Correlation between copy number variation genes (focal events) and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1348J1G
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1348J1G
Overview
Introduction

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

Summary

Testing the association between copy number variation 27 focal events and 6 molecular subtypes across 159 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_14q24.3 cnv correlated to 'CN_CNMF'.

  • del_1p36.32 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_1p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_3p24.1 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q26.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_11p15.4 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_12q21.32 cnv correlated to 'CN_CNMF'.

  • del_16q21 cnv correlated to 'CN_CNMF'.

  • del_17p13.2 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

  • del_17q11.2 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_22q12.3 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 27 focal events and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 29 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 11p15 4 56 (35%) 103 3.96e-15
(6.18e-13) 		3.07e-05
(0.00449) 		0.000981
(0.131) 		1.3e-06
(0.000195) 		2.43e-06
(0.000363) 		5.62e-05
(0.00809)
del 3p24 1 60 (38%) 99 2.93e-09
(4.48e-07) 		0.00353
(0.434) 		7.42e-07
(0.000112) 		9.23e-05
(0.0132) 		1.19e-05
(0.00175) 		0.0006
(0.0823)
del 1p12 111 (70%) 48 6.7e-13
(1.04e-10) 		9.17e-06
(0.00136) 		0.000344
(0.0485) 		0.00454
(0.536) 		0.000848
(0.115) 		0.00429
(0.51)
del 1p36 32 101 (64%) 58 2.46e-17
(3.86e-15) 		0.00951
(0.989) 		0.102
(1.00) 		0.00358
(0.436) 		0.00156
(0.203) 		0.0109
(1.00)
del 3q26 1 93 (58%) 66 2.49e-08
(3.79e-06) 		0.647
(1.00) 		0.14
(1.00) 		0.000844
(0.115) 		0.251
(1.00) 		0.0147
(1.00)
del 11q22 1 44 (28%) 115 5.56e-11
(8.56e-09) 		0.201
(1.00) 		0.108
(1.00) 		0.0111
(1.00) 		0.000574
(0.0792) 		0.00995
(1.00)
del 17p13 2 64 (40%) 95 0.0205
(1.00) 		0.000461
(0.064) 		0.00131
(0.173) 		0.00754
(0.822) 		0.00589
(0.677) 		0.0133
(1.00)
amp 1q21 3 30 (19%) 129 1.82e-18
(2.88e-16) 		0.621
(1.00) 		1
(1.00) 		0.28
(1.00) 		0.286
(1.00) 		0.495
(1.00)
amp 14q24 3 10 (6%) 149 0.00155
(0.203) 		0.198
(1.00) 		0.759
(1.00) 		0.722
(1.00) 		0.0249
(1.00) 		0.593
(1.00)
del 12q21 32 3 (2%) 156 5.33e-05
(0.00773) 		0.438
(1.00)
del 16q21 5 (3%) 154 0.00039
(0.0545) 		0.115
(1.00) 		0.524
(1.00) 		0.289
(1.00) 		0.292
(1.00) 		0.359
(1.00)
del 17q11 2 42 (26%) 117 0.117
(1.00) 		0.00349
(0.433) 		0.00214
(0.274) 		0.00328
(0.41) 		0.00017
(0.0241) 		0.00215
(0.274)
del 22q12 3 59 (37%) 100 0.0376
(1.00) 		0.00888
(0.932) 		0.00773
(0.835) 		0.0195
(1.00) 		0.00815
(0.864) 		0.000931
(0.125)
amp 4q31 1 12 (8%) 147 0.0901
(1.00) 		0.0838
(1.00) 		0.819
(1.00) 		0.00369
(0.446) 		0.192
(1.00) 		0.689
(1.00)
amp 12q13 3 16 (10%) 143 0.0378
(1.00) 		0.132
(1.00) 		0.125
(1.00) 		0.149
(1.00) 		0.00802
(0.858) 		0.12
(1.00)
amp 17q21 31 15 (9%) 144 0.103
(1.00) 		0.828
(1.00) 		0.675
(1.00) 		0.00632
(0.714) 		0.376
(1.00) 		0.583
(1.00)
del 1q44 21 (13%) 138 0.0773
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.0777
(1.00) 		0.253
(1.00)
del 4q22 1 14 (9%) 145 0.0306
(1.00) 		0.356
(1.00) 		0.23
(1.00) 		0.507
(1.00) 		0.0262
(1.00) 		0.47
(1.00)
del 4q32 3 14 (9%) 145 0.0506
(1.00) 		0.165
(1.00) 		0.44
(1.00) 		0.697
(1.00) 		0.156
(1.00) 		0.161
(1.00)
del 5q23 1 11 (7%) 148 0.00621
(0.708) 		0.922
(1.00) 		0.45
(1.00) 		0.185
(1.00) 		0.373
(1.00) 		0.723
(1.00)
del 6p12 3 8 (5%) 151 0.0724
(1.00) 		0.288
(1.00) 		0.2
(1.00) 		0.0392
(1.00) 		0.705
(1.00) 		0.161
(1.00)
del 6q16 1 23 (14%) 136 0.0176
(1.00) 		0.061
(1.00) 		0.0157
(1.00) 		0.00209
(0.27) 		0.0469
(1.00) 		0.00498
(0.577)
del 8p22 24 (15%) 135 0.242
(1.00) 		0.131
(1.00) 		0.236
(1.00) 		0.165
(1.00) 		0.119
(1.00) 		0.0448
(1.00)
del 9p24 2 15 (9%) 144 0.0256
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.0107
(1.00) 		0.585
(1.00) 		0.744
(1.00)
del 9q21 12 14 (9%) 145 0.0546
(1.00) 		0.628
(1.00) 		0.296
(1.00) 		0.167
(1.00) 		0.616
(1.00) 		0.567
(1.00)
del 22q13 31 64 (40%) 95 0.0249
(1.00) 		0.0109
(1.00) 		0.0164
(1.00) 		0.0355
(1.00) 		0.0134
(1.00) 		0.003
(0.378)
del xp21 1 46 (29%) 113 0.00677
(0.759) 		0.00706
(0.783) 		0.00368
(0.446) 		0.0456
(1.00) 		0.0046
(0.538) 		0.0073
(0.803)
'amp_1q21.3' versus 'CN_CNMF'

