Correlation between copy number variations of arm-level result and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1KP8042
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Stomach Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KP8042
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 78 arm-level results and 6 molecular subtypes across 306 patients, 90 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_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'.

  • 18p gain cnv correlated to 'METHLYATION_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

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

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

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_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' and 'METHLYATION_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 15q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 90 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
1q gain 0 (0%) 263 1.99e-07
(8.54e-05) 		0.000347
(0.129) 		0.00046
(0.169) 		4.35e-05
(0.0172) 		0.000138
(0.0528) 		0.00826
(1.00)
20q gain 0 (0%) 149 1.47e-24
(6.65e-22) 		1.89e-13
(8.43e-11) 		5e-08
(2.15e-05) 		0.000145
(0.0553) 		0.00315
(1.00) 		7.81e-09
(3.37e-06)
19p loss 0 (0%) 273 1.37e-11
(6.05e-09) 		7.32e-06
(0.00301) 		8.4e-05
(0.0325) 		0.000268
(0.101) 		0.0381
(1.00) 		4.05e-06
(0.00169)
20p gain 0 (0%) 178 1.86e-17
(8.35e-15) 		7.59e-09
(3.29e-06) 		4.06e-05
(0.0161) 		0.0322
(1.00) 		0.0201
(1.00) 		1.89e-05
(0.00769)
4p loss 0 (0%) 251 4.58e-12
(2.03e-09) 		7.32e-05
(0.0285) 		0.00568
(1.00) 		0.0085
(1.00) 		7.01e-06
(0.00289) 		2.28e-05
(0.00918)
4q loss 0 (0%) 253 3.37e-14
(1.51e-11) 		5.91e-06
(0.00245) 		0.0151
(1.00) 		0.00522
(1.00) 		1.85e-06
(0.000779) 		1.5e-05
(0.0061)
16p loss 0 (0%) 277 2.1e-11
(9.23e-09) 		2.54e-05
(0.0102) 		2.86e-05
(0.0115) 		0.000483
(0.177) 		0.0555
(1.00) 		0.224
(1.00)
5q loss 0 (0%) 271 1.59e-12
(7.04e-10) 		1.65e-06
(0.000697) 		0.00338
(1.00) 		0.0014
(0.493) 		0.00505
(1.00) 		0.00015
(0.0567)
17p loss 0 (0%) 242 6.31e-12
(2.79e-09) 		7.73e-07
(0.000329) 		0.00014
(0.0535) 		0.00792
(1.00) 		0.0366
(1.00) 		0.0197
(1.00)
19q loss 0 (0%) 283 2.73e-07
(0.000117) 		2.05e-05
(0.0083) 		0.00279
(0.961) 		0.00783
(1.00) 		0.0761
(1.00) 		1.39e-05
(0.00568)
5p gain 0 (0%) 264 1.92e-06
(0.000808) 		0.00614
(1.00) 		0.000414
(0.154) 		0.0997
(1.00) 		0.136
(1.00) 		0.0641
(1.00)
6p gain 0 (0%) 279 3.37e-05
