Correlation between copy number variation genes and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C13X84ZJ
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/C13X84ZJ
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 34 peak regions and 8 molecular subtypes across 158 patients, 56 significant findings detected with Q value < 0.25.

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

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

  • Amp Peak 3(3p14.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 4(3q22.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 5(5q35.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 7(7q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 8(16p11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(17q25.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 1(1p36.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 3(3p22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 4(4q32.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 6(5q15) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 7(5q35.2) cnvs correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 10(6q25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 11(9p21.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 12(11q22.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 13(11q24.2) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • Del Peak 15(14q32.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 16(14q32.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 17(15q15.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • Del Peak 22(22q12.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 23(Xq21.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 24(Xq28) 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 34 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 56 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 7(7q22 1) 0 (0%) 69 2.75e-09
(7.27e-07) 		4.13e-07
(0.000104) 		1.08e-10
(2.87e-08) 		2.64e-08
(6.85e-06) 		0.00385
(0.769) 		0.0787
(1.00) 		0.186
(1.00) 		0.0719
(1.00)
Del Peak 3(3p22 1) 0 (0%) 145 1.26e-05
(0.00311) 		1.98e-07
(5.04e-05) 		0.00157
(0.335) 		3.76e-05
(0.00907) 		0.00815
(1.00) 		0.0732
(1.00) 		0.124
(1.00) 		0.000844
(0.185)
Del Peak 11(9p21 3) 0 (0%) 134 1.68e-06
(0.000423) 		2.99e-08
(7.74e-06) 		1.22e-08
(3.21e-06) 		0.000149
(0.0352) 		0.0474
(1.00) 		0.112
(1.00) 		0.1
(1.00) 		0.00232
(0.485)
Del Peak 12(11q22 3) 0 (0%) 142 0.000468
(0.105) 		0.000577
(0.129) 		0.000441
(0.0996) 		0.000153
(0.0359) 		0.502
(1.00) 		0.123
(1.00) 		0.473
(1.00) 		0.0315
(1.00)
Del Peak 1(1p36 31) 0 (0%) 124 4.51e-11
(1.2e-08) 		0.000877
(0.191) 		3.14e-06
(0.000782) 		0.0166
(1.00) 		0.214
(1.00) 		0.492
(1.00) 		0.701
(1.00) 		0.67
(1.00)
Del Peak 4(4q32 1) 0 (0%) 135 1.57e-08
(4.11e-06) 		1.95e-08
(5.09e-06) 		2.91e-07
(7.39e-05) 		0.00146
(0.315) 		0.11
(1.00) 		0.516
(1.00) 		0.895
(1.00) 		0.0806
(1.00)
Del Peak 7(5q35 2) 0 (0%) 147 0.0171
(1.00) 		5.45e-05
(0.013) 		0.000644
(0.144) 		6.21e-06
(0.00154) 		0.179
(1.00) 		0.0376
(1.00) 		0.57
(1.00) 		0.0979
(1.00)
Del Peak 22(22q12 2) 0 (0%) 118 1.76e-06
(0.000439) 		1.43e-05
(0.00351) 		0.000111
(0.0262) 		0.00354
(0.718) 		0.126
(1.00) 		0.0507
(1.00) 		0.278
(1.00) 		0.498
(1.00)
Del Peak 23(Xq21 31) 0 (0%) 136 8.01e-08
(2.07e-05) 		3.67e-05
(0.00889) 		5.16e-05
(0.0124) 		0.00164
(0.347) 		0.154
(1.00) 		0.141
(1.00) 		0.151
(1.00) 		0.0087
(1.00)
Amp Peak 3(3p14 1) 0 (0%) 115 1.3e-18
(3.53e-16) 		0.0179
(1.00) 		2.97e-05
(0.00722) 		0.00357
(0.722) 		0.00305
(0.632) 		0.202
(1.00) 		0.365
(1.00) 		0.0292
(1.00)
Amp Peak 4(3q22 3) 0 (0%) 105 1.67e-19
(4.54e-17) 		0.0484
(1.00) 		0.000169
(0.0394) 		0.0596
(1.00) 		0.0231
(1.00) 		0.268
