Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C19S1P81
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19S1P81
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 51 arm-level results and 8 molecular subtypes across 220 patients, 49 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 11p loss cnv correlated to 'METHLYATION_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 51 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 49 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
1p loss 67 (30%) 153 0.00361
(0.974) 		0.00862
(1.00) 		4.56e-47
(1.57e-44) 		1.46e-42
(4.96e-40) 		1.61e-24
(5.41e-22) 		1.37e-30
(4.66e-28) 		1.41e-19
(4.72e-17) 		3.05e-05
(0.00951)
19q loss 76 (35%) 144 0.247
(1.00) 		0.145
(1.00) 		1.4e-45
(4.79e-43) 		9.63e-33
(3.27e-30) 		9.57e-22
(3.22e-19) 		4.5e-27
(1.52e-24) 		3.01e-17
(9.94e-15) 		3.32e-05
(0.0103)
7p gain 37 (17%) 183 0.175
(1.00) 		0.162
(1.00) 		1.86e-17
(6.17e-15) 		3.65e-07
(0.000118) 		8.17e-12
(2.65e-09) 		0.000204
(0.0615) 		0.000552
(0.164) 		0.0071
(1.00)
4p loss 15 (7%) 205 0.415
(1.00) 		0.329
(1.00) 		0.000882
(0.259) 		0.000169
(0.0513) 		0.000108
(0.0328) 		0.000418
(0.125) 		4.98e-06
(0.00159) 		0.833
(1.00)
7q gain 51 (23%) 169 0.282
(1.00) 		0.144
(1.00) 		6.78e-15
(2.21e-12) 		6.01e-06
(0.00192) 		6.56e-08
(2.13e-05) 		0.00139
(0.396) 		0.00423
(1.00) 		0.128
(1.00)
1q loss 9 (4%) 211 0.0889
(1.00) 		0.0971
(1.00) 		8.38e-05
(0.0256) 		3.23e-05
(0.01) 		0.00603
(1.00) 		0.00013
(0.0397) 		0.0106
(1.00) 		0.715
(1.00)
10p loss 31 (14%) 189 0.271
(1.00) 		0.241
(1.00) 		2.3e-17
(7.62e-15) 		7.92e-17
(2.61e-14) 		4.79e-19
(1.59e-16) 		0.0016
(0.454) 		0.0191
(1.00) 		0.0066
(1.00)
10q loss 32 (15%) 188 0.271
(1.00) 		0.241
(1.00) 		3.46e-16
(1.14e-13) 		6.63e-16
(2.17e-13) 		3.81e-20
(1.28e-17) 		0.00109
(0.318) 		0.0128
(1.00) 		0.0178
(1.00)
22q loss 15 (7%) 205 1
(1.00) 		0.763
(1.00) 		7.15e-06
(0.00227) 		0.00075
(0.221) 		1.92e-05
(0.00605) 		0.0451
(1.00) 		0.149
(1.00) 		0.149
(1.00)
10p gain 21 (10%) 199 6.41e-07
(0.000206) 		2.89e-05
(0.00905) 		0.0175
(1.00) 		0.094
(1.00) 		0.54
(1.00) 		0.93
(1.00)
19q gain 9 (4%) 211 0.00034
(0.102) 		0.0103
(1.00) 		0.000336
(0.101) 		0.0217
(1.00) 		0.115
(1.00) 		0.162
(1.00)
20p gain 17 (8%) 203 1.66e-05
(0.00528) 		0.00225
(0.627) 		1.7e-05
(0.00537) 		0.259
(1.00) 		0.0281
(1.00) 		0.267
(1.00)
20q gain 16 (7%) 204 8.04e-05