(0.0134) 		7.73e-05
(0.03) 		0.0133
(1.00) 		0.0342
(1.00) 		0.00107
(0.378) 		0.0261
(1.00)
6q gain 0 (0%) 284 9.53e-05
(0.0368) 		0.000437
(0.161) 		0.0127
(1.00) 		0.0489
(1.00) 		0.0086
(1.00) 		0.0539
(1.00)
7p gain 0 (0%) 210 7.19e-14
(3.21e-11) 		5.13e-05
(0.0202) 		0.0311
(1.00) 		0.0502
(1.00) 		0.0768
(1.00) 		0.192
(1.00)
7q gain 0 (0%) 229 2.11e-13
(9.4e-11) 		0.00063
(0.229) 		0.166
(1.00) 		0.483
(1.00) 		0.0899
(1.00) 		0.703
(1.00)
8p gain 0 (0%) 216 2.76e-10
(1.21e-07) 		0.000489
(0.179) 		0.17
(1.00) 		0.0239
(1.00) 		0.0178
(1.00) 		0.429
(1.00)
8q gain 0 (0%) 184 4.29e-10
(1.87e-07) 		6.92e-07
(0.000295) 		0.00866
(1.00) 		0.0209
(1.00) 		0.00726
(1.00) 		0.0306
(1.00)
13q gain 0 (0%) 241 1.2e-06
(0.000509) 		0.000605
(0.221) 		0.367
(1.00) 		0.344
(1.00) 		0.56
(1.00) 		0.00968
(1.00)
9p loss 0 (0%) 255 1.45e-11
(6.37e-09) 		3.46e-06
(0.00144) 		0.00736
(1.00) 		0.0165
(1.00) 		0.0639
(1.00) 		0.0171
(1.00)
11p loss 0 (0%) 288 0.000611
(0.222) 		0.000291
(0.109) 		0.803
(1.00) 		0.0945
(1.00) 		0.145
(1.00) 		0.275
(1.00)
12p loss 0 (0%) 285 4.38e-05
(0.0173) 		6.83e-05
(0.0266) 		0.0044
(1.00) 		0.000993
(0.355) 		0.0769
(1.00) 		0.0127
(1.00)
14q loss 0 (0%) 278 8.18e-06
(0.00335) 		0.000127
(0.0488) 		0.0133
(1.00) 		0.0559
(1.00) 		0.0136
(1.00) 		0.0119
(1.00)
15q loss 0 (0%) 281 1.45e-07
(6.24e-05) 		3.75e-05
(0.0149) 		0.0598
(1.00) 		0.00334
(1.00) 		0.0116
(1.00) 		0.00534
(1.00)
16q loss 0 (0%) 274 3.96e-11
(1.74e-08) 		5.71e-06
(0.00238) 		0.00126
(0.445) 		0.00275
(0.953) 		0.0704
(1.00) 		0.64
(1.00)
21q loss 0 (0%) 244 4.08e-09
(1.77e-06) 		6.7e-06
(0.00277) 		0.0531
(1.00) 		0.0213
(1.00) 		0.076
(1.00) 		0.437
(1.00)
22q loss 0 (0%) 266 7.2e-15
(3.23e-12) 		8.91e-07
(0.000378) 		0.000803
(0.29) 		0.00276
(0.954) 		0.00401
(1.00) 		0.00493
(1.00)
2p gain 0 (0%) 282 0.000434
(0.161) 		0.00206
(0.718) 		0.346
(1.00) 		0.432
(1.00) 		0.319
(1.00) 		0.00426
(1.00)
3q gain 0 (0%) 277 0.000666
(0.241) 		0.188
(1.00) 		0.56
(1.00) 		0.895
(1.00) 		1
(1.00) 		0.159
(1.00)
10p gain 0 (0%) 261 3.76e-09
(1.64e-06) 		0.00281
(0.965) 		0.00109
(0.386) 		0.012
(1.00) 		0.581
(1.00) 		0.00357
(1.00)
10q gain 0 (0%) 280 2.63e-05
(0.0105) 		0.056
(1.00) 		0.113
(1.00) 		0.285
(1.00) 		0.391
(1.00) 		0.393
(1.00)
18p gain 0 (0%) 281 0.00377
(1.00) 		5.64e-05
(0.0221) 		0.0451
(1.00) 		0.34
(1.00) 		0.492
(1.00) 		0.899
(1.00)
1p loss 0 (0%) 292 1.5e-05
(0.0061) 		0.103
(1.00) 		0.167
