1.00) 		0.0931
(1.00) 		0.101
(1.00)
Del Peak 44(22q13 32) 0 (0%) 275 0.000428
(0.229) 		0.000747
(0.386) 		9.76e-13
(6.32e-10) 		0.0049
(1.00) 		0.306
(1.00) 		0.218
(1.00) 		0.00222
(1.00) 		0.00106
(0.537) 		0.394
(1.00) 		0.069
(1.00)
Amp Peak 1(2q33 1) 0 (0%) 334 0.0734
(1.00) 		0.105
(1.00) 		3.05e-05
(0.0174) 		0.258
(1.00) 		0.245
(1.00) 		0.0652
(1.00) 		0.000516
(0.272) 		0.0137
(1.00) 		0.277
(1.00) 		0.258
(1.00)
Amp Peak 2(5p13 2) 0 (0%) 332 0.334
(1.00) 		0.469
(1.00) 		0.000202
(0.11) 		0.15
(1.00) 		0.00999
(1.00) 		0.724
(1.00) 		0.0864
(1.00) 		0.0696
(1.00) 		0.927
(1.00) 		0.581
(1.00)
Amp Peak 4(6p21 1) 0 (0%) 324 0.0902
(1.00) 		0.000996
(0.506) 		3.37e-09
(2.06e-06) 		0.17
(1.00) 		0.83
(1.00) 		0.178
(1.00) 		0.00644
(1.00) 		0.033
(1.00) 		0.776
(1.00) 		0.258
(1.00)
Amp Peak 5(8p11 23) 0 (0%) 269 0.444
(1.00) 		0.231
(1.00) 		2.99e-13
(1.94e-10) 		0.868
(1.00) 		0.864
(1.00) 		0.733
(1.00) 		0.211
(1.00) 		0.783
(1.00) 		0.179
(1.00) 		0.189
(1.00)
Amp Peak 6(8p11 21) 0 (0%) 240 0.355
(1.00) 		0.129
(1.00) 		4.51e-10
(2.8e-07) 		0.886
(1.00) 		0.27
(1.00) 		0.00672
(1.00) 		0.421
(1.00) 		0.606
(1.00) 		0.502
(1.00) 		0.218
(1.00)
Amp Peak 7(8q12 1) 0 (0%) 198 0.15
(1.00) 		0.0646
(1.00) 		9.31e-12
(5.92e-09) 		0.0383
(1.00) 		0.0228
(1.00) 		0.00068
(0.354) 		0.0141
(1.00) 		0.228
(1.00) 		0.126
(1.00) 		0.295
(1.00)
Amp Peak 8(8q24 21) 0 (0%) 174 0.203
(1.00) 		0.107
(1.00) 		7.86e-14
(5.13e-11) 		0.0102
(1.00) 		0.103
(1.00) 		0.0104
(1.00) 		0.00636
(1.00) 		0.445
(1.00) 		0.404
(1.00) 		0.215
(1.00)
Amp Peak 17(19p13 2) 0 (0%) 348 0.0535
(1.00) 		0.0345
(1.00) 		4.82e-05
(0.0273) 		0.283
(1.00) 		0.734
(1.00) 		0.341
(1.00) 		0.501
(1.00) 		0.539
(1.00) 		0.204
(1.00) 		0.385
(1.00)
Amp Peak 19(20p12 3) 0 (0%) 229 0.00188
(0.936) 		0.000844
(0.432) 		1.86e-12
(1.2e-09) 		0.434
(1.00) 		0.0113
(1.00) 		0.478
(1.00) 		0.0305
(1.00) 		0.00972
(1.00) 		0.597
(1.00) 		0.195
(1.00)
Amp Peak 20(20p11 23) 0 (0%) 208 0.0267
(1.00) 		0.000792
(0.408) 		1.26e-16
(8.32e-14) 		0.105
(1.00) 		0.0479
(1.00) 		0.183
(1.00) 		0.000513
(0.271) 		0.00104
(0.527) 		0.455
(1.00) 		0.212
(1.00)
Del Peak 2(1p33) 0 (0%) 306 0.0246
(1.00) 		0.532
(1.00) 		1.09e-11
(6.91e-09) 		0.00668
(1.00) 		0.556
(1.00) 		0.395
(1.00) 		0.0051
(1.00) 		0.0141
(1.00) 		0.893
(1.00) 		0.0519
(1.00)
Del Peak 3(1p13 1) 0 (0%) 310 0.115
(1.00) 		0.374
(1.00) 		6.85e-10
(4.25e-07) 		0.185
(1.00) 		0.56
(1.00) 		0.89
(1.00) 		0.0836
(1.00) 		0.00481
(1.00) 		0.868
(1.00) 		0.379
(1.00)
Del Peak 4(1q43) 0 (0%) 369 0.0983
(1.00) 		0.458
(1.00) 		6.98e-06
(0.00405) 		0.105
(1.00) 		0.393
(1.00) 		0.664
(1.00) 		0.0312
(1.00) 		0.0114
(1.00) 		0.335
(1.00) 		0.301
(1.00)
Del Peak 6(3p26 1) 0 (0%) 353 0.0994
(1.00) 		0.304
(1.00) 		0.00043
(0.229) 		0.268
(1.00) 		0.942
(1.00) 		0.861
(1.00) 		0.539
(1.00) 		0.0883
(1.00) 		0.541
(1.00) 		0.958
(1.00)
Del Peak 12(5q11 2) 0 (0%) 322 0.00129
(0.648) 		0.00378
(1.00) 		4.94e-09
(3.01e-06) 		0.0339
(1.00) 		0.048
(1.00) 		0.0118
(1.00) 		0.00142
(0.711) 		0.00781
(1.00) 		0.835
(1.00) 		0.215
(1.00)
Del Peak 13(5q21 3) 0 (0%) 296 0.118
(1.00) 		0.0281
(1.00) 		1.14e-09
(7.04e-07) 		0.0359
(1.00) 		0.0651
(1.00) 		0.0971
(1.00) 		0.00438
(1.00) 		0.0104
(1.00) 		0.654
(1.00) 		0.36
(1.00)
Del Peak 14(5q23 1) 0 (0%) 306 0.0628
(1.00) 		0.0356
(1.00) 		1.57e-08
(9.52e-06) 		0.087
(1.00) 		0.044
(1.00) 		0.15
(1.00) 		0.0219
(1.00) 		0.0126
(1.00) 		0.622
(1.00) 		0.246
(1.00)
Del Peak 15(6p25 3) 0 (0%) 359 0.971
(1.00) 		0.792
(1.00) 		0.000102
(0.0571) 		0.0527
(1.00) 		0.337
(1.00) 		0.828
(1.00) 		0.353
(1.00) 		0.788
(1.00) 		0.406
(1.00) 		0.453
(1.00)
Del Peak 20(8p11 22) 0 (0%) 333 0.213
(1.00) 		0.118
(1.00) 		8.88e-09
(5.4e-06) 		0.0614
(1.00) 		0.049
(1.00) 		0.00534
(1.00) 		0.0993
(1.00) 		0.0804
(1.00) 		0.359
(1.00) 		0.831
(1.00)
Del Peak 21(8p11 21) 0 (0%) 370 0.0231
(1.00) 		0.351
