Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C13J39ZX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13J39ZX
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 45 arm-level results and 8 molecular subtypes across 497 patients, 102 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',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 13q gain cnv correlated to 'CN_CNMF'.

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

  • 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',  'MRNASEQ_CHIERARCHICAL', 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' and 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_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',  'MRNASEQ_CHIERARCHICAL',  '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',  'METHLYATION_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 45 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 102 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
7q gain 0 (0%) 478 1.76e-23
(5.65e-21) 		3.64e-05
(0.00969) 		0.689
(1.00) 		0.00298
(0.597) 		4.87e-05
(0.0128) 		6.26e-06
(0.00177) 		0.000289
(0.0691) 		2.87e-05
(0.00773)
12p gain 0 (0%) 486 1.03e-12
(3.22e-10) 		3.14e-06
(0.000912) 		0.901
(1.00) 		0.0299
(1.00) 		1.59e-05
(0.00446) 		3.43e-06
(0.000987) 		5.19e-05
(0.0136) 		1.7e-05
(0.00472)
12q gain 0 (0%) 485 1.27e-12
(3.98e-10) 		6.85e-07
(0.000204) 		0.901
(1.00) 		0.0299
(1.00) 		3.88e-06
(0.00111) 		7.94e-07
(0.000235) 		1.64e-05
(0.00459) 		4.85e-06
(0.00138)
16p gain 0 (0%) 485 5.51e-14
(1.75e-11) 		2.82e-05
(0.0076) 		1
(1.00) 		0.0445
(1.00) 		0.000128
(0.0323) 		3.37e-05
(0.00899) 		0.000214
(0.052) 		5.88e-05
(0.0152)
17p gain 0 (0%) 485 2e-09
(6.13e-07) 		6.85e-07
(0.000204) 		0.772
(1.00) 		0.0179
(1.00) 		3.88e-06
(0.00111) 		7.94e-07
(0.000235) 		5.19e-05
(0.0136) 		1.7e-05
(0.00472)
17q gain 0 (0%) 484 3.83e-09
(1.17e-06) 		1.58e-07
(4.73e-05) 		0.795
(1.00) 		0.0206
(1.00) 		1.36e-06
(0.000398) 		1.92e-07
(5.74e-05) 		1.64e-05
(0.00459) 		4.85e-06
(0.00138)
2p loss 0 (0%) 489 5.02e-09
(1.53e-06) 		8.94e-05
(0.0229) 		1
(1.00) 		0.0817
(1.00) 		0.000496
(0.114) 		0.000164
(0.041) 		5.53e-05
(0.0144) 		2.27e-05
(0.00615)
22q loss 0 (0%) 431 6.79e-58
(2.19e-55) 		0.00013
(0.0328) 		0.114
(1.00) 		0.0835
(1.00) 		8.4e-11
(2.6e-08) 		1.98e-10
(6.11e-08) 		4.33e-05
(0.0114) 		9.51e-06
(0.00268)
5q gain 0 (0%) 483 2.6e-18
(8.27e-16) 		3.16e-05
(0.00847) 		0.901
(1.00) 		0.0299
(1.00) 		0.000163