(1.00) 		0.155
(1.00) 		0.0853
(1.00) 		0.836
(1.00)
3p loss 0 (0%) 281 5.51e-07
(0.000235) 		0.00105
(0.373) 		0.0373
(1.00) 		0.0199
(1.00) 		0.00932
(1.00) 		0.0513
(1.00)
3q loss 0 (0%) 292 5.76e-05
(0.0225) 		0.0215
(1.00) 		0.0757
(1.00) 		0.184
(1.00) 		0.003
(1.00) 		0.013
(1.00)
5p loss 0 (0%) 289 2.12e-05
(0.00855) 		0.00483
(1.00) 		0.148
(1.00) 		0.0506
(1.00) 		0.166
(1.00) 		0.0514
(1.00)
7q loss 0 (0%) 293 0.0002
(0.0752) 		0.0436
(1.00) 		0.339
(1.00) 		0.561
(1.00) 		0.0434
(1.00) 		0.26
(1.00)
8p loss 0 (0%) 275 5.9e-06
(0.00245) 		0.0302
(1.00) 		0.0424
(1.00) 		0.0127
(1.00) 		0.0422
(1.00) 		0.298
(1.00)
9q loss 0 (0%) 281 3.06e-05
(0.0122) 		0.00261
(0.909) 		0.291
(1.00) 		0.324
(1.00) 		0.163
(1.00) 		0.341
(1.00)
10p loss 0 (0%) 289 0.000261
(0.0983) 		0.0103
(1.00) 		0.053
(1.00) 		0.00503
(1.00) 		0.331
(1.00) 		0.225
(1.00)
10q loss 0 (0%) 290 0.000133
(0.0511) 		0.00393
(1.00) 		0.272
(1.00) 		0.0296
(1.00) 		0.0936
(1.00) 		0.118
(1.00)
11q loss 0 (0%) 290 0.000269
(0.101) 		0.01
(1.00) 		0.855
(1.00) 		0.543
(1.00) 		0.0853
(1.00) 		0.917
(1.00)
17q loss 0 (0%) 286 0.000103
(0.0396) 		0.0087
(1.00) 		0.011
(1.00) 		0.144
(1.00) 		0.174
(1.00) 		0.0698
(1.00)
18q loss 0 (0%) 254 2.74e-06
(0.00115) 		0.00413
(1.00) 		0.0179
(1.00) 		0.127
(1.00) 		0.044
(1.00) 		0.0271
(1.00)
20p loss 0 (0%) 297 0.00451
(1.00) 		0.0186
(1.00) 		0.000151
(0.0569) 		0.0901
(1.00) 		0.305
(1.00) 		0.894
(1.00)
1p gain 0 (0%) 291 0.00429
(1.00) 		0.571
(1.00) 		0.128
(1.00) 		0.0203
(1.00) 		0.0674
(1.00) 		0.657
(1.00)
2q gain 0 (0%) 283 0.00439
(1.00) 		0.00098
(0.351) 		0.0241
(1.00) 		0.0529
(1.00) 		0.187
(1.00) 		0.0117
(1.00)
3p gain 0 (0%) 295 0.248
(1.00) 		0.0987
(1.00) 		0.555
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 0 (0%) 301 0.0903
(1.00) 		0.286
(1.00) 		0.827
(1.00) 		0.553
(1.00)
5q gain 0 (0%) 296 0.26
(1.00) 		0.95
(1.00) 		0.402
(1.00) 		0.905
(1.00) 		0.76
(1.00) 		0.611
(1.00)
9p gain 0 (0%) 284 0.0258
(1.00) 		0.153
(1.00) 		0.279
(1.00) 		0.524
(1.00) 		0.789
(1.00) 		0.124
(1.00)
9q gain 0 (0%) 277 0.00579
(1.00) 		0.132
(1.00) 		0.358
(1.00) 		0.382
(1.00) 		0.625
(1.00) 		0.67
(1.00)
11p gain 0 (0%) 294 0.845
(1.00) 		0.122
(1.00) 		0.768
(1.00) 		0.0591
(1.00) 		0.27
(1.00) 		0.512
(1.00)
11q gain 0 (0%) 286 0.137
(1.00) 		0.0414
(1.00) 		0.804
(1.00) 		0.26
(1.00) 		0.136
(1.00) 		0.536
(1.00)
12p gain 0 (0%) 271 0.00368
(1.00) 		0.218
(1.00) 		0.0159
(1.00) 		0.126
(1.00) 		0.107
