Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C11R6NRZ
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/C11R6NRZ
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 42 arm-level results and 8 molecular subtypes across 430 patients, 94 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 42 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 94 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
5q gain 13 (3%) 417 6.43e-16
(1.97e-13) 		0.000276
(0.0659) 		0.902
(1.00) 		0.0224
(1.00) 		0.000782
(0.174) 		0.000962
(0.212) 		0.000188
(0.0461) 		8.57e-05
(0.0216)
7p gain 17 (4%) 413 3.79e-21
(1.17e-18) 		0.00114
(0.246) 		1
(1.00) 		0.00541
(1.00) 		0.000677
(0.152) 		0.000554
(0.126) 		0.000268
(0.0642) 		9.98e-05
(0.025)
7q gain 19 (4%) 411 6.81e-24
(2.1e-21) 		0.000166
(0.0411) 		0.502
(1.00) 		0.00126
(0.269) 		0.000262
(0.0635) 		0.000178
(0.0437) 		3.79e-05
(0.00992) 		9.44e-06
(0.00261)
12p gain 12 (3%) 418 7.66e-12
(2.32e-09) 		1.68e-06
(0.000487) 		0.902
(1.00) 		0.0224
(1.00) 		7.26e-06
(0.00203) 		4.95e-06
(0.0014) 		1.44e-05
(0.00394) 		3.71e-06
(0.00106)
12q gain 12 (3%) 418 7.66e-12
(2.32e-09) 		1.68e-06
(0.000487) 		0.902
(1.00) 		0.0224
(1.00) 		7.26e-06
(0.00203) 		4.95e-06
(0.0014) 		1.44e-05
(0.00394) 		3.71e-06
(0.00106)
16p gain 12 (3%) 418 3.91e-13
(1.19e-10) 		0.000351
(0.0818) 		0.504
(1.00) 		0.0245
(1.00) 		0.000245
(0.0597) 		0.000169
(0.0418) 		0.000105
(0.0261) 		4.89e-05
(0.0125)
17p gain 11 (3%) 419 1.49e-07
(4.37e-05) 		6.61e-06
(0.00185) 		0.773
(1.00) 		0.00799
(1.00) 		1.89e-05
(0.00512) 		1.95e-05
(0.00528) 		4.59e-05
(0.0118) 		1.35e-05
(0.0037)
17q gain 12 (3%) 418 1.21e-07
(3.56e-05) 		1.68e-06
(0.000487) 		0.795
(1.00) 		0.00924
(1.00) 		7.26e-06
(0.00203) 		4.95e-06
(0.0014) 		1.44e-05
(0.00394) 		3.71e-06
(0.00106)
2p loss 8 (2%) 422 1.7e-08
(5e-06) 		0.000211
(0.0514) 		1
(1.00) 		0.0385
(1.00) 		0.000655
(0.147) 		0.000335
(0.0793) 		4.59e-05
(0.0118) 		2.06e-05
(0.00554)
22q loss 54 (13%) 376 3.28e-45
(1.02e-42) 		0.00129
(0.274) 		0.122
(1.00) 		0.104
(1.00) 		3.64e-09
(1.08e-06) 		2.17e-07
(6.34e-05) 		0.000267
(0.0642) 		8.28e-05
(0.0209)
2q loss 7 (2%) 423 1.31e-08
(3.88e-06) 		0.00103
(0.226) 		0.837
(1.00) 		0.0398
(1.00) 		0.00217
(0.441) 		0.00122
(0.264) 		0.000164
(0.0407) 		8.14e-05
(0.0207)
5p gain 16 (4%) 414 2.61e-17
(8.03e-15) 		0.00733
(1.00) 		1
(1.00) 		0.0911
(1.00) 		0.00918
(1.00) 		0.0101
(1.00) 		0.000686
(0.153) 		0.00053
(0.121)
15q loss 6 (1%) 424 0.000943
(0.208) 		0.00735
(1.00) 		0.459
(1.00) 		0.228
(1.00) 		0.0175
(1.00) 		0.00936
(1.00) 		0.000579
(0.131) 		0.000319
(0.076)
14q gain 7 (2%) 423 2.19e-07
(6.36e-05) 		0.00103
(0.226) 		1
(1.00) 		0.228
(1.00) 		0.00217
(0.441) 		0.00122
(0.264) 		0.00432
(0.852) 		0.00204
(0.42)
16q gain 10 (2%) 420 3.43e-12
(1.04e-09) 		0.00255
(0.509) 		0.858
(1.00) 		0.114
(1.00) 		0.00179
(0.374) 		0.00147
(0.309) 		0.00137
(0.29) 		0.000634
(0.143)
1q gain 16 (4%) 414 7.85e-05
(0.02) 		0.0375
(1.00) 		0.0155
(1.00) 		0.0911
(1.00) 		0.0328
(1.00) 		0.0235
(1.00) 		0.152
(1.00) 		0.0547
(1.00)
4p gain 4 (1%) 426 3.73e-05
(0.00992) 		0.0167
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.108
(1.00) 		0.0986
(1.00)
4q gain 4 (1%) 426 3.73e-05
(0.00992) 		0.0167
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.108
(1.00) 		0.0986
(1.00)
