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 45 arm-level results and 8 molecular subtypes across 470 patients, 99 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', 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', 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' 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',  'MIRSEQ_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' 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',  '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, 99 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 14 (3%) 456 5.75e-18
(1.79e-15) 		3.24e-05
(0.00851) 		0.901
(1.00) 		0.0299
(1.00) 		0.000812
(0.179) 		0.000952
(0.209) 		0.00104
(0.229) 		0.00014
(0.0351)
7q gain 19 (4%) 451 4.86e-23
(1.53e-20) 		3.72e-05
(0.00968) 		0.689
(1.00) 		0.00298
(0.6) 		0.000286
(0.0687) 		0.000176
(0.0438) 		0.000214
(0.0526) 		4.94e-05
(0.0127)
12p gain 11 (2%) 459 1.79e-12
(5.52e-10) 		3.2e-06
(0.000926) 		0.901
(1.00) 		0.0299
(1.00) 		1.83e-05
(0.00506) 		1.93e-05
(0.00526) 		3.39e-05
(0.00888) 		1.87e-05
(0.00515)
12q gain 12 (3%) 458 2.23e-12
(6.85e-10) 		6.84e-07
(2e-04) 		0.901
(1.00) 		0.0299
(1.00) 		7.78e-06
(0.00219) 		4.91e-06
(0.0014) 		1.09e-05
(0.00303) 		5.32e-06
(0.00151)
16p gain 12 (3%) 458 1.02e-13
(3.17e-11) 		2.89e-05
(0.00764) 		1
(1.00) 		0.0445
(1.00) 		0.000239
(0.0587) 		0.000167
(0.0418) 		9.46e-05
(0.0239) 		7.74e-05
(0.0198)
17p gain 12 (3%) 458 3.73e-09
(1.13e-06) 		6.84e-07
(2e-04) 		0.772
(1.00) 		0.0179
(1.00) 		1.83e-05
(0.00506) 		1.93e-05
(0.00526) 		3.39e-05
(0.00888) 		1.87e-05
(0.00515)
17q gain 13 (3%) 457 5.93e-09
(1.78e-06) 		1.53e-07
(4.49e-05) 		0.795
(1.00) 		0.0206
(1.00) 		7.78e-06
(0.00219) 		4.91e-06
(0.0014) 		1.09e-05
(0.00303) 		5.32e-06
(0.00151)
2p loss 8 (2%) 462 7.39e-09
(2.21e-06) 		8.85e-05
(0.0226) 		1
(1.00) 		0.0817
(1.00) 		0.000731
(0.164) 		0.000334
(0.0799) 		5.28e-05
(0.0136) 		2.87e-05
(0.0076)
22q loss 62 (13%) 408 7.02e-54
(2.22e-51) 		0.000526
(0.122) 		0.114
(1.00) 		0.0835
(1.00) 		1.79e-09
(5.41e-07) 		1.22e-07
(3.59e-05) 		4.79e-05
(0.0124) 		4.64e-06
(0.00134)
7p gain 17 (4%) 453 4.17e-22
(1.31e-19) 		0.000198
(0.0489) 		1
(1.00) 		0.0129
(1.00) 		0.000704
(0.16) 		0.000607
(0.14) 		0.00178
(0.377) 		0.000414
(0.0965)
16q gain 10 (2%) 460 9.96e-13
(3.08e-10) 		0.000255
(0.0615) 		0.856
(1.00) 		0.129
(1.00) 		0.00204
(0.429) 		0.00146
(0.313) 		0.00107
(0.233) 		0.000706
(0.16)
2q loss 7 (1%) 463 5.6e-09
(1.68e-06) 		0.00038
(0.0892) 		0.837
(1.00) 		0.0549
(1.00) 		0.00213
(0.446) 		0.00122
(0.264) 		0.000185
(0.0458) 		0.000108
(0.0273)
5p gain 17 (4%) 453 1.72e-19
(5.39e-17) 		0.000766
(0.172) 		1
(1.00) 		0.125
(1.00) 		0.00945
(1.00) 		0.01
(1.00) 		0.00564
(1.00) 		0.000668
(0.152)
15q loss 6 (1%) 464 0.000427
(0.099) 		0.00547
(1.00) 		0.458
(1.00) 		0.256
(1.00) 		0.0173
(1.00) 		0.00933
(1.00) 		0.000641
(0.147) 		0.000407
(0.0953)
14q gain 8 (2%) 462 7.39e-09
(2.21e-06) 		8.85e-05
(0.0226) 		1
(1.00) 		0.256
(1.00) 		0.00213
(0.446) 		0.00122
(0.264) 		0.00296
(0.597) 		0.00247
(0.509)
20p gain 9 (2%) 461 1.84e-11
(5.6e-09) 		0.000789
(0.176) 		1
(1.00) 		0.0817
(1.00) 		0.0134
(1.00) 		0.0136
(1.00) 		0.0101
(1.00) 		0.00804
(1.00)
20q gain 9 (2%) 461 1.84e-11
(5.6e-09) 		0.000789
(0.176) 		1
(1.00) 		0.0817
(1.00) 		0.0134
(1.00) 		0.0136
(1.00) 		0.0101
(1.00) 		0.00804
(1.00)
1q gain 21 (4%) 449 4.65e-06
(0.00134) 		0.0818
(1.00) 		0.0153
(1.00) 		0.0826
(1.00) 		0.0325