(1.00) 		0.853
(1.00)
12q gain 0 (0%) 278 0.329
(1.00) 		0.187
(1.00) 		0.26
(1.00) 		0.5
(1.00) 		0.183
(1.00) 		0.419
(1.00)
14q gain 0 (0%) 301 0.0438
(1.00) 		0.349
(1.00) 		0.797
(1.00) 		0.072
(1.00)
15q gain 0 (0%) 296 0.0326
(1.00) 		0.58
(1.00) 		0.0709
(1.00) 		0.00161
(0.562) 		0.791
(1.00) 		0.24
(1.00)
16p gain 0 (0%) 293 0.0238
(1.00) 		0.131
(1.00) 		0.0812
(1.00) 		0.292
(1.00) 		1
(1.00) 		0.293
(1.00)
16q gain 0 (0%) 294 0.117
(1.00) 		0.826
(1.00) 		0.306
(1.00) 		0.426
(1.00) 		0.321
(1.00) 		0.208
(1.00)
17p gain 0 (0%) 299 0.0216
(1.00) 		0.458
(1.00) 		0.729
(1.00) 		0.327
(1.00) 		0.5
(1.00) 		0.875
(1.00)
17q gain 0 (0%) 291 0.00983
(1.00) 		0.675
(1.00) 		0.323
(1.00) 		0.416
(1.00) 		0.135
(1.00) 		0.582
(1.00)
18q gain 0 (0%) 292 0.221
(1.00) 		0.0674
(1.00) 		0.0731
(1.00) 		0.338
(1.00) 		0.312
(1.00) 		0.585
(1.00)
19p gain 0 (0%) 293 0.261
(1.00) 		0.0201
(1.00) 		0.874
(1.00) 		0.113
(1.00) 		0.26
(1.00) 		0.78
(1.00)
19q gain 0 (0%) 274 0.431
(1.00) 		0.419
(1.00) 		0.531
(1.00) 		0.443
(1.00) 		0.4
(1.00) 		0.55
(1.00)
21q gain 0 (0%) 303 0.212
(1.00) 		0.861
(1.00)
22q gain 0 (0%) 300 0.0244
(1.00) 		0.233
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.676
(1.00)
Xq gain 0 (0%) 301 0.345
(1.00) 		0.223
(1.00)
1q loss 0 (0%) 302 0.154
(1.00) 		1
(1.00)
2p loss 0 (0%) 300 0.0268
(1.00) 		0.452
(1.00) 		0.351
(1.00) 		0.385
(1.00) 		0.294
(1.00) 		0.0354
(1.00)
2q loss 0 (0%) 301 0.0438
(1.00) 		0.681
(1.00) 		0.587
(1.00) 		0.686
(1.00) 		0.55
(1.00) 		0.0359
(1.00)
6p loss 0 (0%) 291 0.0368
(1.00) 		0.29
(1.00) 		0.444
(1.00) 		0.0292
(1.00) 		0.832
(1.00) 		0.288
(1.00)
6q loss 0 (0%) 287 0.0114
(1.00) 		0.123
(1.00) 		0.0142
(1.00) 		0.0617
(1.00) 		0.789
(1.00) 		0.44
(1.00)
7p loss 0 (0%) 302 0.118
(1.00) 		0.0656
(1.00) 		0.373
(1.00) 		0.797
(1.00) 		0.203
(1.00)
8q loss 0 (0%) 298 0.0115
(1.00) 		0.267
(1.00) 		0.729
(1.00) 		0.327
(1.00) 		0.5
(1.00) 		0.268
(1.00)
12q loss 0 (0%) 294 0.00807
(1.00) 		0.00147
(0.515) 		0.0742
(1.00) 		0.0854
(1.00) 		0.76
(1.00) 		0.0943
(1.00)
13q loss 0 (0%) 295 0.000884
(0.318) 		0.162
(1.00) 		0.174
(1.00) 		0.0854
(1.00) 		0.282
(1.00) 		0.678
(1.00)
18p loss 0 (0%) 266 0.000932
(0.335) 		0.0104
(1.00) 		0.085
(1.00) 		0.114
(1.00) 		0.0223
(1.00) 		0.169
(1.00)
Xq loss 0 (0%) 292 0.0116
(1.00) 		0.116
(1.00) 		0.256
(1.00) 		0.184
(1.00) 		0.282
(1.00) 		0.358
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 8.5e-05