(0.0247) 		0.00128
(0.365) 		7.35e-08
(2.37e-05) 		0.0252
(1.00) 		0.00356
(0.966) 		0.0462
(1.00)
4q loss 24 (11%) 196 0.839
(1.00) 		0.828
(1.00) 		0.0049
(1.00) 		0.000613
(0.181) 		0.002
(0.56) 		0.00355
(0.966) 		6.65e-05
(0.0205) 		0.6
(1.00)
1p gain 6 (3%) 214 0.0272
(1.00) 		0.115
(1.00) 		3.39e-05
(0.0105) 		0.103
(1.00) 		0.234
(1.00) 		0.208
(1.00)
19p gain 11 (5%) 209 2.25e-05
(0.00708) 		0.00124
(0.356) 		0.00122
(0.353) 		0.0102
(1.00) 		0.0861
(1.00) 		0.0595
(1.00)
11p loss 20 (9%) 200 0.815
(1.00) 		0.526
(1.00) 		0.00199
(0.56) 		0.000474
(0.141) 		0.0162
(1.00) 		0.00897
(1.00) 		0.0113
(1.00) 		0.0469
(1.00)
1q gain 8 (4%) 212 0.00126
(0.362) 		0.0898
(1.00) 		0.0312
(1.00) 		0.618
(1.00) 		0.851
(1.00) 		0.569
(1.00)
6p gain 4 (2%) 216 0.213
(1.00) 		0.426
(1.00) 		0.0517
(1.00) 		0.279
(1.00) 		0.0922
(1.00) 		0.717
(1.00)
8p gain 14 (6%) 206 0.0337
(1.00) 		0.26
(1.00) 		0.606
(1.00) 		0.464
(1.00) 		0.205
(1.00) 		0.459
(1.00)
8q gain 17 (8%) 203 0.00467
(1.00) 		0.0872
(1.00) 		0.377
(1.00) 		0.203
(1.00) 		0.125
(1.00) 		0.172
(1.00)
9p gain 4 (2%) 216 0.213
(1.00) 		0.355
(1.00) 		0.0715
(1.00) 		1
(1.00) 		1
(1.00) 		0.159
(1.00)
9q gain 6 (3%) 214 0.0272
(1.00) 		0.274
(1.00) 		0.00231
(0.642) 		0.519
(1.00) 		0.747
(1.00) 		0.37
(1.00)
11p gain 9 (4%) 211 0.5
(1.00) 		0.192
(1.00) 		0.00395
(1.00) 		0.00261
(0.717) 		0.138
(1.00) 		0.426
(1.00)
11q gain 14 (6%) 206 0.353
(1.00) 		0.301
(1.00) 		0.172
(1.00) 		0.107
(1.00) 		0.708
(1.00) 		0.521
(1.00)
12p gain 11 (5%) 209 0.0368
(1.00) 		0.179
(1.00) 		0.286
(1.00) 		0.17
(1.00) 		0.0299
(1.00) 		0.05
(1.00)
12q gain 5 (2%) 215 0.848
(1.00) 		0.885
(1.00) 		0.934
(1.00) 		0.346
(1.00) 		0.0605
(1.00) 		0.157
(1.00)
18p gain 4 (2%) 216 0.213
(1.00) 		0.504
(1.00) 		0.569
(1.00) 		0.279
(1.00) 		0.37
(1.00) 		0.0958
(1.00)
21q gain 3 (1%) 217 0.328
(1.00) 		0.709
(1.00) 		0.158
(1.00) 		0.0879
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 4 (2%) 216 0.825
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.37
(1.00) 		0.37
(1.00) 		0.0958
(1.00)
2q loss 3 (1%) 217 0.796
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.259
(1.00) 		0.0543
(1.00) 		0.387
(1.00)
3p loss 4 (2%) 216 0.553
(1.00) 		0.504
(1.00) 		0.356
(1.00) 		0.279
(1.00) 		0.191
(1.00) 		0.241
(1.00)
3q loss 9 (4%) 211 0.175
(1.00) 		1
(1.00) 		0.128
(1.00) 		0.109
