Correlation between copy number variation genes (focal events) and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C13R0R9Q
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13R0R9Q
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 12 molecular subtypes across 490 patients, 98 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 2p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 3p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3q cnv correlated to 'CN_CNMF'.

  • 4p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p cnv correlated to 'CN_CNMF'.

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

  • 6p cnv correlated to 'CN_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 9q cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

  • 10q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 11q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12q cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 13q cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 14q cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 15q cnv correlated to 'CN_CNMF'.

  • 16p cnv correlated to 'CN_CNMF'.

  • 16q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17p cnv correlated to 'CN_CNMF'.

  • 17q cnv correlated to 'CN_CNMF'.

  • 18p cnv correlated to 'CN_CNMF'.

  • 18q cnv correlated to 'CN_CNMF'.

  • 19p cnv correlated to 'CN_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 20p cnv correlated to 'CN_CNMF'.

  • 20q cnv correlated to 'CN_CNMF'.

  • 21q cnv correlated to 'CN_CNMF'.

  • xq cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 98 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
2p 239 (49%) 251 0.0807
(1.00) 		0.136
(1.00) 		2.04e-12
(9.75e-10) 		2.71e-05
(0.0115) 		0.493
(1.00) 		0.262
(1.00) 		1.25e-06
(0.00056) 		1.62e-05
(0.00689) 		5.93e-05
(0.0247) 		0.00899
(1.00) 		7.5e-06
(0.00326) 		3.83e-05
(0.0161)
1p 235 (48%) 255 0.0118
(1.00) 		0.00263
(0.923) 		2.84e-16
(1.37e-13) 		9.26e-12
(4.43e-09) 		0.676
(1.00) 		0.101
(1.00) 		5.5e-09
(2.6e-06) 		8.57e-11
(4.07e-08) 		0.000149
(0.0599) 		0.000119
(0.0485) 		0.0187
(1.00) 		0.00179
(0.643)
10p 286 (58%) 204 0.483
(1.00) 		0.618
(1.00) 		7.09e-09
(3.33e-06) 		2.74e-06
(0.00122) 		0.242
(1.00) 		0.611
(1.00) 		9.56e-06
(0.00411) 		1.38e-06
(0.000617) 		0.00375
(1.00) 		0.000207
(0.0821) 		6.6e-06
(0.00288) 		0.00345
(1.00)
10q 266 (54%) 224 0.0236
(1.00) 		0.0149
(1.00) 		1.28e-07
(5.88e-05) 		2.87e-06
(0.00127) 		0.903
(1.00) 		0.644
(1.00) 		2.65e-07
(0.000121) 		1.87e-07
(8.58e-05) 		0.0015
(0.545) 		6.44e-05