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
1Q GAIN CNV 4 6 3 30
1Q GAIN WILD-TYPE 133 22 25 83

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.000347 (Fisher's exact test), Q value = 0.13

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
1Q GAIN CNV 2 13 2 20
1Q GAIN WILD-TYPE 35 66 62 58

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Chi-square test), Q value = 0.17

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
1Q GAIN CNV 2 0 5 3 14
1Q GAIN WILD-TYPE 37 37 23 29 33

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.35e-05 (Fisher's exact test), Q value = 0.017

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 73 52
1Q GAIN CNV 0 11 13
1Q GAIN WILD-TYPE 58 62 39

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.053

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 53 101
1Q GAIN CNV 8 1 25
1Q GAIN WILD-TYPE 75 52 76

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.000434 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
2P GAIN CNV 2 4 4 14
2P GAIN WILD-TYPE 135 24 24 99

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 0.000666 (Fisher's exact test), Q value = 0.24

Table S7.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
3Q GAIN CNV 5 8 3 13
3Q GAIN WILD-TYPE 132 20 25 100

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.00081

Table S8.  Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
5P GAIN CNV 6 3 2 31
5P GAIN WILD-TYPE 131 25 26 82

Figure S8.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.000414 (Chi-square test), Q value = 0.15

Table S9.  Gene #8: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
5P GAIN CNV 6 2 1 4 17
5P GAIN WILD-TYPE 33 35 27 28 30

Figure S9.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.013

Table S10.  Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
6P GAIN CNV 2 2 3 20
6P GAIN WILD-TYPE 135 26 25 93

Figure S10.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.03

Table S11.  Gene #10: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
6P GAIN CNV 0 8 0 14
6P GAIN WILD-TYPE 37 71 64 64

Figure S11.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 9.53e-05 (Fisher's exact test), Q value = 0.037

Table S12.  Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
6Q GAIN CNV 2 0 3 17
6Q GAIN WILD-TYPE 135 28 25 96

Figure S12.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.000437 (Fisher's exact test), Q value = 0.16

Table S13.  Gene #11: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
6Q GAIN CNV 0 6 0 12
6Q GAIN WILD-TYPE 37 73 64 66

Figure S13.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 7.19e-14 (Fisher's exact test), Q value = 3.2e-11

Table S14.  Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
7P GAIN CNV 21 25 6 44
7P GAIN WILD-TYPE 116 3 22 69

Figure S14.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5.13e-05 (Fisher's exact test), Q value = 0.02

Table S15.  Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
7P GAIN CNV 12 29 6 33
7P GAIN WILD-TYPE 25 50 58 45

Figure S15.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.11e-13 (Fisher's exact test), Q value = 9.4e-11

Table S16.  Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
7Q GAIN CNV 20 25 5 27
7Q GAIN WILD-TYPE 117 3 23 86

Figure S16.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.23

Table S17.  Gene #13: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
7Q GAIN CNV 11 20 4 25
7Q GAIN WILD-TYPE 26 59 60 53

Figure S17.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 2.76e-10 (Fisher's exact test), Q value = 1.2e-07

Table S18.  Gene #14: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
8P GAIN CNV 29 11 24 26
8P GAIN WILD-TYPE 108 17 4 87

Figure S18.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.000489 (Fisher's exact test), Q value = 0.18

Table S19.  Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
8P GAIN CNV 13 30 6 21
8P GAIN WILD-TYPE 24 49 58 57

Figure S19.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4.29e-10 (Fisher's exact test), Q value = 1.9e-07

Table S20.  Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
8Q GAIN CNV 36 12 26 48
8Q GAIN WILD-TYPE 101 16 2 65

Figure S20.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 6.92e-07 (Fisher's exact test), Q value = 0.00029

Table S21.  Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
8Q GAIN CNV 13 39 7 38
8Q GAIN WILD-TYPE 24 40 57 40

Figure S21.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 3.76e-09 (Fisher's exact test), Q value = 1.6e-06

Table S22.  Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10P GAIN CNV 3 7 3 32
10P GAIN WILD-TYPE 134 21 25 81

Figure S22.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.011

Table S23.  Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10Q GAIN CNV 2 1 3 20
10Q GAIN WILD-TYPE 135 27 25 93

Figure S23.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00051

Table S24.  Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
13Q GAIN CNV 16 15 2 32
13Q GAIN WILD-TYPE 121 13 26 81

Figure S24.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000605 (Fisher's exact test), Q value = 0.22

Table S25.  Gene #24: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
13Q GAIN CNV 7 15 5 28
13Q GAIN WILD-TYPE 30 64 59 50

Figure S25.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 5.64e-05 (Fisher's exact test), Q value = 0.022

Table S26.  Gene #31: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
18P GAIN CNV 0 5 0 14
18P GAIN WILD-TYPE 37 74 64 64

Figure S26.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.86e-17 (Fisher's exact test), Q value = 8.4e-15