11q gain 4 (1%) 426 0.00034
(0.0803) 		0.0167
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.00712
(1.00) 		0.0048
(0.942)
19p gain 3 (1%) 427 0.000497
(0.115) 		0.0748
(1.00) 		0.101
(1.00) 		0.0822
(1.00) 		0.0247
(1.00) 		0.0184
(1.00)
19q gain 4 (1%) 426 3.73e-05
(0.00992) 		0.0167
(1.00) 		0.638
(1.00) 		0.04
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.00712
(1.00) 		0.0048
(0.942)
20p gain 8 (2%) 422 8.67e-10
(2.59e-07) 		0.0166
(1.00) 		1
(1.00) 		0.0385
(1.00) 		0.0135
(1.00) 		0.0115
(1.00) 		0.0122
(1.00) 		0.00555
(1.00)
20q gain 8 (2%) 422 8.67e-10
(2.59e-07) 		0.0166
(1.00) 		1
(1.00) 		0.0385
(1.00) 		0.0135
(1.00) 		0.0115
(1.00) 		0.0122
(1.00) 		0.00555
(1.00)
1p loss 3 (1%) 427 0.000497
(0.115) 		0.533
(1.00) 		0.489
(1.00) 		0.195
(1.00) 		0.294
(1.00) 		0.357
(1.00)
3q loss 3 (1%) 427 0.000497
(0.115) 		0.0748
(1.00) 		0.101
(1.00) 		0.0822
(1.00) 		0.0247
(1.00) 		0.0184
(1.00)
8p loss 4 (1%) 426 3.73e-05
(0.00992) 		0.0419
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.00712
(1.00) 		0.0048
(0.942)
8q loss 4 (1%) 426 3.73e-05
(0.00992) 		0.0419
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.00712
(1.00) 		0.0048
(0.942)
9p loss 10 (2%) 420 5.24e-10
(1.57e-07) 		0.897
(1.00) 		0.557
(1.00) 		0.074
(1.00) 		0.25
(1.00) 		0.527
(1.00) 		0.182
(1.00) 		0.158
(1.00)
9q loss 14 (3%) 416 1.46e-10
(4.4e-08) 		0.796
(1.00) 		0.213
(1.00) 		0.00228
(0.458) 		0.442
(1.00) 		0.823
(1.00) 		0.193
(1.00) 		0.256
(1.00)
10p loss 4 (1%) 426 3.73e-05
(0.00992) 		0.26
(1.00) 		0.244
(1.00) 		0.0895
(1.00) 		0.108
(1.00) 		0.0986
(1.00)
10q loss 4 (1%) 426 3.73e-05
(0.00992) 		0.26
(1.00) 		0.244
(1.00) 		0.0895
(1.00) 		0.108
(1.00) 		0.0986
(1.00)
11p loss 5 (1%) 425 2.71e-06
(0.000778) 		0.057
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.0498
(1.00) 		0.132
(1.00) 		0.038
(1.00) 		0.0221
(1.00)
11q loss 6 (1%) 424 2.51e-05
(0.00672) 		0.0332
(1.00) 		0.391
(1.00) 		0.776
(1.00) 		0.0188
(1.00) 		0.0674
(1.00) 		0.013
(1.00) 		0.00681
(1.00)
18p loss 4 (1%) 426 0.00034
(0.0803) 		0.175
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.244
(1.00) 		0.0895
(1.00) 		0.0726
(1.00) 		0.0383
(1.00)
18q loss 4 (1%) 426 0.00034
(0.0803) 		0.175
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.244
(1.00) 		0.0895
(1.00) 		0.0726
(1.00) 		0.0383
(1.00)
21q loss 5 (1%) 425 3.11e-05
(0.00832) 		0.017
(1.00) 		0.389
(1.00) 		0.04
(1.00) 		0.0498
(1.00) 		0.132
(1.00) 		0.038
(1.00) 		0.0221
(1.00)
11p gain 5 (1%) 425 0.00195
(0.403) 		0.00598
(1.00) 		0.0175
(1.00) 		0.00936
(1.00) 		0.00204
(0.42) 		0.00124
(0.266)
21q gain 3 (1%) 427 0.00344
(0.68) 		0.0748
(1.00) 		0.101
(1.00) 		0.0822
(1.00) 		0.0247
(1.00) 		0.0184
(1.00)
6q loss 3 (1%) 427 0.0272
(1.00) 		0.0748
(1.00) 		0.101
(1.00) 		0.0822
(1.00) 		0.0247
(1.00) 		0.0184
(1.00)
13q loss 11 (3%) 419 0.00211
(0.43) 		0.0235
(1.00) 		0.0784
(1.00) 		0.856
(1.00) 		0.0981
(1.00) 		0.117
(1.00) 		0.012
(1.00) 		0.00289
(0.575)
17p loss 7 (2%) 423 0.0018
(0.374) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.886
(1.00) 		0.112
(1.00) 		0.493
(1.00)
19p loss 4 (1%) 426 0.232
(1.00) 		0.0167
(1.00) 		0.286
(1.00) 		0.348
(1.00) 		0.0373
(1.00) 		0.0348
(1.00) 		0.00712
(1.00) 		0.0048
(0.942)
'1q gain mutation analysis' versus 'CN_CNMF'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.02