(0.0408) 		4.26e-05
(0.0113) 		0.00146
(0.309) 		0.000106
(0.0269)
7p gain 0 (0%) 480 1.59e-22
(5.09e-20) 		0.000218
(0.0529) 		1
(1.00) 		0.0129
(1.00) 		0.000389
(0.0906) 		6.9e-05
(0.0178) 		0.00232
(0.478) 		0.000272
(0.0652)
2q loss 0 (0%) 490 3.78e-09
(1.16e-06) 		0.000378
(0.0884) 		0.837
(1.00) 		0.0549
(1.00) 		0.00144
(0.307) 		0.00065
(0.146) 		0.000192
(0.0475) 		8.85e-05
(0.0227)
5p gain 0 (0%) 480 6.97e-20
(2.22e-17) 		0.000747
(0.166) 		1
(1.00) 		0.125
(1.00) 		0.00247
(0.499) 		0.000522
(0.119) 		0.00691
(1.00) 		0.000541
(0.123)
14q gain 0 (0%) 489 5.02e-09
(1.53e-06) 		8.94e-05
(0.0229) 		1
(1.00) 		0.256
(1.00) 		0.000496
(0.114) 		0.000164
(0.041) 		0.00467
(0.906) 		0.00229
(0.475)
16q gain 0 (0%) 487 5.67e-13
(1.79e-10) 		0.000247
(0.0595) 		0.856
(1.00) 		0.129
(1.00) 		0.00144
(0.308) 		0.000429
(0.0995) 		0.00169
(0.355) 		0.000547
(0.124)
15q loss 0 (0%) 490 0.000464
(0.107) 		0.00241
(0.494) 		0.458
(1.00) 		0.256
(1.00) 		0.00491
(0.948) 		0.00175
(0.367) 		0.000664
(0.149) 		0.000342
(0.0805)
20p gain 0 (0%) 488 1.11e-11
(3.44e-09) 		0.000767
(0.17) 		1
(1.00) 		0.0817
(1.00) 		0.00397
(0.789) 		0.00123
(0.27) 		0.0124
(1.00) 		0.00619
(1.00)
20q gain 0 (0%) 488 1.11e-11
(3.44e-09) 		0.000767
(0.17) 		1
(1.00) 		0.0817
(1.00) 		0.00397
(0.789) 		0.00123
(0.27) 		0.0124
(1.00) 		0.00619
(1.00)
1q gain 0 (0%) 476 3.29e-06
(0.000951) 		0.0812
(1.00) 		0.0153
(1.00) 		0.0826
(1.00) 		0.0148
(1.00) 		0.00133
(0.288) 		0.224
(1.00) 		0.204
(1.00)
4p gain 0 (0%) 493 1.85e-05
(0.0051) 		0.0192
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.112
(1.00) 		0.0975
(1.00)
4q gain 0 (0%) 493 1.85e-05
(0.0051) 		0.0192
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.112
(1.00) 		0.0975
(1.00)
11q gain 0 (0%) 493 0.000204
(0.0503) 		0.0192
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.965)
13q gain 0 (0%) 494 0.000294
(0.07) 		0.0495
(1.00) 		0.101
(1.00) 		0.0769
(1.00)
19p gain 0 (0%) 493 1.85e-05
(0.0051) 		0.0192
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.0264
(1.00) 		0.0191
(1.00)
19q gain 0 (0%) 492 1.12e-06
(0.00033) 		0.00434
(0.855) 		0.636
(1.00) 		0.0551
(1.00) 		0.0147
(1.00) 		0.00587
(1.00) 		0.00778
(1.00) 		0.00503
(0.965)
1p loss 0 (0%) 494 0.000294
(0.07) 		0.559
(1.00) 		0.495
(1.00) 		0.214
(1.00) 		0.3
(1.00) 		0.276
(1.00)
3q loss 0 (0%) 494 0.000294
(0.07) 		0.0495
(1.00) 		0.101
(1.00) 		0.0769
(1.00) 		0.0264
(1.00) 		0.0191
(1.00)
8p loss 0 (0%) 493 1.85e-05