(1.00) 		0.324
(1.00) 		0.0449
(1.00)
Amp Peak 5(5q35 2) 0 (0%) 134 1.92e-05
(0.00471) 		0.0226
(1.00) 		0.0703
(1.00) 		0.000813
(0.18) 		0.033
(1.00) 		0.218
(1.00) 		0.0706
(1.00) 		0.394
(1.00)
Amp Peak 9(17q25 2) 0 (0%) 46 2.17e-05
(0.0053) 		0.0343
(1.00) 		0.000751
(0.167) 		0.0037
(0.743) 		0.642
(1.00) 		0.869
(1.00) 		0.553
(1.00) 		0.602
(1.00)
Del Peak 10(6q25 3) 0 (0%) 141 0.000426
(0.0968) 		0.000179
(0.0415) 		0.0142
(1.00) 		0.0852
(1.00) 		0.764
(1.00) 		0.296
(1.00) 		0.774
(1.00) 		0.134
(1.00)
Del Peak 13(11q24 2) 0 (0%) 141 0.00322
(0.658) 		0.000179
(0.0415) 		0.00174
(0.366) 		0.00114
(0.248) 		0.279
(1.00) 		0.0646
(1.00) 		0.619
(1.00) 		0.0519
(1.00)
Del Peak 15(14q32 2) 0 (0%) 123 5.24e-13
(1.4e-10) 		0.0508
(1.00) 		0.000837
(0.184) 		0.0147
(1.00) 		0.901
(1.00) 		0.354
(1.00) 		0.855
(1.00) 		0.346
(1.00)
Del Peak 16(14q32 2) 0 (0%) 123 1.29e-14
(3.49e-12) 		0.0141
(1.00) 		0.000376
(0.086) 		0.00519
(1.00) 		0.901
(1.00) 		0.354
(1.00) 		0.855
(1.00) 		0.346
(1.00)
Del Peak 17(15q15 1) 0 (0%) 137 5.22e-05
(0.0125) 		0.00311
(0.64) 		0.000415
(0.0946) 		0.0293
(1.00) 		0.277
(1.00) 		0.223
(1.00) 		0.4
(1.00) 		0.0758
(1.00)
Amp Peak 1(2q32 2) 0 (0%) 124 1.75e-07
(4.51e-05) 		0.0102
(1.00) 		0.058
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.83
(1.00) 		0.293
(1.00) 		0.327
(1.00)
Amp Peak 2(2q32 2) 0 (0%) 124 1.75e-07
(4.51e-05) 		0.0102
(1.00) 		0.058
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.83
(1.00) 		0.293
(1.00) 		0.327
(1.00)
Amp Peak 8(16p11 2) 0 (0%) 73 2.1e-12
(5.62e-10) 		0.431
(1.00) 		0.0149
(1.00) 		0.0117
(1.00) 		0.0896
(1.00) 		0.0546
(1.00) 		0.0261
(1.00) 		0.0538
(1.00)
Del Peak 6(5q15) 0 (0%) 147 0.0628
(1.00) 		0.00811
(1.00) 		0.015
(1.00) 		0.000285
(0.0656) 		0.732
(1.00) 		0.0376
(1.00) 		0.656
(1.00) 		0.056
(1.00)
Del Peak 14(14q11 2) 0 (0%) 123 2.48e-13
(6.67e-11) 		0.0813
(1.00) 		0.00492
(0.965) 		0.0433
(1.00) 		0.917
(1.00) 		0.527
(1.00) 		0.855
(1.00) 		0.346
(1.00)
Del Peak 19(19p13 3) 0 (0%) 142 0.000168
(0.0393) 		0.00731
(1.00) 		0.056
(1.00) 		0.0148
(1.00) 		0.801
(1.00) 		0.115
(1.00) 		0.258
(1.00) 		0.141
(1.00)
Del Peak 24(Xq28) 0 (0%) 137 3.2e-07
(8.11e-05) 		0.00123
(0.266) 		0.00151
(0.323) 		0.0185
(1.00) 		0.277
(1.00) 		0.519
(1.00) 		0.451
(1.00) 		0.0519
(1.00)
Amp Peak 6(6p12 3) 0 (0%) 152 0.2
(1.00) 		0.0204
(1.00) 		0.556
(1.00) 		0.152
(1.00) 		0.534
(1.00) 		0.386
(1.00) 		0.32
(1.00) 		0.516
(1.00)
Amp Peak 10(19p13 2) 0 (0%) 142 0.705
(1.00) 		0.0407
(1.00) 		0.0497
(1.00) 		0.321
(1.00) 		0.981
(1.00) 		0.889
(1.00) 		0.927
(1.00) 		0.368
(1.00)
Del Peak 2(2q36 3) 0 (0%) 151 0.0183
(1.00) 		0.00312
(0.64) 		0.497
(1.00) 		0.138
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.257
(1.00) 		0.375
(1.00)
Del Peak 5(5p14 2) 0 (0%) 147 0.0196
(1.00) 		0.00811
(1.00) 		0.15
(1.00) 		0.00585
(1.00) 		0.228
(1.00) 		0.427
(1.00) 		0.57
(1.00) 		0.567
(1.00)
Del Peak 8(6p12 3) 0 (0%) 143 0.0043
(0.855) 		0.00301
(0.626) 		0.177
(1.00) 		0.448
(1.00) 		0.766
(1.00) 		0.933
(1.00) 		1
(1.00) 		0.361
(1.00)
Del Peak 9(6q22 31) 0 (0%) 142 0.00747
(1.00) 		0.0043
(0.855) 		0.0084
(1.00) 		0.0527
(1.00) 		0.401
(1.00) 		0.259
(1.00) 		0.33
(1.00) 		0.0496
(1.00)
Del Peak 18(16q24 1) 0 (0%) 151 0.0729
(1.00) 		0.00448
(0.882) 		0.0352
(1.00) 		0.00212
(0.445) 		0.102
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.181
(1.00)
Del Peak 20(19q13 2) 0 (0%) 144 0.00962
(1.00) 		0.0176
(1.00) 		0.0147
(1.00) 		0.00832
(1.00) 		0.133
(1.00) 		0.383
(1.00) 		0.034
(1.00) 		0.408
(1.00)
Del Peak 21(19q13 42) 0 (0%) 143 0.0185
(1.00) 		0.029
(1.00) 		0.0454
(1.00) 		0.0311
(1.00) 		0.537
(1.00) 		0.383
(1.00) 		0.152
(1.00) 		0.9
(1.00)
'Amp Peak 1(2q32.2)' versus 'CN_CNMF'

