Thyroid Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 432 patients, 95 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',  'METHLYATION_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, 95 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%) 419 3.8e-16
(1.16e-13) 		0.000147
(0.0363) 		0.901
(1.00) 		0.0299
(1.00) 		0.000812
(0.176) 		0.000952
(0.206) 		0.000192
(0.0467) 		8.84e-05
(0.0222)
7p gain 17 (4%) 415 1.8e-21
(5.53e-19) 		0.000397
(0.0917) 		1
(1.00) 		0.0129
(1.00) 		0.000704
(0.154) 		0.000607
(0.135) 		0.000271
(0.0652) 		0.000103
(0.0257)
7q gain 19 (4%) 413 2.84e-24
(8.79e-22) 		7.69e-05
(0.0195) 		0.689
(1.00) 		0.00298
(0.594) 		0.000286
(0.0682) 		0.000176
(0.0429) 		3.84e-05
(0.00996) 		9.67e-06
(0.00267)
12p gain 12 (3%) 420 5.23e-12
(1.59e-09) 		1.01e-06
(0.000292) 		0.901
(1.00) 		0.0299
(1.00) 		7.78e-06
(0.00217) 		4.91e-06
(0.00138) 		1.46e-05
(0.00401) 		3.89e-06
(0.00111)
12q gain 12 (3%) 420 5.23e-12
(1.59e-09) 		1.01e-06
(0.000292) 		0.901
(1.00) 		0.0299
(1.00) 		7.78e-06
(0.00217) 		4.91e-06
(0.00138) 		1.46e-05
(0.00401) 		3.89e-06
(0.00111)
16p gain 12 (3%) 420 2.57e-13
(7.84e-11) 		4.7e-05
(0.0121) 		1
(1.00) 		0.0445
(1.00) 		0.000239
(0.0577) 		0.000167
(0.0411) 		0.000137
(0.0341) 		5.08e-05
(0.013)
17p gain 11 (3%) 421 1.04e-07
(3.05e-05) 		4.25e-06
(0.0012) 		0.772
(1.00) 		0.0179
(1.00) 		1.83e-05
(0.00495) 		1.93e-05
(0.0052) 		4.67e-05
(0.0121) 		1.41e-05
(0.00387)
17q gain 12 (3%) 420 7.49e-08
(2.2e-05) 		1.01e-06
(0.000292) 		0.795
(1.00) 		0.0206
(1.00) 		7.78e-06
(0.00217) 		4.91e-06
(0.00138) 		1.46e-05
(0.00401) 		3.89e-06
(0.00111)
2p loss 8 (2%) 424 1.32e-08
(3.91e-06) 		0.000197
(0.0478) 		1
(1.00) 		0.0817
(1.00) 		0.000731
(0.159) 		0.000334
(0.0775) 		4.73e-05
(0.0121) 		2.14e-05
(0.00575)
22q loss 54 (12%) 378 1.18e-45
(3.64e-43) 		0.00135
(0.286) 		0.114
(1.00) 		0.0835
(1.00) 		3.69e-09
(1.1e-06) 		2.07e-07
(6.01e-05) 		0.000284
(0.0679) 		8.99e-05
(0.0225)
2q loss 7 (2%) 425 1.01e-08
(3e-06) 		0.000476
(0.108) 		0.837
(1.00) 		0.0549
(1.00) 		0.00213
(0.433) 		0.00122
(0.261) 		0.000168
(0.0411) 		8.4e-05
(0.0212)
5p gain 16 (4%) 416 1.4e-17
(4.28e-15) 		0.00411
(0.806) 		1
(1.00) 		0.125
(1.00) 		0.00945
(1.00) 		0.01
(1.00) 		0.000633
(0.14) 		0.000544
(0.122)
16q gain 10 (2%) 422 2.33e-12
(7.1e-10) 		0.000314
(0.0735) 		0.856
(1.00) 		0.129
(1.00) 		0.00204
(0.421) 		0.00146
(0.309) 		0.00165
(0.346) 		0.000643
(0.142)
15q loss 6 (1%) 426 0.000556
(0.125) 		0.0112
(1.00) 		0.458
(1.00) 		0.256
(1.00) 		0.0173
(1.00) 		0.00933
(1.00) 		0.000592
(0.132) 		0.000328
(0.0764)
14q gain 7 (2%) 425 1.77e-07
(5.18e-05) 		0.000476
(0.108) 		1
(1.00) 		0.256
(1.00) 		0.00213
(0.433) 		0.00122
(0.261) 		0.00437
(0.853) 		0.00209
(0.426)
1q gain 16 (4%) 416 5.82e-05
(0.0148) 		0.255
(1.00) 		0.0153
(1.00) 		0.0826
(1.00) 		0.0325
(1.00) 		0.0233
(1.00) 		0.136
(1.00) 		0.0514
(1.00)
4p gain 4 (1%) 428 3.24e-05
(0.00862) 		0.0212
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.109
(1.00) 		0.0989
(1.00)
4q gain 4 (1%) 428 3.24e-05
(0.00862) 		0.0212
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.109
(1.00) 		0.0989
(1.00)
11q gain 4 (1%) 428 0.000308
(0.0731) 		0.0212
