Correlation between copy number variations of arm-level result and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1CF9NSJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1CF9NSJ
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 73 arm-level events and 10 molecular subtypes across 331 patients, 43 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 43 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
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 Chi-square test Fisher's exact test Chi-square test Fisher's exact test
8p loss 104 (31%) 227 0.000279
(0.182) 		1.22e-08
(8.35e-06) 		0.543
(1.00) 		0.904
(1.00) 		2.99e-05
(0.02) 		8.54e-05
(0.0564) 		0.000218
(0.143) 		0.369
(1.00) 		0.00471
(1.00) 		0.807
(1.00)
10p loss 22 (7%) 309 2.78e-07
(0.000189) 		0.000263
(0.172) 		0.00682
(1.00) 		0.031
(1.00) 		0.000162
(0.107) 		0.000271
(0.177) 		0.164
(1.00) 		0.000798
(0.512) 		0.328
(1.00) 		0.282
(1.00)
7p gain 58 (18%) 273 1.77e-09
(1.22e-06) 		5.18e-08
(3.54e-05) 		0.541
(1.00) 		0.663
(1.00) 		4.03e-05
(0.0269) 		0.00343
(1.00) 		0.21
(1.00) 		0.0813
(1.00) 		0.156
(1.00) 		0.909
(1.00)
7q gain 56 (17%) 275 9.23e-09
(6.35e-06) 		2.75e-08
(1.88e-05) 		0.586
(1.00) 		0.551
(1.00) 		5.99e-05
(0.0397) 		0.00478
(1.00) 		0.233
(1.00) 		0.264
(1.00) 		0.11
(1.00) 		0.927
(1.00)
8p gain 38 (11%) 293 4.01e-10
(2.77e-07) 		9.22e-06
(0.0062) 		0.00511
(1.00) 		0.0193
(1.00) 		0.0187
(1.00) 		0.0245
(1.00) 		0.103
(1.00) 		0.121
(1.00) 		0.0223
(1.00) 		0.48
(1.00)
8q gain 67 (20%) 264 2.51e-12
(1.73e-09) 		1.13e-05
(0.0076) 		0.00216
(1.00) 		0.00746
(1.00) 		0.000434
(0.283) 		0.000625
(0.404) 		0.000888
(0.566) 		0.0441
(1.00) 		0.000946
(0.603) 		0.239
(1.00)
6p loss 11 (3%) 320 0.000259
(0.17) 		0.00479
(1.00) 		0.255
(1.00) 		0.155
(1.00) 		0.00156
(0.984) 		2.98e-05
(0.02) 		0.351
(1.00) 		0.262
(1.00) 		0.639
(1.00) 		0.702
(1.00)
17p loss 44 (13%) 287 9.89e-13
(6.87e-10) 		0.00931
(1.00) 		0.00344
(1.00) 		0.0141
(1.00) 		0.000839
(0.537) 		4.12e-05
(0.0274) 		0.174
(1.00) 		0.00273
(1.00) 		0.0636
(1.00) 		0.462
(1.00)
1q gain 15 (5%) 316 3.5e-05
(0.0234) 		0.00555
(1.00) 		0.0223
(1.00) 		0.224
(1.00) 		0.0127
(1.00) 		0.00431
(1.00) 		0.241
(1.00) 		0.419
(1.00) 		0.524
(1.00) 		1
(1.00)
3p gain 23 (7%) 308 4.26e-06
(0.00288) 		0.0118
(1.00) 		0.219
(1.00) 		0.838
(1.00) 		0.247
(1.00) 		0.215
(1.00) 		0.802
(1.00) 		0.892
(1.00) 		0.731
(1.00) 		0.623
(1.00)
3q gain 31 (9%) 300 6.46e-08
(4.41e-05) 		0.0586
(1.00) 		0.0839
(1.00) 		0.434
(1.00) 		0.0413
(1.00) 		0.111
(1.00) 		0.625
(1.00) 		0.432
(1.00) 		0.272
(1.00) 		0.389
