Stomach 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 77 arm-level results and 6 molecular subtypes across 306 patients, 62 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16p 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'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_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'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 77 arm-level results and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 62 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
4q loss 47 (15%) 259 1.17e-14
(4.94e-12) 		0.000173
(0.0653) 		0.664
(1.00) 		0.55
(1.00) 		0.00291
(0.991) 		1.56e-07
(6.32e-05)
17p loss 58 (19%) 248 3.45e-18
(1.47e-15) 		0.000157
(0.0597) 		0.281
(1.00) 		0.0973
(1.00) 		0.00285
(0.975) 		0.00067
(0.247)
22q loss 39 (13%) 267 9.26e-17
(3.93e-14) 		8.17e-06
(0.00327) 		0.664
(1.00) 		1
(1.00) 		0.000238
(0.0894) 		0.000908
(0.33)
7p gain 89 (29%) 217 1.21e-18
(5.19e-16) 		0.000148
(0.0564) 		1
(1.00) 		0.523
(1.00) 		0.00664
(1.00) 		0.0132
(1.00)
8q gain 108 (35%) 198 4.09e-05
(0.0158) 		1.52e-05
(0.00598) 		0.364
(1.00) 		0.779
(1.00) 		0.00768
(1.00) 		0.116
(1.00)
13q gain 62 (20%) 244 2.58e-08
(1.07e-05) 		0.000677
(0.249) 		0.721
(1.00) 		0.885
(1.00) 		0.399
(1.00) 		0.135
(1.00)
20p gain 122 (40%) 184 2.71e-19
(1.16e-16) 		7.9e-05
(0.0302) 		0.129
(1.00) 		0.0165
(1.00) 		0.17
(1.00) 		0.0174
(1.00)
20q gain 149 (49%) 157 2.59e-29
(1.11e-26) 		4.18e-08
(1.71e-05) 		0.227
(1.00) 		0.0227
(1.00) 		0.00809
(1.00) 		0.00118
(0.429)
3q loss 15 (5%) 291 9.73e-06
(0.00384) 		0.0174
(1.00) 		0.233
(1.00) 		0.000629
(0.234) 		0.0137
(1.00)
4p loss 49 (16%) 257 7.25e-11
(3.02e-08) 		0.000706
(0.259) 		0.457
(1.00) 		0.674
(1.00) 		0.00646
(1.00) 		2.88e-07
(0.000116)
5q loss 34 (11%) 272 2.59e-12
(1.09e-09) 		0.00166
(0.593) 		1
(1.00) 		1
(1.00) 		0.0289
(1.00) 		0.000219
(0.0822)
9p loss 47 (15%) 259 4.54e-17
(1.93e-14) 		0.000291
(0.109) 		0.698
(1.00) 		0.863
(1.00) 		0.00646
(1.00) 		0.00453
(1.00)
16q loss 26 (8%) 280 7.49e-10
(3.1e-07) 		0.000502
(0.187) 		1
(1.00) 		0.349
(1.00) 		0.0386
(1.00) 		0.215
(1.00)
1p gain 15 (5%) 291 3.44e-05
(0.0134) 		0.924
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.627
(1.00) 		0.926
(1.00)
1q gain 41 (13%) 265 2.96e-11
(1.24e-08) 		0.00499
(1.00) 		1
(1.00) 		0.73
(1.00) 		0.00209
(0.732) 		0.0318
(1.00)
2p gain 21 (7%) 285 4.42e-06
(0.00177) 		0.00225
(0.782) 		0.488
(1.00) 		0.23
(1.00) 		0.00766
(1.00)
2q gain 22 (7%) 284 6.4e-05
(0.0246) 		0.00225
(0.782) 		0.233
(1.00) 		0.268
(1.00) 		0.436
(1.00) 		0.067
(1.00)
5p gain 36 (12%) 270 8.5e-08
(3.47e-05) 		0.0208
(1.00) 		0.281
(1.00) 		0.464
(1.00) 		0.106
(1.00) 		0.117
(1.00)
6p gain 23 (8%) 283 1.57e-05
(0.00619) 		0.0041
(1.00) 		1
(1.00) 		1
(1.00) 		0.00644
(1.00) 		0.257
(1.00)
6q gain 20 (7%) 286 5.05e-05
(0.0194) 		0.00235
(0.813) 		1
(1.00) 		1
(1.00) 		0.0159
(1.00) 		0.139
(1.00)
7q gain 72 (24%) 234 1.59e-16
(6.72e-14) 		0.00384
(1.00) 		1
(1.00) 		1
(1.00) 		0.0156