(1.00) 		0.0233
(1.00) 		0.198
(1.00) 		0.242
(1.00)
4p gain 4 (1%) 466 2.31e-05
(0.00624) 		0.0195
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.073
(1.00) 		0.137
(1.00)
4q gain 4 (1%) 466 2.31e-05
(0.00624) 		0.0195
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.073
(1.00) 		0.137
(1.00)
11q gain 4 (1%) 466 0.000241
(0.0587) 		0.0195
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00761
(1.00) 		0.00564
(1.00)
13q gain 3 (1%) 467 0.000348
(0.0828) 		0.0496
(1.00)
19p gain 4 (1%) 466 2.31e-05
(0.00624) 		0.0195
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.026
(1.00) 		0.0208
(1.00)
19q gain 5 (1%) 465 1.49e-06
(0.000433) 		0.00437
(0.874) 		0.636
(1.00) 		0.0551
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00761
(1.00) 		0.00564
(1.00)
1p loss 3 (1%) 467 0.000348
(0.0828) 		0.412
(1.00) 		0.487
(1.00) 		0.195
(1.00) 		0.202
(1.00) 		0.367
(1.00)
3q loss 3 (1%) 467 0.000348
(0.0828) 		0.0496
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.026
(1.00) 		0.0208
(1.00)
8p loss 4 (1%) 466 2.31e-05
(0.00624) 		0.0474
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00761
(1.00) 		0.00564
(1.00)
8q loss 4 (1%) 466 2.31e-05
(0.00624) 		0.0474
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00761
(1.00) 		0.00564
(1.00)
9p loss 11 (2%) 459 1.04e-11
(3.19e-09) 		0.365
(1.00) 		0.559
(1.00) 		0.206
(1.00) 		0.249
(1.00) 		0.527
(1.00) 		0.151
(1.00) 		0.192
(1.00)
9q loss 16 (3%) 454 1.1e-13
(3.41e-11) 		0.288
(1.00) 		0.21
(1.00) 		0.00441
(0.874) 		0.441
(1.00) 		0.823
(1.00) 		0.193
(1.00) 		0.274
(1.00)
10p loss 6 (1%) 464 9.28e-08
(2.75e-05) 		0.0793
(1.00) 		0.12
(1.00) 		0.0427
(1.00) 		0.0256
(1.00) 		0.0361
(1.00)
10q loss 5 (1%) 465 1.49e-06
(0.000433) 		0.177
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.073
(1.00) 		0.137
(1.00)
11p loss 6 (1%) 464 9.28e-08
(2.75e-05) 		0.0202
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.0495
(1.00) 		0.166
(1.00) 		0.0256
(1.00) 		0.0361
(1.00)
11q loss 8 (2%) 462 4.79e-06
(0.00137) 		0.0278
(1.00) 		0.388
(1.00) 		0.798
(1.00) 		0.0186
(1.00) 		0.0672
(1.00) 		0.00877
(1.00) 		0.00798
(1.00)
18p loss 4 (1%) 466 0.000241
(0.0587) 		0.191
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.111
(1.00) 		0.0414
(1.00)
18q loss 4 (1%) 466 0.000241
(0.0587) 		0.191
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.242
(1.00) 		0.0893
(1.00) 		0.111
(1.00) 		0.0414
(1.00)
21q loss 5 (1%) 465 1.96e-05
(0.00531) 		0.0132
(1.00) 		0.384
(1.00) 		0.0551
(1.00) 		0.0495
(1.00) 		0.166
(1.00) 		0.0256
(1.00) 		0.0361
(1.00)
11p gain 5 (1%) 465 0.00151
(0.321) 		0.00437
(0.874) 		0.0173
(1.00) 		0.00933
(1.00) 		0.00222
(0.459) 		0.00152
(0.322)
18p gain 3 (1%) 467 0.00273
(0.56) 		0.0496
(1.00)
18q gain 3 (1%) 467 0.00273
(0.56) 		0.0496
(1.00)
21q gain 3 (1%) 467 0.00273
(0.56) 		0.0496
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.026
(1.00) 		0.0208
(1.00)
6q loss 3 (1%) 467 0.0234
(1.00) 		0.0496
(1.00) 		0.101
(1.00) 		0.0821
(1.00) 		0.026
(1.00) 		0.0208
(1.00)
13q loss 11 (2%) 459 0.0136
(1.00) 		0.0184
(1.00) 		0.0779
(1.00) 		1
(1.00) 		0.0941
(1.00) 		0.116
(1.00) 		0.00769
(1.00) 		0.0142
(1.00)
17p loss 7 (1%) 463 0.00134
(0.288) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.886
(1.00) 		0.403
(1.00) 		0.495
(1.00)
19p loss 4 (1%) 466 0.138
(1.00) 		0.0195
(1.00) 		0.281
(1.00) 		0.369
(1.00) 		0.0371
(1.00) 		0.0346
(1.00) 		0.00761
(1.00) 		0.00564
(1.00)
'1q gain mutation analysis' versus 'CN_CNMF'