Table S1.  Gene #1: '1q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
1Q GAIN MUTATED 7 9 0
1Q GAIN WILD-TYPE 28 321 65

Figure S1.  Get High-res Image Gene #1: '1q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4p gain mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S2.  Gene #2: '4p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
4P GAIN MUTATED 4 0 0
4P GAIN WILD-TYPE 31 330 65

Figure S2.  Get High-res Image Gene #2: '4p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4q gain mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S3.  Gene #3: '4q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
4Q GAIN MUTATED 4 0 0
4Q GAIN WILD-TYPE 31 330 65

Figure S3.  Get High-res Image Gene #3: '4q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 2.61e-17 (Fisher's exact test), Q value = 8e-15

Table S4.  Gene #4: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
5P GAIN MUTATED 15 1 0
5P GAIN WILD-TYPE 20 329 65

Figure S4.  Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000686 (Fisher's exact test), Q value = 0.15

Table S5.  Gene #4: '5p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
5P GAIN MUTATED 10 0 6
5P GAIN WILD-TYPE 109 143 138

Figure S5.  Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'5p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.12

Table S6.  Gene #4: '5p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
5P GAIN MUTATED 10 6 0
5P GAIN WILD-TYPE 98 163 129

Figure S6.  Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain mutation analysis' versus 'CN_CNMF'

P value = 6.43e-16 (Fisher's exact test), Q value = 2e-13

Table S7.  Gene #5: '5q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
5Q GAIN MUTATED 13 0 0
5Q GAIN WILD-TYPE 22 330 65

Figure S7.  Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.066

Table S8.  Gene #5: '5q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
5Q GAIN MUTATED 11 0 2
5Q GAIN WILD-TYPE 124 55 238

Figure S8.  Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'5q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000782 (Fisher's exact test), Q value = 0.17