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00722
(1.00) 		0.00489
(0.944)
19p gain 3 (1%) 429 0.000448
(0.103) 		0.0552
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.025
(1.00) 		0.0187
(1.00)
19q gain 4 (1%) 428 3.24e-05
(0.00862) 		0.0212
(1.00) 		0.636
(1.00) 		0.0551
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00722
(1.00) 		0.00489
(0.944)
20p gain 8 (2%) 424 6.44e-10
(1.93e-07) 		0.00221
(0.445) 		1
(1.00) 		0.0817
(1.00) 		0.0134
(1.00) 		0.0136
(1.00) 		0.0122
(1.00) 		0.00562
(1.00)
20q gain 8 (2%) 424 6.44e-10
(1.93e-07) 		0.00221
(0.445) 		1
(1.00) 		0.0817
(1.00) 		0.0134
(1.00) 		0.0136
(1.00) 		0.0122
(1.00) 		0.00562
(1.00)
1p loss 3 (1%) 429 0.000448
(0.103) 		0.729
(1.00) 		0.487
(1.00) 		0.195
(1.00) 		0.295
(1.00) 		0.359
(1.00)
3q loss 3 (1%) 429 0.000448
(0.103) 		0.0552
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.025
(1.00) 		0.0187
(1.00)
8p loss 4 (1%) 428 3.24e-05
(0.00862) 		0.0532
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00722
(1.00) 		0.00489
(0.944)
8q loss 4 (1%) 428 3.24e-05
(0.00862) 		0.0532
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00722
(1.00) 		0.00489
(0.944)
9p loss 10 (2%) 422 3.74e-10
(1.12e-07) 		0.609
(1.00) 		0.559
(1.00) 		0.206
(1.00) 		0.249
(1.00) 		0.527
(1.00) 		0.182
(1.00) 		0.143
(1.00)
9q loss 14 (3%) 418 8.23e-11
(2.48e-08) 		0.212
(1.00) 		0.21
(1.00) 		0.00441
(0.855) 		0.441
(1.00) 		0.823
(1.00) 		0.193
(1.00) 		0.256
(1.00)
10p loss 4 (1%) 428 3.24e-05
(0.00862) 		0.473
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.109
(1.00) 		0.0989
(1.00)
10q loss 4 (1%) 428 3.24e-05
(0.00862) 		0.473
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.109
(1.00) 		0.0989
(1.00)
11p loss 5 (1%) 427 2.27e-06
(0.000652) 		0.0689
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.0495
(1.00) 		0.166
(1.00) 		0.0383
(1.00) 		0.0225
(1.00)
11q loss 6 (1%) 426 2.33e-05
(0.00624) 		0.024
(1.00) 		0.388
(1.00) 		0.798
(1.00) 		0.0186
(1.00) 		0.0672
(1.00) 		0.0131
(1.00) 		0.00695
(1.00)
18p loss 4 (1%) 428 0.000308
(0.0731) 		0.204
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.109
(1.00) 		0.0389
(1.00)
18q loss 4 (1%) 428 0.000308
(0.0731) 		0.204
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.109
(1.00) 		0.0389
(1.00)
21q loss 5 (1%) 427 2.73e-05
(0.00728) 		0.0225
(1.00) 		0.384
(1.00) 		0.0551
(1.00) 		0.0495
(1.00) 		0.166
(1.00) 		0.0383
(1.00) 		0.0225
(1.00)
11p gain 5 (1%) 427 0.00181
(0.377) 		0.00503
(0.946) 		0.0173
(1.00) 		0.00933
(1.00) 		0.00207
(0.425) 		0.00127
(0.271)
21q gain 3 (1%) 429 0.00322
(0.635) 		0.0552
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.025
(1.00) 		0.0187
(1.00)
6q loss 3 (1%) 429 0.0261
(1.00) 		0.0552
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.025
(1.00) 		0.0187
(1.00)
13q loss 11 (3%) 421 0.00193
(0.399) 		0.0337
(1.00) 		0.0779
(1.00) 		1
(1.00) 		0.0941
(1.00) 		0.116
(1.00) 		0.0161
(1.00) 		0.00298
(0.594)
17p loss 7 (2%) 425 0.00165
(0.346) 		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%) 428 0.23
(1.00) 		0.0212
(1.00) 		0.281
(1.00) 		0.369
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00722
(1.00) 		0.00489
(0.944)
'1q gain mutation analysis' versus 'CN_CNMF'