P value = 1.75e-07 (Fisher's exact test), Q value = 4.5e-05

Table S1.  Gene #1: 'Amp Peak 1(2q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 1(2Q32.2) CNV 12 20 2
AMP PEAK 1(2Q32.2) WILD-TYPE 24 32 68

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(2q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.75e-07 (Fisher's exact test), Q value = 4.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 2(2Q32.2) CNV 12 20 2
AMP PEAK 2(2Q32.2) WILD-TYPE 24 32 68

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

'Amp Peak 3(3p14.1)' versus 'CN_CNMF'

P value = 1.3e-18 (Fisher's exact test), Q value = 3.5e-16

Table S3.  Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 3(3P14.1) CNV 31 8 4
AMP PEAK 3(3P14.1) WILD-TYPE 5 44 66

Figure S3.  Get High-res Image Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(3p14.1)' versus 'MRNASEQ_CNMF'

P value = 2.97e-05 (Fisher's exact test), Q value = 0.0072

Table S4.  Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
AMP PEAK 3(3P14.1) CNV 3 18 11 7
AMP PEAK 3(3P14.1) WILD-TYPE 48 24 14 16

Figure S4.  Get High-res Image Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 4(3q22.3)' versus 'CN_CNMF'

P value = 1.67e-19 (Fisher's exact test), Q value = 4.5e-17

Table S5.  Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 4(3Q22.3) CNV 34 13 6
AMP PEAK 4(3Q22.3) WILD-TYPE 2 39 64

Figure S5.  Get High-res Image Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q22.3)' versus 'MRNASEQ_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.039

Table S6.  Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
AMP PEAK 4(3Q22.3) CNV 6 18 12 12
AMP PEAK 4(3Q22.3) WILD-TYPE 45 24 13 11

Figure S6.  Get High-res Image Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 5(5q35.2)' versus 'CN_CNMF'

P value = 1.92e-05 (Fisher's exact test), Q value = 0.0047

Table S7.  Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 5(5Q35.2) CNV 1 18 5
AMP PEAK 5(5Q35.2) WILD-TYPE 35 34 65

Figure S7.  Get High-res Image Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(5q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000813 (Fisher's exact test), Q value = 0.18

Table S8.  Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
AMP PEAK 5(5Q35.2) CNV 1 7 15
AMP PEAK 5(5Q35.2) WILD-TYPE 22 67 29

Figure S8.  Get High-res Image Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(7q22.1)' versus 'CN_CNMF'

P value = 2.75e-09 (Fisher's exact test), Q value = 7.3e-07

Table S9.  Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 7(7Q22.1) CNV 34 16 39
AMP PEAK 7(7Q22.1) WILD-TYPE 2 36 31