(0.0267) 		4.83e-05
(0.0201) 		0.014
(1.00)
xq 187 (38%) 303 0.0393
(1.00) 		0.201
(1.00) 		6.76e-09
(3.18e-06) 		6.7e-06
(0.00292) 		0.479
(1.00) 		0.945
(1.00) 		0.000157
(0.063) 		0.0013
(0.483) 		1.87e-09
(8.82e-07) 		0.00735
(1.00) 		3.07e-08
(1.43e-05) 		4.58e-06
(0.00202)
4p 337 (69%) 153 0.00729
(1.00) 		0.0498
(1.00) 		1.22e-11
(5.8e-09) 		5.91e-07
(0.000269) 		0.096
(1.00) 		0.372
(1.00) 		0.000402
(0.156) 		4.03e-05
(0.0169) 		0.00181
(0.648) 		0.773
(1.00) 		0.00131
(0.483) 		0.000575
(0.221)
4q 312 (64%) 178 0.00375
(1.00) 		0.0159
(1.00) 		4.78e-11
(2.28e-08) 		9.85e-07
(0.000444) 		0.361
(1.00) 		0.705
(1.00) 		2.08e-06
(0.000928) 		9.62e-07
(0.000435) 		0.0121
(1.00) 		0.11
(1.00) 		0.0117
(1.00) 		0.000577
(0.222)
7q 265 (54%) 225 0.0215
(1.00) 		0.049
(1.00) 		7.86e-09
(3.68e-06) 		7.91e-05
(0.0327) 		1
(1.00) 		0.297
(1.00) 		0.00029
(0.114) 		4.11e-05
(0.0172) 		0.000317
(0.124) 		0.0065
(1.00) 		0.00532
(1.00) 		0.00776
(1.00)
12p 262 (53%) 228 0.000726
(0.277) 		0.0242
(1.00) 		3.68e-08
(1.71e-05) 		0.000521
(0.201) 		0.284
(1.00) 		0.485
(1.00) 		3.34e-05
(0.0141) 		0.000132
(0.0536) 		0.000332
(0.129) 		0.0433
(1.00) 		0.0147
(1.00) 		0.0198
(1.00)
1q 256 (52%) 234 0.257
(1.00) 		0.297
(1.00) 		6.06e-10
(2.87e-07) 		5.1e-08
(2.36e-05) 		0.553
(1.00) 		0.137
(1.00) 		1.16e-06
(0.000523) 		2.7e-08
(1.26e-05) 		0.00195
(0.692) 		0.000947
(0.357) 		0.0237
(1.00) 		0.00397
(1.00)
2q 177 (36%) 313 0.249
(1.00) 		0.223
(1.00) 		3.37e-06
(0.00149) 		0.0116
(1.00) 		0.383
(1.00) 		0.136
(1.00) 		0.00018
(0.0717) 		1.16e-05
(0.00497) 		0.000695
(0.265) 		0.0579
(1.00) 		7.89e-06
(0.00342) 		0.0019
(0.678)
7p 292 (60%) 198 0.0285
(1.00) 		0.0121
(1.00) 		2.89e-07
(0.000132) 		5.66e-06
(0.00248) 		0.701
(1.00) 		0.327
(1.00) 		0.00186
(0.664) 		0.000119
(0.0484) 		0.000113
(0.0463) 		0.0941
(1.00) 		0.00167
(0.604) 		0.00738
(1.00)
16q 262 (53%) 228 0.69
(1.00) 		0.519
(1.00) 		2.17e-06
(0.000964) 		0.0572
(1.00) 		0.0963
(1.00) 		0.966
(1.00) 		0.000276
(0.109) 		0.000125
(0.0507) 		0.00165
(0.598) 		0.0209
(1.00) 		0.000283
(0.111) 		0.00125
(0.469)
11p 240 (49%) 250 0.0802
(1.00) 		0.135
(1.00) 		4.46e-06
(0.00197) 		7.44e-05
(0.0308) 		0.27
(1.00) 		1.9e-05
(0.00808) 		0.105
(1.00) 		0.0639
(1.00) 		0.00125
(0.469) 		0.296
(1.00) 		0.00267
(0.935) 		0.0764
(1.00)
3p 410 (84%) 80 0.413
(1.00) 		0.237
(1.00) 		8.34e-06
(0.0036) 		0.000109
(0.045) 		0.886
(1.00) 		0.0354
(1.00) 		0.00148
(0.54) 		0.0149
(1.00) 		0.00125
(0.468) 		0.00473
(1.00) 		0.00128
(0.477) 		0.0317
(1.00)
5q 377 (77%) 113 0.489
(1.00) 		0.364