(1.00) 		0.226
(1.00)
8p gain 81 (26%) 225 4.12e-05
(0.0159) 		0.00238
(0.821) 		0.543
(1.00) 		0.84
(1.00) 		0.0121
(1.00) 		0.657
(1.00)
10p gain 42 (14%) 264 3.14e-10
(1.3e-07) 		0.0017
(0.604) 		0.412
(1.00) 		0.557
(1.00) 		0.723
(1.00) 		0.0594
(1.00)
10q gain 25 (8%) 281 8.66e-06
(0.00344) 		0.0622
(1.00) 		0.607
(1.00) 		0.643
(1.00) 		0.316
(1.00) 		0.692
(1.00)
16p gain 14 (5%) 292 0.000637
(0.236) 		0.0569
(1.00) 		0.607
(1.00) 		0.643
(1.00) 		0.618
(1.00) 		0.251
(1.00)
1p loss 14 (5%) 292 4.12e-06
(0.00166) 		0.543
(1.00) 		0.488
(1.00) 		0.131
(1.00) 		1
(1.00)
3p loss 26 (8%) 280 4.42e-08
(1.81e-05) 		0.00759
(1.00) 		0.233
(1.00) 		0.00362
(1.00) 		0.0155
(1.00)
5p loss 15 (5%) 291 1.67e-05
(0.00654) 		0.0979
(1.00) 		0.488
(1.00) 		0.848
(1.00) 		0.199
(1.00)
7q loss 12 (4%) 294 2.9e-05
(0.0113) 		0.0674
(1.00) 		0.233
(1.00) 		0.0179
(1.00) 		0.0179
(1.00)
8p loss 27 (9%) 279 1.19e-06
(0.000481) 		0.121
(1.00) 		0.664
(1.00) 		0.73
(1.00) 		0.0142
(1.00) 		0.0301
(1.00)
9q loss 25 (8%) 281 3.15e-08
(1.3e-05) 		0.00141
(0.506) 		1
(1.00) 		0.163
(1.00) 		0.0301
(1.00)
10p loss 17 (6%) 289 0.000108
(0.0412) 		0.0103
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.343
(1.00) 		0.337
(1.00)
10q loss 17 (6%) 289 8.39e-06
(0.00335) 		0.00576
(1.00) 		0.345
(1.00) 		0.481
(1.00) 		0.24
(1.00) 		0.209
(1.00)
11p loss 19 (6%) 287 1.63e-05
(0.00638) 		0.00172
(0.611) 		1
(1.00) 		0.0974
(1.00) 		0.059
(1.00) 		0.106
(1.00)
11q loss 17 (6%) 289 9.49e-06
(0.00376) 		0.00503
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.0689
(1.00) 		0.32
(1.00)
12p loss 19 (6%) 287 0.00014
(0.0534) 		0.00784
(1.00) 		0.108
(1.00) 		0.0284
(1.00) 		0.24
(1.00) 		0.0907
(1.00)
13q loss 9 (3%) 297 0.000419
(0.156) 		0.225
(1.00) 		0.488
(1.00) 		0.389
(1.00) 		0.486
(1.00)
14q loss 25 (8%) 281 8.66e-06
(0.00344) 		0.0622
(1.00) 		0.345
(1.00) 		0.481
(1.00) 		0.0535
(1.00) 		0.0677
(1.00)
15q loss 22 (7%) 284 1.09e-07
(4.42e-05) 		0.00666
(1.00) 		0.607
(1.00) 		0.745
(1.00) 		0.571
(1.00) 		0.114
(1.00)
16p loss 24 (8%) 282 1.01e-10
(4.18e-08) 		0.00734
(1.00) 		1
(1.00) 		1
(1.00) 		0.115
(1.00) 		0.32
(1.00)
17q loss 19 (6%) 287 2.17e-05
(0.00845) 		0.323
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.0491
(1.00) 		0.00713
(1.00)
18q loss 51 (17%) 255 1.13e-07
(4.6e-05) 		0.0306
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.127
(1.00) 		0.187
(1.00)
19p loss 30 (10%) 276 1.87e-12
(7.88e-10) 		0.0122
(1.00) 		0.0089
(1.00) 		0.0106
(1.00) 		0.219
(1.00) 		0.00203
(0.711)
19q loss 21 (7%) 285 3.32e-08
(1.37e-05) 		0.00548
(1.00) 		0.0211
(1.00) 		0.0358
(1.00) 		0.101
(1.00) 		0.00326
(1.00)
20p loss 10 (3%) 296 0.000171
(0.0645) 		0.00222
(0.776) 		0.488
(1.00) 		0.374
(1.00) 		1
(1.00)
21q loss 53 (17%) 253 1.73e-11
(7.25e-09) 		0.0209
(1.00) 		0.281
(1.00) 		0.0973
(1.00) 		0.00354
(1.00) 		0.452
(1.00)
3p gain 9 (3%) 297 0.433
(1.00) 		0.225
(1.00) 		0.488
(1.00) 		0.365
(1.00) 		0.577
(1.00)
3q gain 26 (8%) 280 0.00134
(0.482) 		0.256
(1.00) 		0.0211
