Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C10P0X6T
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10P0X6T
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 76 arm-level results and 10 molecular subtypes across 413 patients, 75 significant findings detected with Q value < 0.25.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q 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 76 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 75 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 267 (65%) 146 1.18e-11
(8.21e-09) 		9.69e-15
(6.82e-12) 		9.42e-47
(6.77e-44) 		1.06e-09
(7.32e-07) 		0.00104
(0.649) 		1.24e-05
(0.00826) 		3.95e-16
(2.8e-13) 		5.98e-18
(4.25e-15) 		0.103
(1.00) 		0.429
(1.00)
14q loss 94 (23%) 319 9.75e-08
(6.68e-05) 		2.1e-06
(0.00142) 		1.58e-22
(1.13e-19) 		1.2e-06
(0.000814) 		0.000251
(0.163) 		0.00308
(1.00) 		1.54e-07
(0.000105) 		1.76e-06
(0.00119) 		0.532
(1.00) 		0.194
(1.00)
18p loss 209 (51%) 204 2.04e-14
(1.43e-11) 		6.47e-10
(4.46e-07) 		2.44e-46
(1.75e-43) 		5.15e-13
(3.6e-10) 		0.00081
(0.511) 		8.24e-05
(0.0541) 		5.92e-13
(4.13e-10) 		4.6e-14
(3.23e-11) 		0.251
(1.00) 		0.497
(1.00)
13q gain 211 (51%) 202 1.08e-05
(0.00717) 		4.14e-05
(0.0274) 		2.95e-33
(2.11e-30) 		0.000267
(0.173) 		0.101
(1.00) 		0.0212
(1.00) 		8.39e-07
(0.000572) 		8.46e-06
(0.00567) 		0.045
(1.00) 		0.466
(1.00)
18q loss 225 (54%) 188 1.4e-13
(9.83e-11) 		1.62e-09
(1.12e-06) 		8.88e-46
(6.36e-43) 		3.62e-15
(2.55e-12) 		0.00975
(1.00) 		0.000662
(0.419) 		1.01e-11
(7.05e-09) 		1.74e-15
(1.23e-12) 		0.0612
(1.00) 		0.499
(1.00)
17p loss 164 (40%) 249 4.44e-06
(0.00299) 		5.88e-05
(0.0388) 		4.44e-23
(3.18e-20) 		2.31e-07
(0.000158) 		0.028
(1.00) 		0.0336
(1.00) 		0.00041
(0.264) 		5.09e-05
(0.0336) 		0.147
(1.00) 		0.0464
(1.00)
7p gain 200 (48%) 213 0.0012
(0.745) 		0.00141
(0.877) 		1.92e-15
(1.35e-12) 		9.14e-05
(0.0599) 		0.316
(1.00) 		0.0199
(1.00) 		1.22e-06
(0.000829) 		7.19e-05
(0.0473) 		0.425
(1.00) 		0.958
(1.00)
20p gain 188 (46%) 225 0.00223
(1.00) 		5.92e-06
(0.00398) 		4.29e-20
(3.05e-17) 		0.0127
(1.00) 		0.0229
(1.00) 		0.0648
(1.00) 		8.67e-06
(0.0058) 		3.55e-07
(0.000242) 		0.174
(1.00) 		0.0758
(1.00)
8p loss 93 (23%) 320 0.000293
(0.189) 		0.00823
(1.00) 		7.76e-17
(5.51e-14) 		0.00104
(0.649) 		0.229
(1.00) 		0.0337
(1.00) 		0.000218
(0.142) 		0.0025
(1.00) 		0.2
(1.00) 		0.356
(1.00)
7q gain 175 (42%) 238 0.00419
(1.00) 		0.0146
(1.00) 		7.05e-11
(4.88e-08) 		0.00278
(1.00) 		0.667
(1.00) 		0.0751
(1.00) 		0.000163
(0.106) 		0.000453
(0.291) 		0.474
(1.00) 		0.752
(1.00)
16p gain 67 (16%) 346 0.0127
(1.00) 		0.0111
(1.00) 		1.08e-14
(7.62e-12) 		0.138
(1.00) 		0.258
(1.00) 		0.0488
(1.00) 		0.00986