P value = 1.82e-18 (Chi-square test), Q value = 2.9e-16

Table S1.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
AMP PEAK 1(1Q21.3) MUTATED 21 1 5 3 0 0
AMP PEAK 1(1Q21.3) WILD-TYPE 2 23 52 43 7 2

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q24.3' versus 'CN_CNMF'

P value = 0.00155 (Chi-square test), Q value = 0.2

Table S2.  Gene #4: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
AMP PEAK 4(14Q24.3) MUTATED 0 0 1 9 0 0
AMP PEAK 4(14Q24.3) WILD-TYPE 23 24 56 37 7 2

Figure S2.  Get High-res Image Gene #4: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'CN_CNMF'

P value = 2.46e-17 (Chi-square test), Q value = 3.9e-15

Table S3.  Gene #6: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 1(1P36.32) MUTATED 21 2 54 15 7 2
DEL PEAK 1(1P36.32) WILD-TYPE 2 22 3 31 0 0

Figure S3.  Get High-res Image Gene #6: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.2

Table S4.  Gene #6: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 55 42
DEL PEAK 1(1P36.32) MUTATED 12 40 28
DEL PEAK 1(1P36.32) WILD-TYPE 22 15 14

Figure S4.  Get High-res Image Gene #6: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

'del_1p12' versus 'CN_CNMF'

P value = 6.7e-13 (Chi-square test), Q value = 1e-10

Table S5.  Gene #7: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 2(1P12) MUTATED 21 3 53 25 7 2
DEL PEAK 2(1P12) WILD-TYPE 2 21 4 21 0 0