(1.00) 		5.81e-07
(0.000343) 		0.366
(1.00) 		0.156
(1.00) 		0.024
(1.00) 		0.483
(1.00) 		0.308
(1.00) 		0.0997
(1.00) 		0.549
(1.00)
Del Peak 22(9p21 3) 0 (0%) 357 0.251
(1.00) 		0.264
(1.00) 		4.51e-05
(0.0256) 		0.204
(1.00) 		0.768
(1.00) 		0.214
(1.00) 		0.0637
(1.00) 		0.127
(1.00) 		0.904
(1.00) 		0.663
(1.00)
Del Peak 23(10p15 3) 0 (0%) 345 0.261
(1.00) 		0.141
(1.00) 		2.25e-08
(1.35e-05) 		0.0291
(1.00) 		0.0673
(1.00) 		0.104
(1.00) 		0.126
(1.00) 		0.034
(1.00) 		0.68
(1.00) 		0.566
(1.00)
Del Peak 24(10q21 1) 0 (0%) 331 0.00928
(1.00) 		0.0374
(1.00) 		2.24e-11
(1.41e-08) 		0.194
(1.00) 		0.277
(1.00) 		0.144
(1.00) 		0.191
(1.00) 		0.0431
(1.00) 		0.887
(1.00) 		0.831
(1.00)
Del Peak 25(10q23 31) 0 (0%) 319 0.249
(1.00) 		0.0829
(1.00) 		3.46e-07
(0.000205) 		0.0801
(1.00) 		0.123
(1.00) 		0.375
(1.00) 		0.0348
(1.00) 		0.165
(1.00) 		0.885
(1.00) 		0.985
(1.00)
Del Peak 26(10q25 2) 0 (0%) 320 0.172
(1.00) 		0.0105
(1.00) 		1.91e-11
(1.21e-08) 		0.0139
(1.00) 		0.03
(1.00) 		0.319
(1.00) 		0.00312
(1.00) 		0.0025
(1.00) 		0.921
(1.00) 		0.593
(1.00)
Del Peak 27(12p13 2) 0 (0%) 369 0.0404
(1.00) 		0.00796
(1.00) 		9.87e-08
(5.89e-05) 		0.207
(1.00) 		0.383
(1.00) 		0.87
(1.00) 		0.0262
(1.00) 		0.00369
(1.00) 		0.695
(1.00) 		0.973
(1.00)
Del Peak 28(13q14 13) 0 (0%) 395 0.395
(1.00) 		0.876
(1.00) 		0.000128
(0.0703) 		0.153
(1.00) 		0.212
(1.00) 		0.34
(1.00) 		0.228
(1.00) 		0.452
(1.00) 		0.614
(1.00) 		0.834
(1.00)
Del Peak 43(21q11 2) 0 (0%) 288 0.00298
(1.00) 		0.0933
(1.00) 		3.37e-09
(2.06e-06) 		0.0302
(1.00) 		0.236
(1.00) 		0.455
(1.00) 		0.000897
(0.458) 		0.0187
(1.00) 		0.923
(1.00) 		0.47
(1.00)
Amp Peak 3(5q22 3) 0 (0%) 373 0.78
(1.00) 		0.629
(1.00) 		0.0293
(1.00) 		0.875
(1.00) 		0.394
(1.00) 		0.494
(1.00) 		0.165
(1.00) 		0.112
(1.00) 		0.693
(1.00) 		0.839
(1.00)
Amp Peak 10(12p13 33) 0 (0%) 309 0.463
(1.00) 		0.882
(1.00) 		0.0612
(1.00) 		0.247
(1.00) 		0.429
(1.00) 		0.958
(1.00) 		0.334
(1.00) 		0.977
(1.00) 		0.304
(1.00) 		0.173
(1.00)
Amp Peak 18(19q13 11) 0 (0%) 330 0.332
(1.00) 		0.0177
(1.00) 		0.002
(0.988) 		0.517
(1.00) 		0.173
(1.00) 		0.688
(1.00) 		0.0736
(1.00) 		0.167
(1.00) 		0.417
(1.00) 		0.491
(1.00)
Del Peak 5(2q37 2) 0 (0%) 392 0.928
(1.00) 		0.0598
(1.00) 		0.977
(1.00) 		0.701
(1.00) 		0.23
(1.00) 		0.208
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.447
(1.00) 		0.447
(1.00)
Del Peak 7(3p14 2) 0 (0%) 338 0.466
(1.00) 		0.744
(1.00) 		0.205
(1.00) 		0.735
(1.00) 		0.566
(1.00) 		0.29
(1.00) 		0.632
(1.00) 		0.483
(1.00) 		0.203
(1.00) 		0.536
(1.00)
Del Peak 8(3q26 31) 0 (0%) 374 0.122
(1.00) 		0.605
(1.00) 		0.00818
(1.00) 		0.497
(1.00) 		0.288
(1.00) 		0.369
(1.00) 		0.458
(1.00) 		0.0223
(1.00) 		0.15
(1.00) 		0.939
(1.00)
Del Peak 16(6q26) 0 (0%) 353 0.383
(1.00) 		0.304
(1.00) 		0.157
(1.00) 		0.356
(1.00) 		0.189
(1.00) 		0.355
(1.00) 		0.873
(1.00) 		0.697
(1.00) 		0.797
(1.00) 		0.53
(1.00)
Del Peak 17(7q31 1) 0 (0%) 402 1
(1.00) 		0.504
(1.00) 		0.816
(1.00) 		0.795
(1.00) 		0.354
(1.00) 		0.219
(1.00) 		0.49
(1.00) 		1
(1.00) 		1
(1.00) 		0.564
(1.00)
Del Peak 33(16p13 3) 0 (0%) 368 0.334
(1.00) 		0.155
(1.00) 		0.208
(1.00) 		0.376
(1.00) 		0.418
(1.00) 		0.913
(1.00) 		0.62
(1.00) 		0.572
(1.00) 		0.842
(1.00) 		0.739
(1.00)
Del Peak 34(16q23 1) 0 (0%) 364 0.259
(1.00) 		0.00785
(1.00) 		0.131
(1.00) 		0.337
(1.00) 		0.489
(1.00) 		0.821
(1.00) 		0.0421
(1.00) 		0.0701
(1.00) 		0.977
(1.00) 		0.505
(1.00)
Del Peak 36(17q24 3) 0 (0%) 354 0.102
(1.00) 		0.676
(1.00) 		0.00348
(1.00) 		0.0118
(1.00) 		0.874
(1.00) 		0.338
(1.00) 		0.00329
(1.00) 		0.0329
(1.00) 		0.681
(1.00) 		0.979
(1.00)
Del Peak 41(19p13 3) 0 (0%) 356 0.268
(1.00) 		0.198
(1.00) 		0.00362
(1.00) 		0.565
(1.00) 		0.88
(1.00) 		0.0676
(1.00) 		0.0512
(1.00) 		0.0244
(1.00) 		0.582
(1.00) 		0.0166
(1.00)
'Amp Peak 1(2q33.1)' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.017