P value = 4.65e-06 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
1Q GAIN MUTATED 9 11 1
1Q GAIN WILD-TYPE 25 352 72

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 = 2.31e-05 (Fisher's exact test), Q value = 0.0062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
4P GAIN MUTATED 4 0 0
4P GAIN WILD-TYPE 30 363 73

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 = 2.31e-05 (Fisher's exact test), Q value = 0.0062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
4Q GAIN MUTATED 4 0 0
4Q GAIN WILD-TYPE 30 363 73

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 = 1.72e-19 (Fisher's exact test), Q value = 5.4e-17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
5P GAIN MUTATED 16 1 0
5P GAIN WILD-TYPE 18 362 73

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

'5p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000766 (Fisher's exact test), Q value = 0.17

Table S5.  Gene #4: '5p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
5P GAIN MUTATED 12 2 3
5P GAIN WILD-TYPE 128 69 256

Figure S5.  Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'5p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000668 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
5P GAIN MUTATED 6 0 10
5P GAIN WILD-TYPE 167 133 107

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 = 5.75e-18 (Fisher's exact test), Q value = 1.8e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
5Q GAIN MUTATED 14 0 0
5Q GAIN WILD-TYPE 20 363 73

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 = 3.24e-05 (Fisher's exact test), Q value = 0.0085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
5Q GAIN MUTATED 12 1 1
5Q GAIN WILD-TYPE 128 70 258

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 = 0.00104 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
5Q GAIN MUTATED 10 1 2
5Q GAIN WILD-TYPE 116 152 142

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 = 0.00014 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
5Q GAIN MUTATED 3 0 10
5Q GAIN WILD-TYPE 170 133 107

