Correlation between copy number variation genes and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C11C1TW4
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/C11C1TW4
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 563 patients, 117 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 4(2p24.3) 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 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and '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 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(5q35.3) cnvs correlated to 'MRNA_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_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', 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' 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 'MRNA_CNMF' and '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, 117 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 3.62e-11
(2.46e-08) 		3.18e-11
(2.17e-08) 		3.48e-07
(0.000226) 		2.34e-13
(1.6e-10) 		1.23e-20
(8.56e-18) 		1.32e-06
(0.000844) 		8.62e-06
(0.00538) 		5.85e-05
(0.0356) 		1.11e-05
(0.00686) 		0.000357
(0.208)
Amp Peak 9(7q11 21) 0 (0%) 111 9.85e-06
(0.00614) 		4.88e-07
(0.000315) 		4.69e-06
(0.00295) 		7.42e-09
(4.96e-06) 		1.72e-09
(1.15e-06) 		0.00585
(1.00) 		0.00417
(1.00) 		0.336
(1.00) 		0.004
(1.00) 		0.00143
(0.801)
Del Peak 22(10p13) 0 (0%) 104 3.17e-07
(0.000206) 		9.94e-06
(0.00618) 		0.00282
(1.00) 		1.28e-07
(8.44e-05) 		1.11e-15
(7.68e-13) 		0.035
(1.00) 		0.000132
(0.0792) 		0.00458
(1.00) 		0.0885
(1.00) 		0.41
(1.00)
Del Peak 26(11p15 5) 0 (0%) 436 3.9e-10
(2.62e-07) 		1.15e-06
(0.000737) 		0.23
(1.00) 		1.5e-06
(0.000956) 		2.1e-15
(1.44e-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%) 412 1.46e-06
(0.000933) 		7.39e-08
(4.88e-05) 		0.00977
(1.00) 		1.31e-06
(0.00084) 		4.09e-07
(0.000265) 		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 1.02e-05
(0.00635) 		4.54e-05
(0.0278) 		0.0107
(1.00) 		1.92e-06
(0.00122) 		1.06e-10
(7.19e-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%) 499 1.69e-07
(0.000111) 		0.000183
(0.108) 		0.0397
(1.00) 		8.34e-05
(0.0506) 		3.51e-06
(0.00222) 		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%) 323 2.33e-12
(1.59e-09) 		2.56e-07
(0.000167) 		0.248
(1.00) 		0.00825
(1.00) 		1.86e-20
(1.29e-17) 		0.017
(1.00) 		0.0116
(1.00) 		1.32e-05
(0.00816) 		0.164
(1.00) 		0.0199
(1.00)
Amp Peak 23(19q12) 0 (0%) 360 1.29e-10
(8.73e-08) 		3.97e-08
(2.63e-05) 		0.218
(1.00) 		0.00449
(1.00) 		1.5e-15
(1.03e-12) 		0.0553
(1.00) 		0.0174
(1.00) 		0.000213
(0.125) 		0.0823
(1.00) 		0.0438
(1.00)
Del Peak 21(10p15 3) 0 (0%) 106 1.64e-06
(0.00104) 		0.000166
(0.0989) 		0.0133
(1.00) 		1.85e-07
(0.000121) 		1.45e-14
(9.97e-12) 		0.035
(1.00) 		0.00523
(1.00) 		0.0278
(1.00) 		0.0147
(1.00) 		0.41
(1.00)
Del Peak 23(10p11 23) 0 (0%) 100 2.94e-10
(1.98e-07) 		9.54e-07
(0.000613) 		0.00054
(0.314) 		1.26e-08
(8.38e-06) 		9.85e-17
(6.84e-14) 		0.027
(1.00) 		0.000786
(0.453) 		0.0175
(1.00) 		0.0443
(1.00) 		0.084
(1.00)
Del Peak 24(10q23 31) 0 (0%) 64 4.77e-07
(0.000308) 		0.000124
(0.0745) 		0.00781
(1.00) 		7.23e-05
(0.0439) 		1.19e-16
(8.24e-14) 		0.196
(1.00) 		0.0105
(1.00) 		0.131
(1.00) 		0.369
(1.00) 		0.16
(1.00)
Del Peak 27(11p11 2) 0 (0%) 462 5.47e-08
(3.62e-05) 		0.000192
(0.113) 		0.921
(1.00) 		2.44e-05
(0.015) 		2.18e-13
(1.49e-10) 		0.000701
(0.405) 		0.825
(1.00) 		0.576
(1.00) 		0.051
(1.00) 		0.706
(1.00)
Amp Peak 11(7q31 2) 0 (0%) 103 0.000978
(0.559) 		0.00013
(0.0782) 		0.00207
(1.00) 		0.000144
(0.0859) 		2.21e-07
(0.000144) 		0.0107
(1.00) 		0.103
(1.00) 		0.183
(1.00) 		0.256
(1.00) 		0.00355
(1.00)
Amp Peak 12(7q36 1) 0 (0%) 98 4.64e-05
(0.0283) 		0.000671
(0.388) 		0.059
(1.00) 		4.59e-05
(0.0281) 		1.41e-05
(0.00873) 		0.00363
(1.00) 		0.227
(1.00) 		0.249
(1.00) 		0.0292
(1.00) 		0.00467
(1.00)
Del Peak 15(5q35 3) 0 (0%) 509 4.89e-06
(0.00308) 		0.00216
(1.00) 		0.00156
(0.872) 		2.27e-05
(0.014) 		5.69e-05
(0.0347) 		0.00732
(1.00) 		0.84
(1.00) 		0.407
(1.00) 		0.208
(1.00) 		0.841
(1.00)
Del Peak 19(9p21 3) 0 (0%) 155 6.36e-06
(0.00398) 		0.000114
(0.0691) 		0.554
(1.00) 		0.00153