Table S27.  Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
20P GAIN CNV 23 25 15 65
20P GAIN WILD-TYPE 114 3 13 48

Figure S27.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 7.59e-09 (Fisher's exact test), Q value = 3.3e-06

Table S28.  Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
20P GAIN CNV 21 29 8 47
20P GAIN WILD-TYPE 16 50 56 31

Figure S28.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 4.06e-05 (Chi-square test), Q value = 0.016

Table S29.  Gene #35: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
20P GAIN CNV 11 7 5 16 29
20P GAIN WILD-TYPE 28 30 23 16 18

Figure S29.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0077

Table S30.  Gene #35: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
20P GAIN CNV 36 14 44
20P GAIN WILD-TYPE 20 47 76

Figure S30.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.47e-24 (Fisher's exact test), Q value = 6.7e-22

Table S31.  Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
20Q GAIN CNV 27 26 18 86
20Q GAIN WILD-TYPE 110 2 10 27

Figure S31.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1.89e-13 (Fisher's exact test), Q value = 8.4e-11

Table S32.  Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
20Q GAIN CNV 21 36 12 64
20Q GAIN WILD-TYPE 16 43 52 14

Figure S32.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 5e-08 (Chi-square test), Q value = 2.2e-05

Table S33.  Gene #36: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
20Q GAIN CNV 12 9 9 18 39
20Q GAIN WILD-TYPE 27 28 19 14 8

Figure S33.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000145 (Fisher's exact test), Q value = 0.055

Table S34.  Gene #36: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 73 52
20Q GAIN CNV 19 31 37
20Q GAIN WILD-TYPE 39 42 15

Figure S34.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.81e-09 (Fisher's exact test), Q value = 3.4e-06

Table S35.  Gene #36: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
20Q GAIN CNV 47 20 52
20Q GAIN WILD-TYPE 9 41 68

Figure S35.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.0061

Table S36.  Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
1P LOSS CNV 0 0 0 14
1P LOSS WILD-TYPE 137 28 28 99

Figure S36.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 5.51e-07 (Fisher's exact test), Q value = 0.00024

Table S37.  Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
3P LOSS CNV 1 1 1 22
3P LOSS WILD-TYPE 136 27 27 91

Figure S37.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 5.76e-05 (Fisher's exact test), Q value = 0.023

Table S38.  Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
3Q LOSS CNV 0 1 0 13
3Q LOSS WILD-TYPE 137 27 28 100

Figure S38.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 4.58e-12 (Fisher's exact test), Q value = 2e-09

Table S39.  Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
4P LOSS CNV 6 4 1 44
4P LOSS WILD-TYPE 131 24 27 69

Figure S39.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 7.32e-05 (Fisher's exact test), Q value = 0.028

Table S40.  Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
4P LOSS CNV 1 15 5 25
4P LOSS WILD-TYPE 36 64 59 53

Figure S40.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 7.01e-06 (Fisher's exact test), Q value = 0.0029

Table S41.  Gene #46: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 53 101
4P LOSS CNV 11 1 31
4P LOSS WILD-TYPE 72 52 70

Figure S41.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.28e-05 (Fisher's exact test), Q value = 0.0092

Table S42.  Gene #46: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
4P LOSS CNV 21 3 19
4P LOSS WILD-TYPE 35 58 101

Figure S42.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 3.37e-14 (Fisher's exact test), Q value = 1.5e-11

Table S43.  Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
4Q LOSS CNV 4 3 1 45
4Q LOSS WILD-TYPE 133 25 27 68

Figure S43.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 5.91e-06 (Fisher's exact test), Q value = 0.0024

Table S44.  Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
4Q LOSS CNV 1 17 3 25
4Q LOSS WILD-TYPE 36 62 61 53

Figure S44.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.85e-06 (Fisher's exact test), Q value = 0.00078

Table S45.  Gene #47: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 53 101
4Q LOSS CNV 11 0 29
4Q LOSS WILD-TYPE 72 53 72

Figure S45.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.0061

Table S46.  Gene #47: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
4Q LOSS CNV 20 2 18
4Q LOSS WILD-TYPE 36 59 102

Figure S46.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.0085

Table S47.  Gene #48: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
5P LOSS CNV 0 1 1 15
5P LOSS WILD-TYPE 137 27 27 98