Figure S9.  Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(7q22.1)' versus 'METHLYATION_CNMF'

P value = 4.13e-07 (Fisher's exact test), Q value = 1e-04

Table S10.  Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
AMP PEAK 7(7Q22.1) CNV 17 12 49
AMP PEAK 7(7Q22.1) WILD-TYPE 20 31 13

Figure S10.  Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 7(7q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.08e-10 (Fisher's exact test), Q value = 2.9e-08

Table S11.  Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
AMP PEAK 7(7Q22.1) CNV 14 38 11 19
AMP PEAK 7(7Q22.1) WILD-TYPE 37 4 14 4

Figure S11.  Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 7(7q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-08 (Fisher's exact test), Q value = 6.9e-06

Table S12.  Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
AMP PEAK 7(7Q22.1) CNV 8 60 14
AMP PEAK 7(7Q22.1) WILD-TYPE 15 14 30

Figure S12.  Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(16p11.2)' versus 'CN_CNMF'

P value = 2.1e-12 (Fisher's exact test), Q value = 5.6e-10

Table S13.  Gene #8: 'Amp Peak 8(16p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 8(16P11.2) CNV 36 26 23
AMP PEAK 8(16P11.2) WILD-TYPE 0 26 47

Figure S13.  Get High-res Image Gene #8: 'Amp Peak 8(16p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(17q25.2)' versus 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.0053

Table S14.  Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
AMP PEAK 9(17Q25.2) CNV 35 29 48
AMP PEAK 9(17Q25.2) WILD-TYPE 1 23 22

Figure S14.  Get High-res Image Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(17q25.2)' versus 'MRNASEQ_CNMF'

P value = 0.000751 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
AMP PEAK 9(17Q25.2) CNV 27 38 19 17
AMP PEAK 9(17Q25.2) WILD-TYPE 24 4 6 6

Figure S15.  Get High-res Image Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'CN_CNMF'

P value = 4.51e-11 (Fisher's exact test), Q value = 1.2e-08

Table S16.  Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 1(1P36.31) CNV 1 28 5
DEL PEAK 1(1P36.31) WILD-TYPE 35 24 65

Figure S16.  Get High-res Image Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.31)' versus 'METHLYATION_CNMF'

P value = 0.000877 (Fisher's exact test), Q value = 0.19

Table S17.  Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 1(1P36.31) CNV 6 18 7
DEL PEAK 1(1P36.31) WILD-TYPE 31 25 55

Figure S17.  Get High-res Image Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CNMF'

P value = 3.14e-06 (Fisher's exact test), Q value = 0.00078

Table S18.  Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 1(1P36.31) CNV 22 4 2 0
DEL PEAK 1(1P36.31) WILD-TYPE 29 38 23 23

Figure S18.  Get High-res Image Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 3(3p22.1)' versus 'CN_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0031

Table S19.  Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 3(3P22.1) CNV 0 12 1
DEL PEAK 3(3P22.1) WILD-TYPE 36 40 69

Figure S19.  Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 3(3p22.1)' versus 'METHLYATION_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 5e-05

Table S20.  Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 3(3P22.1) CNV 0 12 0
DEL PEAK 3(3P22.1) WILD-TYPE 37 31 62

Figure S20.  Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 3(3p22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.0091

Table S21.  Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
DEL PEAK 3(3P22.1) CNV 2 0 10
DEL PEAK 3(3P22.1) WILD-TYPE 21 74 34

Figure S21.  Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(3p22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000844 (Fisher's exact test), Q value = 0.18

Table S22.  Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 52 64
DEL PEAK 3(3P22.1) CNV 4 5 1
DEL PEAK 3(3P22.1) WILD-TYPE 6 47 63

Figure S22.  Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(4q32.1)' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 4.1e-06

Table S23.  Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 4(4Q32.1) CNV 0 20 3
DEL PEAK 4(4Q32.1) WILD-TYPE 36 32 67

Figure S23.  Get High-res Image Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 4(4q32.1)' versus 'METHLYATION_CNMF'

P value = 1.95e-08 (Fisher's exact test), Q value = 5.1e-06

Table S24.  Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 4(4Q32.1) CNV 1 17 1
DEL PEAK 4(4Q32.1) WILD-TYPE 36 26 61

Figure S24.  Get High-res Image Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 4(4q32.1)' versus 'MRNASEQ_CNMF'