(1.00) 		9.94e-05
(0.065) 		0.126
(1.00) 		0.0474
(1.00)
11p loss 22 (5%) 391 0.494
(1.00) 		0.106
(1.00) 		8.34e-05
(0.0547) 		0.000281
(0.182) 		0.727
(1.00) 		0.514
(1.00) 		0.929
(1.00) 		0.64
(1.00) 		0.0401
(1.00) 		0.162
(1.00)
11q loss 27 (7%) 386 0.365
(1.00) 		0.0666
(1.00) 		7.92e-06
(0.00532) 		9.61e-06
(0.00641) 		0.652
(1.00) 		0.594
(1.00) 		0.663
(1.00) 		1
(1.00) 		0.358
(1.00) 		0.202
(1.00)
2q gain 39 (9%) 374 0.0577
(1.00) 		0.0512
(1.00) 		0.000173
(0.112) 		0.00235
(1.00) 		0.121
(1.00) 		0.589
(1.00) 		0.00294
(1.00) 		0.00261
(1.00) 		0.529
(1.00) 		0.405
(1.00)
8p gain 80 (19%) 333 1
(1.00) 		0.988
(1.00) 		9.22e-06
(0.00616) 		0.0562
(1.00) 		0.25
(1.00) 		0.162
(1.00) 		0.47
(1.00) 		0.849
(1.00) 		0.615
(1.00) 		0.571
(1.00)
8q gain 162 (39%) 251 0.793
(1.00) 		0.151
(1.00) 		9.39e-12
(6.55e-09) 		0.000666
(0.421) 		0.65
(1.00) 		0.0565
(1.00) 		0.15
(1.00) 		0.136
(1.00) 		0.0986
(1.00) 		0.154
(1.00)
11p gain 18 (4%) 395 0.15
(1.00) 		0.0019
(1.00) 		0.000314
(0.203) 		0.000575
(0.367) 		1
(1.00) 		0.605
(1.00) 		0.00559
(1.00) 		0.0421
(1.00) 		0.634
(1.00) 		0.882
(1.00)
11q gain 22 (5%) 391 0.0297
(1.00) 		0.00397
(1.00) 		3.72e-06
(0.00251) 		0.00141
(0.877) 		0.299
(1.00) 		0.677
(1.00) 		0.00062
(0.394) 		0.0098
(1.00) 		0.386
(1.00) 		0.693
(1.00)
16q gain 66 (16%) 347 0.0138
(1.00) 		0.0185
(1.00) 		1.44e-16
(1.02e-13) 		0.136
(1.00) 		0.181
(1.00) 		0.0488
(1.00) 		0.00285
(1.00) 		0.000408
(0.263) 		0.314
(1.00) 		0.232
(1.00)
1p loss 51 (12%) 362 0.00249
(1.00) 		0.000927
(0.582) 		7.09e-08
(4.87e-05) 		0.00329
(1.00) 		0.71
(1.00) 		0.597
(1.00) 		0.00432
(1.00) 		0.00144
(0.895) 		0.18
(1.00) 		0.274
(1.00)
4p loss 84 (20%) 329 0.00199
(1.00) 		0.0369
(1.00) 		1.05e-11
(7.31e-09) 		0.00299
(1.00) 		0.157
(1.00) 		0.255
(1.00) 		0.00875
(1.00) 		0.0234
(1.00) 		0.083
(1.00) 		0.29
(1.00)
4q loss 68 (16%) 345 0.0047
(1.00) 		0.0161
(1.00) 		2.26e-10
(1.56e-07) 		0.00223
(1.00) 		0.11
(1.00) 		0.231
(1.00) 		0.0388
(1.00) 		0.217
(1.00) 		0.00266
(1.00) 		0.0359
(1.00)
5q loss 38 (9%) 375 0.0926
(1.00) 		0.122
(1.00) 		1.11e-05
(0.00741) 		0.293
(1.00) 		0.381
(1.00) 		0.284
(1.00) 		0.0297
(1.00) 		0.0743
(1.00) 		0.551
(1.00) 		0.48
(1.00)
9p loss 27 (7%) 386 0.874
(1.00) 		0.197
(1.00) 		4.4e-05
(0.0291) 		0.0746
(1.00) 		0.241
(1.00) 		0.177
(1.00) 		0.301
(1.00) 		0.807
(1.00) 		0.53
(1.00) 		0.744
(1.00)
9q loss 26 (6%) 387 0.358
(1.00) 		0.171
(1.00) 		2.55e-06
(0.00172) 		0.000619
(0.394) 		0.241
(1.00) 		0.177
(1.00) 		0.0587
(1.00) 		0.371
(1.00) 		0.114
(1.00) 		0.675
(1.00)
12p loss 21 (5%) 392 0.097
(1.00) 		0.126
(1.00) 		7.1e-05
(0.0468) 		0.207
(1.00) 		0.53
(1.00) 		0.972
(1.00) 		0.282