Table S1.  Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 1(2Q33.1) CNV 49 18 8 4
AMP PEAK 1(2Q33.1) WILD-TYPE 121 169 24 20

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(5p13.2)' versus 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 2(5P13.2) CNV 46 20 10 5
AMP PEAK 2(5P13.2) WILD-TYPE 124 167 22 19

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S3.  Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 4(6P21.1) CNV 61 16 8 4
AMP PEAK 4(6P21.1) WILD-TYPE 109 171 24 20

Figure S3.  Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(8p11.23)' versus 'CN_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 1.9e-10

Table S4.  Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 5(8P11.23) CNV 56 47 17 24
AMP PEAK 5(8P11.23) WILD-TYPE 114 140 15 0

Figure S4.  Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(8p11.21)' versus 'CN_CNMF'

P value = 4.51e-10 (Fisher's exact test), Q value = 2.8e-07

Table S5.  Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 6(8P11.21) CNV 75 55 21 22
AMP PEAK 6(8P11.21) WILD-TYPE 95 132 11 2

Figure S5.  Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q12.1)' versus 'CN_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 5.9e-09

Table S6.  Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 7(8Q12.1) CNV 106 64 23 22
AMP PEAK 7(8Q12.1) WILD-TYPE 64 123 9 2

Figure S6.  Get High-res Image Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.86e-14 (Fisher's exact test), Q value = 5.1e-11

Table S7.  Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 8(8Q24.21) CNV 119 73 23 24
AMP PEAK 8(8Q24.21) WILD-TYPE 51 114 9 0

Figure S7.  Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0079

Table S8.  Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 9(11P15.5) CNV 1 17 3 13
AMP PEAK 9(11P15.5) WILD-TYPE 30 45 27 10

Figure S8.  Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000201 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 9(11P15.5) CNV 14 2 18
AMP PEAK 9(11P15.5) WILD-TYPE 42 42 28

Figure S9.  Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(11p15.5)' versus 'CN_CNMF'

P value = 1.54e-09 (Fisher's exact test), Q value = 9.5e-07

Table S10.  Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 9(11P15.5) CNV 54 17 14 1
AMP PEAK 9(11P15.5) WILD-TYPE 116 170 18 23

Figure S10.  Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CNMF'

P value = 7.21e-08 (Fisher's exact test), Q value = 4.3e-05

Table S11.  Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 11(13Q12.13) CNV 14 52 8 18
AMP PEAK 11(13Q12.13) WILD-TYPE 17 10 22 5

Figure S11.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CHIERARCHICAL'

P value = 5.27e-06 (Fisher's exact test), Q value = 0.0031

Table S12.  Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 11(13Q12.13) CNV 39 15 38
AMP PEAK 11(13Q12.13) WILD-TYPE 17 29 8

Figure S12.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'CN_CNMF'

P value = 5.04e-36 (Fisher's exact test), Q value = 3.4e-33

Table S13.  Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 11(13Q12.13) CNV 158 57 18 17
AMP PEAK 11(13Q12.13) WILD-TYPE 12 130 14 7

Figure S13.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
AMP PEAK 11(13Q12.13) CNV 79 42 33
AMP PEAK 11(13Q12.13) WILD-TYPE 26 44 30

Figure S14.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00075

Table S15.  Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 11(13Q12.13) CNV 22 46 26 16
AMP PEAK 11(13Q12.13) WILD-TYPE 9 13 21 38

Figure S15.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
AMP PEAK 11(13Q12.13) CNV 16 43 51
AMP PEAK 11(13Q12.13) WILD-TYPE 33 19 29

Figure S16.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'MRNA_CNMF'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.036

Table S17.  Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 12(13Q22.1) CNV 15 49 10 17
AMP PEAK 12(13Q22.1) WILD-TYPE 16 13 20 6

Figure S17.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.031

Table S18.  Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 12(13Q22.1) CNV 38 16 37
AMP PEAK 12(13Q22.1) WILD-TYPE 18 28 9

Figure S18.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'CN_CNMF'

P value = 7.2e-33 (Fisher's exact test), Q value = 4.8e-30

Table S19.  Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 12(13Q22.1) CNV 158 63 17 16
AMP PEAK 12(13Q22.1) WILD-TYPE 12 124 15 8