(0.856) 		3.77e-10
(2.54e-07) 		0.0417
(1.00) 		0.0878
(1.00) 		0.0182
(1.00) 		0.0274
(1.00) 		0.00319
(1.00)
Del Peak 25(10q26 3) 0 (0%) 63 1.16e-07
(7.63e-05) 		0.000142
(0.0852) 		0.0777
(1.00) 		0.00043
(0.251) 		1.89e-13
(1.3e-10) 		0.0145
(1.00) 		0.117
(1.00) 		0.0761
(1.00) 		0.25
(1.00) 		0.378
(1.00)
Del Peak 32(13q14 2) 0 (0%) 327 1.62e-07
(0.000106) 		0.000164
(0.0973) 		0.109
(1.00) 		0.08
(1.00) 		1.1e-15
(7.63e-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%) 459 0.00185
(1.00) 		0.000115
(0.0696) 		0.479
(1.00) 		0.0527
(1.00) 		4.31e-07
(0.000279) 		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%) 468 2.65e-07
(0.000173) 		0.048
(1.00) 		0.936
(1.00) 		0.00783
(1.00) 		1.3e-16
(9e-14) 		0.259
(1.00) 		0.552
(1.00) 		0.5
(1.00) 		0.0908
(1.00) 		0.793
(1.00)
Del Peak 31(12q15) 0 (0%) 486 0.000124
(0.0745) 		0.000563
(0.327) 		0.247
(1.00) 		0.0467
(1.00) 		5.4e-07
(0.000347) 		0.514
(1.00) 		0.527
(1.00) 		0.724
(1.00) 		0.585
(1.00) 		0.943
(1.00)
Del Peak 33(14q13 1) 0 (0%) 388 8.84e-06
(0.00552) 		0.0129
(1.00) 		0.618
(1.00) 		0.421
(1.00) 		3.36e-30
(2.34e-27) 		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%) 393 1.61e-07
(0.000106) 		0.00516
(1.00) 		0.0656
(1.00) 		0.871
(1.00) 		7.68e-39
(5.36e-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%) 407 6.25e-09
(4.18e-06) 		0.00555
(1.00) 		0.422
(1.00) 		0.835
(1.00) 		8.42e-41
(5.89e-38) 		0.00996
(1.00) 		0.515
(1.00) 		0.108
(1.00) 		0.222
(1.00) 		0.0846
(1.00)
Del Peak 40(17p13 1) 0 (0%) 468 0.000167
(0.0991) 		0.453
(1.00) 		0.88
(1.00) 		0.605
(1.00) 		1.42e-15
(9.77e-13) 		0.133
(1.00) 		0.709
(1.00) 		0.447
(1.00) 		0.645
(1.00) 		0.295
(1.00)
Del Peak 41(17q11 2) 0 (0%) 492 7.43e-06
(0.00465) 		0.000862
(0.495) 		0.00192
(1.00) 		0.00959
(1.00) 		5.32e-07
(0.000343) 		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%) 474 0.399
(1.00) 		0.839
(1.00) 		0.179
(1.00) 		0.0074
(1.00) 		1.63e-08
(1.09e-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%) 410 0.91
(1.00) 		0.545
(1.00) 		0.239
(1.00) 		0.097
(1.00) 		1.76e-08
(1.17e-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%) 467 0.156
(1.00) 		0.739
(1.00) 		0.403
(1.00) 		0.441
(1.00) 		8.32e-09
(5.55e-06) 		0.931
(1.00) 		0.426
(1.00) 		0.177
(1.00) 		0.775
(1.00) 		0.439
(1.00)
Amp Peak 4(2p24 3) 0 (0%) 517 0.026
(1.00) 		0.0372
(1.00) 		0.748
(1.00) 		0.385
(1.00) 		0.000238
(0.139) 		0.0574
(1.00) 		0.209
(1.00) 		0.112
(1.00) 		0.93
(1.00) 		1
(1.00)
Amp Peak 5(3q26 33) 0 (0%) 455 0.0157
(1.00) 		0.14
(1.00) 		0.9
(1.00) 		0.724
(1.00) 		3.56e-06
(0.00225) 		0.00452
(1.00) 		0.0685
(1.00) 		0.358
(1.00) 		0.546
(1.00) 		0.321
(1.00)
Amp Peak 15(12p13 32) 0 (0%) 482 0.468
(1.00) 		0.875
(1.00) 		0.716
(1.00) 		0.812
(1.00) 		1.96e-05
(0.0121) 		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%) 432 0.0651
(1.00) 		0.397
(1.00) 		0.309
(1.00) 		0.121
(1.00) 		1.7e-09
(1.14e-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%) 471 0.462
(1.00) 		0.624
(1.00) 		0.751
(1.00) 		0.515
(1.00) 		2.83e-07
(0.000184) 		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%) 485 0.0141
(1.00) 		0.232
(1.00) 		0.402
(1.00) 		0.709
(1.00) 		5.98e-05
(0.0364) 		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%) 519 0.00176
(0.984) 		0.213
(1.00) 		0.437
(1.00) 		0.0651
(1.00) 		1.6e-06
(0.00102) 		0.00338
(1.00) 		0.478
(1.00) 		0.86
(1.00) 		0.181
(1.00) 		0.21
(1.00)
Del Peak 9(3p21 1) 0 (0%) 511 0.231
(1.00) 		0.603
(1.00) 		0.911
(1.00) 		0.104
(1.00) 		0.000187
(0.11) 		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%) 508 0.566
(1.00) 		0.865
(1.00) 		0.98
(1.00) 		0.708
(1.00) 		5.68e-06
(0.00357) 		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%) 508 0.829
(1.00) 		0.252
(1.00) 		0.617
(1.00) 		0.378
(1.00) 		0.000235
(0.138) 		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%) 473 0.00309
(1.00) 		0.0159
(1.00) 		0.088
(1.00) 		0.0519
(1.00) 		0.000153
(0.0909) 		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%) 410 0.797
(1.00) 		0.96
(1.00) 		0.554
(1.00) 		0.029
(1.00) 		9.83e-11
(6.67e-08) 		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%) 390 0.768
(1.00) 		0.236