(1.00) 		0.117
(1.00) 		0.453
(1.00) 		0.149
(1.00)
4p gain 5 (2%) 301 0.0396
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.689
(1.00)
5q gain 9 (3%) 297 0.00202
(0.71) 		1
(1.00) 		0.108
(1.00) 		0.101
(1.00) 		0.2
(1.00) 		0.535
(1.00)
9p gain 20 (7%) 286 0.14
(1.00) 		0.493
(1.00) 		0.345
(1.00) 		0.481
(1.00) 		0.94
(1.00) 		0.359
(1.00)
9q gain 25 (8%) 281 0.0146
(1.00) 		0.471
(1.00) 		0.185
(1.00) 		0.219
(1.00) 		0.74
(1.00) 		0.638
(1.00)
11p gain 11 (4%) 295 0.511
(1.00) 		0.112
(1.00) 		1
(1.00) 		0.7
(1.00) 		0.548
(1.00)
11q gain 18 (6%) 288 0.101
(1.00) 		0.03
(1.00) 		0.488
(1.00) 		0.266
(1.00) 		0.822
(1.00)
12p gain 30 (10%) 276 0.00259
(0.891) 		0.0664
(1.00) 		0.233
(1.00) 		0.268
(1.00) 		0.108
(1.00) 		0.759
(1.00)
12q gain 23 (8%) 283 0.296
(1.00) 		0.279
(1.00) 		0.108
(1.00) 		0.279
(1.00) 		0.24
(1.00) 		0.359
(1.00)
14q gain 4 (1%) 302 0.0834
(1.00) 		0.776
(1.00) 		1
(1.00)
15q gain 10 (3%) 296 0.0159
(1.00) 		0.274
(1.00) 		0.7
(1.00) 		0.0527
(1.00)
16q gain 11 (4%) 295 0.00147
(0.526) 		0.87
(1.00) 		0.607
(1.00) 		0.643
(1.00) 		0.848
(1.00) 		0.123
(1.00)
17p gain 7 (2%) 299 0.0109
(1.00) 		0.803
(1.00) 		1
(1.00) 		0.346
(1.00) 		1
(1.00)
17q gain 13 (4%) 293 0.00272
(0.934) 		0.976
(1.00) 		1
(1.00) 		0.0906
(1.00) 		0.792
(1.00)
18p gain 21 (7%) 285 0.00376
(1.00) 		0.000849
(0.31) 		0.664
(1.00) 		0.84
(1.00) 		0.0303
(1.00) 		0.777
(1.00)
18q gain 13 (4%) 293 0.0558
(1.00) 		0.0934
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.0701
(1.00) 		0.132
(1.00)
19p gain 12 (4%) 294 0.362
(1.00) 		0.0797
(1.00) 		0.345
(1.00) 		0.356
(1.00) 		0.066
(1.00) 		0.264
(1.00)
19q gain 28 (9%) 278 0.0159
(1.00) 		0.1
(1.00) 		0.412
(1.00) 		0.23
(1.00) 		0.592
(1.00) 		0.453
(1.00)
22q gain 6 (2%) 300 0.0199
(1.00) 		0.19
(1.00) 		0.453
(1.00) 		0.369
(1.00)
Xq gain 4 (1%) 302 0.0834
(1.00) 		0.123
(1.00) 		1
(1.00)
1q loss 4 (1%) 302 0.0573
(1.00) 		0.75
(1.00) 		0.227
(1.00) 		0.689
(1.00)
2p loss 4 (1%) 302 0.0573
(1.00) 		0.542
(1.00) 		1
(1.00) 		1
(1.00) 		0.173
(1.00)
2q loss 5 (2%) 301 0.0272
(1.00) 		0.223
(1.00) 		1
(1.00) 		1
(1.00) 		0.087
(1.00)
6p loss 14 (5%) 292 0.00607
(1.00) 		0.552
(1.00) 		0.488
(1.00) 		0.191
(1.00) 		0.254
(1.00)
6q loss 18 (6%) 288 0.00198
(0.699) 		0.272
(1.00) 		0.607
(1.00) 		0.0105
(1.00) 		0.431
(1.00) 		0.405
(1.00)
7p loss 5 (2%) 301 0.0272
(1.00) 		0.861
(1.00) 		0.233
(1.00) 		0.453
(1.00) 		0.283
(1.00)
8q loss 8 (3%) 298 0.0013
(0.469) 		0.337
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.0559
(1.00)
12q loss 11 (4%) 295 0.00593
(1.00) 		0.00147
(0.525) 		0.233
(1.00) 		0.374
(1.00) 		0.0561
(1.00)
18p loss 36 (12%) 270 0.000781
(0.286) 		0.102
(1.00) 		0.698
(1.00) 		0.863
(1.00) 		0.219
(1.00) 		0.126
(1.00)
Xq loss 13 (4%) 293 0.00107
(0.388) 		0.0516
(1.00) 		0.607
(1.00) 		0.745
(1.00) 		0.257
(1.00) 		0.383
(1.00)
'1p gain mutation analysis' versus 'CN_CNMF'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
1P GAIN MUTATED 0 11 4
1P GAIN WILD-TYPE 153 107 31