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 = 4.17e-22 (Fisher's exact test), Q value = 1.3e-19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
7P GAIN MUTATED 17 0 0
7P GAIN WILD-TYPE 17 363 73

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 = 0.000198 (Fisher's exact test), Q value = 0.049

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
7P GAIN MUTATED 12 3 2
7P GAIN WILD-TYPE 128 68 257

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 = 0.16

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 = 0.14

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_CHIERARCHICAL'

P value = 0.000414 (Fisher's exact test), Q value = 0.097

Table S17.  Gene #6: '7p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
7P GAIN MUTATED 4 1 12
7P GAIN WILD-TYPE 169 132 105

Figure S17.  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 = 4.86e-23 (Fisher's exact test), Q value = 1.5e-20

Table S18.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
7Q GAIN MUTATED 18 0 1
7Q GAIN WILD-TYPE 16 363 72

Figure S18.  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 = 3.72e-05 (Fisher's exact test), Q value = 0.0097

Table S19.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
7Q GAIN MUTATED 14 3 2
7Q GAIN WILD-TYPE 126 68 257

Figure S19.  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 = 0.069

Table S20.  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 S20.  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 = 0.044

Table S21.  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 S21.  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 = 0.000214 (Fisher's exact test), Q value = 0.053

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
7Q GAIN MUTATED 14 2 3
7Q GAIN WILD-TYPE 112 151 141

Figure S22.  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 = 4.94e-05 (Fisher's exact test), Q value = 0.013

Table S23.  Gene #7: '7q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
7Q GAIN MUTATED 4 1 14
7Q GAIN WILD-TYPE 169 132 103

Figure S23.  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 = 0.000241 (Fisher's exact test), Q value = 0.059

Table S24.  Gene #9: '11q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
11Q GAIN MUTATED 3 0 1
11Q GAIN WILD-TYPE 31 363 72

Figure S24.  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 = 1.79e-12 (Fisher's exact test), Q value = 5.5e-10

Table S25.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
12P GAIN MUTATED 10 0 1
12P GAIN WILD-TYPE 24 363 72

Figure S25.  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 = 3.2e-06 (Fisher's exact test), Q value = 0.00093

Table S26.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
12P GAIN MUTATED 11 0 0
12P GAIN WILD-TYPE 129 71 259

Figure S26.  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 = 1.83e-05 (Fisher's exact test), Q value = 0.0051

Table S27.  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 11 0 0 0
12P GAIN WILD-TYPE 119 50 89 138

Figure S27.  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 = 1.93e-05 (Fisher's exact test), Q value = 0.0053

Table S28.  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 11 0 0
12P GAIN WILD-TYPE 131 191 74

Figure S28.  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 = 3.39e-05 (Fisher's exact test), Q value = 0.0089

Table S29.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
12P GAIN MUTATED 10 0 1
12P GAIN WILD-TYPE 116 153 143

Figure S29.  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 = 1.87e-05 (Fisher's exact test), Q value = 0.0052

Table S30.  Gene #10: '12p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
12P GAIN MUTATED 1 0 10
12P GAIN WILD-TYPE 172 133 107

Figure S30.  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 = 2.23e-12 (Fisher's exact test), Q value = 6.9e-10

Table S31.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
12Q GAIN MUTATED 10 0 2
12Q GAIN WILD-TYPE 24 363 71

Figure S31.  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 = 6.84e-07 (Fisher's exact test), Q value = 2e-04

Table S32.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
12Q GAIN MUTATED 12 0 0
12Q GAIN WILD-TYPE 128 71 259

Figure S32.  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 S33.  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 S33.  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 S34.  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 S34.  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 = 1.09e-05 (Fisher's exact test), Q value = 0.003

Table S35.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
12Q GAIN MUTATED 11 0 1
12Q GAIN WILD-TYPE 115 153 143

Figure S35.  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 = 5.32e-06 (Fisher's exact test), Q value = 0.0015

Table S36.  Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
12Q GAIN MUTATED 1 0 11
12Q GAIN WILD-TYPE 172 133 106