(1.00)
5p gain 9 (3%) 322 4.8e-05
(0.0319) 		0.07
(1.00) 		0.298
(1.00) 		0.387
(1.00) 		0.0934
(1.00) 		0.399
(1.00) 		0.209
(1.00) 		0.0857
(1.00) 		0.142
(1.00) 		0.678
(1.00)
9p gain 13 (4%) 318 2.43e-05
(0.0163) 		0.351
(1.00) 		0.484
(1.00) 		0.2
(1.00) 		0.297
(1.00) 		0.68
(1.00) 		0.506
(1.00) 		0.746
(1.00) 		0.424
(1.00) 		0.39
(1.00)
9q gain 26 (8%) 305 1.63e-10
(1.12e-07) 		0.0822
(1.00) 		0.0281
(1.00) 		0.0112
(1.00) 		0.00884
(1.00) 		0.0713
(1.00) 		0.113
(1.00) 		0.0864
(1.00) 		0.206
(1.00) 		0.361
(1.00)
12q gain 8 (2%) 323 0.00023
(0.151) 		0.0191
(1.00) 		0.848
(1.00) 		0.863
(1.00) 		0.0795
(1.00) 		0.747
(1.00) 		0.492
(1.00) 		0.861
(1.00) 		0.621
(1.00) 		0.612
(1.00)
21q gain 9 (3%) 322 4.8e-05
(0.0319) 		0.07
(1.00) 		0.445
(1.00) 		0.326
(1.00) 		0.104
(1.00) 		0.106
(1.00) 		0.135
(1.00) 		0.14
(1.00) 		0.136
(1.00) 		0.142
(1.00)
4p loss 10 (3%) 321 0.000587
(0.381) 		0.259
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.076
(1.00) 		0.0933
(1.00) 		0.0249
(1.00) 		0.000177
(0.116) 		0.245
(1.00) 		0.235
(1.00)
5q loss 9 (3%) 322 4.8e-05
(0.0319) 		0.362
(1.00) 		0.255
(1.00) 		0.155
(1.00) 		0.361
(1.00) 		0.246
(1.00) 		0.265
(1.00) 		0.154
(1.00) 		0.752
(1.00) 		0.424
(1.00)
6q loss 20 (6%) 311 7.41e-06
(0.00499) 		0.000846
(0.541) 		0.0761
(1.00) 		0.502
(1.00) 		0.00126
(0.796) 		0.000729
(0.47) 		0.327
(1.00) 		0.0127
(1.00) 		0.191
(1.00) 		0.51
(1.00)
10q loss 24 (7%) 307 2.31e-08
(1.59e-05) 		0.0196
(1.00) 		0.0392
(1.00) 		0.0498
(1.00) 		0.0291
(1.00) 		0.0108
(1.00) 		0.234
(1.00) 		0.0228
(1.00) 		0.029
(1.00) 		0.155
(1.00)
12p loss 30 (9%) 301 6.27e-05
(0.0414) 		0.127
(1.00) 		0.186
(1.00) 		0.647
(1.00) 		0.00918
(1.00) 		0.0285
(1.00) 		0.434
(1.00) 		0.202
(1.00) 		0.206
(1.00) 		0.45
(1.00)
13q loss 44 (13%) 287 8.48e-07
(0.000576) 		0.301
(1.00) 		0.543
(1.00) 		0.545
(1.00) 		0.163
(1.00) 		0.167
(1.00) 		0.575
(1.00) 		0.061
(1.00) 		0.572
(1.00) 		0.777
(1.00)
15q loss 19 (6%) 312 6.59e-07
(0.000449) 		0.0177
(1.00) 		0.0413
(1.00) 		0.0879
(1.00) 		0.0367
(1.00) 		0.0313
(1.00) 		0.0769
(1.00) 		0.00755
(1.00) 		0.0849
(1.00) 		0.466
(1.00)
16q loss 65 (20%) 266 1.19e-12
(8.25e-10) 		0.00106
(0.672) 		0.492
(1.00) 		0.299
(1.00) 		0.00467
(1.00) 		0.011
(1.00) 		0.0426
(1.00) 		0.00493
(1.00) 		0.0793
(1.00) 		0.339
(1.00)
18p loss 41 (12%) 290 6.74e-06
(0.00455) 		0.00732
(1.00) 		0.0633
(1.00) 		0.0794
(1.00) 		0.021
(1.00) 		0.0193
(1.00) 		0.274
(1.00) 		0.291
(1.00) 		0.0973
(1.00) 		0.081
(1.00)
18q loss 61 (18%) 270 9.2e-07
(0.000625) 		0.0274
(1.00) 		0.016
(1.00) 		0.0188
