Correlation between copy number variation genes and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1ZS2TGN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZS2TGN
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 29 peak regions and 8 molecular subtypes across 497 patients, 53 significant findings detected with Q value < 0.25.

  • Amp Peak 1(Xq22.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 2(2p23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 3(2q35) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Del Peak 9(8p23.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(8p22) cnvs correlated to 'CN_CNMF'.

  • Del Peak 11(8p12) cnvs correlated to 'CN_CNMF'.

  • Del Peak 12(8q24.22) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 13(9q21.13) cnvs correlated to 'CN_CNMF'.

  • Del Peak 14(10q21.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 15(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 16(11p15.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 17(13q12.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 18(13q21.31) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 19(15q25.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(18p11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 24(18q22.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 25(19p13.2) cnvs correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 28(21q21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 29(22q13.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 30(22q13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 31(22q13.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 32(22q13.32) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 29 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Del Peak 2(2p23 1) 0 (0%) 485 3.57e-10
(7.57e-08) 		2.82e-05
(0.00532) 		0.772
(1.00) 		0.0179
(1.00) 		3.88e-06
(0.00076) 		5.46e-06
(0.00107) 		1.27e-06
(0.000258) 		3.68e-07
(7.57e-05)
Del Peak 3(2q35) 0 (0%) 486 5.96e-12
(1.27e-09) 		2.39e-05
(0.00455) 		0.562
(1.00) 		0.00287
(0.443) 		1.59e-05
(0.00308) 		3.43e-06
(0.000675) 		1.27e-06
(0.000258) 		3.68e-07
(7.57e-05)
Del Peak 12(8q24 22) 0 (0%) 490 4.61e-05
(0.00853) 		0.00241
(0.374) 		0.837
(1.00) 		0.0549
(1.00) 		0.00144
(0.239) 		0.00065
(0.113) 		0.000192
(0.0344) 		8.85e-05
(0.0159)
Del Peak 32(22q13 32) 0 (0%) 410 1.16e-89
(2.5e-87) 		3.67e-05
(0.00683) 		0.205
(1.00) 		0.0795
(1.00) 		9.86e-09
(2.08e-06) 		1.04e-06
(0.000212) 		0.00204
(0.326) 		0.00123
(0.21)
Del Peak 29(22q13 1) 0 (0%) 411 1.42e-91
(3.09e-89) 		7.1e-05
(0.013) 		0.205
(1.00) 		0.0795
(1.00) 		1.86e-08
(3.9e-06) 		1.99e-06
(0.000398) 		0.00343
(0.521) 		0.0023
(0.365)
Del Peak 30(22q13 2) 0 (0%) 411 1.42e-91
(3.09e-89) 		7.1e-05
(0.013) 		0.205
(1.00) 		0.0795
(1.00) 		1.86e-08
(3.9e-06) 		1.99e-06
(0.000398) 		0.00343
(0.521) 		0.0023
(0.365)
Del Peak 31(22q13 31) 0 (0%) 411 1.42e-91
(3.09e-89) 		7.1e-05
(0.013) 		0.205
(1.00) 		0.0795
(1.00) 		1.86e-08
(3.9e-06) 		1.99e-06
(0.000398) 		0.00343
(0.521) 		0.0023
(0.365)
Del Peak 15(10q23 31) 0 (0%) 486 3.37e-05
(0.00633) 		0.0182
(1.00) 		0.0336
(1.00) 		0.0641
(1.00) 		0.0077
(1.00) 		0.00142
(0.238) 		0.042