(0.0051) 		0.047
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.965)
8q loss 0 (0%) 493 1.85e-05
(0.0051) 		0.047
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.965)
9p loss 0 (0%) 485 1.08e-11
(3.36e-09) 		0.272
(1.00) 		0.559
(1.00) 		0.206
(1.00) 		0.157
(1.00) 		0.206
(1.00) 		0.185
(1.00) 		0.159
(1.00)
9q loss 0 (0%) 480 1.58e-13
(4.99e-11) 		0.204
(1.00) 		0.21
(1.00) 		0.00441
(0.86) 		0.268
(1.00) 		0.295
(1.00) 		0.235
(1.00) 		0.228
(1.00)
10p loss 0 (0%) 491 6.62e-08
(2e-05) 		0.0979
(1.00) 		0.047
(1.00) 		0.0135
(1.00) 		0.0399
(1.00) 		0.0333
(1.00)
10q loss 0 (0%) 492 1.12e-06
(0.00033) 		0.175
(1.00) 		0.102
(1.00) 		0.0405
(1.00) 		0.112
(1.00) 		0.0975
(1.00)
11p loss 0 (0%) 490 7.74e-08
(2.33e-05) 		0.00947
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.0148
(1.00) 		0.0419
(1.00) 		0.0399
(1.00) 		0.0333
(1.00)
11q loss 0 (0%) 488 3.24e-06
(0.00094) 		0.0149
(1.00) 		0.388
(1.00) 		0.798
(1.00) 		0.044
(1.00) 		0.039
(1.00) 		0.0138
(1.00) 		0.0075
(1.00)
18p loss 0 (0%) 493 0.000204
(0.0503) 		0.19
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.22
(1.00) 		0.12
(1.00) 		0.0743
(1.00) 		0.0671
(1.00)
18q loss 0 (0%) 493 0.000204
(0.0503) 		0.19
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.22
(1.00) 		0.12
(1.00) 		0.0743
(1.00) 		0.0671
(1.00)
21q loss 0 (0%) 491 0.000192
(0.0475) 		0.0979
(1.00) 		0.384
(1.00) 		0.0551
(1.00) 		0.0439
(1.00) 		0.112
(1.00) 		0.0399
(1.00) 		0.0333
(1.00)
11p gain 0 (0%) 492 0.00134
(0.288) 		0.00434
(0.855) 		0.0147
(1.00) 		0.00587
(1.00) 		0.00228
(0.474) 		0.00132
(0.286)
18p gain 0 (0%) 494 0.00245
(0.499) 		0.0495
(1.00) 		0.101
(1.00) 		0.0769
(1.00)
18q gain 0 (0%) 494 0.00245
(0.499) 		0.0495
(1.00) 		0.101
(1.00) 		0.0769
(1.00)
21q gain 0 (0%) 494 0.00245
(0.499) 		0.0495
(1.00) 		0.101
(1.00) 		0.0769
(1.00) 		0.0264
(1.00) 		0.0191
(1.00)
6q loss 0 (0%) 494 0.0218
(1.00) 		0.0495
(1.00) 		0.101
(1.00) 		0.0769
(1.00) 		0.0264
(1.00) 		0.0191
(1.00)
13q loss 0 (0%) 486 0.0123
(1.00) 		0.0182
(1.00) 		0.0779
(1.00) 		1
(1.00) 		0.0182
(1.00) 		0.00154
(0.325) 		0.00774
(1.00) 		0.0164
(1.00)
17p loss 0 (0%) 490 0.00118
(0.26) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.79
(1.00) 		0.819
(1.00) 		0.518
(1.00) 		0.499
(1.00)
19p loss 0 (0%) 493 0.132
(1.00) 		0.0192
(1.00) 		0.281
(1.00) 		0.369
(1.00) 		0.0366
(1.00) 		0.0186
(1.00) 		0.00778
(1.00) 		0.00503
(0.965)
'1q gain' versus 'CN_CNMF'