Figure S47.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.59e-12 (Fisher's exact test), Q value = 7e-10

Table S48.  Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
5Q LOSS CNV 0 2 1 32
5Q LOSS WILD-TYPE 137 26 27 81

Figure S48.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.65e-06 (Fisher's exact test), Q value = 7e-04

Table S49.  Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
5Q LOSS CNV 0 10 1 21
5Q LOSS WILD-TYPE 37 69 63 57

Figure S49.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.057

Table S50.  Gene #49: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
5Q LOSS CNV 15 2 9
5Q LOSS WILD-TYPE 41 59 111

Figure S50.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.075

Table S51.  Gene #53: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
7Q LOSS CNV 0 0 1 12
7Q LOSS WILD-TYPE 137 28 27 101

Figure S51.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 5.9e-06 (Fisher's exact test), Q value = 0.0024

Table S52.  Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
8P LOSS CNV 4 3 0 24
8P LOSS WILD-TYPE 133 25 28 89

Figure S52.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.45e-11 (Fisher's exact test), Q value = 6.4e-09

Table S53.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
9P LOSS CNV 4 3 3 41
9P LOSS WILD-TYPE 133 25 25 72

Figure S53.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.46e-06 (Fisher's exact test), Q value = 0.0014

Table S54.  Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
9P LOSS CNV 0 12 5 26
9P LOSS WILD-TYPE 37 67 59 52

Figure S54.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.012

Table S55.  Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
9Q LOSS CNV 2 1 2 20
9Q LOSS WILD-TYPE 135 27 26 93

Figure S55.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.098

Table S56.  Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10P LOSS CNV 1 2 0 14
10P LOSS WILD-TYPE 136 26 28 99

Figure S56.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.000133 (Fisher's exact test), Q value = 0.051

Table S57.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10Q LOSS CNV 0 3 1 12
10Q LOSS WILD-TYPE 137 25 27 101

Figure S57.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.000611 (Fisher's exact test), Q value = 0.22

Table S58.  Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
11P LOSS CNV 2 0 1 15
11P LOSS WILD-TYPE 135 28 27 98

Figure S58.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

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

Table S59.  Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
11P LOSS CNV 0 2 0 11
11P LOSS WILD-TYPE 37 77 64 67

Figure S59.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.1

Table S60.  Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
11Q LOSS CNV 1 0 1 14
11Q LOSS WILD-TYPE 136 28 27 99

Figure S60.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.017

Table S61.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
12P LOSS CNV 2 1 0 18
12P LOSS WILD-TYPE 135 27 28 95

Figure S61.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 6.83e-05 (Fisher's exact test), Q value = 0.027

Table S62.  Gene #62: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
12P LOSS CNV 0 2 1 14
12P LOSS WILD-TYPE 37 77 63 64

Figure S62.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 8.18e-06 (Fisher's exact test), Q value = 0.0034

Table S63.  Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
14Q LOSS CNV 3 1 1 23
14Q LOSS WILD-TYPE 134 27 27 90

Figure S63.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.049

Table S64.  Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
14Q LOSS CNV 0 7 1 16
14Q LOSS WILD-TYPE 37 72 63 62

Figure S64.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1.45e-07 (Fisher's exact test), Q value = 6.2e-05

Table S65.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
15Q LOSS CNV 0 2 2 21
15Q LOSS WILD-TYPE 137 26 26 92

Figure S65.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.015

Table S66.  Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
15Q LOSS CNV 0 7 0 15
15Q LOSS WILD-TYPE 37 72 64 63

Figure S66.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 2.1e-11 (Fisher's exact test), Q value = 9.2e-09

Table S67.  Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
16P LOSS CNV 0 0 1 28
16P LOSS WILD-TYPE 137 28 27 85

Figure S67.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 2.54e-05 (Fisher's exact test), Q value = 0.01

Table S68.  Gene #67: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
16P LOSS CNV 0 10 0 15
16P LOSS WILD-TYPE 37 69 64 63

Figure S68.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 2.86e-05 (Chi-square test), Q value = 0.011

Table S69.  Gene #67: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
16P LOSS CNV 2 0 1 0 12
16P LOSS WILD-TYPE 37 37 27 32 35

Figure S69.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000483 (Fisher's exact test), Q value = 0.18