(1.00) 		0.866
(1.00) 		0.125
(1.00) 		1.08e-06
(0.000693) 		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%) 487 0.00831
(1.00) 		0.00296
(1.00) 		0.188
(1.00) 		0.0064
(1.00) 		0.000175
(0.103) 		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%) 478 0.00121
(0.684) 		0.869
(1.00) 		0.926
(1.00) 		0.8
(1.00) 		2e-10
(1.35e-07) 		0.376
(1.00) 		0.632
(1.00) 		0.487
(1.00) 		0.587
(1.00) 		0.261
(1.00)
Del Peak 43(19q13 41) 0 (0%) 464 0.00103
(0.587) 		1.23e-05
(0.0076) 		0.0018
(1.00) 		0.00108
(0.616) 		0.0012
(0.68) 		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%) 504 0.00118
(0.669) 		0.0168
(1.00) 		0.000108
(0.0652) 		0.00239
(1.00) 		0.14
(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%) 440 0.00431
(1.00) 		0.00119
(0.677) 		0.155
(1.00) 		0.209
(1.00) 		6.6e-10
(4.44e-07) 		0.00951
(1.00) 		0.605
(1.00) 		0.253
(1.00) 		0.337
(1.00) 		0.644
(1.00)
Amp Peak 6(4p16 3) 0 (0%) 517 0.348
(1.00) 		0.852
(1.00) 		0.828
(1.00) 		0.403
(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%) 537 0.718
(1.00) 		0.588
(1.00) 		0.324
(1.00) 		0.769
(1.00) 		0.452
(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%) 533 0.169
(1.00) 		0.691
(1.00) 		0.17
(1.00) 		0.115
(1.00) 		0.014
(1.00) 		0.0677
(1.00) 		0.186
(1.00) 		0.368
(1.00) 		1
(1.00)
Amp Peak 19(14q32 33) 0 (0%) 529 0.368
(1.00) 		0.434
(1.00) 		0.0211
(1.00) 		0.943
(1.00) 		0.794
(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%) 518 0.00312
(1.00) 		0.00458
(1.00) 		0.0751
(1.00) 		0.221
(1.00) 		0.00696
(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%) 496 0.00429
(1.00) 		0.0716
(1.00) 		0.108
(1.00) 		0.0796
(1.00) 		0.000771
(0.445) 		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%) 464 0.797
(1.00) 		0.0418
(1.00) 		0.503
(1.00) 		0.233
(1.00) 		0.614
(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%) 428 0.133
(1.00) 		0.107
(1.00) 		0.369
(1.00) 		0.33
(1.00) 		0.00118
(0.671) 		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%) 503 0.248
(1.00) 		0.299
(1.00) 		0.97
(1.00) 		0.871
(1.00) 		0.0973
(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%) 516 0.833
(1.00) 		0.979
(1.00) 		0.761
(1.00) 		0.228
(1.00) 		0.176
(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%) 516 0.309
(1.00) 		0.409
(1.00) 		0.402
(1.00) 		0.679
(1.00) 		0.619
(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%) 531 0.729
(1.00) 		0.555
(1.00) 		0.685
(1.00) 		0.315
(1.00) 		0.612
(1.00) 		0.187
(1.00) 		0.799
(1.00) 		0.335
(1.00) 		0.539
(1.00) 		0.904
(1.00)
Del Peak 8(2q37 1) 0 (0%) 507 0.0601
(1.00) 		0.023
(1.00) 		0.239
(1.00) 		0.00097
(0.556) 		0.00684
(1.00) 		0.0265
(1.00) 		0.647
(1.00) 		0.72
(1.00) 		0.181
(1.00) 		0.687
(1.00)
Del Peak 12(3q29) 0 (0%) 499 0.0674
(1.00) 		0.191
(1.00) 		0.612
(1.00) 		0.984
(1.00) 		0.00683
(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%) 485 0.0176
(1.00) 		0.0695
(1.00) 		0.35
(1.00) 		0.178
(1.00) 		0.0582
(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%) 496 0.517
(1.00) 		0.13
(1.00) 		0.256
(1.00) 		0.355
(1.00) 		0.0382
(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%) 492 0.19
(1.00) 		0.116
(1.00) 		0.84
(1.00) 		0.401
(1.00) 		0.292
(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%) 488 0.0112
(1.00) 		0.013
(1.00) 		0.129
(1.00) 		0.056
(1.00) 		0.077
(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%) 474 0.389
(1.00) 		0.248
(1.00) 		0.0617
(1.00) 		0.578
(1.00) 		0.0942
(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%) 468 0.0364
(1.00) 		0.61
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.0045
(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%) 484 0.192
(1.00) 		0.205
(1.00) 		0.498
(1.00) 		0.421
(1.00) 		0.00203
(1.00) 		0.0928
(1.00) 		0.0315
(1.00) 		0.00134
(0.753) 		0.159
(1.00) 		0.697
(1.00)
Del Peak 45(22q13 32) 0 (0%) 355 0.749
(1.00) 		0.305
(1.00) 		0.0194
(1.00) 		0.088
(1.00) 		0.000804
(0.462) 		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 = 1.63e-08 (Fisher's exact test), Q value = 1.1e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 1(1P36.21) CNV 50 20 19
AMP PEAK 1(1P36.21) WILD-TYPE 111 194 169