(1.00) 		0.0144
(1.00)
Del Peak 17(13q12 3) 0 (0%) 482 0.0227
(1.00) 		0.00119
(0.205) 		0.388
(1.00) 		0.44
(1.00) 		0.00143
(0.239) 		0.00489
(0.724) 		0.0574
(1.00) 		0.0235
(1.00)
Del Peak 25(19p13 2) 0 (0%) 491 0.00453
(0.675) 		0.00165
(0.271) 		0.682
(1.00) 		0.256
(1.00) 		0.00491
(0.724) 		0.00175
(0.286) 		0.000664
(0.115) 		0.000342
(0.0606)
Amp Peak 1(Xq22 3) 0 (0%) 481 1.63e-06
(0.000328) 		0.491
(1.00) 		0.856
(1.00) 		0.129
(1.00) 		0.603
(1.00) 		0.562
(1.00) 		0.0849
(1.00) 		0.0398
(1.00)
Del Peak 6(6q22 31) 0 (0%) 491 0.00036
(0.0634) 		0.00545
(0.774) 		0.0379
(1.00) 		0.798
(1.00) 		0.0147
(1.00) 		0.00587
(0.828) 		0.0138
(1.00) 		0.0075
(1.00)
Del Peak 9(8p23 2) 0 (0%) 493 1.85e-05
(0.00356) 		0.047
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.729)
Del Peak 10(8p22) 0 (0%) 493 1.85e-05
(0.00356) 		0.047
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.729)
Del Peak 11(8p12) 0 (0%) 493 1.85e-05
(0.00356) 		0.047
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.729)
Del Peak 13(9q21 13) 0 (0%) 474 1.17e-13
(2.5e-11) 		0.114
(1.00) 		0.182
(1.00) 		0.0136
(1.00) 		0.151
(1.00) 		0.101
(1.00) 		0.0394
(1.00) 		0.0293
(1.00)
Del Peak 14(10q21 2) 0 (0%) 486 0.000558
(0.0976) 		0.066
(1.00) 		0.162
(1.00) 		1
(1.00) 		0.023
(1.00) 		0.00489
(0.724) 		0.436
(1.00) 		0.563
(1.00)
Del Peak 16(11p15 1) 0 (0%) 490 7.74e-08
(1.6e-05) 		0.00947
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.0148
(1.00) 		0.0419
(1.00) 		0.0399
(1.00) 		0.0333
(1.00)
Del Peak 18(13q21 31) 0 (0%) 480 0.0272
(1.00) 		0.0297
(1.00) 		0.0908
(1.00) 		1
(1.00) 		0.00176
(0.286) 		3.48e-05
(0.0065) 		0.00652
(0.913) 		0.00169
(0.277)
Del Peak 19(15q25 3) 0 (0%) 489 0.00133
(0.226) 		0.013
(1.00) 		0.444
(1.00) 		0.0817
(1.00) 		0.027
(1.00) 		0.014
(1.00) 		0.00301
(0.461) 		0.00229
(0.365)
Del Peak 23(18p11 21) 0 (0%) 493 0.000204
(0.0364) 		0.19
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.22
(1.00) 		0.12
(1.00) 		0.0743
(1.00) 		0.0671
(1.00)
Del Peak 24(18q22 2) 0 (0%) 492 0.00134
(0.226) 		0.0613
(1.00) 		1
(1.00) 		0.256
(1.00) 		0.102
(1.00) 		0.0405
(1.00) 		0.0261
(1.00) 		0.0138
(1.00)
Del Peak 28(21q21 1) 0 (0%) 488 5.72e-05
(0.0105) 		0.319
(1.00) 		0.147
(1.00) 		0.206
(1.00) 		0.252
(1.00) 		0.378
(1.00) 		0.0757
(1.00) 		0.0732
(1.00)
Del Peak 4(5p15 2) 0 (0%) 493 0.348
(1.00) 		0.371
(1.00)
Del Peak 8(7q34) 0 (0%) 493 0.641
(1.00) 		0.799
(1.00) 		0.748
(1.00) 		0.531
(1.00) 		0.689
(1.00) 		0.829
(1.00)
Del Peak 21(16q23 3) 0 (0%) 491 0.0484
(1.00) 		0.125
(1.00) 		0.444
(1.00) 		0.103
(1.00) 		0.138
(1.00) 		0.29
(1.00) 		0.223
(1.00) 		0.292
(1.00)
Del Peak 22(17p13 1) 0 (0%) 489 0.00181
(0.291) 		0.884
(1.00) 		1
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.594
(1.00) 		0.364
(1.00) 		0.313
(1.00)
Del Peak 33(Xq22 1) 0 (0%) 491 0.0733
(1.00) 		0.433
(1.00) 		0.0993
(1.00) 		0.12
(1.00) 		0.632
(1.00) 		0.309
(1.00) 		0.453
(1.00) 		0.39
(1.00)
Del Peak 34(Xq22 3) 0 (0%) 493 0.0539
(1.00) 		0.047
(1.00) 		0.281
(1.00) 		0.369
(1.00) 		0.0865
(1.00) 		0.12
(1.00) 		0.0743
(1.00) 		0.0671
(1.00)
'Amp Peak 1(Xq22.3)' versus 'CN_CNMF'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.00033