P value = 3.29e-06 (Fisher's exact test), Q value = 0.00095

Table S1.  Gene #1: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
1Q GAIN CNV 9 11 1
1Q GAIN WILD-TYPE 25 374 77

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

'4p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S2.  Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
4P GAIN CNV 4 0 0
4P GAIN WILD-TYPE 30 385 78

Figure S2.  Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S3.  Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
4Q GAIN CNV 4 0 0
4Q GAIN WILD-TYPE 30 385 78

Figure S3.  Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 6.97e-20 (Fisher's exact test), Q value = 2.2e-17

Table S4.  Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
5P GAIN CNV 16 1 0
5P GAIN WILD-TYPE 18 384 78

Figure S4.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000747 (Fisher's exact test), Q value = 0.17

Table S5.  Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
5P GAIN CNV 12 2 3
5P GAIN WILD-TYPE 137 72 271

Figure S5.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000522 (Fisher's exact test), Q value = 0.12

Table S6.  Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
5P GAIN CNV 12 5 0 0
5P GAIN WILD-TYPE 111 186 53 91

Figure S6.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000541 (Fisher's exact test), Q value = 0.12

Table S7.  Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
5P GAIN CNV 10 6 0
5P GAIN WILD-TYPE 104 162 142

Figure S7.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2.6e-18 (Fisher's exact test), Q value = 8.3e-16

Table S8.  Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
5Q GAIN CNV 14 0 0
5Q GAIN WILD-TYPE 20 385 78

Figure S8.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.0085

Table S9.  Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
5Q GAIN CNV 12 1 1
5Q GAIN WILD-TYPE 137 73 273

Figure S9.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.041

Table S10.  Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
5Q GAIN CNV 12 0 0 2
5Q GAIN WILD-TYPE 128 56 106 154

Figure S10.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.26e-05 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
5Q GAIN CNV 12 2 0 0
5Q GAIN WILD-TYPE 111 189 53 91

Figure S11.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.027

Table S12.  Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
5Q GAIN CNV 10 3 0
5Q GAIN WILD-TYPE 104 165 142

Figure S12.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.59e-22 (Fisher's exact test), Q value = 5.1e-20

Table S13.  Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
7P GAIN CNV 17 0 0
7P GAIN WILD-TYPE 17 385 78

Figure S13.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.053

Table S14.  Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
7P GAIN CNV 12 3 2
7P GAIN WILD-TYPE 137 71 272

Figure S14.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000389 (Fisher's exact test), Q value = 0.091

Table S15.  Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
7P GAIN CNV 13 0 1 2
7P GAIN WILD-TYPE 127 56 105 154

Figure S15.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.9e-05 (Fisher's exact test), Q value = 0.018

Table S16.  Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
7P GAIN CNV 13 2 0 1
7P GAIN WILD-TYPE 110 189 53 90

Figure S16.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000272 (Fisher's exact test), Q value = 0.065

Table S17.  Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
7P GAIN CNV 12 4 1
7P GAIN WILD-TYPE 102 164 141

Figure S17.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.76e-23 (Fisher's exact test), Q value = 5.7e-21

Table S18.  Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
7Q GAIN CNV 18 0 1
7Q GAIN WILD-TYPE 16 385 77

Figure S18.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.0097

Table S19.  Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
7Q GAIN CNV 14 3 2
7Q GAIN WILD-TYPE 135 71 272

Figure S19.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4.87e-05 (Fisher's exact test), Q value = 0.013

Table S20.  Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
7Q GAIN CNV 15 0 1 2
7Q GAIN WILD-TYPE 125 56 105 154

Figure S20.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0018

Table S21.  Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
7Q GAIN CNV 15 2 0 1
7Q GAIN WILD-TYPE 108 189 53 90

Figure S21.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.069

Table S22.  Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
7Q GAIN CNV 14 2 3
7Q GAIN WILD-TYPE 113 146 146

Figure S22.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.0077

Table S23.  Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
7Q GAIN CNV 14 4 1
7Q GAIN WILD-TYPE 100 164 141

Figure S23.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.05

Table S24.  Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
11Q GAIN CNV 3 0 1
11Q GAIN WILD-TYPE 31 385 77

Figure S24.  Get High-res Image Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 3.2e-10

Table S25.  Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 24 385 77

Figure S25.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.14e-06 (Fisher's exact test), Q value = 0.00091

Table S26.  Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
12P GAIN CNV 11 0 0
12P GAIN WILD-TYPE 138 74 274

Figure S26.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0045

Table S27.  Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
12P GAIN CNV 11 0 0 0
12P GAIN WILD-TYPE 129 56 106 156

Figure S27.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.43e-06 (Fisher's exact test), Q value = 0.00099

Table S28.  Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
12P GAIN CNV 11 0 0 0
12P GAIN WILD-TYPE 112 191 53 91