P value = 5.82e-05 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
1Q GAIN MUTATED 7 9 0
1Q GAIN WILD-TYPE 27 323 66

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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
4P GAIN MUTATED 4 0 0
4P GAIN WILD-TYPE 30 332 66

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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
4Q GAIN MUTATED 4 0 0
4Q GAIN WILD-TYPE 30 332 66

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 = 1.4e-17 (Fisher's exact test), Q value = 4.3e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
5P GAIN MUTATED 15 1 0
5P GAIN WILD-TYPE 19 331 66

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 = 0.000633 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
5P GAIN MUTATED 10 0 6
5P GAIN WILD-TYPE 110 144 138

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 = 0.000544 (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 109 169 130
5P GAIN MUTATED 10 6 0
5P GAIN WILD-TYPE 99 163 130

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 = 3.8e-16 (Fisher's exact test), Q value = 1.2e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
5Q GAIN MUTATED 13 0 0
5Q GAIN WILD-TYPE 21 332 66

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 = 0.000147 (Fisher's exact test), Q value = 0.036

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
5Q GAIN MUTATED 11 1 1
5Q GAIN WILD-TYPE 125 64 230

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 = 0.000812 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
5Q GAIN MUTATED 11 0 0 2
5Q GAIN WILD-TYPE 119 50 89 136

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 = 0.000952 (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 142 191 74
5Q GAIN MUTATED 11 2 0
5Q GAIN WILD-TYPE 131 189 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 = 0.000192 (Fisher's exact test), Q value = 0.047

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
5Q GAIN MUTATED 10 0 3
5Q GAIN WILD-TYPE 110 144 141

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 = 8.84e-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 109 169 130
5Q GAIN MUTATED 10 3 0
5Q GAIN WILD-TYPE 99 166 130

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 = 1.8e-21 (Fisher's exact test), Q value = 5.5e-19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
7P GAIN MUTATED 17 0 0
7P GAIN WILD-TYPE 17 332 66

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 = 0.000397 (Fisher's exact test), Q value = 0.092

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
7P GAIN MUTATED 12 3 2
7P GAIN WILD-TYPE 124 62 229

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 = 0.000704 (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 130 50 89 138
7P GAIN MUTATED 13 0 1 2
7P GAIN WILD-TYPE 117 50 88 136

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 = 0.000607 (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 142 191 74
7P GAIN MUTATED 13 2 1
7P GAIN WILD-TYPE 129 189 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 = 0.000271 (Fisher's exact test), Q value = 0.065

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
7P GAIN MUTATED 12 1 3
7P GAIN WILD-TYPE 108 143 141

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 = 0.000103 (Fisher's exact test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
7P GAIN MUTATED 12 3 1
7P GAIN WILD-TYPE 97 166 129

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 = 2.84e-24 (Fisher's exact test), Q value = 8.8e-22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
7Q GAIN MUTATED 19 0 0
7Q GAIN WILD-TYPE 15 332 66

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 = 7.69e-05 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
7Q GAIN MUTATED 14 3 2
7Q GAIN WILD-TYPE 122 62 229

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 = 0.000286 (Fisher's exact test), Q value = 0.068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
7Q GAIN MUTATED 14 0 1 2
7Q GAIN WILD-TYPE 116 50 88 136

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 = 0.000176 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
7Q GAIN MUTATED 14 2 1
7Q GAIN WILD-TYPE 128 189 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 = 3.84e-05 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
7Q GAIN MUTATED 14 1 3
7Q GAIN WILD-TYPE 106 143 141