Figure S36.  Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.083

Table S37.  Gene #12: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
13Q GAIN MUTATED 3 0 0
13Q GAIN WILD-TYPE 31 363 73

Figure S37.  Get High-res Image Gene #12: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q gain mutation analysis' versus 'CN_CNMF'

P value = 7.39e-09 (Fisher's exact test), Q value = 2.2e-06

Table S38.  Gene #13: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
14Q GAIN MUTATED 7 0 1
14Q GAIN WILD-TYPE 27 363 72

Figure S38.  Get High-res Image Gene #13: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S39.  Gene #13: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
14Q GAIN MUTATED 8 0 0
14Q GAIN WILD-TYPE 132 71 259

Figure S39.  Get High-res Image Gene #13: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.02e-13 (Fisher's exact test), Q value = 3.2e-11

Table S40.  Gene #14: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
16P GAIN MUTATED 11 0 1
16P GAIN WILD-TYPE 23 363 72

Figure S40.  Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.0076

Table S41.  Gene #14: '16p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
16P GAIN MUTATED 10 2 0
16P GAIN WILD-TYPE 130 69 259

Figure S41.  Get High-res Image Gene #14: '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 = 0.059

Table S42.  Gene #14: '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 #14: '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 = 0.042

Table S43.  Gene #14: '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 #14: '16p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.46e-05 (Fisher's exact test), Q value = 0.024

Table S44.  Gene #14: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
16P GAIN MUTATED 10 0 2
16P GAIN WILD-TYPE 116 153 142

Figure S44.  Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'16p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.74e-05 (Fisher's exact test), Q value = 0.02

Table S45.  Gene #14: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
16P GAIN MUTATED 2 0 10
16P GAIN WILD-TYPE 171 133 107

Figure S45.  Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 9.96e-13 (Fisher's exact test), Q value = 3.1e-10

Table S46.  Gene #15: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
16Q GAIN MUTATED 10 0 0
16Q GAIN WILD-TYPE 24 363 73

Figure S46.  Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.061

Table S47.  Gene #15: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
16Q GAIN MUTATED 8 2 0
16Q GAIN WILD-TYPE 132 69 259

Figure S47.  Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.23

Table S48.  Gene #15: '16q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
16Q GAIN MUTATED 8 0 2
16Q GAIN WILD-TYPE 118 153 142

Figure S48.  Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000706 (Fisher's exact test), Q value = 0.16

Table S49.  Gene #15: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
16Q GAIN MUTATED 2 0 8
16Q GAIN WILD-TYPE 171 133 109

Figure S49.  Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'CN_CNMF'

P value = 3.73e-09 (Fisher's exact test), Q value = 1.1e-06

Table S50.  Gene #16: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
17P GAIN MUTATED 9 2 1
17P GAIN WILD-TYPE 25 361 72

Figure S50.  Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.84e-07 (Fisher's exact test), Q value = 2e-04

Table S51.  Gene #16: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
17P GAIN MUTATED 12 0 0
17P GAIN WILD-TYPE 128 71 259

Figure S51.  Get High-res Image Gene #16: '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 = 0.0051

Table S52.  Gene #16: '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 S52.  Get High-res Image Gene #16: '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 = 0.0053

Table S53.  Gene #16: '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 S53.  Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0089

Table S54.  Gene #16: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
17P GAIN MUTATED 10 0 1
17P GAIN WILD-TYPE 116 153 143

Figure S54.  Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.0052

Table S55.  Gene #16: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
17P GAIN MUTATED 1 0 10
17P GAIN WILD-TYPE 172 133 107

Figure S55.  Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 5.93e-09 (Fisher's exact test), Q value = 1.8e-06

Table S56.  Gene #17: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
17Q GAIN MUTATED 9 2 2
17Q GAIN WILD-TYPE 25 361 71

Figure S56.  Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 4.5e-05

Table S57.  Gene #17: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
17Q GAIN MUTATED 13 0 0
17Q GAIN WILD-TYPE 127 71 259