(1.00) 		0.00691
(1.00) 		0.000607
(0.393) 		0.366
(1.00) 		0.058
(1.00) 		0.21
(1.00) 		0.188
(1.00)
22q loss 24 (7%) 307 2.16e-06
(0.00147) 		0.0569
(1.00) 		0.442
(1.00) 		0.805
(1.00) 		0.0291
(1.00) 		0.00277
(1.00) 		0.353
(1.00) 		0.0709
(1.00) 		0.524
(1.00) 		0.764
(1.00)
xq loss 20 (6%) 311 2.67e-06
(0.00181) 		0.00116
(0.735) 		0.193
(1.00) 		0.235
(1.00) 		0.0226
(1.00) 		0.0294
(1.00) 		0.078
(1.00) 		0.0117
(1.00) 		0.0499
(1.00) 		0.135
(1.00)
1p gain 9 (3%) 322 0.00156
(0.984) 		0.07
(1.00) 		0.0411
(1.00) 		0.495
(1.00) 		0.104
(1.00) 		0.106
(1.00) 		0.442
(1.00) 		0.172
(1.00) 		0.422
(1.00) 		0.545
(1.00)
2p gain 4 (1%) 327 0.268
(1.00) 		0.108
(1.00) 		0.394
(1.00) 		0.326
(1.00) 		0.82
(1.00) 		0.832
(1.00) 		0.335
(1.00) 		1
(1.00)
2q gain 3 (1%) 328 0.117
(1.00) 		0.383
(1.00) 		0.779
(1.00) 		0.637
(1.00) 		0.535
(1.00) 		0.545
(1.00) 		0.125
(1.00) 		0.74
(1.00)
4p gain 5 (2%) 326 0.163
(1.00) 		0.33
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.766
(1.00) 		0.842
(1.00) 		0.484
(1.00)
4q gain 4 (1%) 327 0.268
(1.00) 		0.316
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.915
(1.00) 		0.861
(1.00) 		0.895
(1.00)
5q gain 7 (2%) 324 0.000838
(0.537) 		0.122
(1.00) 		0.183
(1.00) 		0.633
(1.00) 		0.184
(1.00) 		0.402
(1.00) 		0.178
(1.00) 		0.827
(1.00)
6p gain 3 (1%) 328 0.0779
(1.00) 		0.383
(1.00) 		0.112
(1.00) 		0.637
(1.00) 		0.612
(1.00) 		0.352
(1.00) 		0.603
(1.00) 		0.865
(1.00)
10p gain 8 (2%) 323 0.00393
(1.00) 		0.315
(1.00) 		0.784
(1.00) 		0.635
(1.00) 		0.604
(1.00) 		0.398
(1.00) 		0.0248
(1.00) 		0.00854
(1.00) 		0.221
(1.00) 		0.0196
(1.00)
10q gain 9 (3%) 322 0.00156
(0.984) 		0.362
(1.00) 		0.0403
(1.00) 		0.0376
(1.00) 		0.484
(1.00) 		0.246
(1.00) 		0.227
(1.00) 		0.21
(1.00) 		0.538
(1.00) 		0.314
(1.00)
11p gain 11 (3%) 320 0.000974
(0.62) 		0.164
(1.00) 		0.768
(1.00) 		0.585
(1.00) 		0.057
(1.00) 		0.347
(1.00) 		0.984
(1.00) 		0.711
(1.00) 		0.836
(1.00) 		0.766
(1.00)
11q gain 11 (3%) 320 0.000974
(0.62) 		0.164
(1.00) 		0.768
(1.00) 		0.585
(1.00) 		0.057
(1.00) 		0.347
(1.00) 		0.984
(1.00) 		0.711
(1.00) 		0.836
(1.00) 		0.766
(1.00)
12p gain 5 (2%) 326 0.00632
(1.00) 		0.0379
(1.00) 		0.166
(1.00) 		0.385
(1.00) 		0.598
(1.00) 		0.525
(1.00) 		0.156
(1.00) 		0.928
(1.00)
13q gain 4 (1%) 327 0.181
(1.00) 		0.316
(1.00) 		0.211
(1.00) 		0.461
(1.00) 		0.762
(1.00) 		0.263
(1.00) 		0.335
(1.00) 		0.895
(1.00)
14q gain 6 (2%) 325 0.00795
(1.00) 		0.0805
(1.00) 		0.784
(1.00) 		0.635
(1.00) 		0.25
(1.00) 		0.214
(1.00) 		0.607
(1.00) 		0.127
(1.00) 		0.0375
(1.00) 		0.888
(1.00)