P value = 2.91e-07 (Fisher's exact test), Q value = 7.4e-05

Table S25.  Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 4(4Q32.1) CNV 18 1 0 0
DEL PEAK 4(4Q32.1) WILD-TYPE 33 41 25 23

Figure S25.  Get High-res Image Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 6(5q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.066

Table S26.  Gene #16: 'Del Peak 6(5q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
DEL PEAK 6(5Q15) CNV 6 1 1
DEL PEAK 6(5Q15) WILD-TYPE 17 73 43

Figure S26.  Get High-res Image Gene #16: 'Del Peak 6(5q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q35.2)' versus 'METHLYATION_CNMF'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.013

Table S27.  Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 7(5Q35.2) CNV 1 9 0
DEL PEAK 7(5Q35.2) WILD-TYPE 36 34 62

Figure S27.  Get High-res Image Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(5q35.2)' versus 'MRNASEQ_CNMF'

P value = 0.000644 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 7(5Q35.2) CNV 9 0 0 0
DEL PEAK 7(5Q35.2) WILD-TYPE 42 42 25 23

Figure S28.  Get High-res Image Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 7(5q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.21e-06 (Fisher's exact test), Q value = 0.0015

Table S29.  Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
DEL PEAK 7(5Q35.2) CNV 7 0 2
DEL PEAK 7(5Q35.2) WILD-TYPE 16 74 42

Figure S29.  Get High-res Image Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q25.3)' versus 'CN_CNMF'

P value = 0.000426 (Fisher's exact test), Q value = 0.097

Table S30.  Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 10(6Q25.3) CNV 1 13 3
DEL PEAK 10(6Q25.3) WILD-TYPE 35 39 67

Figure S30.  Get High-res Image Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(6q25.3)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.041

Table S31.  Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 10(6Q25.3) CNV 2 12 2
DEL PEAK 10(6Q25.3) WILD-TYPE 35 31 60

Figure S31.  Get High-res Image Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(9p21.3)' versus 'CN_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00042

Table S32.  Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 11(9P21.3) CNV 1 19 4
DEL PEAK 11(9P21.3) WILD-TYPE 35 33 66

Figure S32.  Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.99e-08 (Fisher's exact test), Q value = 7.7e-06

Table S33.  Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 11(9P21.3) CNV 4 17 0
DEL PEAK 11(9P21.3) WILD-TYPE 33 26 62

Figure S33.  Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 1.22e-08 (Fisher's exact test), Q value = 3.2e-06

Table S34.  Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 11(9P21.3) CNV 20 0 1 0
DEL PEAK 11(9P21.3) WILD-TYPE 31 42 24 23

Figure S34.  Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 11(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000149 (Fisher's exact test), Q value = 0.035

Table S35.  Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
DEL PEAK 11(9P21.3) CNV 8 3 10
DEL PEAK 11(9P21.3) WILD-TYPE 15 71 34

Figure S35.  Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(11q22.3)' versus 'CN_CNMF'

P value = 0.000468 (Fisher's exact test), Q value = 0.11

Table S36.  Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 12(11Q22.3) CNV 0 12 4
DEL PEAK 12(11Q22.3) WILD-TYPE 36 40 66

Figure S36.  Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(11q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000577 (Fisher's exact test), Q value = 0.13

Table S37.  Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 12(11Q22.3) CNV 2 11 2
DEL PEAK 12(11Q22.3) WILD-TYPE 35 32 60

Figure S37.  Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(11q22.3)' versus 'MRNASEQ_CNMF'

P value = 0.000441 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 12(11Q22.3) CNV 13 1 1 0
DEL PEAK 12(11Q22.3) WILD-TYPE 38 41 24 23

Figure S38.  Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 12(11q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.036

Table S39.  Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
DEL PEAK 12(11Q22.3) CNV 6 1 8
DEL PEAK 12(11Q22.3) WILD-TYPE 17 73 36

Figure S39.  Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(11q24.2)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.041

Table S40.  Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 13(11Q24.2) CNV 2 12 2
DEL PEAK 13(11Q24.2) WILD-TYPE 35 31 60

Figure S40.  Get High-res Image Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(11q24.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.25

Table S41.  Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
DEL PEAK 13(11Q24.2) CNV 5 2 9
DEL PEAK 13(11Q24.2) WILD-TYPE 18 72 35

Figure S41.  Get High-res Image Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.48e-13 (Fisher's exact test), Q value = 6.7e-11

Table S42.  Gene #24: 'Del Peak 14(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 14(14Q11.2) CNV 3 30 2
DEL PEAK 14(14Q11.2) WILD-TYPE 33 22 68