(1.00) 		0.762
(1.00) 		0.72
(1.00) 		0.208
(1.00)
12q loss 20 (5%) 393 0.19
(1.00) 		0.154
(1.00) 		0.000101
(0.0662) 		0.153
(1.00) 		0.706
(1.00) 		0.939
(1.00) 		0.446
(1.00) 		0.818
(1.00) 		0.411
(1.00) 		0.362
(1.00)
15q loss 99 (24%) 314 0.00753
(1.00) 		0.00873
(1.00) 		9.29e-22
(6.62e-19) 		0.00458
(1.00) 		0.0541
(1.00) 		0.597
(1.00) 		0.0437
(1.00) 		0.000451
(0.289) 		0.488
(1.00) 		0.0435
(1.00)
20p loss 33 (8%) 380 0.0135
(1.00) 		0.00818
(1.00) 		8.88e-08
(6.09e-05) 		0.0514
(1.00) 		0.756
(1.00) 		0.645
(1.00) 		0.0631
(1.00) 		0.0393
(1.00) 		0.906
(1.00) 		0.53
(1.00)
21q loss 71 (17%) 342 0.0103
(1.00) 		0.00693
(1.00) 		2.6e-06
(0.00175) 		0.258
(1.00) 		0.605
(1.00) 		0.827
(1.00) 		0.103
(1.00) 		0.0245
(1.00) 		0.0731
(1.00) 		0.608
(1.00)
22q loss 81 (20%) 332 0.000473
(0.303) 		0.000623
(0.395) 		1.06e-11
(7.37e-09) 		0.0894
(1.00) 		0.0623
(1.00) 		0.0152
(1.00) 		0.0621
(1.00) 		0.0011
(0.687) 		0.624
(1.00) 		0.123
(1.00)
1p gain 11 (3%) 402 0.576
(1.00) 		0.909
(1.00) 		0.0365
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.0783
(1.00) 		0.46
(1.00) 		1
(1.00)
1q gain 47 (11%) 366 0.0527
(1.00) 		0.604
(1.00) 		0.0788
(1.00) 		0.307
(1.00) 		0.567
(1.00) 		0.181
(1.00) 		0.0943
(1.00) 		0.931
(1.00) 		0.437
(1.00) 		0.837
(1.00)
2p gain 40 (10%) 373 0.0975
(1.00) 		0.0566
(1.00) 		0.00409
(1.00) 		0.046
(1.00) 		0.141
(1.00) 		0.488
(1.00) 		0.0059
(1.00) 		0.00433
(1.00) 		0.508
(1.00) 		0.355
(1.00)
3p gain 20 (5%) 393 0.378
(1.00) 		0.43
(1.00) 		0.071
(1.00) 		0.367
(1.00) 		0.715
(1.00) 		0.175
(1.00) 		0.464
(1.00) 		0.86
(1.00) 		0.626
(1.00) 		0.184
(1.00)
3q gain 30 (7%) 383 0.458
(1.00) 		0.0551
(1.00) 		0.000969
(0.607) 		0.22
(1.00) 		0.393
(1.00) 		0.444
(1.00) 		0.178
(1.00) 		0.585
(1.00) 		0.357
(1.00) 		0.824
(1.00)
4p gain 3 (1%) 410 0.746
(1.00) 		0.473
(1.00) 		0.225
(1.00) 		0.214
(1.00) 		0.208
(1.00) 		0.0334
(1.00)
4q gain 5 (1%) 408 0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.832
(1.00) 		0.579
(1.00) 		0.335
(1.00)
5p gain 39 (9%) 374 0.286
(1.00) 		0.0479
(1.00) 		0.00223
(1.00) 		0.0236
(1.00) 		0.513
(1.00) 		0.987
(1.00) 		0.341
(1.00) 		0.338
(1.00) 		0.685
(1.00) 		0.53
(1.00)
5q gain 21 (5%) 392 0.656
(1.00) 		0.319
(1.00) 		0.0391
(1.00) 		0.188
(1.00) 		0.369
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.948
(1.00)
6p gain 50 (12%) 363 0.516
(1.00) 		0.0107
(1.00) 		0.0267
(1.00) 		0.675
(1.00) 		0.619
(1.00) 		0.955
(1.00) 		0.299
(1.00) 		0.732
(1.00) 		0.513
(1.00) 		0.246
(1.00)
6q gain 45 (11%) 368 0.334
(1.00) 		0.0267
(1.00) 		0.0317
(1.00) 		0.352
(1.00) 		0.877
(1.00) 		0.847
(1.00) 		0.443
(1.00) 		0.943
(1.00) 		0.441
(1.00) 		0.309
(1.00)
9p gain 46 (11%) 367 0.0317