15q gain 4 (1%) 327 0.181
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.206
(1.00) 		0.607
(1.00) 		0.322
(1.00) 		0.831
(1.00) 		0.4
(1.00)
16p gain 15 (5%) 316 0.0027
(1.00) 		0.233
(1.00) 		0.521
(1.00) 		0.39
(1.00) 		0.218
(1.00) 		0.0157
(1.00) 		0.0696
(1.00) 		0.136
(1.00) 		0.0977
(1.00) 		0.127
(1.00)
16q gain 5 (2%) 326 0.421
(1.00) 		0.863
(1.00) 		0.677
(1.00) 		0.466
(1.00) 		0.532
(1.00) 		0.635
(1.00) 		0.598
(1.00) 		0.67
(1.00) 		0.773
(1.00) 		0.559
(1.00)
17p gain 3 (1%) 328 0.543
(1.00) 		0.0561
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.955
(1.00) 		1
(1.00)
17q gain 5 (2%) 326 0.0589
(1.00) 		0.526
(1.00) 		0.471
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.858
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.773
(1.00) 		0.521
(1.00)
18p gain 10 (3%) 321 0.000587
(0.381) 		0.854
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.282
(1.00) 		0.923
(1.00) 		0.921
(1.00) 		0.843
(1.00) 		0.843
(1.00) 		0.936
(1.00)
18q gain 5 (2%) 326 0.00632
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.385
(1.00) 		0.535
(1.00) 		0.556
(1.00) 		0.525
(1.00) 		0.618
(1.00) 		0.928
(1.00)
19p gain 4 (1%) 327 0.0174
(1.00) 		0.316
(1.00) 		0.0199
(1.00) 		0.0384
(1.00) 		0.612
(1.00) 		0.352
(1.00) 		0.564
(1.00) 		0.645
(1.00)
19q gain 5 (2%) 326 0.00632
(1.00) 		0.33
(1.00) 		0.784
(1.00) 		0.635
(1.00) 		0.0809
(1.00) 		0.013
(1.00) 		0.544
(1.00) 		0.263
(1.00) 		0.285
(1.00) 		0.315
(1.00)
20p gain 11 (3%) 320 0.0106
(1.00) 		0.0216
(1.00) 		0.371
(1.00) 		0.145
(1.00) 		0.0621
(1.00) 		0.0336
(1.00) 		0.202
(1.00) 		0.728
(1.00) 		0.00912
(1.00) 		0.194
(1.00)
20q gain 13 (4%) 318 0.0145
(1.00) 		0.0286
(1.00) 		0.418
(1.00) 		0.489
(1.00) 		0.211
(1.00) 		0.341
(1.00) 		0.354
(1.00) 		0.578
(1.00) 		0.265
(1.00) 		0.446
(1.00)
xq gain 3 (1%) 328 0.0779
(1.00) 		0.383
(1.00) 		0.779
(1.00) 		0.78
(1.00) 		0.136
(1.00) 		0.545
(1.00) 		0.125
(1.00) 		0.412
(1.00)
1p loss 9 (3%) 322 0.00156
(0.984) 		0.07
(1.00) 		0.255
(1.00) 		0.155
(1.00) 		0.0934
(1.00) 		0.0263
(1.00) 		0.182
(1.00) 		0.0272
(1.00) 		0.19
(1.00) 		0.272
(1.00)
2p loss 6 (2%) 325 0.00795
(1.00) 		0.22
(1.00) 		0.289
(1.00) 		0.0798
(1.00) 		0.636
(1.00) 		0.476
(1.00) 		0.238
(1.00) 		0.509
(1.00)
2q loss 8 (2%) 323 0.000705
(0.456) 		0.355
(1.00) 		0.604
(1.00) 		0.113
(1.00) 		0.445
(1.00) 		0.217
(1.00) 		0.148
(1.00) 		0.301
(1.00)
3p loss 5 (2%) 326 0.0589
(1.00) 		0.158
(1.00) 		0.0809
(1.00) 		0.197
(1.00) 		0.409
(1.00) 		0.0756
(1.00) 		0.511
(1.00) 		0.498
(1.00)
3q loss 3 (1%) 328 0.543
(1.00) 		0.635
(1.00) 		0.642