(1.00) 		0.547
(1.00) 		0.453
(1.00) 		0.96
(1.00) 		0.849
(1.00)
5p loss 11 (5%) 209 1
(1.00) 		0.388
(1.00) 		0.0162
(1.00) 		0.0317
(1.00) 		0.847
(1.00) 		0.36
(1.00) 		0.161
(1.00) 		0.766
(1.00)
5q loss 9 (4%) 211 0.615
(1.00) 		0.0971
(1.00) 		0.0453
(1.00) 		0.0734
(1.00) 		0.0439
(1.00) 		0.0217
(1.00) 		0.00506
(1.00) 		0.139
(1.00)
6p loss 7 (3%) 213 0.12
(1.00) 		0.0431
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.693
(1.00) 		0.157
(1.00)
6q loss 21 (10%) 199 0.00431
(1.00) 		0.0237
(1.00) 		0.362
(1.00) 		0.332
(1.00) 		0.0529
(1.00) 		0.32
(1.00)
8p loss 3 (1%) 217 0.17
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.125
(1.00) 		0.387
(1.00)
9p loss 38 (17%) 182 0.384
(1.00) 		0.828
(1.00) 		0.00289
(0.791) 		0.0555
(1.00) 		0.692
(1.00) 		0.245
(1.00) 		0.804
(1.00) 		0.915
(1.00)
9q loss 6 (3%) 214 0.0702
(1.00) 		0.0542
(1.00) 		0.0111
(1.00) 		0.000882
(0.259) 		0.00806
(1.00) 		0.795
(1.00)
11q loss 4 (2%) 216 0.00243
(0.669) 		0.238
(1.00) 		0.00187
(0.527) 		0.279
(1.00) 		0.697
(1.00) 		0.0958
(1.00)
12q loss 8 (4%) 212 0.0444
(1.00) 		0.153
(1.00) 		0.686
(1.00) 		0.618
(1.00) 		0.182
(1.00) 		0.833
(1.00)
13q loss 28 (13%) 192 1
(1.00) 		0.388
(1.00) 		0.635
(1.00) 		0.171
(1.00) 		0.86
(1.00) 		0.537
(1.00) 		0.914
(1.00) 		0.364
(1.00)
14q loss 24 (11%) 196 0.00111
(0.322) 		0.0183
(1.00) 		0.00126
(0.362) 		0.452
(1.00) 		0.0127
(1.00) 		0.103
(1.00)
15q loss 12 (5%) 208 0.00582
(1.00) 		0.0161
(1.00) 		0.000977
(0.285) 		0.00504
(1.00) 		0.248
(1.00) 		0.89
(1.00)
16q loss 6 (3%) 214 0.662
(1.00) 		0.115
(1.00) 		0.302
(1.00) 		0.519
(1.00) 		0.549
(1.00) 		1
(1.00)
18p loss 15 (7%) 205 0.344
(1.00) 		0.413
(1.00) 		0.144
(1.00) 		0.0484
(1.00) 		0.119
(1.00) 		0.117
(1.00) 		0.0755
(1.00) 		0.354
(1.00)
18q loss 16 (7%) 204 0.0889
(1.00) 		0.0971
(1.00) 		0.00296
(0.807) 		0.00953
(1.00) 		0.0024
(0.664) 		0.0264
(1.00) 		0.0111
(1.00) 		0.51
(1.00)
19p loss 10 (5%) 210 0.302
(1.00) 		0.0773
(1.00) 		0.0618
(1.00) 		0.0581
(1.00) 		0.0747
(1.00) 		0.0204
(1.00) 		0.0118
(1.00) 		0.744
(1.00)
21q loss 8 (4%) 212 0.588
(1.00) 		0.423
(1.00) 		0.46
(1.00) 		0.618
(1.00) 		0.33
(1.00) 		0.197
(1.00)
Xq loss 6 (3%) 214 0.132
(1.00) 		0.203
(1.00) 		0.698
(1.00) 		0.103
(1.00) 		0.234
(1.00) 		0.208
(1.00)
'1p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.39e-05 (Chi-square test), Q value = 0.01