Figure S5.  Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 9.17e-06 (Fisher's exact test), Q value = 0.0014

Table S6.  Gene #7: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 42
DEL PEAK 2(1P12) MUTATED 24 67 20
DEL PEAK 2(1P12) WILD-TYPE 16 10 22

Figure S6.  Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.048

Table S7.  Gene #7: 'del_1p12' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 53 24
DEL PEAK 2(1P12) MUTATED 31 46 12
DEL PEAK 2(1P12) WILD-TYPE 23 7 12

Figure S7.  Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000848 (Fisher's exact test), Q value = 0.11

Table S8.  Gene #7: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 55 42
DEL PEAK 2(1P12) MUTATED 18 47 24
DEL PEAK 2(1P12) WILD-TYPE 16 8 18

Figure S8.  Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 2.93e-09 (Chi-square test), Q value = 4.5e-07

Table S9.  Gene #9: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 4(3P24.1) MUTATED 12 1 10 33 4 0
DEL PEAK 4(3P24.1) WILD-TYPE 11 23 47 13 3 2

Figure S9.  Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 7.42e-07 (Fisher's exact test), Q value = 0.00011

Table S10.  Gene #9: 'del_3p24.1' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 53 24
DEL PEAK 4(3P24.1) MUTATED 34 11 3
DEL PEAK 4(3P24.1) WILD-TYPE 20 42 21

Figure S10.  Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.013

Table S11.  Gene #9: 'del_3p24.1' versus Molecular Subtype #4: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 41 18 52
DEL PEAK 4(3P24.1) MUTATED 2 11 4 31
DEL PEAK 4(3P24.1) WILD-TYPE 18 30 14 21

Figure S11.  Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #4: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0017

Table S12.  Gene #9: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 55 42
DEL PEAK 4(3P24.1) MUTATED 24 12 12
DEL PEAK 4(3P24.1) WILD-TYPE 10 43 30

Figure S12.  Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.082

Table S13.  Gene #9: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 43 56
DEL PEAK 4(3P24.1) MUTATED 6 11 31
DEL PEAK 4(3P24.1) WILD-TYPE 26 32 25

Figure S13.  Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 2.49e-08 (Chi-square test), Q value = 3.8e-06

Table S14.  Gene #10: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 5(3Q26.1) MUTATED 12 0 42 32 5 2
DEL PEAK 5(3Q26.1) WILD-TYPE 11 24 15 14 2 0

Figure S14.  Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000844 (Fisher's exact test), Q value = 0.11

Table S15.  Gene #10: 'del_3q26.1' versus Molecular Subtype #4: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 41 18 52
DEL PEAK 5(3Q26.1) MUTATED 7 29 4 33
DEL PEAK 5(3Q26.1) WILD-TYPE 13 12 14 19

Figure S15.  Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #4: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 3.96e-15 (Chi-square test), Q value = 6.2e-13

Table S16.  Gene #19: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 14(11P15.4) MUTATED 8 4 1 35 6 2
DEL PEAK 14(11P15.4) WILD-TYPE 15 20 56 11 1 0

Figure S16.  Get High-res Image Gene #19: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.0045

Table S17.  Gene #19: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 42
DEL PEAK 14(11P15.4) MUTATED 23 14 19
DEL PEAK 14(11P15.4) WILD-TYPE 17 63 23

Figure S17.  Get High-res Image Gene #19: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 0.000981 (Fisher's exact test), Q value = 0.13

Table S18.  Gene #19: 'del_11p15.4' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 53 24
DEL PEAK 14(11P15.4) MUTATED 29 11 6
DEL PEAK 14(11P15.4) WILD-TYPE 25 42 18

Figure S18.  Get High-res Image Gene #19: 'del_11p15.4' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.00019