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

'1q gain mutation analysis' versus 'CN_CNMF'

P value = 2.96e-11 (Fisher's exact test), Q value = 1.2e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
1Q GAIN MUTATED 2 27 12
1Q GAIN WILD-TYPE 151 91 23

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

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 4.42e-06 (Fisher's exact test), Q value = 0.0018

Table S3.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
2P GAIN MUTATED 1 13 7
2P GAIN WILD-TYPE 152 105 28

Figure S3.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.025

Table S4.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
2Q GAIN MUTATED 2 14 6
2Q GAIN WILD-TYPE 151 104 29

Figure S4.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 8.5e-08 (Fisher's exact test), Q value = 3.5e-05

Table S5.  Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
5P GAIN MUTATED 4 29 3
5P GAIN WILD-TYPE 149 89 32

Figure S5.  Get High-res Image Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.0062

Table S6.  Gene #10: '6p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
6P GAIN MUTATED 2 19 2
6P GAIN WILD-TYPE 151 99 33

Figure S6.  Get High-res Image Gene #10: '6p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 5.05e-05 (Fisher's exact test), Q value = 0.019

Table S7.  Gene #11: '6q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
6Q GAIN MUTATED 2 17 1
6Q GAIN WILD-TYPE 151 101 34

Figure S7.  Get High-res Image Gene #11: '6q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.21e-18 (Fisher's exact test), Q value = 5.2e-16

Table S8.  Gene #12: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
7P GAIN MUTATED 13 49 27
7P GAIN WILD-TYPE 140 69 8

Figure S8.  Get High-res Image Gene #12: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.056

Table S9.  Gene #12: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
7P GAIN MUTATED 8 24 7 34
7P GAIN WILD-TYPE 29 55 57 44

Figure S9.  Get High-res Image Gene #12: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 1.59e-16 (Fisher's exact test), Q value = 6.7e-14

Table S10.  Gene #13: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
7Q GAIN MUTATED 12 33 27
7Q GAIN WILD-TYPE 141 85 8

Figure S10.  Get High-res Image Gene #13: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.016

Table S11.  Gene #14: '8p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
8P GAIN MUTATED 33 27 21
8P GAIN WILD-TYPE 120 91 14

Figure S11.  Get High-res Image Gene #14: '8p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.016