Table S1.  Gene #1: 'Amp Peak 1(Xq22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
AMP PEAK 1(XQ22.3) CNV 8 8 0
AMP PEAK 1(XQ22.3) WILD-TYPE 26 377 78

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(Xq22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(2p23.1)' versus 'CN_CNMF'

P value = 3.57e-10 (Fisher's exact test), Q value = 7.6e-08

Table S2.  Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 2(2P23.1) CNV 9 1 2
DEL PEAK 2(2P23.1) WILD-TYPE 25 384 76

Figure S2.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(2p23.1)' versus 'METHLYATION_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.0053

Table S3.  Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 2(2P23.1) CNV 10 2 0
DEL PEAK 2(2P23.1) WILD-TYPE 139 72 274

Figure S3.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 2(2p23.1)' versus 'MRNASEQ_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.00076

Table S4.  Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 2(2P23.1) CNV 12 0 0 0
DEL PEAK 2(2P23.1) WILD-TYPE 128 56 106 156

Figure S4.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 2(2p23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.46e-06 (Fisher's exact test), Q value = 0.0011

Table S5.  Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 2(2P23.1) CNV 11 0 1 0
DEL PEAK 2(2P23.1) WILD-TYPE 112 191 52 91

Figure S5.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(2p23.1)' versus 'MIRSEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00026

Table S6.  Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
DEL PEAK 2(2P23.1) CNV 11 0 0
DEL PEAK 2(2P23.1) WILD-TYPE 116 148 149

Figure S6.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 2(2p23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.68e-07 (Fisher's exact test), Q value = 7.6e-05

Table S7.  Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
DEL PEAK 2(2P23.1) CNV 11 0 0
DEL PEAK 2(2P23.1) WILD-TYPE 103 168 142

Figure S7.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q35)' versus 'CN_CNMF'

P value = 5.96e-12 (Fisher's exact test), Q value = 1.3e-09

Table S8.  Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 3(2Q35) CNV 10 1 0
DEL PEAK 3(2Q35) WILD-TYPE 24 384 78

Figure S8.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 3(2q35)' versus 'METHLYATION_CNMF'

P value = 2.39e-05 (Fisher's exact test), Q value = 0.0045

Table S9.  Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 3(2Q35) CNV 10 1 0
DEL PEAK 3(2Q35) WILD-TYPE 139 73 274

Figure S9.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 3(2q35)' versus 'MRNASEQ_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0031

Table S10.  Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 3(2Q35) CNV 11 0 0 0
DEL PEAK 3(2Q35) WILD-TYPE 129 56 106 156

Figure S10.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 3(2q35)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.43e-06 (Fisher's exact test), Q value = 0.00067

Table S11.  Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 3(2Q35) CNV 11 0 0 0
DEL PEAK 3(2Q35) WILD-TYPE 112 191 53 91

Figure S11.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q35)' versus 'MIRSEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00026

Table S12.  Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
DEL PEAK 3(2Q35) CNV 11 0 0
DEL PEAK 3(2Q35) WILD-TYPE 116 148 149

Figure S12.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 3(2q35)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.68e-07 (Fisher's exact test), Q value = 7.6e-05

Table S13.  Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
DEL PEAK 3(2Q35) CNV 11 0 0
DEL PEAK 3(2Q35) WILD-TYPE 103 168 142