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 = 9.67e-06 (Fisher's exact test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
7Q GAIN MUTATED 14 3 1
7Q GAIN WILD-TYPE 95 166 129

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 = 0.000308 (Fisher's exact test), Q value = 0.073

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
11Q GAIN MUTATED 3 0 1
11Q GAIN WILD-TYPE 31 332 65

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 = 5.23e-12 (Fisher's exact test), Q value = 1.6e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
12P GAIN MUTATED 10 0 2
12P GAIN WILD-TYPE 24 332 64

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 = 1.01e-06 (Fisher's exact test), Q value = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
12P GAIN MUTATED 12 0 0
12P GAIN WILD-TYPE 124 65 231

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 = 7.78e-06 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
12P GAIN MUTATED 12 0 0 0
12P GAIN WILD-TYPE 118 50 89 138

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 = 4.91e-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 142 191 74
12P GAIN MUTATED 12 0 0
12P GAIN WILD-TYPE 130 191 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 = 1.46e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
12P GAIN MUTATED 11 0 1
12P GAIN WILD-TYPE 109 144 143

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 = 3.89e-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 109 169 130
12P GAIN MUTATED 11 1 0
12P GAIN WILD-TYPE 98 168 130

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 = 5.23e-12 (Fisher's exact test), Q value = 1.6e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
12Q GAIN MUTATED 10 0 2
12Q GAIN WILD-TYPE 24 332 64

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 = 1.01e-06 (Fisher's exact test), Q value = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
12Q GAIN MUTATED 12 0 0
12Q GAIN WILD-TYPE 124 65 231

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 = 7.78e-06 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
12Q GAIN MUTATED 12 0 0 0
12Q GAIN WILD-TYPE 118 50 89 138

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 = 4.91e-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 142 191 74
12Q GAIN MUTATED 12 0 0
12Q GAIN WILD-TYPE 130 191 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 = 1.46e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
12Q GAIN MUTATED 11 0 1
12Q GAIN WILD-TYPE 109 144 143

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 = 3.89e-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 109 169 130
12Q GAIN MUTATED 11 1 0
12Q GAIN WILD-TYPE 98 168 130

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 = 1.77e-07 (Fisher's exact test), Q value = 5.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
14Q GAIN MUTATED 6 0 1
14Q GAIN WILD-TYPE 28 332 65

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 = 0.000476 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
14Q GAIN MUTATED 7 0 0
14Q GAIN WILD-TYPE 129 65 231

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 = 2.57e-13 (Fisher's exact test), Q value = 7.8e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
16P GAIN MUTATED 11 0 1
16P GAIN WILD-TYPE 23 332 65

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 = 4.7e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
16P GAIN MUTATED 10 2 0
16P GAIN WILD-TYPE 126 63 231

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 = 0.000239 (Fisher's exact test), Q value = 0.058

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
16P GAIN MUTATED 11 0 0 1
16P GAIN WILD-TYPE 119 50 89 137

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 = 0.000167 (Fisher's exact test), Q value = 0.041

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
16P GAIN MUTATED 11 1 0
16P GAIN WILD-TYPE 131 190 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 = 0.000137 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
16P GAIN MUTATED 10 0 2
16P GAIN WILD-TYPE 110 144 142

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 = 5.08e-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 109 169 130
16P GAIN MUTATED 10 2 0
16P GAIN WILD-TYPE 99 167 130

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 = 2.33e-12 (Fisher's exact test), Q value = 7.1e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
16Q GAIN MUTATED 10 0 0
16Q GAIN WILD-TYPE 24 332 66

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

'16q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.073

Table S47.  Gene #14: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
16Q GAIN MUTATED 8 2 0
16Q GAIN WILD-TYPE 128 63 231

Figure S47.  Get High-res Image Gene #14: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000643 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #14: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
16Q GAIN MUTATED 8 2 0
16Q GAIN WILD-TYPE 101 167 130

Figure S48.  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 = 1.04e-07 (Fisher's exact test), Q value = 3.1e-05

Table S49.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
17P GAIN MUTATED 8 2 1
17P GAIN WILD-TYPE 26 330 65

Figure S49.  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 = 4.25e-06 (Fisher's exact test), Q value = 0.0012

Table S50.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
17P GAIN MUTATED 11 0 0
17P GAIN WILD-TYPE 125 65 231

Figure S50.  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 = 1.83e-05 (Fisher's exact test), Q value = 0.0049