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 = 1.76e-08 (Fisher's exact test), Q value = 1.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 2(1Q32.1) CNV 73 43 37
AMP PEAK 2(1Q32.1) WILD-TYPE 88 171 151

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 = 8.32e-09 (Fisher's exact test), Q value = 5.6e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 3(1Q44) CNV 53 21 22
AMP PEAK 3(1Q44) WILD-TYPE 108 193 166

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

'Amp Peak 4(2p24.3)' versus 'CN_CNMF'

P value = 0.000238 (Fisher's exact test), Q value = 0.14

Table S4.  Gene #4: 'Amp Peak 4(2p24.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 4(2P24.3) CNV 24 7 15
AMP PEAK 4(2P24.3) WILD-TYPE 137 207 173

Figure S4.  Get High-res Image Gene #4: 'Amp Peak 4(2p24.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 3.56e-06 (Fisher's exact test), Q value = 0.0022

Table S5.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 5(3Q26.33) CNV 52 25 31
AMP PEAK 5(3Q26.33) WILD-TYPE 109 189 157

Figure S5.  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 = 0.000115 (Fisher's exact test), Q value = 0.07

Table S6.  Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 7(4Q12) CNV 16 50 32
AMP PEAK 7(4Q12) WILD-TYPE 114 116 181

Figure S6.  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 = 4.31e-07 (Fisher's exact test), Q value = 0.00028

Table S7.  Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 7(4Q12) CNV 52 22 30
AMP PEAK 7(4Q12) WILD-TYPE 109 192 158

Figure S7.  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 = 3.62e-11 (Fisher's exact test), Q value = 2.5e-08

Table S8.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 8(7P11.2) CNV 139 66 147 91
AMP PEAK 8(7P11.2) WILD-TYPE 8 28 5 25

Figure S8.  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 = 3.18e-11 (Fisher's exact test), Q value = 2.2e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 8(7P11.2) CNV 124 119 200
AMP PEAK 8(7P11.2) WILD-TYPE 6 47 13

Figure S9.  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 = 3.48e-07 (Fisher's exact test), Q value = 0.00023

Table S10.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 157 72 104
AMP PEAK 8(7P11.2) CNV 136 124 58 95
AMP PEAK 8(7P11.2) WILD-TYPE 3 33 14 9

Figure S10.  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 = 2.34e-13 (Fisher's exact test), Q value = 1.6e-10

Table S11.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
AMP PEAK 8(7P11.2) CNV 153 172 88
AMP PEAK 8(7P11.2) WILD-TYPE 10 7 42

Figure S11.  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 = 1.23e-20 (Fisher's exact test), Q value = 8.6e-18

Table S12.  Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 8(7P11.2) CNV 149 213 132
AMP PEAK 8(7P11.2) WILD-TYPE 12 1 56

Figure S12.  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 S13.  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 S13.  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 = 0.0054

Table S14.  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 S14.  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 = 0.036

Table S15.  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 S15.  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 = 0.0069

Table S16.  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 S16.  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 S17.  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 S17.  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 = 9.85e-06 (Fisher's exact test), Q value = 0.0061

Table S18.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 9(7Q11.21) CNV 133 62 124 84
AMP PEAK 9(7Q11.21) WILD-TYPE 14 32 28 32

Figure S18.  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 = 4.88e-07 (Fisher's exact test), Q value = 0.00032

Table S19.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 9(7Q11.21) CNV 109 108 186
AMP PEAK 9(7Q11.21) WILD-TYPE 21 58 27

Figure S19.  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 = 4.69e-06 (Fisher's exact test), Q value = 0.003

Table S20.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 157 72 104
AMP PEAK 9(7Q11.21) CNV 126 113 48 90
AMP PEAK 9(7Q11.21) WILD-TYPE 13 44 24 14

Figure S20.  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 = 7.42e-09 (Fisher's exact test), Q value = 5e-06

Table S21.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
AMP PEAK 9(7Q11.21) CNV 143 155 79
AMP PEAK 9(7Q11.21) WILD-TYPE 20 24 51

Figure S21.  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 = 1.72e-09 (Fisher's exact test), Q value = 1.2e-06

Table S22.  Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 9(7Q11.21) CNV 144 186 122
AMP PEAK 9(7Q11.21) WILD-TYPE 17 28 66

Figure S22.  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 = 1.02e-05 (Fisher's exact test), Q value = 0.0064