Figure S57.  Get High-res Image Gene #17: '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 S58.  Gene #17: '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 S58.  Get High-res Image Gene #17: '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 S59.  Gene #17: '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 S59.  Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.003

Table S60.  Gene #17: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
17Q GAIN MUTATED 11 0 1
17Q GAIN WILD-TYPE 115 153 143

Figure S60.  Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.32e-06 (Fisher's exact test), Q value = 0.0015

Table S61.  Gene #17: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
17Q GAIN MUTATED 1 0 11
17Q GAIN WILD-TYPE 172 133 106

Figure S61.  Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
19P GAIN MUTATED 4 0 0
19P GAIN WILD-TYPE 30 363 73

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

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00043

Table S63.  Gene #21: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
19Q GAIN MUTATED 5 0 0
19Q GAIN WILD-TYPE 29 363 73

Figure S63.  Get High-res Image Gene #21: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 5.6e-09

Table S64.  Gene #22: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
20P GAIN MUTATED 9 0 0
20P GAIN WILD-TYPE 25 363 73

Figure S64.  Get High-res Image Gene #22: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000789 (Fisher's exact test), Q value = 0.18

Table S65.  Gene #22: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
20P GAIN MUTATED 7 2 0
20P GAIN WILD-TYPE 133 69 259

Figure S65.  Get High-res Image Gene #22: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 5.6e-09

Table S66.  Gene #23: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
20Q GAIN MUTATED 9 0 0
20Q GAIN WILD-TYPE 25 363 73

Figure S66.  Get High-res Image Gene #23: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000789 (Fisher's exact test), Q value = 0.18

Table S67.  Gene #23: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
20Q GAIN MUTATED 7 2 0
20Q GAIN WILD-TYPE 133 69 259

Figure S67.  Get High-res Image Gene #23: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.083

Table S68.  Gene #25: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
1P LOSS MUTATED 3 0 0
1P LOSS WILD-TYPE 31 363 73

Figure S68.  Get High-res Image Gene #25: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'CN_CNMF'

P value = 7.39e-09 (Fisher's exact test), Q value = 2.2e-06

Table S69.  Gene #26: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
2P LOSS MUTATED 7 0 1
2P LOSS WILD-TYPE 27 363 72

Figure S69.  Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'METHLYATION_CNMF'

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

Table S70.  Gene #26: '2p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 132 71 259

Figure S70.  Get High-res Image Gene #26: '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 S71.  Gene #26: '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 S71.  Get High-res Image Gene #26: '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 = 0.08

Table S72.  Gene #26: '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 S72.  Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.28e-05 (Fisher's exact test), Q value = 0.014

Table S73.  Gene #26: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
2P LOSS MUTATED 8 0 0
2P LOSS WILD-TYPE 118 153 144

Figure S73.  Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.0076

Table S74.  Gene #26: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
2P LOSS MUTATED 0 0 8
2P LOSS WILD-TYPE 173 133 109

Figure S74.  Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 5.6e-09 (Fisher's exact test), Q value = 1.7e-06

Table S75.  Gene #27: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 27 363 73

Figure S75.  Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.089

Table S76.  Gene #27: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 133 71 259

Figure S76.  Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.046

Table S77.  Gene #27: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
2Q LOSS MUTATED 7 0 0
2Q LOSS WILD-TYPE 119 153 144

Figure S77.  Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.027

Table S78.  Gene #27: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
2Q LOSS MUTATED 0 0 7
2Q LOSS WILD-TYPE 173 133 110

Figure S78.  Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.083

Table S79.  Gene #28: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
3Q LOSS MUTATED 3 0 0
3Q LOSS WILD-TYPE 31 363 73

Figure S79.  Get High-res Image Gene #28: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S80.  Gene #30: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
8P LOSS MUTATED 4 0 0
8P LOSS WILD-TYPE 30 363 73

Figure S80.  Get High-res Image Gene #30: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q loss mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S81.  Gene #31: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
8Q LOSS MUTATED 4 0 0
8Q LOSS WILD-TYPE 30 363 73

Figure S81.  Get High-res Image Gene #31: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 1.04e-11 (Fisher's exact test), Q value = 3.2e-09