(1.00) 		0.262
(1.00) 		0.28
(1.00) 		0.433
(1.00) 		0.0817
(1.00) 		0.13
(1.00) 		0.0783
(1.00) 		0.35
(1.00) 		0.767
(1.00) 		0.763
(1.00)
9q gain 39 (9%) 374 0.0568
(1.00) 		0.305
(1.00) 		0.0641
(1.00) 		0.113
(1.00) 		0.017
(1.00) 		0.0254
(1.00) 		0.595
(1.00) 		0.875
(1.00) 		0.0589
(1.00) 		0.635
(1.00)
10p gain 18 (4%) 395 0.669
(1.00) 		0.55
(1.00) 		0.104
(1.00) 		0.0477
(1.00) 		0.951
(1.00) 		0.696
(1.00) 		0.826
(1.00) 		0.45
(1.00) 		0.761
(1.00) 		0.941
(1.00)
10q gain 7 (2%) 406 0.114
(1.00) 		0.042
(1.00) 		0.877
(1.00) 		0.615
(1.00) 		0.202
(1.00) 		0.151
(1.00)
12p gain 66 (16%) 347 0.361
(1.00) 		0.0912
(1.00) 		0.00442
(1.00) 		0.0146
(1.00) 		0.537
(1.00) 		0.574
(1.00) 		0.146
(1.00) 		0.561
(1.00) 		0.069
(1.00) 		0.21
(1.00)
12q gain 60 (15%) 353 0.245
(1.00) 		0.19
(1.00) 		0.00181
(1.00) 		0.00291
(1.00) 		0.417
(1.00) 		0.546
(1.00) 		0.208
(1.00) 		0.874
(1.00) 		0.0121
(1.00) 		0.268
(1.00)
14q gain 15 (4%) 398 0.484
(1.00) 		0.45
(1.00) 		0.0566
(1.00) 		0.276
(1.00) 		0.0499
(1.00) 		0.367
(1.00) 		0.306
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.805
(1.00)
15q gain 5 (1%) 408 0.0732
(1.00) 		0.683
(1.00) 		0.0374
(1.00) 		0.0636
(1.00) 		0.473
(1.00) 		0.427
(1.00)
17p gain 9 (2%) 404 0.618
(1.00) 		0.893
(1.00) 		0.626
(1.00) 		0.0996
(1.00) 		0.737
(1.00) 		0.891
(1.00)
17q gain 48 (12%) 365 0.0898
(1.00) 		0.0218
(1.00) 		0.000913
(0.574) 		0.00739
(1.00) 		0.25
(1.00) 		0.185
(1.00) 		0.000475
(0.304) 		0.00605
(1.00) 		0.0581
(1.00) 		0.753
(1.00)
18p gain 15 (4%) 398 0.117
(1.00) 		0.828
(1.00) 		0.00548
(1.00) 		0.0139
(1.00) 		0.334
(1.00) 		0.603
(1.00) 		0.216
(1.00) 		0.0234
(1.00) 		0.144
(1.00) 		0.388
(1.00)
18q gain 9 (2%) 404 0.0232
(1.00) 		0.0303
(1.00) 		0.0747
(1.00) 		0.0666
(1.00) 		0.274
(1.00) 		0.327
(1.00)
19p gain 34 (8%) 379 0.0744
(1.00) 		0.222
(1.00) 		0.00554
(1.00) 		0.0512
(1.00) 		0.229
(1.00) 		0.233
(1.00) 		0.75
(1.00) 		0.104
(1.00) 		0.588
(1.00) 		0.573
(1.00)
19q gain 41 (10%) 372 0.0676
(1.00) 		0.0935
(1.00) 		0.437
(1.00) 		0.0666
(1.00) 		0.0262
(1.00) 		0.0721
(1.00) 		0.00506
(1.00) 		0.419
(1.00) 		0.924
(1.00) 		0.942
(1.00)
21q gain 11 (3%) 402 0.192
(1.00) 		0.295
(1.00) 		0.0858
(1.00) 		0.339
(1.00) 		0.193
(1.00) 		0.48
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.684
(1.00)
Xq gain 12 (3%) 401 0.0689
(1.00) 		0.735
(1.00) 		0.0331
(1.00) 		0.631
(1.00) 		0.133
(1.00) 		0.352
(1.00) 		0.892
(1.00) 		0.225
(1.00) 		0.352
(1.00) 		0.41
(1.00)
1q loss 18 (4%) 395 0.271
(1.00) 		0.112
(1.00) 		0.0103
(1.00) 		0.269
(1.00) 		0.401
(1.00) 		0.594
(1.00) 		0.345
(1.00) 		0.0298
(1.00) 		0.941
(1.00) 		0.44
(1.00)
2p loss 4 (1%) 409 0.569
(1.00) 		0.142