Table S1.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
1P GAIN MUTATED 0 6 0 0 0
1P GAIN WILD-TYPE 60 36 35 70 11

Figure S1.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.86e-17 (Fisher's exact test), Q value = 6.2e-15

Table S2.  Gene #4: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
7P GAIN MUTATED 5 30 2
7P GAIN WILD-TYPE 89 20 74

Figure S2.  Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.65e-07 (Fisher's exact test), Q value = 0.00012

Table S3.  Gene #4: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
7P GAIN MUTATED 10 17 2 2
7P GAIN WILD-TYPE 66 14 17 47

Figure S3.  Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.17e-12 (Chi-square test), Q value = 2.7e-09

Table S4.  Gene #4: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
7P GAIN MUTATED 10 23 2 2 0
7P GAIN WILD-TYPE 50 19 33 68 11

Figure S4.  Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.062

Table S5.  Gene #4: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
7P GAIN MUTATED 2 31 4
7P GAIN WILD-TYPE 30 86 65

Figure S5.  Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000552 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #4: '7p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 32 87
7P GAIN MUTATED 14 14 1 8
7P GAIN WILD-TYPE 36 36 31 79

Figure S6.  Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 6.78e-15 (Fisher's exact test), Q value = 2.2e-12

Table S7.  Gene #5: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
7Q GAIN MUTATED 10 34 7
7Q GAIN WILD-TYPE 84 16 69

Figure S7.  Get High-res Image Gene #5: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.01e-06 (Fisher's exact test), Q value = 0.0019

Table S8.  Gene #5: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
7Q GAIN MUTATED 16 19 3 5
7Q GAIN WILD-TYPE 60 12 16 44

Figure S8.  Get High-res Image Gene #5: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.56e-08 (Chi-square test), Q value = 2.1e-05

Table S9.  Gene #5: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
7Q GAIN MUTATED 17 23 4 6 0
7Q GAIN WILD-TYPE 43 19 31 64 11

Figure S9.  Get High-res Image Gene #5: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'10p gain mutation analysis' versus 'CN_CNMF'

P value = 6.41e-07 (Fisher's exact test), Q value = 0.00021

Table S10.  Gene #10: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
10P GAIN MUTATED 20 0 1
10P GAIN WILD-TYPE 74 50 75

Figure S10.  Get High-res Image Gene #10: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.009

Table S11.  Gene #10: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
10P GAIN MUTATED 17 0 1 0
10P GAIN WILD-TYPE 59 31 18 49

Figure S11.  Get High-res Image Gene #10: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0071

Table S12.  Gene #16: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
19P GAIN MUTATED 2 9 0
19P GAIN WILD-TYPE 92 41 76

Figure S12.  Get High-res Image Gene #16: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.1

Table S13.  Gene #17: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
19Q GAIN MUTATED 2 7 0
19Q GAIN WILD-TYPE 92 43 76

Figure S13.  Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000336 (Chi-square test), Q value = 0.1

Table S14.  Gene #17: '19q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
19Q GAIN MUTATED 1 7 0 1 0
19Q GAIN WILD-TYPE 59 35 35 69 11

Figure S14.  Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0053

Table S15.  Gene #18: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
20P GAIN MUTATED 4 12 1
20P GAIN WILD-TYPE 90 38 75

Figure S15.  Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.7e-05 (Chi-square test), Q value = 0.0054

Table S16.  Gene #18: '20p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
20P GAIN MUTATED 2 11 1 2 0
20P GAIN WILD-TYPE 58 31 34 68 11

Figure S16.  Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 8.04e-05 (Fisher's exact test), Q value = 0.025

Table S17.  Gene #19: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
20Q GAIN MUTATED 4 11 1
20Q GAIN WILD-TYPE 90 39 75