(1.00) 		0.78
(1.00)
4q loss 6 (2%) 325 0.0351
(1.00) 		0.589
(1.00) 		0.784
(1.00) 		0.385
(1.00) 		0.25
(1.00) 		0.214
(1.00) 		0.357
(1.00) 		0.255
(1.00) 		0.486
(1.00) 		0.509
(1.00)
5p loss 5 (2%) 326 0.00632
(1.00) 		0.231
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.013
(1.00) 		0.82
(1.00) 		0.832
(1.00) 		0.861
(1.00) 		1
(1.00)
8q loss 10 (3%) 321 0.0358
(1.00) 		0.16
(1.00) 		0.845
(1.00) 		0.851
(1.00) 		0.00963
(1.00) 		0.0052
(1.00) 		0.263
(1.00) 		0.444
(1.00) 		0.0816
(1.00) 		0.0155
(1.00)
9p loss 14 (4%) 317 0.00101
(0.638) 		0.62
(1.00) 		0.0855
(1.00) 		0.348
(1.00) 		0.128
(1.00) 		0.0754
(1.00) 		0.101
(1.00) 		0.501
(1.00) 		0.104
(1.00) 		0.495
(1.00)
9q loss 5 (2%) 326 0.0589
(1.00) 		0.451
(1.00) 		0.445
(1.00) 		0.863
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.366
(1.00) 		0.842
(1.00) 		0.689
(1.00)
12q loss 12 (4%) 319 0.000759
(0.488) 		0.344
(1.00) 		0.297
(1.00) 		0.495
(1.00) 		0.199
(1.00) 		0.134
(1.00) 		0.464
(1.00) 		0.266
(1.00) 		0.493
(1.00) 		0.91
(1.00)
14q loss 13 (4%) 318 0.0624
(1.00) 		0.101
(1.00) 		0.464
(1.00) 		0.348
(1.00) 		0.136
(1.00) 		0.119
(1.00) 		0.0219
(1.00) 		0.0323
(1.00) 		0.0258
(1.00) 		0.0244
(1.00)
16p loss 23 (7%) 308 0.00924
(1.00) 		0.143
(1.00) 		0.599
(1.00) 		0.599
(1.00) 		0.247
(1.00) 		0.526
(1.00) 		0.164
(1.00) 		0.154
(1.00) 		0.551
(1.00) 		0.377
(1.00)
17q loss 8 (2%) 323 0.000705
(0.456) 		0.0123
(1.00) 		0.452
(1.00) 		0.314
(1.00) 		0.101
(1.00) 		0.0684
(1.00) 		0.471
(1.00) 		0.0213
(1.00) 		0.19
(1.00) 		0.272
(1.00)
19p loss 11 (3%) 320 0.0106
(1.00) 		0.689
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.508
(1.00) 		0.637
(1.00) 		0.229
(1.00) 		0.0616
(1.00) 		0.0699
(1.00) 		0.497
(1.00)
19q loss 11 (3%) 320 0.0106
(1.00) 		0.689
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.508
(1.00) 		0.637
(1.00) 		0.229
(1.00) 		0.0616
(1.00) 		0.0699
(1.00) 		0.497
(1.00)
20p loss 12 (4%) 319 1
(1.00) 		0.11
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.537
(1.00) 		0.885
(1.00) 		0.308
(1.00) 		0.241
(1.00) 		0.0859
(1.00)
20q loss 5 (2%) 326 0.163
(1.00) 		0.231
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.385
(1.00) 		0.523
(1.00) 		0.169
(1.00) 		0.819
(1.00) 		0.283
(1.00)
21q loss 13 (4%) 318 0.00175
(1.00) 		0.351
(1.00) 		0.505
(1.00) 		0.445
(1.00) 		0.0308
(1.00) 		0.0324
(1.00) 		0.818
(1.00) 		0.424
(1.00) 		0.701
(1.00) 		0.951
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 3.5e-05 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
1Q GAIN MUTATED 0 2 13
1Q GAIN WILD-TYPE 44 181 91