Figure S28.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.014

Table S29.  Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 117 148 148

Figure S29.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0047

Table S30.  Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
12P GAIN CNV 10 1 0
12P GAIN WILD-TYPE 104 167 142

Figure S30.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.27e-12 (Fisher's exact test), Q value = 4e-10

Table S31.  Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
12Q GAIN CNV 10 0 2
12Q GAIN WILD-TYPE 24 385 76

Figure S31.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 2e-04

Table S32.  Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
12Q GAIN CNV 12 0 0
12Q GAIN WILD-TYPE 137 74 274

Figure S32.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0011

Table S33.  Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
12Q GAIN CNV 12 0 0 0
12Q GAIN WILD-TYPE 128 56 106 156

Figure S33.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.94e-07 (Fisher's exact test), Q value = 0.00023

Table S34.  Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
12Q GAIN CNV 12 0 0 0
12Q GAIN WILD-TYPE 111 191 53 91

Figure S34.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0046

Table S35.  Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
12Q GAIN CNV 11 0 1
12Q GAIN WILD-TYPE 116 148 148

Figure S35.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0014

Table S36.  Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
12Q GAIN CNV 11 1 0
12Q GAIN WILD-TYPE 103 167 142

Figure S36.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.07

Table S37.  Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
13Q GAIN CNV 3 0 0
13Q GAIN WILD-TYPE 31 385 78

Figure S37.  Get High-res Image Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.5e-06

Table S38.  Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
14Q GAIN CNV 7 0 1
14Q GAIN WILD-TYPE 27 385 77

Figure S38.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 8.94e-05 (Fisher's exact test), Q value = 0.023

Table S39.  Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
14Q GAIN CNV 8 0 0
14Q GAIN WILD-TYPE 141 74 274

Figure S39.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
14Q GAIN CNV 8 0 0 0
14Q GAIN WILD-TYPE 132 56 106 156

Figure S40.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S41.  Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
14Q GAIN CNV 8 0 0 0
14Q GAIN WILD-TYPE 115 191 53 91

Figure S41.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 5.51e-14 (Fisher's exact test), Q value = 1.7e-11

Table S42.  Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
16P GAIN CNV 11 0 1
16P GAIN WILD-TYPE 23 385 77

Figure S42.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.0076

Table S43.  Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
16P GAIN CNV 10 2 0
16P GAIN WILD-TYPE 139 72 274

Figure S43.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.032

Table S44.  Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
16P GAIN CNV 11 0 0 1
16P GAIN WILD-TYPE 129 56 106 155

Figure S44.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.009

Table S45.  Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
16P GAIN CNV 11 1 0 0
16P GAIN WILD-TYPE 112 190 53 91

Figure S45.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.052

Table S46.  Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
16P GAIN CNV 10 0 2
16P GAIN WILD-TYPE 117 148 147

Figure S46.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.015

Table S47.  Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
16P GAIN CNV 10 2 0
16P GAIN WILD-TYPE 104 166 142

Figure S47.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5.67e-13 (Fisher's exact test), Q value = 1.8e-10

Table S48.  Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
16Q GAIN CNV 10 0 0
16Q GAIN WILD-TYPE 24 385 78

Figure S48.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.000247 (Fisher's exact test), Q value = 0.059

Table S49.  Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
16Q GAIN CNV 8 2 0
16Q GAIN WILD-TYPE 141 72 274

Figure S49.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000429 (Fisher's exact test), Q value = 0.099

Table S50.  Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
16Q GAIN CNV 9 1 0 0
16Q GAIN WILD-TYPE 114 190 53 91

Figure S50.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000547 (Fisher's exact test), Q value = 0.12

Table S51.  Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
16Q GAIN CNV 8 2 0
16Q GAIN WILD-TYPE 106 166 142

Figure S51.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2e-09 (Fisher's exact test), Q value = 6.1e-07

Table S52.  Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
17P GAIN CNV 9 2 1
17P GAIN WILD-TYPE 25 383 77