Table S51.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
17P GAIN MUTATED 11 0 0 0
17P GAIN WILD-TYPE 119 50 89 138

Figure S51.  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 = 1.93e-05 (Fisher's exact test), Q value = 0.0052

Table S52.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
17P GAIN MUTATED 11 0 0
17P GAIN WILD-TYPE 131 191 74

Figure S52.  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 = 4.67e-05 (Fisher's exact test), Q value = 0.012

Table S53.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
17P GAIN MUTATED 10 0 1
17P GAIN WILD-TYPE 110 144 143

Figure S53.  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 = 1.41e-05 (Fisher's exact test), Q value = 0.0039

Table S54.  Gene #15: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
17P GAIN MUTATED 10 1 0
17P GAIN WILD-TYPE 99 168 130

Figure S54.  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 = 7.49e-08 (Fisher's exact test), Q value = 2.2e-05

Table S55.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
17Q GAIN MUTATED 8 2 2
17Q GAIN WILD-TYPE 26 330 64

Figure S55.  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 = 1.01e-06 (Fisher's exact test), Q value = 0.00029

Table S56.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
17Q GAIN MUTATED 12 0 0
17Q GAIN WILD-TYPE 124 65 231

Figure S56.  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 = 7.78e-06 (Fisher's exact test), Q value = 0.0022

Table S57.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
17Q GAIN MUTATED 12 0 0 0
17Q GAIN WILD-TYPE 118 50 89 138

Figure S57.  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 = 4.91e-06 (Fisher's exact test), Q value = 0.0014

Table S58.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
17Q GAIN MUTATED 12 0 0
17Q GAIN WILD-TYPE 130 191 74

Figure S58.  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 = 1.46e-05 (Fisher's exact test), Q value = 0.004

Table S59.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
17Q GAIN MUTATED 11 0 1
17Q GAIN WILD-TYPE 109 144 143

Figure S59.  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 = 3.89e-06 (Fisher's exact test), Q value = 0.0011

Table S60.  Gene #16: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
17Q GAIN MUTATED 11 1 0
17Q GAIN WILD-TYPE 98 168 130

Figure S60.  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 = 0.000448 (Fisher's exact test), Q value = 0.1

Table S61.  Gene #17: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
19P GAIN MUTATED 3 0 0
19P GAIN WILD-TYPE 31 332 66

Figure S61.  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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S62.  Gene #18: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
19Q GAIN MUTATED 4 0 0
19Q GAIN WILD-TYPE 30 332 66

Figure S62.  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 = 6.44e-10 (Fisher's exact test), Q value = 1.9e-07

Table S63.  Gene #19: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
20P GAIN MUTATED 8 0 0
20P GAIN WILD-TYPE 26 332 66

Figure S63.  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 = 6.44e-10 (Fisher's exact test), Q value = 1.9e-07

Table S64.  Gene #20: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
20Q GAIN MUTATED 8 0 0
20Q GAIN WILD-TYPE 26 332 66

Figure S64.  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 = 0.000448 (Fisher's exact test), Q value = 0.1

Table S65.  Gene #22: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
1P LOSS MUTATED 3 0 0
1P LOSS WILD-TYPE 31 332 66

Figure S65.  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 = 1.32e-08 (Fisher's exact test), Q value = 3.9e-06

Table S66.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
2P LOSS MUTATED 7 0 1
2P LOSS WILD-TYPE 27 332 65

Figure S66.  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 = 0.000197 (Fisher's exact test), Q value = 0.048

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 128 65 231

Figure S67.  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 = 0.000731 (Fisher's exact test), Q value = 0.16

Table S68.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
2P LOSS MUTATED 8 0 0 0
2P LOSS WILD-TYPE 122 50 89 138

Figure S68.  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 = 0.000334 (Fisher's exact test), Q value = 0.078

Table S69.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 134 191 74

Figure S69.  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 = 4.73e-05 (Fisher's exact test), Q value = 0.012

Table S70.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 112 144 144

Figure S70.  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 = 2.14e-05 (Fisher's exact test), Q value = 0.0057

Table S71.  Gene #23: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 101 169 130

Figure S71.  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 = 1.01e-08 (Fisher's exact test), Q value = 3e-06

Table S72.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 27 332 66

Figure S72.  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 = 0.000476 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 65 231
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 129 65 231