Table S19.  Gene #19: 'del_11p15.4' versus Molecular Subtype #4: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 41 18 52
DEL PEAK 14(11P15.4) MUTATED 6 4 4 32
DEL PEAK 14(11P15.4) WILD-TYPE 14 37 14 20

Figure S19.  Get High-res Image Gene #19: 'del_11p15.4' versus Molecular Subtype #4: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00036

Table S20.  Gene #19: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 55 42
DEL PEAK 14(11P15.4) MUTATED 24 10 12
DEL PEAK 14(11P15.4) WILD-TYPE 10 45 30

Figure S20.  Get High-res Image Gene #19: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.62e-05 (Fisher's exact test), Q value = 0.0081

Table S21.  Gene #19: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 43 56
DEL PEAK 14(11P15.4) MUTATED 9 6 31
DEL PEAK 14(11P15.4) WILD-TYPE 23 37 25

Figure S21.  Get High-res Image Gene #19: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 5.56e-11 (Chi-square test), Q value = 8.6e-09

Table S22.  Gene #20: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 15(11Q22.1) MUTATED 6 3 2 31 1 1
DEL PEAK 15(11Q22.1) WILD-TYPE 17 21 55 15 6 1

Figure S22.  Get High-res Image Gene #20: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000574 (Fisher's exact test), Q value = 0.079

Table S23.  Gene #20: 'del_11q22.1' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 55 42
DEL PEAK 15(11Q22.1) MUTATED 19 11 8
DEL PEAK 15(11Q22.1) WILD-TYPE 15 44 34

Figure S23.  Get High-res Image Gene #20: 'del_11q22.1' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

'del_12q21.32' versus 'CN_CNMF'

P value = 5.33e-05 (Chi-square test), Q value = 0.0077

Table S24.  Gene #21: 'del_12q21.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 16(12Q21.32) MUTATED 0 1 1 0 0 1
DEL PEAK 16(12Q21.32) WILD-TYPE 23 23 56 46 7 1

Figure S24.  Get High-res Image Gene #21: 'del_12q21.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q21' versus 'CN_CNMF'

P value = 0.00039 (Chi-square test), Q value = 0.055

Table S25.  Gene #22: 'del_16q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 24 57 46 7 2
DEL PEAK 17(16Q21) MUTATED 0 0 0 4 0 1
DEL PEAK 17(16Q21) WILD-TYPE 23 24 57 42 7 1

Figure S25.  Get High-res Image Gene #22: 'del_16q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.000461 (Fisher's exact test), Q value = 0.064

Table S26.  Gene #23: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 42
DEL PEAK 18(17P13.2) MUTATED 9 43 12
DEL PEAK 18(17P13.2) WILD-TYPE 31 34 30

Figure S26.  Get High-res Image Gene #23: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.17

Table S27.  Gene #23: 'del_17p13.2' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 53 24
DEL PEAK 18(17P13.2) MUTATED 17 30 4
DEL PEAK 18(17P13.2) WILD-TYPE 37 23 20

Figure S27.  Get High-res Image Gene #23: 'del_17p13.2' versus Molecular Subtype #3: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.024

Table S28.  Gene #24: 'del_17q11.2' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 55 42
DEL PEAK 19(17Q11.2) MUTATED 8 24 3
DEL PEAK 19(17Q11.2) WILD-TYPE 26 31 39

Figure S28.  Get High-res Image Gene #24: 'del_17q11.2' versus Molecular Subtype #5: 'MIRSEQ_MATURE_CNMF'

'del_22q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000931 (Fisher's exact test), Q value = 0.12

Table S29.  Gene #25: 'del_22q12.3' versus Molecular Subtype #6: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 43 56
DEL PEAK 20(22Q12.3) MUTATED 12 24 11
DEL PEAK 20(22Q12.3) WILD-TYPE 20 19 45

Figure S29.  Get High-res Image Gene #25: 'del_22q12.3' versus Molecular Subtype #6: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 159

  • Number of significantly focal cnvs = 27

  • Number of molecular subtypes = 6

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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