(1.00) 		0.433
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.132
(1.00)
2q loss 6 (1%) 407 1
(1.00) 		0.0661
(1.00) 		0.601
(1.00) 		0.071
(1.00) 		0.269
(1.00) 		0.0816
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.0588
(1.00)
3p loss 27 (7%) 386 0.528
(1.00) 		0.2
(1.00) 		0.00251
(1.00) 		0.252
(1.00) 		0.427
(1.00) 		0.972
(1.00) 		0.772
(1.00) 		0.195
(1.00) 		0.212
(1.00) 		0.143
(1.00)
3q loss 12 (3%) 401 0.816
(1.00) 		0.692
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.306
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.423
(1.00) 		0.822
(1.00)
5p loss 25 (6%) 388 0.659
(1.00) 		0.172
(1.00) 		0.00176
(1.00) 		0.102
(1.00) 		0.725
(1.00) 		0.7
(1.00) 		0.434
(1.00) 		0.477
(1.00) 		0.841
(1.00) 		0.907
(1.00)
6p loss 12 (3%) 401 0.538
(1.00) 		0.05
(1.00) 		0.00285
(1.00) 		1
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.34
(1.00) 		0.642
(1.00) 		0.624
(1.00)
6q loss 21 (5%) 392 0.943
(1.00) 		0.529
(1.00) 		0.0743
(1.00) 		0.697
(1.00) 		0.165
(1.00) 		0.711
(1.00) 		0.575
(1.00) 		0.314
(1.00) 		0.864
(1.00) 		1
(1.00)
8q loss 8 (2%) 405 0.402
(1.00) 		0.735
(1.00) 		0.00966
(1.00) 		0.852
(1.00) 		0.273
(1.00) 		0.726
(1.00) 		0.0514
(1.00) 		0.0381
(1.00) 		0.197
(1.00) 		0.436
(1.00)
10p loss 22 (5%) 391 0.63
(1.00) 		0.692
(1.00) 		0.000828
(0.522) 		0.285
(1.00) 		0.109
(1.00) 		0.638
(1.00) 		0.255
(1.00) 		0.0842
(1.00) 		0.24
(1.00) 		0.681
(1.00)
10q loss 24 (6%) 389 0.373
(1.00) 		0.569
(1.00) 		0.000526
(0.336) 		0.152
(1.00) 		0.135
(1.00) 		0.949
(1.00) 		0.303
(1.00) 		0.0297
(1.00) 		0.697
(1.00) 		0.393
(1.00)
13q loss 6 (1%) 407 0.0209
(1.00) 		0.232
(1.00) 		0.038
(1.00) 		0.0214
(1.00) 		0.869
(1.00) 		0.723
(1.00)
16p loss 9 (2%) 404 0.249
(1.00) 		0.571
(1.00) 		0.305
(1.00) 		0.0298
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.383
(1.00) 		0.317
(1.00) 		0.711
(1.00) 		1
(1.00)
16q loss 7 (2%) 406 0.462
(1.00) 		0.917
(1.00) 		0.228
(1.00) 		0.649
(1.00) 		0.558
(1.00) 		0.175
(1.00) 		0.17
(1.00)
17q loss 32 (8%) 381 0.116
(1.00) 		0.134
(1.00) 		0.00216
(1.00) 		0.22
(1.00) 		0.622
(1.00) 		0.411
(1.00) 		0.903
(1.00) 		0.367
(1.00) 		0.322
(1.00) 		0.291
(1.00)
19p loss 14 (3%) 399 1
(1.00) 		0.339
(1.00) 		0.00275
(1.00) 		0.0957
(1.00) 		0.127
(1.00) 		0.123
(1.00) 		0.464
(1.00) 		0.34
(1.00) 		0.693
(1.00) 		0.0876
(1.00)
19q loss 13 (3%) 400 0.922
(1.00) 		0.435
(1.00) 		0.0115
(1.00) 		0.0957
(1.00) 		0.584
(1.00) 		0.196
(1.00) 		0.428
(1.00) 		0.558
(1.00) 		0.57
(1.00) 		0.0611
(1.00)
Xq loss 5 (1%) 408 0.842
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.673
(1.00) 		0.851
(1.00) 		0.14
(1.00)
'2q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.11