(1.00) 		3.59e-07
(0.000164) 		0.00128
(0.475) 		0.0966
(1.00) 		0.565
(1.00) 		0.0147
(1.00) 		0.0874
(1.00) 		0.121
(1.00) 		0.000263
(0.104) 		0.0169
(1.00) 		0.0365
(1.00)
9q 330 (67%) 160 0.0484
(1.00) 		0.0568
(1.00) 		0.000309
(0.121) 		0.0937
(1.00) 		0.812
(1.00) 		0.732
(1.00) 		0.00135
(0.495) 		0.044
(1.00) 		0.0332
(1.00) 		0.000175
(0.0701) 		0.0639
(1.00) 		0.639
(1.00)
11q 228 (47%) 262 0.0535
(1.00) 		0.217
(1.00) 		3.75e-08
(1.74e-05) 		0.00019
(0.0756) 		0.225
(1.00) 		0.0108
(1.00) 		0.0585
(1.00) 		0.00417
(1.00) 		0.00135
(0.495) 		0.691
(1.00) 		0.00863
(1.00) 		0.0463
(1.00)
12q 199 (41%) 291 0.00223
(0.784) 		0.0868
(1.00) 		7.88e-06
(0.00342) 		0.00305
(1.00) 		0.106
(1.00) 		0.313
(1.00) 		0.0123
(1.00) 		0.000134
(0.054) 		0.122
(1.00) 		0.0883
(1.00) 		0.000863
(0.327) 		0.0689
(1.00)
14q 289 (59%) 201 0.157
(1.00) 		0.653
(1.00) 		0.00315
(1.00) 		0.0041
(1.00) 		0.698
(1.00) 		0.234
(1.00) 		0.000232
(0.092) 		1.4e-05
(0.00601) 		0.00276
(0.962) 		0.0159
(1.00) 		0.0955
(1.00) 		0.0233
(1.00)
3q 378 (77%) 112 0.634
(1.00) 		0.83
(1.00) 		0.000593
(0.227) 		0.0527
(1.00) 		0.579
(1.00) 		0.0182
(1.00) 		0.0563
(1.00) 		0.00996
(1.00) 		0.0358
(1.00) 		0.387
(1.00) 		0.197
(1.00) 		0.799
(1.00)
5p 380 (78%) 110 0.708
(1.00) 		0.573
(1.00) 		5.56e-09
(2.62e-06) 		0.00426
(1.00) 		0.266
(1.00) 		0.319
(1.00) 		0.21
(1.00) 		0.987
(1.00) 		0.618
(1.00) 		0.00469
(1.00) 		0.196
(1.00) 		0.694
(1.00)
6p 215 (44%) 275 0.315
(1.00) 		0.468
(1.00) 		0.00011
(0.0452) 		0.00311
(1.00) 		0.442
(1.00) 		0.468
(1.00) 		0.00216
(0.762) 		0.00336
(1.00) 		0.59
(1.00) 		0.423
(1.00) 		0.109
(1.00) 		0.0343
(1.00)
6q 200 (41%) 290 0.223
(1.00) 		0.43
(1.00) 		0.000428
(0.166) 		0.0236
(1.00) 		0.572
(1.00) 		0.398
(1.00) 		0.127
(1.00) 		0.14
(1.00) 		0.135
(1.00) 		0.81
(1.00) 		0.336
(1.00) 		0.0426
(1.00)
13q 344 (70%) 146 0.83
(1.00) 		0.917
(1.00) 		0.0294
(1.00) 		0.0257
(1.00) 		0.308
(1.00) 		0.242
(1.00) 		0.576
(1.00) 		0.0911
(1.00) 		0.496
(1.00) 		0.146
(1.00) 		0.000151
(0.0609) 		0.0733
(1.00)
15q 241 (49%) 249 0.985
(1.00) 		0.564
(1.00) 		0.000109
(0.0448) 		0.00959
(1.00) 		1
(1.00) 		0.105
(1.00) 		0.0924
(1.00) 		0.0339
(1.00) 		0.01
(1.00) 		0.0403
(1.00) 		0.0048
(1.00) 		0.0148
(1.00)
16p 241 (49%) 249 0.601
(1.00) 		0.364
(1.00) 		8.24e-07
(0.000373) 		0.0275
(1.00) 		0.0309
(1.00) 		0.51
(1.00) 		0.112
(1.00) 		0.0251
(1.00) 		0.0321
(1.00) 		0.0693
(1.00) 		0.000856
(0.325) 		0.0595
(1.00)
17p 350 (71%) 140 0.46
(1.00) 		0.29
(1.00) 		1.48e-06
(0.000661) 		0.00331
(1.00) 		0.309
(1.00) 		0.043