Table S23.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 10(7Q21.2) CNV 131 62 135 91
AMP PEAK 10(7Q21.2) WILD-TYPE 16 32 17 25

Figure S23.  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 = 4.54e-05 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 10(7Q21.2) CNV 114 118 187
AMP PEAK 10(7Q21.2) WILD-TYPE 16 48 26

Figure S24.  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 = 1.92e-06 (Fisher's exact test), Q value = 0.0012

Table S25.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
AMP PEAK 10(7Q21.2) CNV 140 160 87
AMP PEAK 10(7Q21.2) WILD-TYPE 23 19 43

Figure S25.  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 = 1.06e-10 (Fisher's exact test), Q value = 7.2e-08

Table S26.  Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 10(7Q21.2) CNV 145 196 127
AMP PEAK 10(7Q21.2) WILD-TYPE 16 18 61

Figure S26.  Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S27.  Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 11(7Q31.2) CNV 107 118 188
AMP PEAK 11(7Q31.2) WILD-TYPE 23 48 25

Figure S27.  Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 0.000144 (Fisher's exact test), Q value = 0.086

Table S28.  Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
AMP PEAK 11(7Q31.2) CNV 141 151 88
AMP PEAK 11(7Q31.2) WILD-TYPE 22 28 42

Figure S28.  Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

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

P value = 2.21e-07 (Fisher's exact test), Q value = 0.00014

Table S29.  Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 11(7Q31.2) CNV 141 190 129
AMP PEAK 11(7Q31.2) WILD-TYPE 20 24 59

Figure S29.  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 = 4.64e-05 (Fisher's exact test), Q value = 0.028

Table S30.  Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 12(7Q36.1) CNV 131 62 132 92
AMP PEAK 12(7Q36.1) WILD-TYPE 16 32 20 24

Figure S30.  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 = 4.59e-05 (Fisher's exact test), Q value = 0.028

Table S31.  Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
AMP PEAK 12(7Q36.1) CNV 138 158 89
AMP PEAK 12(7Q36.1) WILD-TYPE 25 21 41

Figure S31.  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 = 1.41e-05 (Fisher's exact test), Q value = 0.0087

Table S32.  Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 12(7Q36.1) CNV 139 191 135
AMP PEAK 12(7Q36.1) WILD-TYPE 22 23 53

Figure S32.  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 = 1.69e-07 (Fisher's exact test), Q value = 0.00011

Table S33.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 13(8Q24.21) CNV 8 24 6 19
AMP PEAK 13(8Q24.21) WILD-TYPE 139 70 146 97

Figure S33.  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 = 0.000183 (Fisher's exact test), Q value = 0.11

Table S34.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 13(8Q24.21) CNV 9 33 15
AMP PEAK 13(8Q24.21) WILD-TYPE 121 133 198

Figure S34.  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 = 8.34e-05 (Fisher's exact test), Q value = 0.051

Table S35.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
AMP PEAK 13(8Q24.21) CNV 12 13 29
AMP PEAK 13(8Q24.21) WILD-TYPE 151 166 101

Figure S35.  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 = 3.51e-06 (Fisher's exact test), Q value = 0.0022

Table S36.  Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 13(8Q24.21) CNV 31 8 25
AMP PEAK 13(8Q24.21) WILD-TYPE 130 206 163

Figure S36.  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 = 1.96e-05 (Fisher's exact test), Q value = 0.012

Table S37.  Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 15(12P13.32) CNV 41 18 22
AMP PEAK 15(12P13.32) WILD-TYPE 120 196 166

Figure S37.  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 = 1.7e-09 (Fisher's exact test), Q value = 1.1e-06

Table S38.  Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 16(12Q14.1) CNV 67 37 27
AMP PEAK 16(12Q14.1) WILD-TYPE 94 177 161

Figure S38.  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 = 2.83e-07 (Fisher's exact test), Q value = 0.00018

Table S39.  Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 17(12Q15) CNV 49 24 19
AMP PEAK 17(12Q15) WILD-TYPE 112 190 169

Figure S39.  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 = 5.98e-05 (Fisher's exact test), Q value = 0.036

Table S40.  Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 21(17Q25.1) CNV 39 18 21
AMP PEAK 21(17Q25.1) WILD-TYPE 122 196 167

Figure S40.  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 = 2.33e-12 (Fisher's exact test), Q value = 1.6e-09

Table S41.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 22(19P13.2) CNV 56 37 100 25
AMP PEAK 22(19P13.2) WILD-TYPE 91 57 52 91

Figure S41.  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 = 2.56e-07 (Fisher's exact test), Q value = 0.00017

Table S42.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 22(19P13.2) CNV 78 47 93
AMP PEAK 22(19P13.2) WILD-TYPE 52 119 120

Figure S42.  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 = 1.86e-20 (Fisher's exact test), Q value = 1.3e-17

Table S43.  Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 22(19P13.2) CNV 47 145 48
AMP PEAK 22(19P13.2) WILD-TYPE 114 69 140

Figure S43.  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 = 0.0082

Table S44.  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 S44.  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 = 1.29e-10 (Fisher's exact test), Q value = 8.7e-08

Table S45.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
AMP PEAK 23(19Q12) CNV 55 29 83 17
AMP PEAK 23(19Q12) WILD-TYPE 92 65 69 99

Figure S45.  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 = 3.97e-08 (Fisher's exact test), Q value = 2.6e-05

Table S46.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
AMP PEAK 23(19Q12) CNV 64 32 88
AMP PEAK 23(19Q12) WILD-TYPE 66 134 125