Table S12.  Gene #15: '8q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
8Q GAIN MUTATED 37 50 21
8Q GAIN WILD-TYPE 116 68 14

Figure S12.  Get High-res Image Gene #15: '8q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.006

Table S13.  Gene #15: '8q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
8Q GAIN MUTATED 12 30 6 35
8Q GAIN WILD-TYPE 25 49 58 43

Figure S13.  Get High-res Image Gene #15: '8q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'10p gain mutation analysis' versus 'CN_CNMF'

P value = 3.14e-10 (Fisher's exact test), Q value = 1.3e-07

Table S14.  Gene #18: '10p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
10P GAIN MUTATED 3 33 6
10P GAIN WILD-TYPE 150 85 29

Figure S14.  Get High-res Image Gene #18: '10p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q gain mutation analysis' versus 'CN_CNMF'

P value = 8.66e-06 (Fisher's exact test), Q value = 0.0034

Table S15.  Gene #19: '10q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
10Q GAIN MUTATED 3 21 1
10Q GAIN WILD-TYPE 150 97 34

Figure S15.  Get High-res Image Gene #19: '10q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 2.58e-08 (Fisher's exact test), Q value = 1.1e-05

Table S16.  Gene #24: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
13Q GAIN MUTATED 12 34 16
13Q GAIN WILD-TYPE 141 84 19

Figure S16.  Get High-res Image Gene #24: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000677 (Fisher's exact test), Q value = 0.25

Table S17.  Gene #24: '13q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
13Q GAIN MUTATED 5 15 5 27
13Q GAIN WILD-TYPE 32 64 59 51

Figure S17.  Get High-res Image Gene #24: '13q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000637 (Fisher's exact test), Q value = 0.24

Table S18.  Gene #27: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
16P GAIN MUTATED 1 12 1
16P GAIN WILD-TYPE 152 106 34

Figure S18.  Get High-res Image Gene #27: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 2.71e-19 (Fisher's exact test), Q value = 1.2e-16

Table S19.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
20P GAIN MUTATED 25 67 30
20P GAIN WILD-TYPE 128 51 5

Figure S19.  Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.9e-05 (Fisher's exact test), Q value = 0.03

Table S20.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
20P GAIN MUTATED 18 29 11 41
20P GAIN WILD-TYPE 19 50 53 37

Figure S20.  Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 2.59e-29 (Fisher's exact test), Q value = 1.1e-26

Table S21.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
20Q GAIN MUTATED 27 90 32
20Q GAIN WILD-TYPE 126 28 3

Figure S21.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.18e-08 (Fisher's exact test), Q value = 1.7e-05

Table S22.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
20Q GAIN MUTATED 19 38 13 55
20Q GAIN WILD-TYPE 18 41 51 23

Figure S22.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 4.12e-06 (Fisher's exact test), Q value = 0.0017

Table S23.  Gene #39: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
1P LOSS MUTATED 0 14 0
1P LOSS WILD-TYPE 153 104 35

Figure S23.  Get High-res Image Gene #39: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 4.42e-08 (Fisher's exact test), Q value = 1.8e-05

Table S24.  Gene #43: '3p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
3P LOSS MUTATED 1 23 2
3P LOSS WILD-TYPE 152 95 33

Figure S24.  Get High-res Image Gene #43: '3p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 9.73e-06 (Fisher's exact test), Q value = 0.0038

Table S25.  Gene #44: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
3Q LOSS MUTATED 0 14 1
3Q LOSS WILD-TYPE 153 104 34

Figure S25.  Get High-res Image Gene #44: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'3q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000629 (Fisher's exact test), Q value = 0.23

Table S26.  Gene #44: '3q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 55 92
3Q LOSS MUTATED 0 0 9
3Q LOSS WILD-TYPE 89 55 83

Figure S26.  Get High-res Image Gene #44: '3q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 7.25e-11 (Fisher's exact test), Q value = 3e-08

Table S27.  Gene #45: '4p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
4P LOSS MUTATED 5 39 5
4P LOSS WILD-TYPE 148 79 30

Figure S27.  Get High-res Image Gene #45: '4p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.88e-07 (Fisher's exact test), Q value = 0.00012

Table S28.  Gene #45: '4p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
4P LOSS MUTATED 23 8 5
4P LOSS WILD-TYPE 36 96 68