(1.00) 		0.219
(1.00) 		0.0446
(1.00) 		0.00212
(0.75) 		0.386
(1.00) 		0.0764
(1.00) 		0.0657
(1.00)
17q 246 (50%) 244 0.576
(1.00) 		0.0303
(1.00) 		8.86e-06
(0.00382) 		0.0131
(1.00) 		0.914
(1.00) 		0.938
(1.00) 		0.0555
(1.00) 		0.0205
(1.00) 		0.0532
(1.00) 		0.168
(1.00) 		0.00509
(1.00) 		0.122
(1.00)
18p 286 (58%) 204 0.0718
(1.00) 		0.0168
(1.00) 		1.54e-05
(0.00657) 		0.00143
(0.522) 		0.619
(1.00) 		0.529
(1.00) 		0.102
(1.00) 		0.513
(1.00) 		0.00124
(0.466) 		0.0505
(1.00) 		0.00276
(0.962) 		0.025
(1.00)
18q 287 (59%) 203 0.362
(1.00) 		0.0742
(1.00) 		3.66e-05
(0.0154) 		0.0175
(1.00) 		0.697
(1.00) 		0.678
(1.00) 		0.171
(1.00) 		0.761
(1.00) 		0.161
(1.00) 		0.319
(1.00) 		0.0499
(1.00) 		0.119
(1.00)
19p 273 (56%) 217 0.232
(1.00) 		0.0409
(1.00) 		1.06e-07
(4.91e-05) 		0.0043
(1.00) 		0.183
(1.00) 		0.562
(1.00) 		0.384
(1.00) 		0.00648
(1.00) 		0.0625
(1.00) 		0.332
(1.00) 		0.101
(1.00) 		0.219
(1.00)
19q 265 (54%) 225 0.273
(1.00) 		0.411
(1.00) 		1.23e-08
(5.72e-06) 		0.00181
(0.648) 		0.0742
(1.00) 		0.146
(1.00) 		0.051
(1.00) 		0.0259
(1.00) 		0.155
(1.00) 		0.541
(1.00) 		0.0126
(1.00) 		0.119
(1.00)
20p 295 (60%) 195 0.146
(1.00) 		0.46
(1.00) 		7.64e-07
(0.000347) 		0.00574
(1.00) 		0.644
(1.00) 		0.0339
(1.00) 		0.445
(1.00) 		0.012
(1.00) 		0.319
(1.00) 		0.859
(1.00) 		0.0902
(1.00) 		1
(1.00)
20q 289 (59%) 201 0.803
(1.00) 		0.947
(1.00) 		2.02e-05
(0.00857) 		0.0177
(1.00) 		0.878
(1.00) 		0.312
(1.00) 		0.567
(1.00) 		0.0461
(1.00) 		0.081
(1.00) 		0.0247
(1.00) 		0.0797
(1.00) 		0.822
(1.00)
21q 316 (64%) 174 0.702
(1.00) 		0.403
(1.00) 		5.16e-06
(0.00226) 		0.00283
(0.981) 		0.546
(1.00) 		0.707
(1.00) 		0.0556
(1.00) 		0.0108
(1.00) 		0.000889
(0.336) 		0.00862
(1.00) 		0.122
(1.00) 		0.0126
(1.00)
8p 360 (73%) 130 0.88
(1.00) 		0.626
(1.00) 		0.00593
(1.00) 		0.0518
(1.00) 		0.488
(1.00) 		0.438
(1.00) 		0.876
(1.00) 		0.624
(1.00) 		0.103
(1.00) 		0.62
(1.00) 		0.3
(1.00) 		0.618
(1.00)
8q 296 (60%) 194 0.126
(1.00) 		0.123
(1.00) 		0.0923
(1.00) 		0.355
(1.00) 		0.615
(1.00) 		0.816
(1.00) 		0.226
(1.00) 		0.378
(1.00) 		0.0375
(1.00) 		0.688
(1.00) 		0.14
(1.00) 		0.648
(1.00)
9p 364 (74%) 126 0.212
(1.00) 		0.0212
(1.00) 		0.00149
(0.541) 		0.0118
(1.00) 		0.724
(1.00) 		0.778
(1.00) 		0.00665
(1.00) 		0.304
(1.00) 		0.18
(1.00) 		0.104
(1.00) 		0.379
(1.00) 		0.615
(1.00)
22q 313 (64%) 177 0.17
(1.00) 		0.335
(1.00) 		0.0314
(1.00) 		0.747
(1.00) 		0.574
(1.00) 		0.364
(1.00) 		0.518
(1.00) 		0.408
(1.00) 		0.147
(1.00) 		0.0387
(1.00) 		0.0953
(1.00) 		0.361
(1.00)
'1p' versus 'CN_CNMF'