Figure S46.  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 = 1.5e-15 (Fisher's exact test), Q value = 1e-12

Table S47.  Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
AMP PEAK 23(19Q12) CNV 38 123 42
AMP PEAK 23(19Q12) WILD-TYPE 123 91 146

Figure S47.  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 S48.  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 S48.  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 = 1.6e-06 (Fisher's exact test), Q value = 0.001

Table S49.  Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 7(2Q22.1) CNV 26 4 14
DEL PEAK 7(2Q22.1) WILD-TYPE 135 210 174

Figure S49.  Get High-res Image Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.000187 (Fisher's exact test), Q value = 0.11

Table S50.  Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 9(3P21.1) CNV 23 7 22
DEL PEAK 9(3P21.1) WILD-TYPE 138 207 166

Figure S50.  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 = 5.68e-06 (Fisher's exact test), Q value = 0.0036

Table S51.  Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 10(3Q13.31) CNV 27 6 22
DEL PEAK 10(3Q13.31) WILD-TYPE 134 208 166

Figure S51.  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 = 0.000235 (Fisher's exact test), Q value = 0.14

Table S52.  Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 11(3Q22.1) CNV 24 8 23
DEL PEAK 11(3Q22.1) WILD-TYPE 137 206 165

Figure S52.  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 = 0.000153 (Fisher's exact test), Q value = 0.091

Table S53.  Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 14(4Q34.3) CNV 41 20 29
DEL PEAK 14(4Q34.3) WILD-TYPE 120 194 159

Figure S53.  Get High-res Image Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 15(5q35.3)' versus 'MRNA_CNMF'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.0031

Table S54.  Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 15(5Q35.3) CNV 8 22 6 15
DEL PEAK 15(5Q35.3) WILD-TYPE 139 72 146 101

Figure S54.  Get High-res Image Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(5q35.3)' versus 'MIR_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.014

Table S55.  Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 15(5Q35.3) CNV 6 15 26
DEL PEAK 15(5Q35.3) WILD-TYPE 157 164 104

Figure S55.  Get High-res Image Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 15(5q35.3)' versus 'CN_CNMF'

P value = 5.69e-05 (Fisher's exact test), Q value = 0.035

Table S56.  Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 15(5Q35.3) CNV 18 7 29
DEL PEAK 15(5Q35.3) WILD-TYPE 143 207 159

Figure S56.  Get High-res Image Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 9.83e-11 (Fisher's exact test), Q value = 6.7e-08

Table S57.  Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 16(6Q22.31) CNV 77 42 34
DEL PEAK 16(6Q22.31) WILD-TYPE 84 172 154

Figure S57.  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 = 1.08e-06 (Fisher's exact test), Q value = 0.00069

Table S58.  Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 17(6Q26) CNV 75 58 40
DEL PEAK 17(6Q26) WILD-TYPE 86 156 148

Figure S58.  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 = 6.36e-06 (Fisher's exact test), Q value = 0.004

Table S59.  Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 19(9P21.3) CNV 100 60 133 77
DEL PEAK 19(9P21.3) WILD-TYPE 47 34 19 39

Figure S59.  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 = 0.000114 (Fisher's exact test), Q value = 0.069

Table S60.  Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 19(9P21.3) CNV 112 109 149
DEL PEAK 19(9P21.3) WILD-TYPE 18 57 64

Figure S60.  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 = 3.77e-10 (Fisher's exact test), Q value = 2.5e-07

Table S61.  Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 19(9P21.3) CNV 108 187 113
DEL PEAK 19(9P21.3) WILD-TYPE 53 27 75

Figure S61.  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 = 1.64e-06 (Fisher's exact test), Q value = 0.001

Table S62.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 21(10P15.3) CNV 129 60 134 85
DEL PEAK 21(10P15.3) WILD-TYPE 18 34 18 31

Figure S62.  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 = 0.000166 (Fisher's exact test), Q value = 0.099

Table S63.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 21(10P15.3) CNV 112 115 181
DEL PEAK 21(10P15.3) WILD-TYPE 18 51 32

Figure S63.  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 = 1.85e-07 (Fisher's exact test), Q value = 0.00012

Table S64.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 21(10P15.3) CNV 143 154 82
DEL PEAK 21(10P15.3) WILD-TYPE 20 25 48

Figure S64.  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 = 1.45e-14 (Fisher's exact test), Q value = 1e-11

Table S65.  Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 21(10P15.3) CNV 137 201 119
DEL PEAK 21(10P15.3) WILD-TYPE 24 13 69

Figure S65.  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 = 3.17e-07 (Fisher's exact test), Q value = 0.00021

Table S66.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 22(10P13) CNV 131 62 135 82
DEL PEAK 22(10P13) WILD-TYPE 16 32 17 34

Figure S66.  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 = 9.94e-06 (Fisher's exact test), Q value = 0.0062

Table S67.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 22(10P13) CNV 112 113 185
DEL PEAK 22(10P13) WILD-TYPE 18 53 28

Figure S67.  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 = 1.28e-07 (Fisher's exact test), Q value = 8.4e-05

Table S68.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 22(10P13) CNV 145 154 83
DEL PEAK 22(10P13) WILD-TYPE 18 25 47

Figure S68.  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 = 1.11e-15 (Fisher's exact test), Q value = 7.7e-13

Table S69.  Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 22(10P13) CNV 137 203 119
DEL PEAK 22(10P13) WILD-TYPE 24 11 69