Figure S13.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.00036 (Fisher's exact test), Q value = 0.063

Table S14.  Gene #5: 'Del Peak 6(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 6(6Q22.31) CNV 4 2 0
DEL PEAK 6(6Q22.31) WILD-TYPE 30 383 78

Figure S14.  Get High-res Image Gene #5: 'Del Peak 6(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(8p23.2)' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0036

Table S15.  Gene #7: 'Del Peak 9(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 9(8P23.2) CNV 4 0 0
DEL PEAK 9(8P23.2) WILD-TYPE 30 385 78

Figure S15.  Get High-res Image Gene #7: 'Del Peak 9(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(8p22)' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0036

Table S16.  Gene #8: 'Del Peak 10(8p22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 10(8P22) CNV 4 0 0
DEL PEAK 10(8P22) WILD-TYPE 30 385 78

Figure S16.  Get High-res Image Gene #8: 'Del Peak 10(8p22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(8p12)' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0036

Table S17.  Gene #9: 'Del Peak 11(8p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 11(8P12) CNV 4 0 0
DEL PEAK 11(8P12) WILD-TYPE 30 385 78

Figure S17.  Get High-res Image Gene #9: 'Del Peak 11(8p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8q24.22)' versus 'CN_CNMF'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.0085

Table S18.  Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 12(8Q24.22) CNV 5 2 0
DEL PEAK 12(8Q24.22) WILD-TYPE 29 383 78

Figure S18.  Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8q24.22)' versus 'MRNASEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.24

Table S19.  Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 12(8Q24.22) CNV 7 0 0 0
DEL PEAK 12(8Q24.22) WILD-TYPE 133 56 106 156

Figure S19.  Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 12(8q24.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.11

Table S20.  Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 12(8Q24.22) CNV 7 0 0 0
DEL PEAK 12(8Q24.22) WILD-TYPE 116 191 53 91

Figure S20.  Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(8q24.22)' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.034

Table S21.  Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
DEL PEAK 12(8Q24.22) CNV 7 0 0
DEL PEAK 12(8Q24.22) WILD-TYPE 120 148 149

Figure S21.  Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 12(8q24.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.85e-05 (Fisher's exact test), Q value = 0.016

Table S22.  Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
DEL PEAK 12(8Q24.22) CNV 7 0 0
DEL PEAK 12(8Q24.22) WILD-TYPE 107 168 142

Figure S22.  Get High-res Image Gene #10: 'Del Peak 12(8q24.22)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(9q21.13)' versus 'CN_CNMF'

P value = 1.17e-13 (Fisher's exact test), Q value = 2.5e-11

Table S23.  Gene #11: 'Del Peak 13(9q21.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 13(9Q21.13) CNV 15 7 1
DEL PEAK 13(9Q21.13) WILD-TYPE 19 378 77

Figure S23.  Get High-res Image Gene #11: 'Del Peak 13(9q21.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(10q21.2)' versus 'CN_CNMF'

P value = 0.000558 (Fisher's exact test), Q value = 0.098

Table S24.  Gene #12: 'Del Peak 14(10q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 14(10Q21.2) CNV 5 6 0
DEL PEAK 14(10Q21.2) WILD-TYPE 29 379 78

Figure S24.  Get High-res Image Gene #12: 'Del Peak 14(10q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(10q23.31)' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.0063

Table S25.  Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 15(10Q23.31) CNV 6 5 0
DEL PEAK 15(10Q23.31) WILD-TYPE 28 380 78

Figure S25.  Get High-res Image Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.24

Table S26.  Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 15(10Q23.31) CNV 8 0 1 2
DEL PEAK 15(10Q23.31) WILD-TYPE 115 191 52 89

Figure S26.  Get High-res Image Gene #13: 'Del Peak 15(10q23.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(11p15.1)' versus 'CN_CNMF'

P value = 7.74e-08 (Fisher's exact test), Q value = 1.6e-05

Table S27.  Gene #14: 'Del Peak 16(11p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 16(11P15.1) CNV 6 0 1
DEL PEAK 16(11P15.1) WILD-TYPE 28 385 77