Figure S19.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00067

Table S20.  Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 12(13Q22.1) CNV 22 49 25 19
AMP PEAK 12(13Q22.1) WILD-TYPE 9 10 22 35

Figure S20.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.043

Table S21.  Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
AMP PEAK 12(13Q22.1) CNV 17 46 52
AMP PEAK 12(13Q22.1) WILD-TYPE 32 16 28

Figure S21.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'MRNA_CNMF'

P value = 0.000447 (Fisher's exact test), Q value = 0.24

Table S22.  Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 13(16P11.2) CNV 5 23 3 13
AMP PEAK 13(16P11.2) WILD-TYPE 26 39 27 10

Figure S22.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.2

Table S23.  Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 13(16P11.2) CNV 13 7 24
AMP PEAK 13(16P11.2) WILD-TYPE 43 37 22

Figure S23.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'CN_CNMF'

P value = 8.55e-19 (Fisher's exact test), Q value = 5.7e-16

Table S24.  Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 13(16P11.2) CNV 88 18 8 2
AMP PEAK 13(16P11.2) WILD-TYPE 82 169 24 22

Figure S24.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000429 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 13(16P11.2) CNV 8 24 13 4
AMP PEAK 13(16P11.2) WILD-TYPE 23 35 34 50

Figure S25.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CNMF'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.017

Table S26.  Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 14(16Q12.1) CNV 3 21 2 13
AMP PEAK 14(16Q12.1) WILD-TYPE 28 41 28 10

Figure S26.  Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.07

Table S27.  Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 14(16Q12.1) CNV 13 4 22
AMP PEAK 14(16Q12.1) WILD-TYPE 43 40 24

Figure S27.  Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'CN_CNMF'

P value = 1.67e-20 (Fisher's exact test), Q value = 1.1e-17

Table S28.  Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 14(16Q12.1) CNV 82 12 7 1
AMP PEAK 14(16Q12.1) WILD-TYPE 88 175 25 23

Figure S28.  Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'CN_CNMF'

P value = 7.53e-07 (Fisher's exact test), Q value = 0.00044

Table S29.  Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 15(17Q12) CNV 62 23 8 8
AMP PEAK 15(17Q12) WILD-TYPE 108 164 24 16

Figure S29.  Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'MRNASEQ_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.026

Table S30.  Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 15(17Q12) CNV 8 26 6 5
AMP PEAK 15(17Q12) WILD-TYPE 23 33 41 49

Figure S30.  Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(17q24.1)' versus 'CN_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 9.7e-06

Table S31.  Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 16(17Q24.1) CNV 59 17 8 8
AMP PEAK 16(17Q24.1) WILD-TYPE 111 170 24 16

Figure S31.  Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(17q24.1)' versus 'MRNASEQ_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0035

Table S32.  Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 16(17Q24.1) CNV 9 26 4 5
AMP PEAK 16(17Q24.1) WILD-TYPE 22 33 43 49

Figure S32.  Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(19p13.2)' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.027

Table S33.  Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 17(19P13.2) CNV 39 13 8 5
AMP PEAK 17(19P13.2) WILD-TYPE 131 174 24 19

Figure S33.  Get High-res Image Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(20p12.3)' versus 'CN_CNMF'

P value = 1.86e-12 (Fisher's exact test), Q value = 1.2e-09

Table S34.  Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 19(20P12.3) CNV 83 58 31 12
AMP PEAK 19(20P12.3) WILD-TYPE 87 129 1 12

Figure S34.  Get High-res Image Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(20p11.23)' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 8.3e-14

Table S35.  Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 20(20P11.23) CNV 102 58 32 13
AMP PEAK 20(20P11.23) WILD-TYPE 68 129 0 11

Figure S35.  Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.024

Table S36.  Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 21(20P11.21) CNV 38 12 31
AMP PEAK 21(20P11.21) WILD-TYPE 18 32 15

Figure S36.  Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(20p11.21)' versus 'CN_CNMF'

P value = 4e-23 (Fisher's exact test), Q value = 2.7e-20

Table S37.  Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 21(20P11.21) CNV 126 58 32 14
AMP PEAK 21(20P11.21) WILD-TYPE 44 129 0 10

Figure S37.  Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CNMF'

P value = 2.41e-07 (Fisher's exact test), Q value = 0.00014

Table S38.  Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 21(20P11.21) CNV 19 44 24 12
AMP PEAK 21(20P11.21) WILD-TYPE 12 15 23 42

Figure S38.  Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00081

Table S39.  Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
AMP PEAK 21(20P11.21) CNV 10 40 49
AMP PEAK 21(20P11.21) WILD-TYPE 39 22 31

Figure S39.  Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNA_CNMF'

P value = 1.07e-10 (Fisher's exact test), Q value = 6.7e-08

Table S40.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 22(20Q11.21) CNV 12 59 14 20
AMP PEAK 22(20Q11.21) WILD-TYPE 19 3 16 3

Figure S40.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.86e-11 (Fisher's exact test), Q value = 1.8e-08

Table S41.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 22(20Q11.21) CNV 50 14 41
AMP PEAK 22(20Q11.21) WILD-TYPE 6 30 5

Figure S41.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'CN_CNMF'

P value = 1.54e-43 (Fisher's exact test), Q value = 1e-40

Table S42.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 22(20Q11.21) CNV 167 74 32 23
AMP PEAK 22(20Q11.21) WILD-TYPE 3 113 0 1

Figure S42.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(20q11.21)' versus 'METHLYATION_CNMF'

P value = 2.19e-09 (Fisher's exact test), Q value = 1.3e-06

Table S43.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
AMP PEAK 22(20Q11.21) CNV 96 46 40
AMP PEAK 22(20Q11.21) WILD-TYPE 9 40 23

Figure S43.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(20q11.21)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.06

Table S44.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
AMP PEAK 22(20Q11.21) CNV 13 29 53 133
AMP PEAK 22(20Q11.21) WILD-TYPE 13 27 10 47

Figure S44.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 1.47e-14 (Fisher's exact test), Q value = 9.6e-12

Table S45.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 22(20Q11.21) CNV 23 58 34 17
AMP PEAK 22(20Q11.21) WILD-TYPE 8 1 13 37

Figure S45.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.85e-12 (Fisher's exact test), Q value = 2.5e-09