Figure S69.  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 S70.  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 S70.  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 = 2.94e-10 (Fisher's exact test), Q value = 2e-07

Table S71.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 23(10P11.23) CNV 130 58 142 86
DEL PEAK 23(10P11.23) WILD-TYPE 17 36 10 30

Figure S71.  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 = 9.54e-07 (Fisher's exact test), Q value = 0.00061

Table S72.  Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 23(10P11.23) CNV 118 114 184
DEL PEAK 23(10P11.23) WILD-TYPE 12 52 29

Figure S72.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.26e-08 (Fisher's exact test), Q value = 8.4e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 23(10P11.23) CNV 145 159 83
DEL PEAK 23(10P11.23) WILD-TYPE 18 20 47

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 = 9.85e-17 (Fisher's exact test), Q value = 6.8e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 23(10P11.23) CNV 138 205 120
DEL PEAK 23(10P11.23) WILD-TYPE 23 9 68

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 = 4.77e-07 (Fisher's exact test), Q value = 0.00031

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 94 152 116
DEL PEAK 24(10Q23.31) CNV 136 72 147 94
DEL PEAK 24(10Q23.31) WILD-TYPE 11 22 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 = 0.000124 (Fisher's exact test), Q value = 0.074

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 24(10Q23.31) CNV 123 132 194
DEL PEAK 24(10Q23.31) WILD-TYPE 7 34 19

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 = 7.23e-05 (Fisher's exact test), Q value = 0.044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 24(10Q23.31) CNV 150 167 101
DEL PEAK 24(10Q23.31) WILD-TYPE 13 12 29

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 = 1.19e-16 (Fisher's exact test), Q value = 8.2e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 24(10Q23.31) CNV 149 212 138
DEL PEAK 24(10Q23.31) WILD-TYPE 12 2 50

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 = 1.16e-07 (Fisher's exact test), Q value = 7.6e-05

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 94 152 116
DEL PEAK 25(10Q26.3) CNV 136 72 148 94
DEL PEAK 25(10Q26.3) WILD-TYPE 11 22 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 = 0.000142 (Fisher's exact test), Q value = 0.085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 25(10Q26.3) CNV 124 133 193
DEL PEAK 25(10Q26.3) WILD-TYPE 6 33 20

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 'CN_CNMF'

P value = 1.89e-13 (Fisher's exact test), Q value = 1.3e-10

Table S81.  Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 25(10Q26.3) CNV 147 211 142
DEL PEAK 25(10Q26.3) WILD-TYPE 14 3 46

Figure S81.  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 = 3.9e-10 (Fisher's exact test), Q value = 2.6e-07

Table S82.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 26(11P15.5) CNV 32 43 13 32
DEL PEAK 26(11P15.5) WILD-TYPE 115 51 139 84

Figure S82.  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 = 1.15e-06 (Fisher's exact test), Q value = 0.00074

Table S83.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 26(11P15.5) CNV 14 60 46
DEL PEAK 26(11P15.5) WILD-TYPE 116 106 167

Figure S83.  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 = 1.5e-06 (Fisher's exact test), Q value = 0.00096

Table S84.  Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 26(11P15.5) CNV 29 32 54
DEL PEAK 26(11P15.5) WILD-TYPE 134 147 76

Figure S84.  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 = 2.1e-15 (Fisher's exact test), Q value = 1.4e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 26(11P15.5) CNV 63 13 51
DEL PEAK 26(11P15.5) WILD-TYPE 98 201 137

Figure S85.  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 S86.  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 S86.  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 = 5.47e-08 (Fisher's exact test), Q value = 3.6e-05

Table S87.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 27(11P11.2) CNV 26 35 10 24
DEL PEAK 27(11P11.2) WILD-TYPE 121 59 142 92

Figure S87.  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 = 0.000192 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 27(11P11.2) CNV 13 47 35
DEL PEAK 27(11P11.2) WILD-TYPE 117 119 178

Figure S88.  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 = 2.44e-05 (Fisher's exact test), Q value = 0.015

Table S89.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 27(11P11.2) CNV 29 20 42
DEL PEAK 27(11P11.2) WILD-TYPE 134 159 88

Figure S89.  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 = 2.18e-13 (Fisher's exact test), Q value = 1.5e-10

Table S90.  Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 27(11P11.2) CNV 55 10 36
DEL PEAK 27(11P11.2) WILD-TYPE 106 204 152

Figure S90.  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 = 2.65e-07 (Fisher's exact test), Q value = 0.00017

Table S91.  Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 28(11Q14.1) CNV 29 34 12 14
DEL PEAK 28(11Q14.1) WILD-TYPE 118 60 140 102

Figure S91.  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 = 1.3e-16 (Fisher's exact test), Q value = 9e-14

Table S92.  Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 28(11Q14.1) CNV 61 10 24
DEL PEAK 28(11Q14.1) WILD-TYPE 100 204 164

Figure S92.  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 = 0.000175 (Fisher's exact test), Q value = 0.1

Table S93.  Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 30(12Q12) CNV 35 15 26
DEL PEAK 30(12Q12) WILD-TYPE 126 199 162

Figure S93.  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 = 0.000124 (Fisher's exact test), Q value = 0.074

Table S94.  Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 31(12Q15) CNV 20 21 7 21
DEL PEAK 31(12Q15) WILD-TYPE 127 73 145 95

Figure S94.  Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 5.4e-07 (Fisher's exact test), Q value = 0.00035