Table S1.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
2Q GAIN MUTATED 28 6 3 2
2Q GAIN WILD-TYPE 142 181 29 22

Figure S1.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.92e-15 (Fisher's exact test), Q value = 1.4e-12

Table S2.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
7P GAIN MUTATED 112 49 23 16
7P GAIN WILD-TYPE 58 138 9 8

Figure S2.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.14e-05 (Fisher's exact test), Q value = 0.06

Table S3.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
7P GAIN MUTATED 71 38 23
7P GAIN WILD-TYPE 34 48 40

Figure S3.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00083

Table S4.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
7P GAIN MUTATED 48 18 10 10
7P GAIN WILD-TYPE 19 40 29 10

Figure S4.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.047

Table S5.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
7P GAIN MUTATED 16 11 59
7P GAIN WILD-TYPE 48 7 43

Figure S5.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 7.05e-11 (Fisher's exact test), Q value = 4.9e-08

Table S6.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
7Q GAIN MUTATED 96 45 21 13
7Q GAIN WILD-TYPE 74 142 11 11

Figure S6.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
7Q GAIN MUTATED 40 16 9 10
7Q GAIN WILD-TYPE 27 42 30 10

Figure S7.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8p gain mutation analysis' versus 'CN_CNMF'

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

Table S8.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
8P GAIN MUTATED 23 32 12 13
8P GAIN WILD-TYPE 147 155 20 11

Figure S8.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 9.39e-12 (Fisher's exact test), Q value = 6.5e-09

Table S9.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
8Q GAIN MUTATED 78 45 17 22
8Q GAIN WILD-TYPE 92 142 15 2

Figure S9.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.2

Table S10.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11P GAIN MUTATED 16 1 1 0
11P GAIN WILD-TYPE 154 186 31 24

Figure S10.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.0025

Table S11.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11Q GAIN MUTATED 19 0 2 1
11Q GAIN WILD-TYPE 151 187 30 23