Figure S73.  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 = 0.000168 (Fisher's exact test), Q value = 0.041

Table S74.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 113 144 144

Figure S74.  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 = 8.4e-05 (Fisher's exact test), Q value = 0.021

Table S75.  Gene #24: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 102 169 130

Figure S75.  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 = 0.000448 (Fisher's exact test), Q value = 0.1

Table S76.  Gene #25: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
3Q LOSS MUTATED 3 0 0
3Q LOSS WILD-TYPE 31 332 66

Figure S76.  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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S77.  Gene #27: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 30 332 66

Figure S77.  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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S78.  Gene #28: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 30 332 66

Figure S78.  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 = 3.74e-10 (Fisher's exact test), Q value = 1.1e-07

Table S79.  Gene #29: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
9P LOSS MUTATED 9 1 0
9P LOSS WILD-TYPE 25 331 66

Figure S79.  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 = 8.23e-11 (Fisher's exact test), Q value = 2.5e-08

Table S80.  Gene #30: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
9Q LOSS MUTATED 11 3 0
9Q LOSS WILD-TYPE 23 329 66

Figure S80.  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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S81.  Gene #31: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
10P LOSS MUTATED 4 0 0
10P LOSS WILD-TYPE 30 332 66

Figure S81.  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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S82.  Gene #32: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
10Q LOSS MUTATED 4 0 0
10Q LOSS WILD-TYPE 30 332 66

Figure S82.  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 = 2.27e-06 (Fisher's exact test), Q value = 0.00065

Table S83.  Gene #33: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
11P LOSS MUTATED 5 0 0
11P LOSS WILD-TYPE 29 332 66

Figure S83.  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 = 2.33e-05 (Fisher's exact test), Q value = 0.0062

Table S84.  Gene #34: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
11Q LOSS MUTATED 5 1 0
11Q LOSS WILD-TYPE 29 331 66

Figure S84.  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 = 0.000556 (Fisher's exact test), Q value = 0.12

Table S85.  Gene #36: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
15Q LOSS MUTATED 4 2 0
15Q LOSS WILD-TYPE 30 330 66

Figure S85.  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 = 0.000592 (Fisher's exact test), Q value = 0.13

Table S86.  Gene #36: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
15Q LOSS MUTATED 6 0 0
15Q LOSS WILD-TYPE 114 144 144

Figure S86.  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 = 0.000328 (Fisher's exact test), Q value = 0.076

Table S87.  Gene #36: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
15Q LOSS MUTATED 6 0 0
15Q LOSS WILD-TYPE 103 169 130

Figure S87.  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 = 0.000308 (Fisher's exact test), Q value = 0.073

Table S88.  Gene #38: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
18P LOSS MUTATED 3 0 1
18P LOSS WILD-TYPE 31 332 65

Figure S88.  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 = 0.000308 (Fisher's exact test), Q value = 0.073

Table S89.  Gene #39: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
18Q LOSS MUTATED 3 0 1
18Q LOSS WILD-TYPE 31 332 65

Figure S89.  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 = 2.73e-05 (Fisher's exact test), Q value = 0.0073

Table S90.  Gene #41: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
21Q LOSS MUTATED 4 0 1
21Q LOSS WILD-TYPE 30 332 65

Figure S90.  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 = 1.18e-45 (Fisher's exact test), Q value = 3.6e-43

Table S91.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 332 66
22Q LOSS MUTATED 8 0 46
22Q LOSS WILD-TYPE 26 332 20

Figure S91.  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 = 3.69e-09 (Fisher's exact test), Q value = 1.1e-06

Table S92.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 50 89 138
22Q LOSS MUTATED 29 3 16 1
22Q LOSS WILD-TYPE 101 47 73 137

Figure S92.  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 = 2.07e-07 (Fisher's exact test), Q value = 6e-05

Table S93.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
22Q LOSS MUTATED 29 6 14
22Q LOSS WILD-TYPE 113 185 60

Figure S93.  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 = 0.000284 (Fisher's exact test), Q value = 0.068

Table S94.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 144 144
22Q LOSS MUTATED 28 14 10
22Q LOSS WILD-TYPE 92 130 134

Figure S94.  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 = 8.99e-05 (Fisher's exact test), Q value = 0.022

Table S95.  Gene #42: '22q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 169 130
22Q LOSS MUTATED 26 10 16
22Q LOSS WILD-TYPE 83 159 114

Figure S95.  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 = 432

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