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
5Q GAIN MUTATED 11 0 0 2
5Q GAIN WILD-TYPE 118 50 89 135

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

'5q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000962 (Fisher's exact test), Q value = 0.21

Table S10.  Gene #5: '5q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
5Q GAIN MUTATED 11 2 0
5Q GAIN WILD-TYPE 130 188 74

Figure S10.  Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000188 (Fisher's exact test), Q value = 0.046

Table S11.  Gene #5: '5q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
5Q GAIN MUTATED 10 0 3
5Q GAIN WILD-TYPE 109 143 141

Figure S11.  Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'5q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.57e-05 (Fisher's exact test), Q value = 0.022

Table S12.  Gene #5: '5q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
5Q GAIN MUTATED 10 3 0
5Q GAIN WILD-TYPE 98 166 129

Figure S12.  Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 3.79e-21 (Fisher's exact test), Q value = 1.2e-18

Table S13.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
7P GAIN MUTATED 17 0 0
7P GAIN WILD-TYPE 18 330 65

Figure S13.  Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S14.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
7P GAIN MUTATED 12 2 3
7P GAIN WILD-TYPE 123 53 237

Figure S14.  Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000677 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
7P GAIN MUTATED 13 0 1 2
7P GAIN WILD-TYPE 116 50 88 135

Figure S15.  Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000554 (Fisher's exact test), Q value = 0.13

Table S16.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
7P GAIN MUTATED 13 2 1
7P GAIN WILD-TYPE 128 188 73

Figure S16.  Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000268 (Fisher's exact test), Q value = 0.064

Table S17.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
7P GAIN MUTATED 12 1 3
7P GAIN WILD-TYPE 107 142 141

Figure S17.  Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'7p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.98e-05 (Fisher's exact test), Q value = 0.025

Table S18.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
7P GAIN MUTATED 12 3 1
7P GAIN WILD-TYPE 96 166 128

Figure S18.  Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 6.81e-24 (Fisher's exact test), Q value = 2.1e-21

Table S19.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
7Q GAIN MUTATED 19 0 0
7Q GAIN WILD-TYPE 16 330 65

Figure S19.  Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.041

Table S20.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
7Q GAIN MUTATED 14 2 3
7Q GAIN WILD-TYPE 121 53 237

Figure S20.  Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000262 (Fisher's exact test), Q value = 0.064

Table S21.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
7Q GAIN MUTATED 14 0 1 2
7Q GAIN WILD-TYPE 115 50 88 135

Figure S21.  Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.044

Table S22.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
7Q GAIN MUTATED 14 2 1
7Q GAIN WILD-TYPE 127 188 73

Figure S22.  Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.79e-05 (Fisher's exact test), Q value = 0.0099

Table S23.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
7Q GAIN MUTATED 14 1 3
7Q GAIN WILD-TYPE 105 142 141

Figure S23.  Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'7q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.44e-06 (Fisher's exact test), Q value = 0.0026

Table S24.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
7Q GAIN MUTATED 14 3 1
7Q GAIN WILD-TYPE 94 166 128

Figure S24.  Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.08

Table S25.  Gene #9: '11q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
11Q GAIN MUTATED 3 0 1
11Q GAIN WILD-TYPE 32 330 64

Figure S25.  Get High-res Image Gene #9: '11q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 7.66e-12 (Fisher's exact test), Q value = 2.3e-09

Table S26.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
12P GAIN MUTATED 10 0 2
12P GAIN WILD-TYPE 25 330 63

Figure S26.  Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00049

Table S27.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
12P GAIN MUTATED 12 0 0
12P GAIN WILD-TYPE 123 55 240

Figure S27.  Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.26e-06 (Fisher's exact test), Q value = 0.002

Table S28.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
12P GAIN MUTATED 12 0 0 0
12P GAIN WILD-TYPE 117 50 89 137

Figure S28.  Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.95e-06 (Fisher's exact test), Q value = 0.0014

Table S29.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
12P GAIN MUTATED 12 0 0
12P GAIN WILD-TYPE 129 190 74

Figure S29.  Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0039

Table S30.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
12P GAIN MUTATED 11 0 1
12P GAIN WILD-TYPE 108 143 143