Table S46.  Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
AMP PEAK 22(20Q11.21) CNV 14 56 62
AMP PEAK 22(20Q11.21) WILD-TYPE 35 6 18

Figure S46.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNA_CNMF'

P value = 9.28e-12 (Fisher's exact test), Q value = 5.9e-09

Table S47.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 23(20Q12) CNV 11 59 13 20
AMP PEAK 23(20Q12) WILD-TYPE 20 3 17 3

Figure S47.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.82e-11 (Fisher's exact test), Q value = 1.1e-08

Table S48.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 23(20Q12) CNV 49 13 41
AMP PEAK 23(20Q12) WILD-TYPE 7 31 5

Figure S48.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'CN_CNMF'

P value = 6.28e-43 (Fisher's exact test), Q value = 4.2e-40

Table S49.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 23(20Q12) CNV 167 75 32 23
AMP PEAK 23(20Q12) WILD-TYPE 3 112 0 1

Figure S49.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(20q12)' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06

Table S50.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
AMP PEAK 23(20Q12) CNV 96 48 41
AMP PEAK 23(20Q12) WILD-TYPE 9 38 22

Figure S50.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(20q12)' versus 'RPPA_CHIERARCHICAL'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.012

Table S51.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
AMP PEAK 23(20Q12) CNV 13 29 55 132
AMP PEAK 23(20Q12) WILD-TYPE 13 27 8 48

Figure S51.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11

Table S52.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 23(20Q12) CNV 23 58 35 18
AMP PEAK 23(20Q12) WILD-TYPE 8 1 12 36

Figure S52.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09

Table S53.  Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
AMP PEAK 23(20Q12) CNV 15 56 63
AMP PEAK 23(20Q12) WILD-TYPE 34 6 17

Figure S53.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNA_CNMF'

P value = 2.87e-10 (Fisher's exact test), Q value = 1.8e-07

Table S54.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
AMP PEAK 24(20Q13.32) CNV 12 59 15 20
AMP PEAK 24(20Q13.32) WILD-TYPE 19 3 15 3

Figure S54.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 6.27e-12 (Fisher's exact test), Q value = 4e-09

Table S55.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
AMP PEAK 24(20Q13.32) CNV 51 14 41
AMP PEAK 24(20Q13.32) WILD-TYPE 5 30 5

Figure S55.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'CN_CNMF'

P value = 3.18e-43 (Fisher's exact test), Q value = 2.1e-40

Table S56.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
AMP PEAK 24(20Q13.32) CNV 168 77 32 23
AMP PEAK 24(20Q13.32) WILD-TYPE 2 110 0 1

Figure S56.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(20q13.32)' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06

Table S57.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
AMP PEAK 24(20Q13.32) CNV 96 48 41
AMP PEAK 24(20Q13.32) WILD-TYPE 9 38 22

Figure S57.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(20q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0075

Table S58.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
AMP PEAK 24(20Q13.32) CNV 13 29 55 135
AMP PEAK 24(20Q13.32) WILD-TYPE 13 27 8 45

Figure S58.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11

Table S59.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
AMP PEAK 24(20Q13.32) CNV 23 58 35 18
AMP PEAK 24(20Q13.32) WILD-TYPE 8 1 12 36

Figure S59.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09

Table S60.  Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
AMP PEAK 24(20Q13.32) CNV 15 56 63
AMP PEAK 24(20Q13.32) WILD-TYPE 34 6 17

Figure S60.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.11)' versus 'MRNA_CNMF'

P value = 6.81e-05 (Fisher's exact test), Q value = 0.038

Table S61.  Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 1(1P36.11) CNV 9 35 3 11
DEL PEAK 1(1P36.11) WILD-TYPE 22 27 27 12

Figure S61.  Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 6.32e-17 (Fisher's exact test), Q value = 4.2e-14

Table S62.  Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 1(1P36.11) CNV 91 28 22 9
DEL PEAK 1(1P36.11) WILD-TYPE 79 159 10 15

Figure S62.  Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'MRNASEQ_CNMF'

P value = 0.000347 (Fisher's exact test), Q value = 0.19

Table S63.  Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 1(1P36.11) CNV 11 31 17 8
DEL PEAK 1(1P36.11) WILD-TYPE 20 28 30 46

Figure S63.  Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p33)' versus 'CN_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 6.9e-09

Table S64.  Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 2(1P33) CNV 69 20 15 3
DEL PEAK 2(1P33) WILD-TYPE 101 167 17 21

Figure S64.  Get High-res Image Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1p13.1)' versus 'CN_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S65.  Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 3(1P13.1) CNV 66 23 13 1
DEL PEAK 3(1P13.1) WILD-TYPE 104 164 19 23

Figure S65.  Get High-res Image Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(1q43)' versus 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.004

Table S66.  Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 4(1Q43) CNV 32 7 5 0
DEL PEAK 4(1Q43) WILD-TYPE 138 180 27 24

Figure S66.  Get High-res Image Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3p26.1)' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.23

Table S67.  Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 6(3P26.1) CNV 36 14 8 2
DEL PEAK 6(3P26.1) WILD-TYPE 134 173 24 22

Figure S67.  Get High-res Image Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 7.5e-10

Table S68.  Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 9(4P16.2) CNV 73 23 19 6
DEL PEAK 9(4P16.2) WILD-TYPE 97 164 13 18

Figure S68.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.13

Table S69.  Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 9(4P16.2) CNV 9 24 16 4
DEL PEAK 9(4P16.2) WILD-TYPE 22 35 31 50

Figure S69.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S70.  Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 9(4P16.2) CNV 3 23 27
DEL PEAK 9(4P16.2) WILD-TYPE 46 39 53

Figure S70.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'CN_CNMF'

P value = 8.5e-12 (Fisher's exact test), Q value = 5.4e-09

Table S71.  Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 10(4Q22.1) CNV 77 28 18 3
DEL PEAK 10(4Q22.1) WILD-TYPE 93 159 14 21

Figure S71.  Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.052

Table S72.  Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 10(4Q22.1) CNV 9 28 15 5
DEL PEAK 10(4Q22.1) WILD-TYPE 22 31 32 49

Figure S72.  Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.016

Table S73.  Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 10(4Q22.1) CNV 3 25 29
DEL PEAK 10(4Q22.1) WILD-TYPE 46 37 51