Figure S28.  Get High-res Image Gene #45: '4p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 1.17e-14 (Fisher's exact test), Q value = 4.9e-12

Table S29.  Gene #46: '4q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
4Q LOSS MUTATED 2 41 4
4Q LOSS WILD-TYPE 151 77 31

Figure S29.  Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.065

Table S30.  Gene #46: '4q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
4Q LOSS MUTATED 0 14 6 22
4Q LOSS WILD-TYPE 37 65 58 56

Figure S30.  Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-07 (Fisher's exact test), Q value = 6.3e-05

Table S31.  Gene #46: '4q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
4Q LOSS MUTATED 22 7 4
4Q LOSS WILD-TYPE 37 97 69

Figure S31.  Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'5p loss mutation analysis' versus 'CN_CNMF'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.0065

Table S32.  Gene #47: '5p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
5P LOSS MUTATED 0 13 2
5P LOSS WILD-TYPE 153 105 33

Figure S32.  Get High-res Image Gene #47: '5p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 2.59e-12 (Fisher's exact test), Q value = 1.1e-09

Table S33.  Gene #48: '5q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
5Q LOSS MUTATED 0 30 4
5Q LOSS WILD-TYPE 153 88 31

Figure S33.  Get High-res Image Gene #48: '5q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.082

Table S34.  Gene #48: '5q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
5Q LOSS MUTATED 14 7 2
5Q LOSS WILD-TYPE 45 97 71

Figure S34.  Get High-res Image Gene #48: '5q loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss mutation analysis' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.011

Table S35.  Gene #52: '7q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
7Q LOSS MUTATED 0 12 0
7Q LOSS WILD-TYPE 153 106 35

Figure S35.  Get High-res Image Gene #52: '7q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00048

Table S36.  Gene #53: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
8P LOSS MUTATED 3 23 1
8P LOSS WILD-TYPE 150 95 34

Figure S36.  Get High-res Image Gene #53: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 4.54e-17 (Fisher's exact test), Q value = 1.9e-14

Table S37.  Gene #55: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
9P LOSS MUTATED 2 44 1
9P LOSS WILD-TYPE 151 74 34

Figure S37.  Get High-res Image Gene #55: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000291 (Fisher's exact test), Q value = 0.11

Table S38.  Gene #55: '9p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
9P LOSS MUTATED 1 11 5 23
9P LOSS WILD-TYPE 36 68 59 55

Figure S38.  Get High-res Image Gene #55: '9p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 3.15e-08 (Fisher's exact test), Q value = 1.3e-05

Table S39.  Gene #56: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
9Q LOSS MUTATED 1 23 1
9Q LOSS WILD-TYPE 152 95 34

Figure S39.  Get High-res Image Gene #56: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.041

Table S40.  Gene #57: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
10P LOSS MUTATED 1 14 2
10P LOSS WILD-TYPE 152 104 33

Figure S40.  Get High-res Image Gene #57: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 8.39e-06 (Fisher's exact test), Q value = 0.0033

Table S41.  Gene #58: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
10Q LOSS MUTATED 0 14 3
10Q LOSS WILD-TYPE 153 104 32

Figure S41.  Get High-res Image Gene #58: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.0064

Table S42.  Gene #59: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
11P LOSS MUTATED 2 17 0
11P LOSS WILD-TYPE 151 101 35

Figure S42.  Get High-res Image Gene #59: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 9.49e-06 (Fisher's exact test), Q value = 0.0038

Table S43.  Gene #60: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
11Q LOSS MUTATED 1 16 0
11Q LOSS WILD-TYPE 152 102 35

Figure S43.  Get High-res Image Gene #60: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.053

Table S44.  Gene #61: '12p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
12P LOSS MUTATED 2 16 1
12P LOSS WILD-TYPE 151 102 34

Figure S44.  Get High-res Image Gene #61: '12p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000419 (Fisher's exact test), Q value = 0.16

Table S45.  Gene #63: '13q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
13Q LOSS MUTATED 0 9 0
13Q LOSS WILD-TYPE 153 109 35

Figure S45.  Get High-res Image Gene #63: '13q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 8.66e-06 (Fisher's exact test), Q value = 0.0034

Table S46.  Gene #64: '14q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
14Q LOSS MUTATED 3 21 1
14Q LOSS WILD-TYPE 150 97 34