Figure S42.  Get High-res Image Gene #24: 'Del Peak 14(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(14q32.2)' versus 'CN_CNMF'

P value = 5.24e-13 (Fisher's exact test), Q value = 1.4e-10

Table S43.  Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 15(14Q32.2) CNV 2 30 3
DEL PEAK 15(14Q32.2) WILD-TYPE 34 22 67

Figure S43.  Get High-res Image Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(14q32.2)' versus 'MRNASEQ_CNMF'

P value = 0.000837 (Fisher's exact test), Q value = 0.18

Table S44.  Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 15(14Q32.2) CNV 19 2 5 3
DEL PEAK 15(14Q32.2) WILD-TYPE 32 40 20 20

Figure S44.  Get High-res Image Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 16(14q32.2)' versus 'CN_CNMF'

P value = 1.29e-14 (Fisher's exact test), Q value = 3.5e-12

Table S45.  Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 16(14Q32.2) CNV 2 31 2
DEL PEAK 16(14Q32.2) WILD-TYPE 34 21 68

Figure S45.  Get High-res Image Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(14q32.2)' versus 'MRNASEQ_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.086

Table S46.  Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 16(14Q32.2) CNV 20 2 5 3
DEL PEAK 16(14Q32.2) WILD-TYPE 31 40 20 20

Figure S46.  Get High-res Image Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 17(15q15.1)' versus 'CN_CNMF'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.012

Table S47.  Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 17(15Q15.1) CNV 2 16 3
DEL PEAK 17(15Q15.1) WILD-TYPE 34 36 67

Figure S47.  Get High-res Image Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(15q15.1)' versus 'MRNASEQ_CNMF'

P value = 0.000415 (Fisher's exact test), Q value = 0.095

Table S48.  Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 17(15Q15.1) CNV 14 1 3 0
DEL PEAK 17(15Q15.1) WILD-TYPE 37 41 22 23

Figure S48.  Get High-res Image Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 0.000168 (Fisher's exact test), Q value = 0.039

Table S49.  Gene #29: 'Del Peak 19(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 19(19P13.3) CNV 1 13 2
DEL PEAK 19(19P13.3) WILD-TYPE 35 39 68

Figure S49.  Get High-res Image Gene #29: 'Del Peak 19(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(22q12.2)' versus 'CN_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.00044

Table S50.  Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 22(22Q12.2) CNV 2 26 12
DEL PEAK 22(22Q12.2) WILD-TYPE 34 26 58

Figure S50.  Get High-res Image Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(22q12.2)' versus 'METHLYATION_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0035

Table S51.  Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 22(22Q12.2) CNV 5 23 9
DEL PEAK 22(22Q12.2) WILD-TYPE 32 20 53

Figure S51.  Get High-res Image Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 22(22q12.2)' versus 'MRNASEQ_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.026

Table S52.  Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 22(22Q12.2) CNV 23 5 5 1
DEL PEAK 22(22Q12.2) WILD-TYPE 28 37 20 22

Figure S52.  Get High-res Image Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 23(Xq21.31)' versus 'CN_CNMF'

P value = 8.01e-08 (Fisher's exact test), Q value = 2.1e-05

Table S53.  Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 23(XQ21.31) CNV 1 19 2
DEL PEAK 23(XQ21.31) WILD-TYPE 35 33 68

Figure S53.  Get High-res Image Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(Xq21.31)' versus 'METHLYATION_CNMF'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.0089

Table S54.  Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
DEL PEAK 23(XQ21.31) CNV 2 15 3
DEL PEAK 23(XQ21.31) WILD-TYPE 35 28 59

Figure S54.  Get High-res Image Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 23(Xq21.31)' versus 'MRNASEQ_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.012

Table S55.  Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
DEL PEAK 23(XQ21.31) CNV 15 1 1 0
DEL PEAK 23(XQ21.31) WILD-TYPE 36 41 24 23

Figure S55.  Get High-res Image Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 24(Xq28)' versus 'CN_CNMF'

P value = 3.2e-07 (Fisher's exact test), Q value = 8.1e-05

Table S56.  Gene #34: 'Del Peak 24(Xq28)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
DEL PEAK 24(XQ28) CNV 1 18 2
DEL PEAK 24(XQ28) WILD-TYPE 35 34 68

Figure S56.  Get High-res Image Gene #34: 'Del Peak 24(Xq28)' versus Molecular Subtype #1: '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 = KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 158

  • Number of copy number variation regions = 34

  • Number of molecular subtypes = 8

  • Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

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