P value = 2.84e-16 (Fisher's exact test), Q value = 1.4e-13

Table S1.  Gene #1: '1p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
1P MUTATED 64 121 50
1P WILD-TYPE 129 41 85

Figure S1.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #3: 'CN_CNMF'

'1p' versus 'METHLYATION_CNMF'

P value = 9.26e-12 (Fisher's exact test), Q value = 4.4e-09

Table S2.  Gene #1: '1p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
1P MUTATED 39 81 40
1P WILD-TYPE 103 33 60

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

'1p' versus 'MRNASEQ_CNMF'

P value = 5.5e-09 (Fisher's exact test), Q value = 2.6e-06

Table S3.  Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
1P MUTATED 43 101 57 31
1P WILD-TYPE 75 42 86 44

Figure S3.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.57e-11 (Fisher's exact test), Q value = 4.1e-08

Table S4.  Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
1P MUTATED 44 100 88
1P WILD-TYPE 49 40 158

Figure S4.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.06

Table S5.  Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
1P MUTATED 73 62 42 43
1P WILD-TYPE 72 68 83 21

Figure S5.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.048

Table S6.  Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
1P MUTATED 50 69 101
1P WILD-TYPE 21 94 129

Figure S6.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 6.06e-10 (Fisher's exact test), Q value = 2.9e-07

Table S7.  Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
1Q MUTATED 79 118 59
1Q WILD-TYPE 114 44 76

Figure S7.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

'1q' versus 'METHLYATION_CNMF'

P value = 5.1e-08 (Fisher's exact test), Q value = 2.4e-05

Table S8.  Gene #2: '1q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
1Q MUTATED 51 82 50
1Q WILD-TYPE 91 32 50

Figure S8.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q' versus 'MRNASEQ_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00052

Table S9.  Gene #2: '1q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
1Q MUTATED 47 101 71 32
1Q WILD-TYPE 71 42 72 43

Figure S9.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.7e-08 (Fisher's exact test), Q value = 1.3e-05

Table S10.  Gene #2: '1q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
1Q MUTATED 51 100 100
1Q WILD-TYPE 42 40 146

Figure S10.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'CN_CNMF'

P value = 2.04e-12 (Fisher's exact test), Q value = 9.8e-10

Table S11.  Gene #3: '2p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
2P MUTATED 60 113 66
2P WILD-TYPE 133 49 69

Figure S11.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #3: 'CN_CNMF'

'2p' versus 'METHLYATION_CNMF'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.011

Table S12.  Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
2P MUTATED 54 76 49
2P WILD-TYPE 88 38 51

Figure S12.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'MRNASEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00056

Table S13.  Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
2P MUTATED 44 93 72 24
2P WILD-TYPE 74 50 71 51

Figure S13.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.62e-05 (Fisher's exact test), Q value = 0.0069

Table S14.  Gene #3: '2p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
2P MUTATED 48 89 96
2P WILD-TYPE 45 51 150

Figure S14.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_CNMF'

P value = 5.93e-05 (Fisher's exact test), Q value = 0.025

Table S15.  Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
2P MUTATED 74 80 41 34
2P WILD-TYPE 71 50 84 30

Figure S15.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.5e-06 (Fisher's exact test), Q value = 0.0033

Table S16.  Gene #3: '2p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
2P MUTATED 83 44 35
2P WILD-TYPE 42 68 56

Figure S16.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.83e-05 (Fisher's exact test), Q value = 0.016

Table S17.  Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
2P MUTATED 69 93
2P WILD-TYPE 109 57

Figure S17.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'CN_CNMF'

P value = 3.37e-06 (Fisher's exact test), Q value = 0.0015

Table S18.  Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
2Q MUTATED 47 81 49
2Q WILD-TYPE 146 81 86

Figure S18.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

'2q' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.072

Table S19.  Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
2Q MUTATED 34 65 58 14
2Q WILD-TYPE 84 78 85 61

Figure S19.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.005

Table S20.  Gene #4: '2q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
2Q MUTATED 44 64 63
2Q WILD-TYPE 49 76 183

Figure S20.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.89e-06 (Fisher's exact test), Q value = 0.0034

Table S21.  Gene #4: '2q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
2Q MUTATED 66 29 24
2Q WILD-TYPE 59 83 67

Figure S21.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p' versus 'CN_CNMF'

P value = 8.34e-06 (Fisher's exact test), Q value = 0.0036

Table S22.  Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
3P MUTATED 143 150 117
3P WILD-TYPE 50 12 18

Figure S22.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

'3p' versus 'METHLYATION_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.045

Table S23.  Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
3P MUTATED 106 104 92
3P WILD-TYPE 36 10 8

Figure S23.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q' versus 'CN_CNMF'

P value = 0.000593 (Fisher's exact test), Q value = 0.23

Table S24.  Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
3Q MUTATED 133 128 117
3Q WILD-TYPE 60 34 18