Table S95.  Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 31(12Q15) CNV 40 12 25
DEL PEAK 31(12Q15) WILD-TYPE 121 202 163

Figure S95.  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 = 1.62e-07 (Fisher's exact test), Q value = 0.00011

Table S96.  Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 32(13Q14.2) CNV 81 43 36 55
DEL PEAK 32(13Q14.2) WILD-TYPE 66 51 116 61

Figure S96.  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 = 0.000164 (Fisher's exact test), Q value = 0.097

Table S97.  Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 32(13Q14.2) CNV 35 77 103
DEL PEAK 32(13Q14.2) WILD-TYPE 95 89 110

Figure S97.  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 = 1.1e-15 (Fisher's exact test), Q value = 7.6e-13

Table S98.  Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 32(13Q14.2) CNV 100 46 90
DEL PEAK 32(13Q14.2) WILD-TYPE 61 168 98

Figure S98.  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 = 8.84e-06 (Fisher's exact test), Q value = 0.0055

Table S99.  Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 33(14Q13.1) CNV 55 37 25 46
DEL PEAK 33(14Q13.1) WILD-TYPE 92 57 127 70

Figure S99.  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 = 3.36e-30 (Fisher's exact test), Q value = 2.3e-27

Table S100.  Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 33(14Q13.1) CNV 104 20 51
DEL PEAK 33(14Q13.1) WILD-TYPE 57 194 137

Figure S100.  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 = 1.61e-07 (Fisher's exact test), Q value = 0.00011

Table S101.  Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 34(14Q24.2) CNV 52 40 22 48
DEL PEAK 34(14Q24.2) WILD-TYPE 95 54 130 68

Figure S101.  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 = 7.68e-39 (Fisher's exact test), Q value = 5.4e-36

Table S102.  Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 34(14Q24.2) CNV 107 11 52
DEL PEAK 34(14Q24.2) WILD-TYPE 54 203 136

Figure S102.  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 = 6.25e-09 (Fisher's exact test), Q value = 4.2e-06

Table S103.  Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 35(14Q31.3) CNV 52 36 16 44
DEL PEAK 35(14Q31.3) WILD-TYPE 95 58 136 72

Figure S103.  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 = 8.42e-41 (Fisher's exact test), Q value = 5.9e-38

Table S104.  Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 35(14Q31.3) CNV 102 6 48
DEL PEAK 35(14Q31.3) WILD-TYPE 59 208 140

Figure S104.  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 = 1.46e-06 (Fisher's exact test), Q value = 0.00093

Table S105.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 36(15Q14) CNV 35 37 22 46
DEL PEAK 36(15Q14) WILD-TYPE 112 57 130 70

Figure S105.  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 = 7.39e-08 (Fisher's exact test), Q value = 4.9e-05

Table S106.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 36(15Q14) CNV 16 69 55
DEL PEAK 36(15Q14) WILD-TYPE 114 97 158

Figure S106.  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 = 1.31e-06 (Fisher's exact test), Q value = 0.00084

Table S107.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
DEL PEAK 36(15Q14) CNV 24 52 54
DEL PEAK 36(15Q14) WILD-TYPE 139 127 76

Figure S107.  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 = 4.09e-07 (Fisher's exact test), Q value = 0.00026

Table S108.  Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 36(15Q14) CNV 69 39 43
DEL PEAK 36(15Q14) WILD-TYPE 92 175 145

Figure S108.  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 = 0.21

Table S109.  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 S109.  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 = 2e-10 (Fisher's exact test), Q value = 1.4e-07

Table S110.  Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 39(17P13.2) CNV 43 8 34
DEL PEAK 39(17P13.2) WILD-TYPE 118 206 154

Figure S110.  Get High-res Image Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.000167 (Fisher's exact test), Q value = 0.099

Table S111.  Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 40(17P13.1) CNV 32 27 13 16
DEL PEAK 40(17P13.1) WILD-TYPE 115 67 139 100

Figure S111.  Get High-res Image Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.42e-15 (Fisher's exact test), Q value = 9.8e-13

Table S112.  Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 40(17P13.1) CNV 53 6 36
DEL PEAK 40(17P13.1) WILD-TYPE 108 208 152

Figure S112.  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 = 7.43e-06 (Fisher's exact test), Q value = 0.0047

Table S113.  Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
DEL PEAK 41(17Q11.2) CNV 35 10 12 5
DEL PEAK 41(17Q11.2) WILD-TYPE 112 84 140 111

Figure S113.  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 = 5.32e-07 (Fisher's exact test), Q value = 0.00034

Table S114.  Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 41(17Q11.2) CNV 31 8 32
DEL PEAK 41(17Q11.2) WILD-TYPE 130 206 156

Figure S114.  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 = 1.23e-05 (Fisher's exact test), Q value = 0.0076

Table S115.  Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
DEL PEAK 43(19Q13.41) CNV 12 49 31
DEL PEAK 43(19Q13.41) WILD-TYPE 118 117 182

Figure S115.  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 = 0.000108 (Fisher's exact test), Q value = 0.065

Table S116.  Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 157 72 104
DEL PEAK 44(21Q22.3) CNV 8 32 8 5
DEL PEAK 44(21Q22.3) WILD-TYPE 131 125 64 99

Figure S116.  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 = 6.6e-10 (Fisher's exact test), Q value = 4.4e-07

Table S117.  Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
DEL PEAK 46(XP22.2) CNV 65 29 29
DEL PEAK 46(XP22.2) WILD-TYPE 96 185 159

Figure S117.  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 = 563

  • 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

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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