Table S70.  Gene #67: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 73 52
16P LOSS CNV 1 3 11
16P LOSS WILD-TYPE 57 70 41

Figure S70.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 3.96e-11 (Fisher's exact test), Q value = 1.7e-08

Table S71.  Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
16Q LOSS CNV 1 0 1 30
16Q LOSS WILD-TYPE 136 28 27 83

Figure S71.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 5.71e-06 (Fisher's exact test), Q value = 0.0024

Table S72.  Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
16Q LOSS CNV 0 9 0 17
16Q LOSS WILD-TYPE 37 70 64 61

Figure S72.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 6.31e-12 (Fisher's exact test), Q value = 2.8e-09

Table S73.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
17P LOSS CNV 6 9 4 45
17P LOSS WILD-TYPE 131 19 24 68

Figure S73.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 7.73e-07 (Fisher's exact test), Q value = 0.00033

Table S74.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
17P LOSS CNV 2 17 4 31
17P LOSS WILD-TYPE 35 62 60 47

Figure S74.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Chi-square test), Q value = 0.054

Table S75.  Gene #69: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
17P LOSS CNV 4 0 10 8 17
17P LOSS WILD-TYPE 35 37 18 24 30

Figure S75.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.04

Table S76.  Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
17Q LOSS CNV 1 2 1 16
17Q LOSS WILD-TYPE 136 26 27 97

Figure S76.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2.74e-06 (Fisher's exact test), Q value = 0.0011

Table S77.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
18Q LOSS CNV 10 8 1 33
18Q LOSS WILD-TYPE 127 20 27 80

Figure S77.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1.37e-11 (Fisher's exact test), Q value = 6.1e-09

Table S78.  Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
19P LOSS CNV 0 2 1 30
19P LOSS WILD-TYPE 137 26 27 83

Figure S78.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 7.32e-06 (Fisher's exact test), Q value = 0.003

Table S79.  Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
19P LOSS CNV 0 7 1 19
19P LOSS WILD-TYPE 37 72 63 59

Figure S79.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 8.4e-05 (Chi-square test), Q value = 0.033

Table S80.  Gene #73: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
19P LOSS CNV 1 0 2 2 13
19P LOSS WILD-TYPE 38 37 26 30 34

Figure S80.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000268 (Fisher's exact test), Q value = 0.1

Table S81.  Gene #73: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 73 52
19P LOSS CNV 0 7 11
19P LOSS WILD-TYPE 58 66 41

Figure S81.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0017

Table S82.  Gene #73: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
19P LOSS CNV 17 2 7
19P LOSS WILD-TYPE 39 59 113

Figure S82.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 2.73e-07 (Fisher's exact test), Q value = 0.00012

Table S83.  Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
19Q LOSS CNV 0 2 1 20
19Q LOSS WILD-TYPE 137 26 27 93

Figure S83.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.0083

Table S84.  Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
19Q LOSS CNV 0 2 1 15
19Q LOSS WILD-TYPE 37 77 63 63

Figure S84.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0057

Table S85.  Gene #74: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 61 120
19Q LOSS CNV 13 2 3
19Q LOSS WILD-TYPE 43 59 117

Figure S85.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.057

Table S86.  Gene #75: '20p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 37 28 32 47
20P LOSS CNV 0 0 5 0 1
20P LOSS WILD-TYPE 39 37 23 32 46

Figure S86.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 4.08e-09 (Fisher's exact test), Q value = 1.8e-06

Table S87.  Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
21Q LOSS CNV 8 4 10 40
21Q LOSS WILD-TYPE 129 24 18 73

Figure S87.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 6.7e-06 (Fisher's exact test), Q value = 0.0028

Table S88.  Gene #76: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
21Q LOSS CNV 1 28 5 18
21Q LOSS WILD-TYPE 36 51 59 60

Figure S88.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.2e-15 (Fisher's exact test), Q value = 3.2e-12

Table S89.  Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
22Q LOSS CNV 0 2 1 37
22Q LOSS WILD-TYPE 137 26 27 76

Figure S89.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 8.91e-07 (Fisher's exact test), Q value = 0.00038

Table S90.  Gene #77: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 79 64 78
22Q LOSS CNV 0 8 2 23
22Q LOSS WILD-TYPE 37 71 62 55

Figure S90.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #2: 'METHLYATION_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 = 78

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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