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

'3p gain' versus 'CN_CNMF'

P value = 4.26e-06 (Fisher's exact test), Q value = 0.0029

Table S2.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
3P GAIN MUTATED 6 2 15
3P GAIN WILD-TYPE 38 181 89

Figure S2.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 6.46e-08 (Fisher's exact test), Q value = 4.4e-05

Table S3.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
3Q GAIN MUTATED 6 3 22
3Q GAIN WILD-TYPE 38 180 82

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.032

Table S4.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
5P GAIN MUTATED 0 0 9
5P GAIN WILD-TYPE 44 183 95

Figure S4.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.77e-09 (Fisher's exact test), Q value = 1.2e-06

Table S5.  Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
7P GAIN MUTATED 16 11 31
7P GAIN WILD-TYPE 28 172 73

Figure S5.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5.18e-08 (Fisher's exact test), Q value = 3.5e-05

Table S6.  Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
7P GAIN MUTATED 34 5 19
7P GAIN WILD-TYPE 62 101 110

Figure S6.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 4.03e-05 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #12: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
7P GAIN MUTATED 35 6 17
7P GAIN WILD-TYPE 86 91 95

Figure S7.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 9.23e-09 (Fisher's exact test), Q value = 6.4e-06

Table S8.  Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
7Q GAIN MUTATED 15 11 30
7Q GAIN WILD-TYPE 29 172 74

Figure S8.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.75e-08 (Fisher's exact test), Q value = 1.9e-05

Table S9.  Gene #13: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
7Q GAIN MUTATED 34 5 17
7Q GAIN WILD-TYPE 62 101 112

Figure S9.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 5.99e-05 (Fisher's exact test), Q value = 0.04

Table S10.  Gene #13: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
7Q GAIN MUTATED 34 6 16
7Q GAIN WILD-TYPE 87 91 96

Figure S10.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 4.01e-10 (Fisher's exact test), Q value = 2.8e-07

Table S11.  Gene #14: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
8P GAIN MUTATED 5 4 29
8P GAIN WILD-TYPE 39 179 75

Figure S11.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0062

Table S12.  Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
8P GAIN MUTATED 24 4 10
8P GAIN WILD-TYPE 72 102 119

Figure S12.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2.51e-12 (Fisher's exact test), Q value = 1.7e-09

Table S13.  Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
8Q GAIN MUTATED 7 14 46
8Q GAIN WILD-TYPE 37 169 58

Figure S13.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0076

Table S14.  Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
8Q GAIN MUTATED 34 9 24
8Q GAIN WILD-TYPE 62 97 105

Figure S14.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.016

Table S15.  Gene #16: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
9P GAIN MUTATED 0 1 12
9P GAIN WILD-TYPE 44 182 92

Figure S15.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1.63e-10 (Fisher's exact test), Q value = 1.1e-07

Table S16.  Gene #17: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
9Q GAIN MUTATED 0 2 24
9Q GAIN WILD-TYPE 44 181 80

Figure S16.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S17.  Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
12Q GAIN MUTATED 0 0 8
12Q GAIN WILD-TYPE 44 183 96

Figure S17.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.032

Table S18.  Gene #37: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
21Q GAIN MUTATED 0 0 9
21Q GAIN WILD-TYPE 44 183 95

Figure S18.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #44: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 86 104 79
4P LOSS MUTATED 0 9 1 0
4P LOSS WILD-TYPE 52 77 103 79

Figure S19.  Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.032

Table S20.  Gene #47: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
5Q LOSS MUTATED 0 0 9
5Q LOSS WILD-TYPE 44 183 95

Figure S20.  Get High-res Image Gene #47: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #48: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
6P LOSS MUTATED 0 1 10
6P LOSS WILD-TYPE 44 182 94

Figure S21.  Get High-res Image Gene #48: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.02

Table S22.  Gene #48: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
6P LOSS MUTATED 0 0 11
6P LOSS WILD-TYPE 115 93 111

Figure S22.  Get High-res Image Gene #48: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 7.41e-06 (Fisher's exact test), Q value = 0.005

Table S23.  Gene #49: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
6Q LOSS MUTATED 2 2 16
6Q LOSS WILD-TYPE 42 181 88

Figure S23.  Get High-res Image Gene #49: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.000279 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #50: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
8P LOSS MUTATED 4 57 43
8P LOSS WILD-TYPE 40 126 61