Figure S11.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0072

Table S12.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
13Q GAIN MUTATED 46 10 8 14
13Q GAIN WILD-TYPE 17 22 22 9

Figure S12.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'13q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.027

Table S13.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
13Q GAIN MUTATED 11 30 6 31
13Q GAIN WILD-TYPE 33 18 7 12

Figure S13.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 2.95e-33 (Fisher's exact test), Q value = 2.1e-30

Table S14.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
13Q GAIN MUTATED 143 42 11 15
13Q GAIN WILD-TYPE 27 145 21 9

Figure S14.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
13Q GAIN MUTATED 70 35 26
13Q GAIN WILD-TYPE 35 51 37

Figure S15.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.39e-07 (Fisher's exact test), Q value = 0.00057

Table S16.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
13Q GAIN MUTATED 49 18 12 13
13Q GAIN WILD-TYPE 18 40 27 7

Figure S16.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.46e-06 (Fisher's exact test), Q value = 0.0057

Table S17.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
13Q GAIN MUTATED 17 9 66
13Q GAIN WILD-TYPE 47 9 36

Figure S17.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.08e-14 (Fisher's exact test), Q value = 7.6e-12

Table S18.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
16P GAIN MUTATED 56 5 5 1
16P GAIN WILD-TYPE 114 182 27 23

Figure S18.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.94e-05 (Fisher's exact test), Q value = 0.065

Table S19.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
16P GAIN MUTATED 3 6 29
16P GAIN WILD-TYPE 61 12 73

Figure S19.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 1.44e-16 (Fisher's exact test), Q value = 1e-13

Table S20.  Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
16Q GAIN MUTATED 58 4 3 1
16Q GAIN WILD-TYPE 112 183 29 23

Figure S20.  Get High-res Image Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.92e-06 (Fisher's exact test), Q value = 0.004

Table S21.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
20P GAIN MUTATED 8 31 8 27
20P GAIN WILD-TYPE 36 17 5 16

Figure S21.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 4.29e-20 (Fisher's exact test), Q value = 3.1e-17

Table S22.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
20P GAIN MUTATED 98 44 31 15
20P GAIN WILD-TYPE 72 143 1 9

Figure S22.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.67e-06 (Fisher's exact test), Q value = 0.0058

Table S23.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
20P GAIN MUTATED 44 14 18 14
20P GAIN WILD-TYPE 23 44 21 6

Figure S23.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.55e-07 (Fisher's exact test), Q value = 0.00024

Table S24.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
20P GAIN MUTATED 15 8 67
20P GAIN WILD-TYPE 49 10 35

Figure S24.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.18e-11 (Fisher's exact test), Q value = 8.2e-09

Table S25.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
20Q GAIN MUTATED 59 10 13 19
20Q GAIN WILD-TYPE 4 22 17 4

Figure S25.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.69e-15 (Fisher's exact test), Q value = 6.8e-12

Table S26.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
20Q GAIN MUTATED 10 43 8 40
20Q GAIN WILD-TYPE 34 5 5 3

Figure S26.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 9.42e-47 (Fisher's exact test), Q value = 6.8e-44

Table S27.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
20Q GAIN MUTATED 160 54 32 21
20Q GAIN WILD-TYPE 10 133 0 3

Figure S27.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 7.3e-07

Table S28.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
20Q GAIN MUTATED 89 37 33
20Q GAIN WILD-TYPE 16 49 30

Figure S28.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0083

Table S29.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 23 48 51
20Q GAIN MUTATED 97 10 18 41
20Q GAIN WILD-TYPE 45 13 30 10

Figure S29.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.95e-16 (Fisher's exact test), Q value = 2.8e-13

Table S30.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
20Q GAIN MUTATED 64 17 23 18
20Q GAIN WILD-TYPE 3 41 16 2

Figure S30.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.98e-18 (Fisher's exact test), Q value = 4.3e-15

Table S31.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
20Q GAIN MUTATED 17 12 93
20Q GAIN WILD-TYPE 47 6 9

Figure S31.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 7.09e-08 (Fisher's exact test), Q value = 4.9e-05