Figure S30.  Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'12p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.71e-06 (Fisher's exact test), Q value = 0.0011

Table S31.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
12P GAIN MUTATED 11 1 0
12P GAIN WILD-TYPE 97 168 129

Figure S31.  Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 7.66e-12 (Fisher's exact test), Q value = 2.3e-09

Table S32.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
12Q GAIN MUTATED 10 0 2
12Q GAIN WILD-TYPE 25 330 63

Figure S32.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00049

Table S33.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
12Q GAIN MUTATED 12 0 0
12Q GAIN WILD-TYPE 123 55 240

Figure S33.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'12q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.26e-06 (Fisher's exact test), Q value = 0.002

Table S34.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
12Q GAIN MUTATED 12 0 0 0
12Q GAIN WILD-TYPE 117 50 89 137

Figure S34.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'12q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.95e-06 (Fisher's exact test), Q value = 0.0014

Table S35.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
12Q GAIN MUTATED 12 0 0
12Q GAIN WILD-TYPE 129 190 74

Figure S35.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0039

Table S36.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
12Q GAIN MUTATED 11 0 1
12Q GAIN WILD-TYPE 108 143 143

Figure S36.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'12q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.71e-06 (Fisher's exact test), Q value = 0.0011

Table S37.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
12Q GAIN MUTATED 11 1 0
12Q GAIN WILD-TYPE 97 168 129

Figure S37.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain mutation analysis' versus 'CN_CNMF'

P value = 2.19e-07 (Fisher's exact test), Q value = 6.4e-05

Table S38.  Gene #12: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
14Q GAIN MUTATED 6 0 1
14Q GAIN WILD-TYPE 29 330 64

Figure S38.  Get High-res Image Gene #12: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.23

Table S39.  Gene #12: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
14Q GAIN MUTATED 7 0 0
14Q GAIN WILD-TYPE 128 55 240

Figure S39.  Get High-res Image Gene #12: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 3.91e-13 (Fisher's exact test), Q value = 1.2e-10

Table S40.  Gene #13: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
16P GAIN MUTATED 11 0 1
16P GAIN WILD-TYPE 24 330 64

Figure S40.  Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000351 (Fisher's exact test), Q value = 0.082

Table S41.  Gene #13: '16p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
16P GAIN MUTATED 10 1 1
16P GAIN WILD-TYPE 125 54 239

Figure S41.  Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000245 (Fisher's exact test), Q value = 0.06

Table S42.  Gene #13: '16p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
16P GAIN MUTATED 11 0 0 1
16P GAIN WILD-TYPE 118 50 89 136

Figure S42.  Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.042

Table S43.  Gene #13: '16p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
16P GAIN MUTATED 11 1 0
16P GAIN WILD-TYPE 130 189 74

Figure S43.  Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000105 (Fisher's exact test), Q value = 0.026

Table S44.  Gene #13: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
16P GAIN MUTATED 10 0 2
16P GAIN WILD-TYPE 109 143 142

Figure S44.  Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'16p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.013

Table S45.  Gene #13: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
16P GAIN MUTATED 10 2 0
16P GAIN WILD-TYPE 98 167 129

Figure S45.  Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 3.43e-12 (Fisher's exact test), Q value = 1e-09

Table S46.  Gene #14: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
16Q GAIN MUTATED 10 0 0
16Q GAIN WILD-TYPE 25 330 65

Figure S46.  Get High-res Image Gene #14: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000634 (Fisher's exact test), Q value = 0.14

Table S47.  Gene #14: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
16Q GAIN MUTATED 8 2 0
16Q GAIN WILD-TYPE 100 167 129

Figure S47.  Get High-res Image Gene #14: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'CN_CNMF'

P value = 1.49e-07 (Fisher's exact test), Q value = 4.4e-05

Table S48.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
17P GAIN MUTATED 8 2 1
17P GAIN WILD-TYPE 27 328 64

Figure S48.  Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.61e-06 (Fisher's exact test), Q value = 0.0018

Table S49.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
17P GAIN MUTATED 11 0 0
17P GAIN WILD-TYPE 124 55 240