Figure S52.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 2e-04

Table S53.  Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
17P GAIN CNV 12 0 0
17P GAIN WILD-TYPE 137 74 274

Figure S53.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0011

Table S54.  Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
17P GAIN CNV 12 0 0 0
17P GAIN WILD-TYPE 128 56 106 156

Figure S54.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.94e-07 (Fisher's exact test), Q value = 0.00023

Table S55.  Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
17P GAIN CNV 12 0 0 0
17P GAIN WILD-TYPE 111 191 53 91

Figure S55.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.014

Table S56.  Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
17P GAIN CNV 10 0 1
17P GAIN WILD-TYPE 117 148 148

Figure S56.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0047

Table S57.  Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
17P GAIN CNV 10 1 0
17P GAIN WILD-TYPE 104 167 142

Figure S57.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 3.83e-09 (Fisher's exact test), Q value = 1.2e-06

Table S58.  Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
17Q GAIN CNV 9 2 2
17Q GAIN WILD-TYPE 25 383 76

Figure S58.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.58e-07 (Fisher's exact test), Q value = 4.7e-05

Table S59.  Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
17Q GAIN CNV 13 0 0
17Q GAIN WILD-TYPE 136 74 274

Figure S59.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 4e-04

Table S60.  Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
17Q GAIN CNV 13 0 0 0
17Q GAIN WILD-TYPE 127 56 106 156

Figure S60.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 5.7e-05

Table S61.  Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
17Q GAIN CNV 13 0 0 0
17Q GAIN WILD-TYPE 110 191 53 91

Figure S61.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0046

Table S62.  Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
17Q GAIN CNV 11 0 1
17Q GAIN WILD-TYPE 116 148 148

Figure S62.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0014

Table S63.  Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
17Q GAIN CNV 11 1 0
17Q GAIN WILD-TYPE 103 167 142

Figure S63.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S64.  Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
19P GAIN CNV 4 0 0
19P GAIN WILD-TYPE 30 385 78

Figure S64.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00033

Table S65.  Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
19Q GAIN CNV 5 0 0
19Q GAIN WILD-TYPE 29 385 78

Figure S65.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 3.4e-09

Table S66.  Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
20P GAIN CNV 9 0 0
20P GAIN WILD-TYPE 25 385 78

Figure S66.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000767 (Fisher's exact test), Q value = 0.17

Table S67.  Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
20P GAIN CNV 7 2 0
20P GAIN WILD-TYPE 142 72 274

Figure S67.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 3.4e-09

Table S68.  Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
20Q GAIN CNV 9 0 0
20Q GAIN WILD-TYPE 25 385 78

Figure S68.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000767 (Fisher's exact test), Q value = 0.17

Table S69.  Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
20Q GAIN CNV 7 2 0
20Q GAIN WILD-TYPE 142 72 274

Figure S69.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.07

Table S70.  Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
1P LOSS CNV 3 0 0
1P LOSS WILD-TYPE 31 385 78

Figure S70.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.5e-06

Table S71.  Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
2P LOSS CNV 7 0 1
2P LOSS WILD-TYPE 27 385 77

Figure S71.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8.94e-05 (Fisher's exact test), Q value = 0.023

Table S72.  Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 141 74 274

Figure S72.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.11

Table S73.  Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
2P LOSS CNV 8 0 0 0
2P LOSS WILD-TYPE 132 56 106 156

Figure S73.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S74.  Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
2P LOSS CNV 8 0 0 0
2P LOSS WILD-TYPE 115 191 53 91

Figure S74.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.014

Table S75.  Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 119 148 149

Figure S75.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0062

Table S76.  Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 106 168 142

Figure S76.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3.78e-09 (Fisher's exact test), Q value = 1.2e-06

Table S77.  Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 27 385 78

Figure S77.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.000378 (Fisher's exact test), Q value = 0.088

Table S78.  Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 142 74 274

Figure S78.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.15

Table S79.  Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
2Q LOSS CNV 7 0 0 0
2Q LOSS WILD-TYPE 116 191 53 91