Figure S24.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'CN_CNMF'

P value = 1.22e-11 (Fisher's exact test), Q value = 5.8e-09

Table S25.  Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4P MUTATED 99 138 100
4P WILD-TYPE 94 24 35

Figure S25.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 5.91e-07 (Fisher's exact test), Q value = 0.00027

Table S26.  Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4P MUTATED 72 92 74
4P WILD-TYPE 70 22 26

Figure S26.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 0.000402 (Fisher's exact test), Q value = 0.16

Table S27.  Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
4P MUTATED 82 116 89 43
4P WILD-TYPE 36 27 54 32

Figure S27.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.03e-05 (Fisher's exact test), Q value = 0.017

Table S28.  Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
4P MUTATED 68 114 148
4P WILD-TYPE 25 26 98

Figure S28.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000575 (Fisher's exact test), Q value = 0.22

Table S29.  Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
4P MUTATED 105 116
4P WILD-TYPE 73 34

Figure S29.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 4.78e-11 (Fisher's exact test), Q value = 2.3e-08

Table S30.  Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4Q MUTATED 95 135 82
4Q WILD-TYPE 98 27 53

Figure S30.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 9.85e-07 (Fisher's exact test), Q value = 0.00044

Table S31.  Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4Q MUTATED 70 92 63
4Q WILD-TYPE 72 22 37

Figure S31.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.00093

Table S32.  Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
4Q MUTATED 72 114 85 34
4Q WILD-TYPE 46 29 58 41

Figure S32.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.62e-07 (Fisher's exact test), Q value = 0.00043

Table S33.  Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
4Q MUTATED 63 111 131
4Q WILD-TYPE 30 29 115

Figure S33.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000577 (Fisher's exact test), Q value = 0.22

Table S34.  Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
4Q MUTATED 96 109
4Q WILD-TYPE 82 41

Figure S34.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 5.56e-09 (Fisher's exact test), Q value = 2.6e-06

Table S35.  Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
5P MUTATED 127 127 126
5P WILD-TYPE 66 35 9

Figure S35.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'CN_CNMF'

P value = 3.59e-07 (Fisher's exact test), Q value = 0.00016

Table S36.  Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
5Q MUTATED 124 134 119
5Q WILD-TYPE 69 28 16

Figure S36.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.1

Table S37.  Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
5Q MUTATED 55 142 161
5Q WILD-TYPE 16 21 69

Figure S37.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.045

Table S38.  Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
6P MUTATED 62 85 68
6P WILD-TYPE 131 77 67

Figure S38.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

'6q' versus 'CN_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.17

Table S39.  Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
6Q MUTATED 58 78 64
6Q WILD-TYPE 135 84 71

Figure S39.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 2.89e-07 (Fisher's exact test), Q value = 0.00013

Table S40.  Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
7P MUTATED 87 118 87
7P WILD-TYPE 106 44 48

Figure S40.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 5.66e-06 (Fisher's exact test), Q value = 0.0025

Table S41.  Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
7P MUTATED 62 84 61
7P WILD-TYPE 80 30 39

Figure S41.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.048

Table S42.  Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
7P MUTATED 49 104 133
7P WILD-TYPE 44 36 113

Figure S42.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.046

Table S43.  Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
7P MUTATED 98 87 54 41
7P WILD-TYPE 47 43 71 23

Figure S43.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q' versus 'CN_CNMF'

P value = 7.86e-09 (Fisher's exact test), Q value = 3.7e-06

Table S44.  Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
7Q MUTATED 75 115 75
7Q WILD-TYPE 118 47 60

Figure S44.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 7.91e-05 (Fisher's exact test), Q value = 0.033

Table S45.  Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
7Q MUTATED 56 76 52
7Q WILD-TYPE 86 38 48

Figure S45.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S46.  Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
7Q MUTATED 58 99 71 33
7Q WILD-TYPE 60 44 72 42

Figure S46.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.017

Table S47.  Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
7Q MUTATED 48 98 115
7Q WILD-TYPE 45 42 131

Figure S47.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.12

Table S48.  Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
7Q MUTATED 87 78 48 41
7Q WILD-TYPE 58 52 77 23

Figure S48.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q' versus 'CN_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.12

Table S49.  Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9Q MUTATED 122 99 109
9Q WILD-TYPE 71 63 26