Figure S49.  Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0051

Table S50.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
17P GAIN MUTATED 11 0 0 0
17P GAIN WILD-TYPE 118 50 89 137

Figure S50.  Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'17p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.0053

Table S51.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
17P GAIN MUTATED 11 0 0
17P GAIN WILD-TYPE 130 190 74

Figure S51.  Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.012

Table S52.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
17P GAIN MUTATED 10 0 1
17P GAIN WILD-TYPE 109 143 143

Figure S52.  Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.0037

Table S53.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
17P GAIN MUTATED 10 1 0
17P GAIN WILD-TYPE 98 168 129

Figure S53.  Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 1.21e-07 (Fisher's exact test), Q value = 3.6e-05

Table S54.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
17Q GAIN MUTATED 8 2 2
17Q GAIN WILD-TYPE 27 328 63

Figure S54.  Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00049

Table S55.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
17Q GAIN MUTATED 12 0 0
17Q GAIN WILD-TYPE 123 55 240

Figure S55.  Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.26e-06 (Fisher's exact test), Q value = 0.002

Table S56.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
17Q GAIN MUTATED 12 0 0 0
17Q GAIN WILD-TYPE 117 50 89 137

Figure S56.  Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.95e-06 (Fisher's exact test), Q value = 0.0014

Table S57.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
17Q GAIN MUTATED 12 0 0
17Q GAIN WILD-TYPE 129 190 74

Figure S57.  Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0039

Table S58.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
17Q GAIN MUTATED 11 0 1
17Q GAIN WILD-TYPE 108 143 143

Figure S58.  Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.71e-06 (Fisher's exact test), Q value = 0.0011

Table S59.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
17Q GAIN MUTATED 11 1 0
17Q GAIN WILD-TYPE 97 168 129

Figure S59.  Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000497 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #17: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
19P GAIN MUTATED 3 0 0
19P GAIN WILD-TYPE 32 330 65

Figure S60.  Get High-res Image Gene #17: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S61.  Gene #18: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
19Q GAIN MUTATED 4 0 0
19Q GAIN WILD-TYPE 31 330 65

Figure S61.  Get High-res Image Gene #18: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 8.67e-10 (Fisher's exact test), Q value = 2.6e-07

Table S62.  Gene #19: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
20P GAIN MUTATED 8 0 0
20P GAIN WILD-TYPE 27 330 65

Figure S62.  Get High-res Image Gene #19: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 8.67e-10 (Fisher's exact test), Q value = 2.6e-07

Table S63.  Gene #20: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
20Q GAIN MUTATED 8 0 0
20Q GAIN WILD-TYPE 27 330 65

Figure S63.  Get High-res Image Gene #20: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000497 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #22: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
1P LOSS MUTATED 3 0 0
1P LOSS WILD-TYPE 32 330 65

Figure S64.  Get High-res Image Gene #22: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'CN_CNMF'

P value = 1.7e-08 (Fisher's exact test), Q value = 5e-06

Table S65.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
2P LOSS MUTATED 7 0 1
2P LOSS WILD-TYPE 28 330 64

Figure S65.  Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.051

Table S66.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 127 55 240

Figure S66.  Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000655 (Fisher's exact test), Q value = 0.15

Table S67.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
2P LOSS MUTATED 8 0 0 0
2P LOSS WILD-TYPE 121 50 89 137

Figure S67.  Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000335 (Fisher's exact test), Q value = 0.079

Table S68.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 133 190 74

Figure S68.  Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.012

Table S69.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 111 143 144

Figure S69.  Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.0055

Table S70.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 100 169 129

Figure S70.  Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 1.31e-08 (Fisher's exact test), Q value = 3.9e-06

Table S71.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 28 330 65

Figure S71.  Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.23

Table S72.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 135 55 240
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 128 55 240

Figure S72.  Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.041

Table S73.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 112 143 144

Figure S73.  Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.14e-05 (Fisher's exact test), Q value = 0.021

Table S74.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 101 169 129

Figure S74.  Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000497 (Fisher's exact test), Q value = 0.12

Table S75.  Gene #25: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
3Q LOSS MUTATED 3 0 0
3Q LOSS WILD-TYPE 32 330 65