Figure S17.  Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.35e-08 (Chi-square test), Q value = 2.4e-05

Table S18.  Gene #19: '20q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
20Q GAIN MUTATED 2 12 1 0 0
20Q GAIN WILD-TYPE 58 30 34 70 11

Figure S18.  Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 4.56e-47 (Fisher's exact test), Q value = 1.6e-44

Table S19.  Gene #21: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
1P LOSS MUTATED 0 0 67
1P LOSS WILD-TYPE 94 50 9

Figure S19.  Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.46e-42 (Fisher's exact test), Q value = 5e-40

Table S20.  Gene #21: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
1P LOSS MUTATED 0 0 4 49
1P LOSS WILD-TYPE 76 31 15 0

Figure S20.  Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.61e-24 (Chi-square test), Q value = 5.4e-22

Table S21.  Gene #21: '1p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
1P LOSS MUTATED 0 0 33 31 3
1P LOSS WILD-TYPE 60 42 2 39 8

Figure S21.  Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'1p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-30 (Fisher's exact test), Q value = 4.7e-28

Table S22.  Gene #21: '1p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
1P LOSS MUTATED 32 4 31
1P LOSS WILD-TYPE 0 113 38

Figure S22.  Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.41e-19 (Fisher's exact test), Q value = 4.7e-17

Table S23.  Gene #21: '1p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 32 87
1P LOSS MUTATED 3 0 25 39
1P LOSS WILD-TYPE 47 50 7 48

Figure S23.  Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'1p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.0095

Table S24.  Gene #21: '1p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 13 118
1P LOSS MUTATED 42 3 22
1P LOSS WILD-TYPE 46 10 96

Figure S24.  Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss mutation analysis' versus 'CN_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.026

Table S25.  Gene #22: '1q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
1Q LOSS MUTATED 0 0 9
1Q LOSS WILD-TYPE 94 50 67

Figure S25.  Get High-res Image Gene #22: '1q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.23e-05 (Fisher's exact test), Q value = 0.01

Table S26.  Gene #22: '1q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
1Q LOSS MUTATED 0 0 0 9
1Q LOSS WILD-TYPE 76 31 19 40

Figure S26.  Get High-res Image Gene #22: '1q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'1q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.04

Table S27.  Gene #22: '1q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
1Q LOSS MUTATED 5 0 4
1Q LOSS WILD-TYPE 27 117 65

Figure S27.  Get High-res Image Gene #22: '1q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.051

Table S28.  Gene #27: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
4P LOSS MUTATED 3 0 0 12
4P LOSS WILD-TYPE 73 31 19 37

Figure S28.  Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Chi-square test), Q value = 0.033

Table S29.  Gene #27: '4p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
4P LOSS MUTATED 0 0 8 7 0
4P LOSS WILD-TYPE 60 42 27 63 11

Figure S29.  Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.13

Table S30.  Gene #27: '4p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
4P LOSS MUTATED 7 2 6
4P LOSS WILD-TYPE 25 115 63

Figure S30.  Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.98e-06 (Fisher's exact test), Q value = 0.0016

Table S31.  Gene #27: '4p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 32 87
4P LOSS MUTATED 0 0 9 6
4P LOSS WILD-TYPE 50 50 23 81

Figure S31.  Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000613 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #28: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
4Q LOSS MUTATED 8 1 0 15
4Q LOSS WILD-TYPE 68 30 19 34

Figure S32.  Get High-res Image Gene #28: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.65e-05 (Fisher's exact test), Q value = 0.02

Table S33.  Gene #28: '4q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 32 87
4Q LOSS MUTATED 1 2 11 10
4Q LOSS WILD-TYPE 49 48 21 77

Figure S33.  Get High-res Image Gene #28: '4q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 2.3e-17 (Fisher's exact test), Q value = 7.6e-15

Table S34.  Gene #36: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
10P LOSS MUTATED 1 27 3
10P LOSS WILD-TYPE 93 23 73