Figure S24.  Get High-res Image Gene #50: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1.22e-08 (Fisher's exact test), Q value = 8.3e-06

Table S25.  Gene #50: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
8P LOSS MUTATED 29 13 62
8P LOSS WILD-TYPE 67 93 67

Figure S25.  Get High-res Image Gene #50: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.99e-05 (Fisher's exact test), Q value = 0.02

Table S26.  Gene #50: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
8P LOSS MUTATED 37 16 51
8P LOSS WILD-TYPE 84 81 61

Figure S26.  Get High-res Image Gene #50: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.54e-05 (Fisher's exact test), Q value = 0.056

Table S27.  Gene #50: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
8P LOSS MUTATED 29 19 56
8P LOSS WILD-TYPE 86 74 66

Figure S27.  Get High-res Image Gene #50: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.000218 (Chi-square test), Q value = 0.14

Table S28.  Gene #50: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 63 51 86 24 97
8P LOSS MUTATED 28 6 32 2 34
8P LOSS WILD-TYPE 35 45 54 22 63

Figure S28.  Get High-res Image Gene #50: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.78e-07 (Fisher's exact test), Q value = 0.00019

Table S29.  Gene #54: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
10P LOSS MUTATED 0 3 19
10P LOSS WILD-TYPE 44 180 85

Figure S29.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.17

Table S30.  Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
10P LOSS MUTATED 7 0 15
10P LOSS WILD-TYPE 89 106 114

Figure S30.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.11

Table S31.  Gene #54: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
10P LOSS MUTATED 7 0 15
10P LOSS WILD-TYPE 114 97 97

Figure S31.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000271 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #54: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
10P LOSS MUTATED 4 1 17
10P LOSS WILD-TYPE 111 92 105

Figure S32.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 2.31e-08 (Fisher's exact test), Q value = 1.6e-05

Table S33.  Gene #55: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
10Q LOSS MUTATED 1 2 21
10Q LOSS WILD-TYPE 43 181 83

Figure S33.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 6.27e-05 (Fisher's exact test), Q value = 0.041

Table S34.  Gene #56: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
12P LOSS MUTATED 0 10 20
12P LOSS WILD-TYPE 44 173 84

Figure S34.  Get High-res Image Gene #56: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 8.48e-07 (Fisher's exact test), Q value = 0.00058

Table S35.  Gene #58: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
13Q LOSS MUTATED 5 10 29
13Q LOSS WILD-TYPE 39 173 75

Figure S35.  Get High-res Image Gene #58: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 6.59e-07 (Fisher's exact test), Q value = 0.00045

Table S36.  Gene #60: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
15Q LOSS MUTATED 0 2 17
15Q LOSS WILD-TYPE 44 181 87

Figure S36.  Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1.19e-12 (Fisher's exact test), Q value = 8.2e-10

Table S37.  Gene #62: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
16Q LOSS MUTATED 2 17 46
16Q LOSS WILD-TYPE 42 166 58

Figure S37.  Get High-res Image Gene #62: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 9.89e-13 (Fisher's exact test), Q value = 6.9e-10

Table S38.  Gene #63: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
17P LOSS MUTATED 1 7 36
17P LOSS WILD-TYPE 43 176 68

Figure S38.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.027

Table S39.  Gene #63: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
17P LOSS MUTATED 7 7 30
17P LOSS WILD-TYPE 108 86 92

Figure S39.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 6.74e-06 (Fisher's exact test), Q value = 0.0045

Table S40.  Gene #65: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
18P LOSS MUTATED 3 11 27
18P LOSS WILD-TYPE 41 172 77

Figure S40.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 9.2e-07 (Fisher's exact test), Q value = 0.00062

Table S41.  Gene #66: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
18Q LOSS MUTATED 5 19 37
18Q LOSS WILD-TYPE 39 164 67

Figure S41.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.0015

Table S42.  Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
22Q LOSS MUTATED 2 3 19
22Q LOSS WILD-TYPE 42 180 85

Figure S42.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0018

Table S43.  Gene #73: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
XQ LOSS MUTATED 0 3 17
XQ LOSS WILD-TYPE 44 180 87

Figure S43.  Get High-res Image Gene #73: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 331

  • Number of significantly arm-level cnvs = 73

  • Number of molecular subtypes = 10

  • 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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