Figure S73.  Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'MRNA_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07

Table S74.  Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 11(4Q35.1) CNV 7 30 3 13
DEL PEAK 11(4Q35.1) WILD-TYPE 24 32 27 10

Figure S74.  Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 11(4q35.1)' versus 'CN_CNMF'

P value = 1.05e-13 (Fisher's exact test), Q value = 6.8e-11

Table S75.  Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 11(4Q35.1) CNV 88 28 16 5
DEL PEAK 11(4Q35.1) WILD-TYPE 82 159 16 19

Figure S75.  Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q35.1)' versus 'METHLYATION_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.043

Table S76.  Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 11(4Q35.1) CNV 46 13 20
DEL PEAK 11(4Q35.1) WILD-TYPE 59 73 43

Figure S76.  Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.13

Table S77.  Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 11(4Q35.1) CNV 11 30 15 7
DEL PEAK 11(4Q35.1) WILD-TYPE 20 29 32 47

Figure S77.  Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'CN_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 3e-06

Table S78.  Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 12(5Q11.2) CNV 60 16 9 6
DEL PEAK 12(5Q11.2) WILD-TYPE 110 171 23 18

Figure S78.  Get High-res Image Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q21.3)' versus 'CN_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 7e-07

Table S79.  Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 13(5Q21.3) CNV 71 24 14 8
DEL PEAK 13(5Q21.3) WILD-TYPE 99 163 18 16

Figure S79.  Get High-res Image Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(5q23.1)' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 9.5e-06

Table S80.  Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 14(5Q23.1) CNV 64 22 13 8
DEL PEAK 14(5Q23.1) WILD-TYPE 106 165 19 16

Figure S80.  Get High-res Image Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(6p25.3)' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.057

Table S81.  Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 15(6P25.3) CNV 13 23 9 9
DEL PEAK 15(6P25.3) WILD-TYPE 157 164 23 15

Figure S81.  Get High-res Image Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'CN_CNMF'

P value = 6.84e-26 (Fisher's exact test), Q value = 4.6e-23

Table S82.  Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 18(8P23.3) CNV 119 32 6 14
DEL PEAK 18(8P23.3) WILD-TYPE 51 155 26 10

Figure S82.  Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'METHLYATION_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0021

Table S83.  Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 18(8P23.3) CNV 62 21 22
DEL PEAK 18(8P23.3) WILD-TYPE 43 65 41

Figure S83.  Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'CN_CNMF'

P value = 2.41e-30 (Fisher's exact test), Q value = 1.6e-27

Table S84.  Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 19(8P22) CNV 129 33 8 15
DEL PEAK 19(8P22) WILD-TYPE 41 154 24 9

Figure S84.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p22)' versus 'METHLYATION_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021

Table S85.  Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 19(8P22) CNV 69 24 24
DEL PEAK 19(8P22) WILD-TYPE 36 62 39

Figure S85.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S86.  Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
DEL PEAK 19(8P22) CNV 5 15 38 82
DEL PEAK 19(8P22) WILD-TYPE 21 41 25 98

Figure S86.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(8p22)' versus 'MRNASEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.012

Table S87.  Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 19(8P22) CNV 17 38 21 11
DEL PEAK 19(8P22) WILD-TYPE 14 21 26 43

Figure S87.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(8p11.22)' versus 'CN_CNMF'

P value = 8.88e-09 (Fisher's exact test), Q value = 5.4e-06

Table S88.  Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 20(8P11.22) CNV 58 18 3 1
DEL PEAK 20(8P11.22) WILD-TYPE 112 169 29 23

Figure S88.  Get High-res Image Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(8p11.21)' versus 'CN_CNMF'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034

Table S89.  Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 21(8P11.21) CNV 35 7 1 0
DEL PEAK 21(8P11.21) WILD-TYPE 135 180 31 24

Figure S89.  Get High-res Image Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.026

Table S90.  Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 22(9P21.3) CNV 35 10 7 4
DEL PEAK 22(9P21.3) WILD-TYPE 135 177 25 20

Figure S90.  Get High-res Image Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.4e-05

Table S91.  Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 23(10P15.3) CNV 38 12 15 3
DEL PEAK 23(10P15.3) WILD-TYPE 132 175 17 21

Figure S91.  Get High-res Image Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q21.1)' versus 'CN_CNMF'

P value = 2.24e-11 (Fisher's exact test), Q value = 1.4e-08

Table S92.  Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 24(10Q21.1) CNV 48 12 17 5
DEL PEAK 24(10Q21.1) WILD-TYPE 122 175 15 19

Figure S92.  Get High-res Image Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10q23.31)' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021

Table S93.  Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 25(10Q23.31) CNV 53 21 15 5
DEL PEAK 25(10Q23.31) WILD-TYPE 117 166 17 19

Figure S93.  Get High-res Image Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'CN_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.2e-08

Table S94.  Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 26(10Q25.2) CNV 57 16 17 3
DEL PEAK 26(10Q25.2) WILD-TYPE 113 171 15 21

Figure S94.  Get High-res Image Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(12p13.2)' versus 'CN_CNMF'

P value = 9.87e-08 (Fisher's exact test), Q value = 5.9e-05

Table S95.  Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 27(12P13.2) CNV 34 4 5 1
DEL PEAK 27(12P13.2) WILD-TYPE 136 183 27 23

Figure S95.  Get High-res Image Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q14.13)' versus 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07

Table S96.  Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 28(13Q14.13) CNV 1 9 6 2
DEL PEAK 28(13Q14.13) WILD-TYPE 169 178 26 22

Figure S96.  Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.012

Table S97.  Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 29(14Q32.11) CNV 7 35 3 11
DEL PEAK 29(14Q32.11) WILD-TYPE 24 27 27 12

Figure S97.  Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S98.  Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
DEL PEAK 29(14Q32.11) CNV 22 7 27
DEL PEAK 29(14Q32.11) WILD-TYPE 34 37 19

Figure S98.  Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(14q32.11)' versus 'CN_CNMF'

P value = 1.61e-20 (Fisher's exact test), Q value = 1.1e-17

Table S99.  Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 29(14Q32.11) CNV 98 22 10 3
DEL PEAK 29(14Q32.11) WILD-TYPE 72 165 22 21