Figure S34.  Get High-res Image Gene #36: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.92e-17 (Fisher's exact test), Q value = 2.6e-14

Table S35.  Gene #36: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
10P LOSS MUTATED 1 22 0 3
10P LOSS WILD-TYPE 75 9 19 46

Figure S35.  Get High-res Image Gene #36: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.79e-19 (Chi-square test), Q value = 1.6e-16

Table S36.  Gene #36: '10p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
10P LOSS MUTATED 1 25 1 3 0
10P LOSS WILD-TYPE 59 17 34 67 11

Figure S36.  Get High-res Image Gene #36: '10p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 3.46e-16 (Fisher's exact test), Q value = 1.1e-13

Table S37.  Gene #37: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
10Q LOSS MUTATED 2 27 3
10Q LOSS WILD-TYPE 92 23 73

Figure S37.  Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.63e-16 (Fisher's exact test), Q value = 2.2e-13

Table S38.  Gene #37: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
10Q LOSS MUTATED 2 22 0 3
10Q LOSS WILD-TYPE 74 9 19 46

Figure S38.  Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.81e-20 (Chi-square test), Q value = 1.3e-17

Table S39.  Gene #37: '10q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
10Q LOSS MUTATED 1 26 1 3 0
10Q LOSS WILD-TYPE 59 16 34 67 11

Figure S39.  Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'11p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000474 (Fisher's exact test), Q value = 0.14

Table S40.  Gene #38: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
11P LOSS MUTATED 15 2 0 0
11P LOSS WILD-TYPE 61 29 19 49

Figure S40.  Get High-res Image Gene #38: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 1.4e-45 (Fisher's exact test), Q value = 4.8e-43

Table S41.  Gene #48: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
19Q LOSS MUTATED 2 3 71
19Q LOSS WILD-TYPE 92 47 5

Figure S41.  Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.63e-33 (Fisher's exact test), Q value = 3.3e-30

Table S42.  Gene #48: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
19Q LOSS MUTATED 7 1 4 49
19Q LOSS WILD-TYPE 69 30 15 0

Figure S42.  Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.57e-22 (Chi-square test), Q value = 3.2e-19

Table S43.  Gene #48: '19q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
19Q LOSS MUTATED 4 1 33 36 2
19Q LOSS WILD-TYPE 56 41 2 34 9

Figure S43.  Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'19q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.5e-27 (Fisher's exact test), Q value = 1.5e-24

Table S44.  Gene #48: '19q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
19Q LOSS MUTATED 32 9 35
19Q LOSS WILD-TYPE 0 108 34

Figure S44.  Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.01e-17 (Fisher's exact test), Q value = 9.9e-15

Table S45.  Gene #48: '19q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 32 87
19Q LOSS MUTATED 4 3 26 43
19Q LOSS WILD-TYPE 46 47 6 44

Figure S45.  Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'19q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.01

Table S46.  Gene #48: '19q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 13 118
19Q LOSS MUTATED 46 2 28
19Q LOSS WILD-TYPE 42 11 90

Figure S46.  Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 7.15e-06 (Fisher's exact test), Q value = 0.0023

Table S47.  Gene #50: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
22Q LOSS MUTATED 4 11 0
22Q LOSS WILD-TYPE 90 39 76

Figure S47.  Get High-res Image Gene #50: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.22

Table S48.  Gene #50: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 31 19 49
22Q LOSS MUTATED 5 8 1 0
22Q LOSS WILD-TYPE 71 23 18 49

Figure S48.  Get High-res Image Gene #50: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.006

Table S49.  Gene #50: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
22Q LOSS MUTATED 1 10 0 3 0
22Q LOSS WILD-TYPE 59 32 35 67 11

Figure S49.  Get High-res Image Gene #50: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 220

  • Number of significantly arm-level cnvs = 51

  • Number of molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, 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

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

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