Figure S79.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.048

Table S80.  Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 120 148 149

Figure S80.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.85e-05 (Fisher's exact test), Q value = 0.023

Table S81.  Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 107 168 142

Figure S81.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.07

Table S82.  Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
3Q LOSS CNV 3 0 0
3Q LOSS WILD-TYPE 31 385 78

Figure S82.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S83.  Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
8P LOSS CNV 4 0 0
8P LOSS WILD-TYPE 30 385 78

Figure S83.  Get High-res Image Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S84.  Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
8Q LOSS CNV 4 0 0
8Q LOSS WILD-TYPE 30 385 78

Figure S84.  Get High-res Image Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 3.4e-09

Table S85.  Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
9P LOSS CNV 10 1 1
9P LOSS WILD-TYPE 24 384 77

Figure S85.  Get High-res Image Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.58e-13 (Fisher's exact test), Q value = 5e-11

Table S86.  Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
9Q LOSS CNV 13 3 1
9Q LOSS WILD-TYPE 21 382 77

Figure S86.  Get High-res Image Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 6.62e-08 (Fisher's exact test), Q value = 2e-05

Table S87.  Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
10P LOSS CNV 6 0 0
10P LOSS WILD-TYPE 28 385 78

Figure S87.  Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00033

Table S88.  Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
10Q LOSS CNV 5 0 0
10Q LOSS WILD-TYPE 29 385 78

Figure S88.  Get High-res Image Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.74e-08 (Fisher's exact test), Q value = 2.3e-05

Table S89.  Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
11P LOSS CNV 6 0 1
11P LOSS WILD-TYPE 28 385 77

Figure S89.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.00094

Table S90.  Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
11Q LOSS CNV 6 2 1
11Q LOSS WILD-TYPE 28 383 77

Figure S90.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000464 (Fisher's exact test), Q value = 0.11

Table S91.  Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
15Q LOSS CNV 4 2 1
15Q LOSS WILD-TYPE 30 383 77

Figure S91.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000664 (Fisher's exact test), Q value = 0.15

Table S92.  Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
15Q LOSS CNV 6 0 0
15Q LOSS WILD-TYPE 121 148 149

Figure S92.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.08

Table S93.  Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
15Q LOSS CNV 6 0 0
15Q LOSS WILD-TYPE 108 168 142

Figure S93.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.05

Table S94.  Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
18P LOSS CNV 3 0 1
18P LOSS WILD-TYPE 31 385 77

Figure S94.  Get High-res Image Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.05

Table S95.  Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
18Q LOSS CNV 3 0 1
18Q LOSS WILD-TYPE 31 385 77

Figure S95.  Get High-res Image Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.048

Table S96.  Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
21Q LOSS CNV 4 1 1
21Q LOSS WILD-TYPE 30 384 77

Figure S96.  Get High-res Image Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.79e-58 (Fisher's exact test), Q value = 2.2e-55

Table S97.  Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 385 78
22Q LOSS CNV 8 0 58
22Q LOSS WILD-TYPE 26 385 20

Figure S97.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.033

Table S98.  Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 74 274
22Q LOSS CNV 35 7 24
22Q LOSS WILD-TYPE 114 67 250

Figure S98.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 8.4e-11 (Fisher's exact test), Q value = 2.6e-08

Table S99.  Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 56 106 156
22Q LOSS CNV 33 5 20 1
22Q LOSS WILD-TYPE 107 51 86 155

Figure S99.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.98e-10 (Fisher's exact test), Q value = 6.1e-08

Table S100.  Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 191 53 91
22Q LOSS CNV 33 6 2 18
22Q LOSS WILD-TYPE 90 185 51 73

Figure S100.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.011

Table S101.  Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 148 149
22Q LOSS CNV 31 14 10
22Q LOSS WILD-TYPE 96 134 139

Figure S101.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.51e-06 (Fisher's exact test), Q value = 0.0027

Table S102.  Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 168 142
22Q LOSS CNV 30 11 14
22Q LOSS WILD-TYPE 84 157 128

Figure S102.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #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 = 497

  • Number of significantly arm-level cnvs = 45

  • 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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