Figure S27.  Get High-res Image Gene #14: 'Del Peak 16(11p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(13q12.3)' versus 'METHLYATION_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.2

Table S28.  Gene #15: 'Del Peak 17(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 17(13Q12.3) CNV 10 3 2
DEL PEAK 17(13Q12.3) WILD-TYPE 139 71 272

Figure S28.  Get High-res Image Gene #15: 'Del Peak 17(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(13q12.3)' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.24

Table S29.  Gene #15: 'Del Peak 17(13q12.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 17(13Q12.3) CNV 10 2 2 0
DEL PEAK 17(13Q12.3) WILD-TYPE 130 54 104 156

Figure S29.  Get High-res Image Gene #15: 'Del Peak 17(13q12.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 18(13q21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.48e-05 (Fisher's exact test), Q value = 0.0065

Table S30.  Gene #16: 'Del Peak 18(13q21.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 18(13Q21.31) CNV 10 0 0 6
DEL PEAK 18(13Q21.31) WILD-TYPE 113 191 53 85

Figure S30.  Get High-res Image Gene #16: 'Del Peak 18(13q21.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(15q25.3)' versus 'CN_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.23

Table S31.  Gene #17: 'Del Peak 19(15q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 19(15Q25.3) CNV 4 3 1
DEL PEAK 19(15Q25.3) WILD-TYPE 30 382 77

Figure S31.  Get High-res Image Gene #17: 'Del Peak 19(15q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(18p11.21)' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.036

Table S32.  Gene #20: 'Del Peak 23(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 23(18P11.21) CNV 3 0 1
DEL PEAK 23(18P11.21) WILD-TYPE 31 385 77

Figure S32.  Get High-res Image Gene #20: 'Del Peak 23(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(18q22.2)' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.23

Table S33.  Gene #21: 'Del Peak 24(18q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 24(18Q22.2) CNV 3 1 1
DEL PEAK 24(18Q22.2) WILD-TYPE 31 384 77

Figure S33.  Get High-res Image Gene #21: 'Del Peak 24(18q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 0.000664 (Fisher's exact test), Q value = 0.11

Table S34.  Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
DEL PEAK 25(19P13.2) CNV 6 0 0
DEL PEAK 25(19P13.2) WILD-TYPE 121 148 149

Figure S34.  Get High-res Image Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 25(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.061

Table S35.  Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
DEL PEAK 25(19P13.2) CNV 6 0 0
DEL PEAK 25(19P13.2) WILD-TYPE 108 168 142

Figure S35.  Get High-res Image Gene #22: 'Del Peak 25(19p13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(21q21.1)' versus 'CN_CNMF'

P value = 5.72e-05 (Fisher's exact test), Q value = 0.011

Table S36.  Gene #23: 'Del Peak 28(21q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 28(21Q21.1) CNV 5 2 2
DEL PEAK 28(21Q21.1) WILD-TYPE 29 383 76

Figure S36.  Get High-res Image Gene #23: 'Del Peak 28(21q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(22q13.1)' versus 'CN_CNMF'

P value = 1.42e-91 (Fisher's exact test), Q value = 3.1e-89

Table S37.  Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 29(22Q13.1) CNV 8 0 78
DEL PEAK 29(22Q13.1) WILD-TYPE 26 385 0

Figure S37.  Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(22q13.1)' versus 'METHLYATION_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.013

Table S38.  Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 29(22Q13.1) CNV 43 7 36
DEL PEAK 29(22Q13.1) WILD-TYPE 106 67 238

Figure S38.  Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 29(22q13.1)' versus 'MRNASEQ_CNMF'

P value = 1.86e-08 (Fisher's exact test), Q value = 3.9e-06

Table S39.  Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 29(22Q13.1) CNV 39 6 26 7
DEL PEAK 29(22Q13.1) WILD-TYPE 101 50 80 149

Figure S39.  Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 29(22q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-06 (Fisher's exact test), Q value = 4e-04

Table S40.  Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 29(22Q13.1) CNV 35 14 7 22
DEL PEAK 29(22Q13.1) WILD-TYPE 88 177 46 69