Figure S99.  Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNASEQ_CNMF'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.041

Table S100.  Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 29(14Q32.11) CNV 11 28 13 5
DEL PEAK 29(14Q32.11) WILD-TYPE 20 31 34 49

Figure S100.  Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNA_CNMF'

P value = 0.000422 (Fisher's exact test), Q value = 0.23

Table S101.  Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 30(15Q11.2) CNV 8 35 5 12
DEL PEAK 30(15Q11.2) WILD-TYPE 23 27 25 11

Figure S101.  Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(15q11.2)' versus 'CN_CNMF'

P value = 1.2e-21 (Fisher's exact test), Q value = 8e-19

Table S102.  Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 30(15Q11.2) CNV 104 29 22 5
DEL PEAK 30(15Q11.2) WILD-TYPE 66 158 10 19

Figure S102.  Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0012

Table S103.  Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 30(15Q11.2) CNV 13 32 19 5
DEL PEAK 30(15Q11.2) WILD-TYPE 18 27 28 49

Figure S103.  Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.065

Table S104.  Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 30(15Q11.2) CNV 6 29 34
DEL PEAK 30(15Q11.2) WILD-TYPE 43 33 46

Figure S104.  Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q21.1)' versus 'CN_CNMF'

P value = 8.15e-18 (Fisher's exact test), Q value = 5.4e-15

Table S105.  Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 31(15Q21.1) CNV 97 30 20 4
DEL PEAK 31(15Q21.1) WILD-TYPE 73 157 12 20

Figure S105.  Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00012

Table S106.  Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 31(15Q21.1) CNV 12 31 17 3
DEL PEAK 31(15Q21.1) WILD-TYPE 19 28 30 51

Figure S106.  Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.012

Table S107.  Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 31(15Q21.1) CNV 4 28 31
DEL PEAK 31(15Q21.1) WILD-TYPE 45 34 49

Figure S107.  Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q22.33)' versus 'CN_CNMF'

P value = 2.48e-21 (Fisher's exact test), Q value = 1.7e-18

Table S108.  Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 32(15Q22.33) CNV 96 23 21 5
DEL PEAK 32(15Q22.33) WILD-TYPE 74 164 11 19

Figure S108.  Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q22.33)' versus 'METHLYATION_CNMF'

P value = 0.000435 (Fisher's exact test), Q value = 0.23

Table S109.  Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 32(15Q22.33) CNV 49 17 22
DEL PEAK 32(15Q22.33) WILD-TYPE 56 69 41

Figure S109.  Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 1.8e-05

Table S110.  Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 32(15Q22.33) CNV 13 33 17 3
DEL PEAK 32(15Q22.33) WILD-TYPE 18 26 30 51

Figure S110.  Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0044

Table S111.  Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 32(15Q22.33) CNV 4 29 33
DEL PEAK 32(15Q22.33) WILD-TYPE 45 33 47

Figure S111.  Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNA_CNMF'

P value = 6.12e-08 (Fisher's exact test), Q value = 3.7e-05

Table S112.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 35(17P12) CNV 10 49 7 16
DEL PEAK 35(17P12) WILD-TYPE 21 13 23 7

Figure S112.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00093

Table S113.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
DEL PEAK 35(17P12) CNV 36 11 35
DEL PEAK 35(17P12) WILD-TYPE 20 33 11

Figure S113.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'CN_CNMF'

P value = 2.81e-35 (Fisher's exact test), Q value = 1.9e-32

Table S114.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 35(17P12) CNV 146 43 24 16
DEL PEAK 35(17P12) WILD-TYPE 24 144 8 8

Figure S114.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(17p12)' versus 'METHLYATION_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06

Table S115.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 35(17P12) CNV 82 30 29
DEL PEAK 35(17P12) WILD-TYPE 23 56 34

Figure S115.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(17p12)' versus 'RPPA_CHIERARCHICAL'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.042

Table S116.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
DEL PEAK 35(17P12) CNV 8 19 43 106
DEL PEAK 35(17P12) WILD-TYPE 18 37 20 74

Figure S116.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.06e-10 (Fisher's exact test), Q value = 6.6e-08

Table S117.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 35(17P12) CNV 20 49 23 11
DEL PEAK 35(17P12) WILD-TYPE 11 10 24 43

Figure S117.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-08 (Fisher's exact test), Q value = 1.9e-05

Table S118.  Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 35(17P12) CNV 11 48 44
DEL PEAK 35(17P12) WILD-TYPE 38 14 36

Figure S118.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'MRNA_CNMF'

P value = 1.51e-12 (Fisher's exact test), Q value = 9.7e-10

Table S119.  Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 37(18P11.31) CNV 6 51 5 16
DEL PEAK 37(18P11.31) WILD-TYPE 25 11 25 7

Figure S119.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S120.  Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
DEL PEAK 37(18P11.31) CNV 36 7 35
DEL PEAK 37(18P11.31) WILD-TYPE 20 37 11

Figure S120.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'CN_CNMF'

P value = 1.93e-42 (Fisher's exact test), Q value = 1.3e-39

Table S121.  Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 37(18P11.31) CNV 145 34 28 13
DEL PEAK 37(18P11.31) WILD-TYPE 25 153 4 11

Figure S121.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(18p11.31)' versus 'METHLYATION_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 2e-10

Table S122.  Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 37(18P11.31) CNV 83 22 31
DEL PEAK 37(18P11.31) WILD-TYPE 22 64 32

Figure S122.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 3.11e-17 (Fisher's exact test), Q value = 2.1e-14

Table S123.  Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 37(18P11.31) CNV 17 52 24 5
DEL PEAK 37(18P11.31) WILD-TYPE 14 7 23 49

Figure S123.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.19e-10 (Fisher's exact test), Q value = 5.1e-07

Table S124.  Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 37(18P11.31) CNV 7 45 46
DEL PEAK 37(18P11.31) WILD-TYPE 42 17 34

Figure S124.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNA_CNMF'

P value = 8.37e-11 (Fisher's exact test), Q value = 5.2e-08

Table S125.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 38(18Q12.2) CNV 8 53 8 17
DEL PEAK 38(18Q12.2) WILD-TYPE 23 9 22 6

Figure S125.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.08e-09 (Fisher's exact test), Q value = 6.7e-07