Table S82.  Gene #32: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
9P LOSS MUTATED 10 1 0
9P LOSS WILD-TYPE 24 362 73

Figure S82.  Get High-res Image Gene #32: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 1.1e-13 (Fisher's exact test), Q value = 3.4e-11

Table S83.  Gene #33: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
9Q LOSS MUTATED 13 3 0
9Q LOSS WILD-TYPE 21 360 73

Figure S83.  Get High-res Image Gene #33: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 2.8e-05

Table S84.  Gene #34: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
10P LOSS MUTATED 6 0 0
10P LOSS WILD-TYPE 28 363 73

Figure S84.  Get High-res Image Gene #34: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00043

Table S85.  Gene #35: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
10Q LOSS MUTATED 5 0 0
10Q LOSS WILD-TYPE 29 363 73

Figure S85.  Get High-res Image Gene #35: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 2.8e-05

Table S86.  Gene #36: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
11P LOSS MUTATED 6 0 0
11P LOSS WILD-TYPE 28 363 73

Figure S86.  Get High-res Image Gene #36: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0014

Table S87.  Gene #37: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
11Q LOSS MUTATED 6 2 0
11Q LOSS WILD-TYPE 28 361 73

Figure S87.  Get High-res Image Gene #37: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000427 (Fisher's exact test), Q value = 0.099

Table S88.  Gene #39: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
15Q LOSS MUTATED 4 2 0
15Q LOSS WILD-TYPE 30 361 73

Figure S88.  Get High-res Image Gene #39: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000641 (Fisher's exact test), Q value = 0.15

Table S89.  Gene #39: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
15Q LOSS MUTATED 6 0 0
15Q LOSS WILD-TYPE 120 153 144

Figure S89.  Get High-res Image Gene #39: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000407 (Fisher's exact test), Q value = 0.095

Table S90.  Gene #39: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
15Q LOSS MUTATED 0 0 6
15Q LOSS WILD-TYPE 173 133 111

Figure S90.  Get High-res Image Gene #39: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.059

Table S91.  Gene #41: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
18P LOSS MUTATED 3 0 1
18P LOSS WILD-TYPE 31 363 72

Figure S91.  Get High-res Image Gene #41: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.059

Table S92.  Gene #42: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
18Q LOSS MUTATED 3 0 1
18Q LOSS WILD-TYPE 31 363 72

Figure S92.  Get High-res Image Gene #42: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0053

Table S93.  Gene #44: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
21Q LOSS MUTATED 4 0 1
21Q LOSS WILD-TYPE 30 363 72

Figure S93.  Get High-res Image Gene #44: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 7.02e-54 (Fisher's exact test), Q value = 2.2e-51

Table S94.  Gene #45: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 363 73
22Q LOSS MUTATED 8 0 54
22Q LOSS WILD-TYPE 26 363 19

Figure S94.  Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000526 (Fisher's exact test), Q value = 0.12

Table S95.  Gene #45: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 71 259
22Q LOSS MUTATED 32 6 24
22Q LOSS WILD-TYPE 108 65 235

Figure S95.  Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.79e-09 (Fisher's exact test), Q value = 5.4e-07

Table S96.  Gene #45: '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 30 3 16 1
22Q LOSS WILD-TYPE 100 47 73 137

Figure S96.  Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 3.6e-05

Table S97.  Gene #45: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 191 74
22Q LOSS MUTATED 30 6 14
22Q LOSS WILD-TYPE 112 185 60

Figure S97.  Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.79e-05 (Fisher's exact test), Q value = 0.012

Table S98.  Gene #45: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 153 144
22Q LOSS MUTATED 31 14 10
22Q LOSS WILD-TYPE 95 139 134

Figure S98.  Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.64e-06 (Fisher's exact test), Q value = 0.0013

Table S99.  Gene #45: '22q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 133 117
22Q LOSS MUTATED 11 13 31
22Q LOSS WILD-TYPE 162 120 86

Figure S99.  Get High-res Image Gene #45: '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 = 470

  • 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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