Figure S40.  Get High-res Image Gene #24: 'Del Peak 29(22q13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(22q13.2)' versus 'CN_CNMF'

P value = 1.42e-91 (Fisher's exact test), Q value = 3.1e-89

Table S41.  Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 30(22Q13.2) CNV 8 0 78
DEL PEAK 30(22Q13.2) WILD-TYPE 26 385 0

Figure S41.  Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 30(22q13.2)' versus 'METHLYATION_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.013

Table S42.  Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 30(22Q13.2) CNV 43 7 36
DEL PEAK 30(22Q13.2) WILD-TYPE 106 67 238

Figure S42.  Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 30(22q13.2)' versus 'MRNASEQ_CNMF'

P value = 1.86e-08 (Fisher's exact test), Q value = 3.9e-06

Table S43.  Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 30(22Q13.2) CNV 39 6 26 7
DEL PEAK 30(22Q13.2) WILD-TYPE 101 50 80 149

Figure S43.  Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 30(22q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-06 (Fisher's exact test), Q value = 4e-04

Table S44.  Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 30(22Q13.2) CNV 35 14 7 22
DEL PEAK 30(22Q13.2) WILD-TYPE 88 177 46 69

Figure S44.  Get High-res Image Gene #25: 'Del Peak 30(22q13.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(22q13.31)' versus 'CN_CNMF'

P value = 1.42e-91 (Fisher's exact test), Q value = 3.1e-89

Table S45.  Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 31(22Q13.31) CNV 8 0 78
DEL PEAK 31(22Q13.31) WILD-TYPE 26 385 0

Figure S45.  Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(22q13.31)' versus 'METHLYATION_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.013

Table S46.  Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 31(22Q13.31) CNV 43 7 36
DEL PEAK 31(22Q13.31) WILD-TYPE 106 67 238

Figure S46.  Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 31(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 1.86e-08 (Fisher's exact test), Q value = 3.9e-06

Table S47.  Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 31(22Q13.31) CNV 39 6 26 7
DEL PEAK 31(22Q13.31) WILD-TYPE 101 50 80 149

Figure S47.  Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 31(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-06 (Fisher's exact test), Q value = 4e-04

Table S48.  Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 31(22Q13.31) CNV 35 14 7 22
DEL PEAK 31(22Q13.31) WILD-TYPE 88 177 46 69

Figure S48.  Get High-res Image Gene #26: 'Del Peak 31(22q13.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(22q13.32)' versus 'CN_CNMF'

P value = 1.16e-89 (Fisher's exact test), Q value = 2.5e-87

Table S49.  Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
DEL PEAK 32(22Q13.32) CNV 8 1 78
DEL PEAK 32(22Q13.32) WILD-TYPE 26 384 0

Figure S49.  Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 32(22q13.32)' versus 'METHLYATION_CNMF'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.0068

Table S50.  Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
DEL PEAK 32(22Q13.32) CNV 44 7 36
DEL PEAK 32(22Q13.32) WILD-TYPE 105 67 238

Figure S50.  Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(22q13.32)' versus 'MRNASEQ_CNMF'

P value = 9.86e-09 (Fisher's exact test), Q value = 2.1e-06

Table S51.  Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
DEL PEAK 32(22Q13.32) CNV 40 6 26 7
DEL PEAK 32(22Q13.32) WILD-TYPE 100 50 80 149

Figure S51.  Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 32(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00021

Table S52.  Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
DEL PEAK 32(22Q13.32) CNV 36 14 7 22
DEL PEAK 32(22Q13.32) WILD-TYPE 87 177 46 69

Figure S52.  Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.21

Table S53.  Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
DEL PEAK 32(22Q13.32) CNV 33 21 20
DEL PEAK 32(22Q13.32) WILD-TYPE 81 147 122

Figure S53.  Get High-res Image Gene #27: 'Del Peak 32(22q13.32)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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 = THCA-TP.transferedmergedcluster.txt

  • Number of patients = 497

  • Number of copy number variation regions = 29

  • 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

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle