Correlation between copy number variation genes (focal events) and molecular subtypes
Mesothelioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1XS5TF1
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5TF1
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 21 focal events and 8 molecular subtypes across 87 patients, 52 significant findings detected with P value < 0.05 and Q value < 0.25.

  • del_1p36.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p21.3 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q35 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_3p21.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q26 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q23.2 cnv correlated to 'CN_CNMF'.

  • del_6q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q25.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_11q23.2 cnv correlated to 'CN_CNMF'.

  • del_12p13.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • del_13q14.11 cnv correlated to 'CN_CNMF'.

  • del_14q32.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_15q15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q24.1 cnv correlated to 'CN_CNMF'.

  • del_22q12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 21 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 52 significant findings detected.

Clinical
Features 		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
del 14q32 31 39 (45%) 48 0.00012
(0.00168) 		0.311
(0.496) 		0.00216
(0.0158) 		1e-05
(0.00042) 		0.0262
(0.0956) 		0.0089
(0.0468) 		0.0426
(0.14) 		0.0795
(0.224)
del 3p21 1 48 (55%) 39 0.0004
(0.00448) 		0.123
(0.292) 		0.00014
(0.00181) 		2e-05
(0.00048) 		0.202
(0.381) 		0.0153
(0.0694) 		0.275
(0.446) 		0.00787
(0.0468)
del 9p21 3 51 (59%) 36 1e-05
(0.00042) 		0.00933
(0.0475) 		0.0191
(0.0781) 		3e-05
(0.00063) 		0.96
(0.986) 		0.13
(0.299) 		0.477
(0.661) 		0.0172
(0.0722)
del 10p15 3 28 (32%) 59 0.00176
(0.0134) 		0.00665
(0.043) 		0.0329
(0.111) 		0.00892
(0.0468) 		1
(1.00) 		0.445
(0.634) 		0.355
(0.54) 		0.444
(0.634)
del 15q15 1 28 (32%) 59 2e-05
(0.00048) 		0.00118
(0.0104) 		0.0275
(0.0961) 		0.0851
(0.23) 		0.36
(0.54) 		0.525
(0.695) 		0.725
(0.823) 		0.0209
(0.0835)
del 1p36 31 33 (38%) 54 1e-05
(0.00042) 		0.184
(0.359) 		0.329
(0.516) 		0.0216
(0.0845) 		0.0817
(0.225) 		0.00872
(0.0468) 		0.433
(0.632) 		0.0713
(0.206)
del 1p21 3 37 (43%) 50 0.108
(0.267) 		0.0269
(0.0961) 		0.00062
(0.00613) 		0.0157
(0.0694) 		0.926
(0.972) 		0.313
(0.496) 		0.593
(0.755) 		0.554
(0.721)
del 4q26 38 (44%) 49 2e-05
(0.00048) 		0.0561
(0.171) 		0.00236
(0.0165) 		0.00082
(0.00765) 		0.276
(0.446) 		0.0516
(0.164) 		0.591
(0.755) 		0.178
(0.353)
del 4q34 3 41 (47%) 46 1e-05
(0.00042) 		0.0169
(0.0722) 		0.0612
(0.184) 		0.00012
(0.00168) 		0.177
(0.353) 		0.242
(0.415) 		0.961
(0.986) 		0.132
(0.299)
del 22q12 2 68 (78%) 19 0.00129
(0.0108) 		5e-05
(0.00084) 		0.106
(0.265) 		0.014
(0.0672) 		0.896
(0.953) 		0.627
(0.776) 		0.0799
(0.224) 		0.679
(0.804)
del 6q22 1 41 (47%) 46 0.00147
(0.0118) 		0.241
(0.415) 		0.157
(0.33) 		0.492
(0.663) 		0.559
(0.723) 		0.2
(0.381) 		0.258
(0.425) 		0.0144
(0.0672)
del 6q26 36 (41%) 51 5e-05
(0.00084) 		0.254
(0.423) 		0.839
(0.909) 		0.799
(0.888) 		0.345
(0.534) 		0.493
(0.663) 		0.347
(0.534) 		0.0435
(0.141)
del 10q25 2 31 (36%) 56 0.00272
(0.0183) 		0.00806
(0.0468) 		0.483
(0.661) 		0.455
(0.642) 		0.717
(0.823) 		0.194
(0.374) 		0.232
(0.415) 		0.148
(0.318)
del 12p13 31 11 (13%) 76 0.117
(0.28) 		0.0125
(0.0617) 		0.0244
(0.093) 		0.15
(0.319) 		0.25
(0.42) 		0.104
(0.265) 		1
(1.00) 		0.23
(0.415)
del 2q35 17 (20%) 70 0.0889
(0.233) 		0.0533
(0.166) 		0.553
(0.721) 		0.0082
(0.0468) 		0.484
(0.661) 		0.0861
(0.23) 		0.68
(0.804) 		0.36
(0.54)
del 5q23 2 17 (20%) 70 0.00024
(0.00288) 		0.378
(0.557) 		0.719
(0.823) 		0.138
(0.308) 		0.742
(0.831) 		0.436
(0.632) 		1
(1.00) 		1
(1.00)
del 11q23 2 18 (21%) 69 0.00056
(0.00588) 		0.715
(0.823) 		0.139
(0.308) 		0.215
(0.394) 		0.469
(0.657) 		0.131
(0.299) 		0.739
(0.831) 		0.111
(0.27)
del 13q14 11 43 (49%) 44 0.0297
(0.102) 		0.179
(0.353) 		0.216
(0.394) 		0.247
(0.419) 		0.963
(0.986) 		0.525
(0.695) 		0.172
(0.353) 		0.91
(0.961)
del 16q24 1 22 (25%) 65 0.026
(0.0956) 		0.675
(0.804) 		0.242
(0.415) 		0.365
(0.543) 		0.605
(0.764) 		0.165
(0.343) 		0.812
(0.898) 		0.212
(0.394)
del 8p23 2 18 (21%) 69 0.865
(0.93) 		0.725
(0.823) 		0.702
(0.823) 		0.937
(0.977) 		0.63
(0.776) 		0.834
(0.909) 		0.839
(0.909) 		0.633
(0.776)
del 16p13 3 6 (7%) 81 0.07
(0.206) 		0.238
(0.415) 		0.143
(0.313) 		0.0988
(0.255) 		0.656
(0.796) 		0.658
(0.796) 		0.869
(0.93) 		0.621
(0.776)
'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S1.  Gene #1: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 1(1P36.31) MUTATED 2 19 5 7
DEL PEAK 1(1P36.31) WILD-TYPE 21 7 19 7

Figure S1.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.084

Table S2.  Gene #1: 'del_1p36.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 1(1P36.31) MUTATED 3 8 11 5 6
DEL PEAK 1(1P36.31) WILD-TYPE 19 4 11 8 11

Figure S2.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00872 (Fisher's exact test), Q value = 0.047

Table S3.  Gene #1: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 1(1P36.31) MUTATED 9 12 5 6 1
DEL PEAK 1(1P36.31) WILD-TYPE 20 13 1 7 13

Figure S3.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p21.3' versus 'METHLYATION_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.096

Table S4.  Gene #2: 'del_1p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 2(1P21.3) MUTATED 5 10 16 6
DEL PEAK 2(1P21.3) WILD-TYPE 9 10 10 21

Figure S4.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0061

Table S5.  Gene #2: 'del_1p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 2(1P21.3) MUTATED 5 11 5 16
DEL PEAK 2(1P21.3) WILD-TYPE 21 11 12 5

Figure S5.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.069

Table S6.  Gene #2: 'del_1p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 2(1P21.3) MUTATED 5 7 10 3 12
DEL PEAK 2(1P21.3) WILD-TYPE 17 5 12 10 5

Figure S6.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0082 (Fisher's exact test), Q value = 0.047

Table S7.  Gene #3: 'del_2q35' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 3(2Q35) MUTATED 1 6 7 1 2
DEL PEAK 3(2Q35) WILD-TYPE 21 6 15 12 15

Figure S7.  Get High-res Image Gene #3: 'del_2q35' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0045

Table S8.  Gene #4: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 4(3P21.1) MUTATED 13 16 18 1
DEL PEAK 4(3P21.1) WILD-TYPE 10 10 6 13

Figure S8.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0018

Table S9.  Gene #4: 'del_3p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 4(3P21.1) MUTATED 21 4 10 13
DEL PEAK 4(3P21.1) WILD-TYPE 5 18 7 8

Figure S9.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S10.  Gene #4: 'del_3p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 4(3P21.1) MUTATED 16 12 4 7 9
DEL PEAK 4(3P21.1) WILD-TYPE 6 0 18 6 8

Figure S10.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.069

Table S11.  Gene #4: 'del_3p21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 4(3P21.1) MUTATED 16 8 3 9 12
DEL PEAK 4(3P21.1) WILD-TYPE 13 17 3 4 2

Figure S11.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00787 (Fisher's exact test), Q value = 0.047

Table S12.  Gene #4: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 17 21 31
DEL PEAK 4(3P21.1) MUTATED 13 4 11 19
DEL PEAK 4(3P21.1) WILD-TYPE 3 13 10 12

Figure S12.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q26' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S13.  Gene #5: 'del_4q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 5(4Q26) MUTATED 3 21 6 8
DEL PEAK 5(4Q26) WILD-TYPE 20 5 18 6

Figure S13.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q26' versus 'MRNASEQ_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.017

Table S14.  Gene #5: 'del_4q26' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 5(4Q26) MUTATED 4 11 9 14
DEL PEAK 5(4Q26) WILD-TYPE 22 11 8 7

Figure S14.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0077

Table S15.  Gene #5: 'del_4q26' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 5(4Q26) MUTATED 2 8 12 5 11
DEL PEAK 5(4Q26) WILD-TYPE 20 4 10 8 6

Figure S15.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S16.  Gene #6: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 6(4Q34.3) MUTATED 3 22 7 9
DEL PEAK 6(4Q34.3) WILD-TYPE 20 4 17 5

Figure S16.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.072

Table S17.  Gene #6: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 6(4Q34.3) MUTATED 4 15 13 9
DEL PEAK 6(4Q34.3) WILD-TYPE 10 5 13 18

Figure S17.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0017

Table S18.  Gene #6: 'del_4q34.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 6(4Q34.3) MUTATED 2 9 14 5 11
DEL PEAK 6(4Q34.3) WILD-TYPE 20 3 8 8 6

Figure S18.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0029

Table S19.  Gene #7: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 7(5Q23.2) MUTATED 0 10 7 0
DEL PEAK 7(5Q23.2) WILD-TYPE 23 16 17 14

Figure S19.  Get High-res Image Gene #7: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.1' versus 'CN_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #8: 'del_6q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 8(6Q22.1) MUTATED 12 19 8 2
DEL PEAK 8(6Q22.1) WILD-TYPE 11 7 16 12

Figure S20.  Get High-res Image Gene #8: 'del_6q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.067

Table S21.  Gene #8: 'del_6q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 17 21 31
DEL PEAK 8(6Q22.1) MUTATED 13 8 9 10
DEL PEAK 8(6Q22.1) WILD-TYPE 3 9 12 21

Figure S21.  Get High-res Image Gene #8: 'del_6q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00084

Table S22.  Gene #9: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 9(6Q26) MUTATED 11 19 4 2
DEL PEAK 9(6Q26) WILD-TYPE 12 7 20 12

Figure S22.  Get High-res Image Gene #9: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.14

Table S23.  Gene #9: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 17 21 31
DEL PEAK 9(6Q26) MUTATED 11 9 6 10
DEL PEAK 9(6Q26) WILD-TYPE 5 8 15 21

Figure S23.  Get High-res Image Gene #9: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S24.  Gene #11: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 11(9P21.3) MUTATED 2 24 20 5
DEL PEAK 11(9P21.3) WILD-TYPE 21 2 4 9

Figure S24.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00933 (Fisher's exact test), Q value = 0.047

Table S25.  Gene #11: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 11(9P21.3) MUTATED 6 17 17 11
DEL PEAK 11(9P21.3) WILD-TYPE 8 3 9 16

Figure S25.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.078

Table S26.  Gene #11: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 11(9P21.3) MUTATED 9 14 12 16
DEL PEAK 11(9P21.3) WILD-TYPE 17 8 5 5

Figure S26.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00063

Table S27.  Gene #11: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 11(9P21.3) MUTATED 4 12 14 9 12
DEL PEAK 11(9P21.3) WILD-TYPE 18 0 8 4 5

Figure S27.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.072

Table S28.  Gene #11: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 17 21 31
DEL PEAK 11(9P21.3) MUTATED 4 12 12 22
DEL PEAK 11(9P21.3) WILD-TYPE 12 5 9 9

Figure S28.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.013

Table S29.  Gene #12: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 12(10P15.3) MUTATED 2 14 10 2
DEL PEAK 12(10P15.3) WILD-TYPE 21 12 14 12

Figure S29.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.043

Table S30.  Gene #12: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 12(10P15.3) MUTATED 1 12 9 6
DEL PEAK 12(10P15.3) WILD-TYPE 13 8 17 21

Figure S30.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.11

Table S31.  Gene #12: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 12(10P15.3) MUTATED 3 8 7 10
DEL PEAK 12(10P15.3) WILD-TYPE 23 14 10 11

Figure S31.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 0.047

Table S32.  Gene #12: 'del_10p15.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 12(10P15.3) MUTATED 1 6 8 5 8
DEL PEAK 12(10P15.3) WILD-TYPE 21 6 14 8 9

Figure S32.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.018

Table S33.  Gene #13: 'del_10q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 13(10Q25.2) MUTATED 3 10 15 3
DEL PEAK 13(10Q25.2) WILD-TYPE 20 16 9 11

Figure S33.  Get High-res Image Gene #13: 'del_10q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.047

Table S34.  Gene #13: 'del_10q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 13(10Q25.2) MUTATED 2 11 13 5
DEL PEAK 13(10Q25.2) WILD-TYPE 12 9 13 22

Figure S34.  Get High-res Image Gene #13: 'del_10q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0059

Table S35.  Gene #14: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 14(11Q23.2) MUTATED 0 3 10 5
DEL PEAK 14(11Q23.2) WILD-TYPE 23 23 14 9

Figure S35.  Get High-res Image Gene #14: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.31' versus 'METHLYATION_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.062

Table S36.  Gene #15: 'del_12p13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 15(12P13.31) MUTATED 1 7 2 1
DEL PEAK 15(12P13.31) WILD-TYPE 13 13 24 26

Figure S36.  Get High-res Image Gene #15: 'del_12p13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.31' versus 'MRNASEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.093

Table S37.  Gene #15: 'del_12p13.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 15(12P13.31) MUTATED 0 5 4 2
DEL PEAK 15(12P13.31) WILD-TYPE 26 17 13 19

Figure S37.  Get High-res Image Gene #15: 'del_12p13.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.11' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #16: 'del_13q14.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 16(13Q14.11) MUTATED 8 19 11 5
DEL PEAK 16(13Q14.11) WILD-TYPE 15 7 13 9

Figure S38.  Get High-res Image Gene #16: 'del_13q14.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0017

Table S39.  Gene #17: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 17(14Q32.31) MUTATED 4 18 7 10
DEL PEAK 17(14Q32.31) WILD-TYPE 19 8 17 4

Figure S39.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.016

Table S40.  Gene #17: 'del_14q32.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 17(14Q32.31) MUTATED 7 17 5 10
DEL PEAK 17(14Q32.31) WILD-TYPE 19 5 12 11

Figure S40.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S41.  Gene #17: 'del_14q32.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 17(14Q32.31) MUTATED 4 9 18 1 7
DEL PEAK 17(14Q32.31) WILD-TYPE 18 3 4 12 10

Figure S41.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.096

Table S42.  Gene #17: 'del_14q32.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 29 22
DEL PEAK 17(14Q32.31) MUTATED 10 16 13
DEL PEAK 17(14Q32.31) WILD-TYPE 26 13 9

Figure S42.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0089 (Fisher's exact test), Q value = 0.047

Table S43.  Gene #17: 'del_14q32.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 17(14Q32.31) MUTATED 8 15 4 9 3
DEL PEAK 17(14Q32.31) WILD-TYPE 21 10 2 4 11

Figure S43.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.14

Table S44.  Gene #17: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 27 21
DEL PEAK 17(14Q32.31) MUTATED 21 7 10
DEL PEAK 17(14Q32.31) WILD-TYPE 16 20 11

Figure S44.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S45.  Gene #18: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 18(15Q15.1) MUTATED 0 9 15 4
DEL PEAK 18(15Q15.1) WILD-TYPE 23 17 9 10

Figure S45.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.01

Table S46.  Gene #18: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 18(15Q15.1) MUTATED 1 12 11 4
DEL PEAK 18(15Q15.1) WILD-TYPE 13 8 15 23

Figure S46.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.096

Table S47.  Gene #18: 'del_15q15.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 22 17 21
DEL PEAK 18(15Q15.1) MUTATED 3 11 6 8
DEL PEAK 18(15Q15.1) WILD-TYPE 23 11 11 13

Figure S47.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.084

Table S48.  Gene #18: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 17 21 31
DEL PEAK 18(15Q15.1) MUTATED 3 8 2 13
DEL PEAK 18(15Q15.1) WILD-TYPE 13 9 19 18

Figure S48.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.096

Table S49.  Gene #20: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 20(16Q24.1) MUTATED 1 7 9 5
DEL PEAK 20(16Q24.1) WILD-TYPE 22 19 15 9

Figure S49.  Get High-res Image Gene #20: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.011

Table S50.  Gene #21: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 26 24 14
DEL PEAK 21(22Q12.2) MUTATED 12 23 23 10
DEL PEAK 21(22Q12.2) WILD-TYPE 11 3 1 4

Figure S50.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00084

Table S51.  Gene #21: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 26 27
DEL PEAK 21(22Q12.2) MUTATED 10 19 25 14
DEL PEAK 21(22Q12.2) WILD-TYPE 4 1 1 13

Figure S51.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.067

Table S52.  Gene #21: 'del_22q12.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 12 22 13 17
DEL PEAK 21(22Q12.2) MUTATED 15 12 18 7 16
DEL PEAK 21(22Q12.2) WILD-TYPE 7 0 4 6 1

Figure S52.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/15089884/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/15104504/MESO-TP.transferedmergedcluster.txt

  • Number of patients = 87

  • Number of significantly focal cnvs = 21

  • Number of molecular subtypes = 8

  • Exclude genes 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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