Figure S46.  Get High-res Image Gene #64: '14q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 1.09e-07 (Fisher's exact test), Q value = 4.4e-05

Table S47.  Gene #65: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
15Q LOSS MUTATED 0 19 3
15Q LOSS WILD-TYPE 153 99 32

Figure S47.  Get High-res Image Gene #65: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16p loss mutation analysis' versus 'CN_CNMF'

P value = 1.01e-10 (Fisher's exact test), Q value = 4.2e-08

Table S48.  Gene #66: '16p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
16P LOSS MUTATED 0 24 0
16P LOSS WILD-TYPE 153 94 35

Figure S48.  Get High-res Image Gene #66: '16p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q loss mutation analysis' versus 'CN_CNMF'

P value = 7.49e-10 (Fisher's exact test), Q value = 3.1e-07

Table S49.  Gene #67: '16q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
16Q LOSS MUTATED 1 25 0
16Q LOSS WILD-TYPE 152 93 35

Figure S49.  Get High-res Image Gene #67: '16q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000502 (Fisher's exact test), Q value = 0.19

Table S50.  Gene #67: '16q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
16Q LOSS MUTATED 0 5 1 14
16Q LOSS WILD-TYPE 37 74 63 64

Figure S50.  Get High-res Image Gene #67: '16q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 3.45e-18 (Fisher's exact test), Q value = 1.5e-15

Table S51.  Gene #68: '17p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
17P LOSS MUTATED 2 49 7
17P LOSS WILD-TYPE 151 69 28

Figure S51.  Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.06

Table S52.  Gene #68: '17p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
17P LOSS MUTATED 3 13 5 27
17P LOSS WILD-TYPE 34 66 59 51

Figure S52.  Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.25

Table S53.  Gene #68: '17p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
17P LOSS MUTATED 21 16 7
17P LOSS WILD-TYPE 38 88 66

Figure S53.  Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss mutation analysis' versus 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.0084

Table S54.  Gene #69: '17q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
17Q LOSS MUTATED 1 16 2
17Q LOSS WILD-TYPE 152 102 33

Figure S54.  Get High-res Image Gene #69: '17q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 4.6e-05

Table S55.  Gene #71: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
18Q LOSS MUTATED 9 37 5
18Q LOSS WILD-TYPE 144 81 30

Figure S55.  Get High-res Image Gene #71: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19p loss mutation analysis' versus 'CN_CNMF'

P value = 1.87e-12 (Fisher's exact test), Q value = 7.9e-10

Table S56.  Gene #72: '19p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
19P LOSS MUTATED 0 29 1
19P LOSS WILD-TYPE 153 89 34

Figure S56.  Get High-res Image Gene #72: '19p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 3.32e-08 (Fisher's exact test), Q value = 1.4e-05

Table S57.  Gene #73: '19q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
19Q LOSS MUTATED 0 20 1
19Q LOSS WILD-TYPE 153 98 34

Figure S57.  Get High-res Image Gene #73: '19q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.064

Table S58.  Gene #74: '20p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
20P LOSS MUTATED 0 10 0
20P LOSS WILD-TYPE 153 108 35

Figure S58.  Get High-res Image Gene #74: '20p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 1.73e-11 (Fisher's exact test), Q value = 7.2e-09

Table S59.  Gene #75: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
21Q LOSS MUTATED 5 40 8
21Q LOSS WILD-TYPE 148 78 27

Figure S59.  Get High-res Image Gene #75: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 9.26e-17 (Fisher's exact test), Q value = 3.9e-14

Table S60.  Gene #76: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 118 35
22Q LOSS MUTATED 0 38 1
22Q LOSS WILD-TYPE 153 80 34

Figure S60.  Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.17e-06 (Fisher's exact test), Q value = 0.0033

Table S61.  Gene #76: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
22Q LOSS MUTATED 0 9 2 21
22Q LOSS WILD-TYPE 37 70 62 57

Figure S61.  Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000238 (Fisher's exact test), Q value = 0.089

Table S62.  Gene #76: '22q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 55 92
22Q LOSS MUTATED 11 0 19
22Q LOSS WILD-TYPE 78 55 73

Figure S62.  Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 306

  • Number of significantly arm-level cnvs = 77

  • Number of molecular subtypes = 6

  • 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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