Figure S49.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.07

Table S50.  Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
9Q MUTATED 38 128 146
9Q WILD-TYPE 33 35 84

Figure S50.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 7.09e-09 (Fisher's exact test), Q value = 3.3e-06

Table S51.  Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
10P MUTATED 81 118 87
10P WILD-TYPE 112 44 48

Figure S51.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 2.74e-06 (Fisher's exact test), Q value = 0.0012

Table S52.  Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
10P MUTATED 63 86 58
10P WILD-TYPE 79 28 42

Figure S52.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 9.56e-06 (Fisher's exact test), Q value = 0.0041

Table S53.  Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
10P MUTATED 66 106 76 31
10P WILD-TYPE 52 37 67 44

Figure S53.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00062

Table S54.  Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
10P MUTATED 52 106 121
10P WILD-TYPE 41 34 125

Figure S54.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000207 (Fisher's exact test), Q value = 0.082

Table S55.  Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
10P MUTATED 51 107 113
10P WILD-TYPE 20 56 117

Figure S55.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.6e-06 (Fisher's exact test), Q value = 0.0029

Table S56.  Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
10P MUTATED 94 55 43
10P WILD-TYPE 31 57 48

Figure S56.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'CN_CNMF'

P value = 1.28e-07 (Fisher's exact test), Q value = 5.9e-05

Table S57.  Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
10Q MUTATED 76 111 79
10Q WILD-TYPE 117 51 56

Figure S57.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0013

Table S58.  Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
10Q MUTATED 59 83 57
10Q WILD-TYPE 83 31 43

Figure S58.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 2.65e-07 (Fisher's exact test), Q value = 0.00012

Table S59.  Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
10Q MUTATED 59 104 69 27
10Q WILD-TYPE 59 39 74 48

Figure S59.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.87e-07 (Fisher's exact test), Q value = 8.6e-05

Table S60.  Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
10Q MUTATED 49 102 108
10Q WILD-TYPE 44 38 138

Figure S60.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.027

Table S61.  Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
10Q MUTATED 53 94 106
10Q WILD-TYPE 18 69 124

Figure S61.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.83e-05 (Fisher's exact test), Q value = 0.02

Table S62.  Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
10Q MUTATED 89 51 43
10Q WILD-TYPE 36 61 48

Figure S62.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'CN_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.002

Table S63.  Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
11P MUTATED 69 87 84
11P WILD-TYPE 124 75 51

Figure S63.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 7.44e-05 (Fisher's exact test), Q value = 0.031

Table S64.  Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
11P MUTATED 49 59 62
11P WILD-TYPE 93 55 38

Figure S64.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p' versus 'RPPA_CHIERARCHICAL'

P value = 1.9e-05 (Fisher's exact test), Q value = 0.0081

Table S65.  Gene #21: '11p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
11P MUTATED 31 25 35 8
11P WILD-TYPE 27 22 14 32

Figure S65.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 3.75e-08 (Fisher's exact test), Q value = 1.7e-05

Table S66.  Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
11Q MUTATED 60 84 84
11Q WILD-TYPE 133 78 51

Figure S66.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.076

Table S67.  Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
11Q MUTATED 49 60 60
11Q WILD-TYPE 93 54 40

Figure S67.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p' versus 'CN_CNMF'

P value = 3.68e-08 (Fisher's exact test), Q value = 1.7e-05

Table S68.  Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
12P MUTATED 73 110 79
12P WILD-TYPE 120 52 56

Figure S68.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 0.000521 (Fisher's exact test), Q value = 0.2

Table S69.  Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
12P MUTATED 61 75 61
12P WILD-TYPE 81 39 39

Figure S69.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.014

Table S70.  Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
12P MUTATED 46 92 87 32
12P WILD-TYPE 72 51 56 43

Figure S70.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000132 (Fisher's exact test), Q value = 0.054

Table S71.  Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
12P MUTATED 58 90 109
12P WILD-TYPE 35 50 137

Figure S71.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 0.000332 (Fisher's exact test), Q value = 0.13

Table S72.  Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
12P MUTATED 73 88 52 36
12P WILD-TYPE 72 42 73 28

Figure S72.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q' versus 'CN_CNMF'

P value = 7.88e-06 (Fisher's exact test), Q value = 0.0034

Table S73.  Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
12Q MUTATED 56 88 55
12Q WILD-TYPE 137 74 80