Table S126.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
DEL PEAK 38(18Q12.2) CNV 39 9 38
DEL PEAK 38(18Q12.2) WILD-TYPE 17 35 8

Figure S126.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'CN_CNMF'

P value = 1.87e-45 (Fisher's exact test), Q value = 1.3e-42

Table S127.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 38(18Q12.2) CNV 157 44 27 19
DEL PEAK 38(18Q12.2) WILD-TYPE 13 143 5 5

Figure S127.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(18q12.2)' versus 'METHLYATION_CNMF'

P value = 8.98e-16 (Fisher's exact test), Q value = 5.9e-13

Table S128.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 38(18Q12.2) CNV 93 29 31
DEL PEAK 38(18Q12.2) WILD-TYPE 12 57 32

Figure S128.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(18q12.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000421 (Fisher's exact test), Q value = 0.23

Table S129.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
DEL PEAK 38(18Q12.2) CNV 9 22 43 113
DEL PEAK 38(18Q12.2) WILD-TYPE 17 34 20 67

Figure S129.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 7.66e-16 (Fisher's exact test), Q value = 5e-13

Table S130.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 38(18Q12.2) CNV 21 53 28 8
DEL PEAK 38(18Q12.2) WILD-TYPE 10 6 19 46

Figure S130.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-08 (Fisher's exact test), Q value = 6.5e-06

Table S131.  Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 38(18Q12.2) CNV 11 48 51
DEL PEAK 38(18Q12.2) WILD-TYPE 38 14 29

Figure S131.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.06e-10 (Fisher's exact test), Q value = 1.9e-07

Table S132.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 39(18Q21.2) CNV 8 53 9 17
DEL PEAK 39(18Q21.2) WILD-TYPE 23 9 21 6

Figure S132.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S133.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
DEL PEAK 39(18Q21.2) CNV 40 9 38
DEL PEAK 39(18Q21.2) WILD-TYPE 16 35 8

Figure S133.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.51e-45 (Fisher's exact test), Q value = 1e-42

Table S134.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 39(18Q21.2) CNV 161 51 28 20
DEL PEAK 39(18Q21.2) WILD-TYPE 9 136 4 4

Figure S134.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.29e-12 (Fisher's exact test), Q value = 2.1e-09

Table S135.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 39(18Q21.2) CNV 94 38 33
DEL PEAK 39(18Q21.2) WILD-TYPE 11 48 30

Figure S135.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000225 (Fisher's exact test), Q value = 0.12

Table S136.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
DEL PEAK 39(18Q21.2) CNV 10 24 46 120
DEL PEAK 39(18Q21.2) WILD-TYPE 16 32 17 60

Figure S136.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 8.74e-13 (Fisher's exact test), Q value = 5.7e-10

Table S137.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 39(18Q21.2) CNV 21 54 29 13
DEL PEAK 39(18Q21.2) WILD-TYPE 10 5 18 41

Figure S137.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 7.14e-07 (Fisher's exact test), Q value = 0.00042

Table S138.  Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 39(18Q21.2) CNV 15 49 53
DEL PEAK 39(18Q21.2) WILD-TYPE 34 13 27

Figure S138.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNA_CNMF'

P value = 6.92e-11 (Fisher's exact test), Q value = 4.3e-08

Table S139.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 40(18Q22.1) CNV 8 54 9 17
DEL PEAK 40(18Q22.1) WILD-TYPE 23 8 21 6

Figure S139.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S140.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
DEL PEAK 40(18Q22.1) CNV 40 10 38
DEL PEAK 40(18Q22.1) WILD-TYPE 16 34 8

Figure S140.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'CN_CNMF'

P value = 1.58e-47 (Fisher's exact test), Q value = 1.1e-44

Table S141.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 40(18Q22.1) CNV 162 50 29 19
DEL PEAK 40(18Q22.1) WILD-TYPE 8 137 3 5

Figure S141.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q22.1)' versus 'METHLYATION_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.3e-09

Table S142.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
DEL PEAK 40(18Q22.1) CNV 94 38 32
DEL PEAK 40(18Q22.1) WILD-TYPE 11 48 31

Figure S142.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(18q22.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000224 (Fisher's exact test), Q value = 0.12

Table S143.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
DEL PEAK 40(18Q22.1) CNV 10 24 45 122
DEL PEAK 40(18Q22.1) WILD-TYPE 16 32 18 58

Figure S143.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 4.05e-12 (Fisher's exact test), Q value = 2.6e-09

Table S144.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 40(18Q22.1) CNV 21 54 29 14
DEL PEAK 40(18Q22.1) WILD-TYPE 10 5 18 40

Figure S144.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-07 (Fisher's exact test), Q value = 0.00016

Table S145.  Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
DEL PEAK 40(18Q22.1) CNV 15 50 53
DEL PEAK 40(18Q22.1) WILD-TYPE 34 12 27

Figure S145.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(20p12.1)' versus 'CN_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 9e-11

Table S146.  Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 42(20P12.1) CNV 61 12 0 6
DEL PEAK 42(20P12.1) WILD-TYPE 109 175 32 18

Figure S146.  Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(20p12.1)' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.082

Table S147.  Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
DEL PEAK 42(20P12.1) CNV 8 24 7 4
DEL PEAK 42(20P12.1) WILD-TYPE 23 35 40 50

Figure S147.  Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(21q11.2)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S148.  Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 43(21Q11.2) CNV 72 30 18 5
DEL PEAK 43(21Q11.2) WILD-TYPE 98 157 14 19

Figure S148.  Get High-res Image Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(22q13.32)' versus 'MRNA_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.23

Table S149.  Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
DEL PEAK 44(22Q13.32) CNV 8 34 4 10
DEL PEAK 44(22Q13.32) WILD-TYPE 23 28 26 13

Figure S149.  Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 44(22q13.32)' versus 'CN_CNMF'

P value = 9.76e-13 (Fisher's exact test), Q value = 6.3e-10

Table S150.  Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
DEL PEAK 44(22Q13.32) CNV 85 28 17 8
DEL PEAK 44(22Q13.32) WILD-TYPE 85 159 15 16

Figure S150.  Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 413

  • Number of copy number variation regions = 68

  • 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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