Figure S75.  Get High-res Image Gene #25: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S76.  Gene #27: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 31 330 65

Figure S76.  Get High-res Image Gene #27: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q loss mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S77.  Gene #28: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 31 330 65

Figure S77.  Get High-res Image Gene #28: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 5.24e-10 (Fisher's exact test), Q value = 1.6e-07

Table S78.  Gene #29: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
9P LOSS MUTATED 9 1 0
9P LOSS WILD-TYPE 26 329 65

Figure S78.  Get High-res Image Gene #29: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 1.46e-10 (Fisher's exact test), Q value = 4.4e-08

Table S79.  Gene #30: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
9Q LOSS MUTATED 11 3 0
9Q LOSS WILD-TYPE 24 327 65

Figure S79.  Get High-res Image Gene #30: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S80.  Gene #31: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
10P LOSS MUTATED 4 0 0
10P LOSS WILD-TYPE 31 330 65

Figure S80.  Get High-res Image Gene #31: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0099

Table S81.  Gene #32: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
10Q LOSS MUTATED 4 0 0
10Q LOSS WILD-TYPE 31 330 65

Figure S81.  Get High-res Image Gene #32: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 2.71e-06 (Fisher's exact test), Q value = 0.00078

Table S82.  Gene #33: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
11P LOSS MUTATED 5 0 0
11P LOSS WILD-TYPE 30 330 65

Figure S82.  Get High-res Image Gene #33: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 2.51e-05 (Fisher's exact test), Q value = 0.0067

Table S83.  Gene #34: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
11Q LOSS MUTATED 5 1 0
11Q LOSS WILD-TYPE 30 329 65

Figure S83.  Get High-res Image Gene #34: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000943 (Fisher's exact test), Q value = 0.21

Table S84.  Gene #36: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
15Q LOSS MUTATED 4 2 0
15Q LOSS WILD-TYPE 31 328 65

Figure S84.  Get High-res Image Gene #36: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000579 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #36: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
15Q LOSS MUTATED 6 0 0
15Q LOSS WILD-TYPE 113 143 144

Figure S85.  Get High-res Image Gene #36: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000319 (Fisher's exact test), Q value = 0.076

Table S86.  Gene #36: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
15Q LOSS MUTATED 6 0 0
15Q LOSS WILD-TYPE 102 169 129

Figure S86.  Get High-res Image Gene #36: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.08

Table S87.  Gene #38: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
18P LOSS MUTATED 3 0 1
18P LOSS WILD-TYPE 32 330 64

Figure S87.  Get High-res Image Gene #38: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.08

Table S88.  Gene #39: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
18Q LOSS MUTATED 3 0 1
18Q LOSS WILD-TYPE 32 330 64

Figure S88.  Get High-res Image Gene #39: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.0083

Table S89.  Gene #41: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
21Q LOSS MUTATED 4 0 1
21Q LOSS WILD-TYPE 31 330 64

Figure S89.  Get High-res Image Gene #41: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 3.28e-45 (Fisher's exact test), Q value = 1e-42

Table S90.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 330 65
22Q LOSS MUTATED 9 0 45
22Q LOSS WILD-TYPE 26 330 20

Figure S90.  Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.64e-09 (Fisher's exact test), Q value = 1.1e-06

Table S91.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 50 89 137
22Q LOSS MUTATED 29 3 16 1
22Q LOSS WILD-TYPE 100 47 73 136

Figure S91.  Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.17e-07 (Fisher's exact test), Q value = 6.3e-05

Table S92.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 190 74
22Q LOSS MUTATED 29 6 14
22Q LOSS WILD-TYPE 112 184 60

Figure S92.  Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.064

Table S93.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 143 144
22Q LOSS MUTATED 28 14 10
22Q LOSS WILD-TYPE 91 129 134

Figure S93.  Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.28e-05 (Fisher's exact test), Q value = 0.021

Table S94.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 169 129
22Q LOSS MUTATED 26 10 16
22Q LOSS WILD-TYPE 82 159 113

Figure S94.  Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 430

  • Number of significantly arm-level cnvs = 42

  • 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

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)
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