Figure S73.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.054

Table S74.  Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
12Q MUTATED 47 70 77
12Q WILD-TYPE 46 70 169

Figure S74.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.061

Table S75.  Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
13Q MUTATED 102 73 51
13Q WILD-TYPE 23 39 40

Figure S75.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.092

Table S76.  Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
14Q MUTATED 57 98 94 34
14Q WILD-TYPE 61 45 49 41

Figure S76.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.006

Table S77.  Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
14Q MUTATED 66 97 120
14Q WILD-TYPE 27 43 126

Figure S77.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.045

Table S78.  Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
15Q MUTATED 72 94 75
15Q WILD-TYPE 121 68 60

Figure S78.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'CN_CNMF'

P value = 8.24e-07 (Fisher's exact test), Q value = 0.00037

Table S79.  Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
16P MUTATED 68 87 86
16P WILD-TYPE 125 75 49

Figure S79.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'CN_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 0.00096

Table S80.  Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
16Q MUTATED 76 98 88
16Q WILD-TYPE 117 64 47

Figure S80.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'MRNASEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.11

Table S81.  Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
16Q MUTATED 54 86 89 27
16Q WILD-TYPE 64 57 54 48

Figure S81.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.051

Table S82.  Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
16Q MUTATED 64 82 110
16Q WILD-TYPE 29 58 136

Figure S82.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000283 (Fisher's exact test), Q value = 0.11

Table S83.  Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
16Q MUTATED 83 46 44
16Q WILD-TYPE 42 66 47

Figure S83.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'CN_CNMF'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.00066

Table S84.  Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
17P MUTATED 113 125 112
17P WILD-TYPE 80 37 23

Figure S84.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'CN_CNMF'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0038

Table S85.  Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
17Q MUTATED 76 105 65
17Q WILD-TYPE 117 57 70

Figure S85.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'CN_CNMF'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0066

Table S86.  Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
18P MUTATED 89 114 83
18P WILD-TYPE 104 48 52

Figure S86.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'CN_CNMF'

P value = 3.66e-05 (Fisher's exact test), Q value = 0.015

Table S87.  Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
18Q MUTATED 90 113 84
18Q WILD-TYPE 103 49 51

Figure S87.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'CN_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 4.9e-05

Table S88.  Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19P MUTATED 78 112 83
19P WILD-TYPE 115 50 52

Figure S88.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 1.23e-08 (Fisher's exact test), Q value = 5.7e-06

Table S89.  Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19Q MUTATED 74 113 78
19Q WILD-TYPE 119 49 57

Figure S89.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'CN_CNMF'

P value = 7.64e-07 (Fisher's exact test), Q value = 0.00035

Table S90.  Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
20P MUTATED 88 113 94
20P WILD-TYPE 105 49 41

Figure S90.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'CN_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0086

Table S91.  Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
20Q MUTATED 89 109 91
20Q WILD-TYPE 104 53 44

Figure S91.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 5.16e-06 (Fisher's exact test), Q value = 0.0023

Table S92.  Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
21Q MUTATED 99 121 96
21Q WILD-TYPE 94 41 39

Figure S92.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'CN_CNMF'

P value = 6.76e-09 (Fisher's exact test), Q value = 3.2e-06

Table S93.  Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
XQ MUTATED 42 79 66
XQ WILD-TYPE 151 83 69

Figure S93.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 6.7e-06 (Fisher's exact test), Q value = 0.0029

Table S94.  Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
XQ MUTATED 32 56 46
XQ WILD-TYPE 110 58 54

Figure S94.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq' versus 'MRNASEQ_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.063

Table S95.  Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
XQ MUTATED 41 67 63 14
XQ WILD-TYPE 77 76 80 61

Figure S95.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq' versus 'MIRSEQ_CNMF'

P value = 1.87e-09 (Fisher's exact test), Q value = 8.8e-07

Table S96.  Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
XQ MUTATED 53 75 23 27
XQ WILD-TYPE 92 55 102 37

Figure S96.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 1.4e-05

Table S97.  Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
XQ MUTATED 73 32 21
XQ WILD-TYPE 52 80 70

Figure S97.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.58e-06 (Fisher's exact test), Q value = 0.002

Table S98.  Gene #40: 'xq' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
XQ MUTATED 48 78
XQ WILD-TYPE 130 72

Figure S98.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

  • Molecular subtype file = LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 490

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, 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

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] 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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