Table S32.  Gene #40: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
1P LOSS MUTATED 36 6 8 1
1P LOSS WILD-TYPE 134 181 24 23

Figure S32.  Get High-res Image Gene #40: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 1.05e-11 (Fisher's exact test), Q value = 7.3e-09

Table S33.  Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
4P LOSS MUTATED 56 11 13 4
4P LOSS WILD-TYPE 114 176 19 20

Figure S33.  Get High-res Image Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 2.26e-10 (Fisher's exact test), Q value = 1.6e-07

Table S34.  Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
4Q LOSS MUTATED 49 8 9 2
4Q LOSS WILD-TYPE 121 179 23 22

Figure S34.  Get High-res Image Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0074

Table S35.  Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
5Q LOSS MUTATED 27 4 3 4
5Q LOSS WILD-TYPE 143 183 29 20

Figure S35.  Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.19

Table S36.  Gene #52: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
8P LOSS MUTATED 24 2 3 9
8P LOSS WILD-TYPE 39 30 27 14

Figure S36.  Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 7.76e-17 (Fisher's exact test), Q value = 5.5e-14

Table S37.  Gene #52: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
8P LOSS MUTATED 73 11 3 6
8P LOSS WILD-TYPE 97 176 29 18

Figure S37.  Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.14

Table S38.  Gene #52: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
8P LOSS MUTATED 25 5 8 9
8P LOSS WILD-TYPE 42 53 31 11

Figure S38.  Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.029

Table S39.  Gene #54: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
9P LOSS MUTATED 19 2 5 1
9P LOSS WILD-TYPE 151 185 27 23

Figure S39.  Get High-res Image Gene #54: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 2.55e-06 (Fisher's exact test), Q value = 0.0017

Table S40.  Gene #55: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
9Q LOSS MUTATED 21 1 4 0
9Q LOSS WILD-TYPE 149 186 28 24

Figure S40.  Get High-res Image Gene #55: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.055

Table S41.  Gene #58: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11P LOSS MUTATED 14 2 6 0
11P LOSS WILD-TYPE 156 185 26 24

Figure S41.  Get High-res Image Gene #58: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.18

Table S42.  Gene #58: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
11P LOSS MUTATED 10 0 0
11P LOSS WILD-TYPE 95 86 63

Figure S42.  Get High-res Image Gene #58: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 7.92e-06 (Fisher's exact test), Q value = 0.0053

Table S43.  Gene #59: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11Q LOSS MUTATED 19 2 6 0
11Q LOSS WILD-TYPE 151 185 26 24

Figure S43.  Get High-res Image Gene #59: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.61e-06 (Fisher's exact test), Q value = 0.0064

Table S44.  Gene #59: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
11Q LOSS MUTATED 14 0 0
11Q LOSS WILD-TYPE 91 86 63

Figure S44.  Get High-res Image Gene #59: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.047

Table S45.  Gene #60: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
12P LOSS MUTATED 17 1 3 0
12P LOSS WILD-TYPE 153 186 29 24

Figure S45.  Get High-res Image Gene #60: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.066

Table S46.  Gene #61: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
12Q LOSS MUTATED 15 1 4 0
12Q LOSS WILD-TYPE 155 186 28 24

Figure S46.  Get High-res Image Gene #61: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

P value = 9.75e-08 (Fisher's exact test), Q value = 6.7e-05

Table S47.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
14Q LOSS MUTATED 31 2 1 9
14Q LOSS WILD-TYPE 32 30 29 14

Figure S47.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.1e-06 (Fisher's exact test), Q value = 0.0014

Table S48.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
14Q LOSS MUTATED 1 17 5 20
14Q LOSS WILD-TYPE 43 31 8 23

Figure S48.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 1.58e-22 (Fisher's exact test), Q value = 1.1e-19

Table S49.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
14Q LOSS MUTATED 78 8 8 0
14Q LOSS WILD-TYPE 92 179 24 24

Figure S49.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00081

Table S50.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
14Q LOSS MUTATED 36 6 6
14Q LOSS WILD-TYPE 69 80 57

Figure S50.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 117 7 76
14Q LOSS MUTATED 14 40 0 7
14Q LOSS WILD-TYPE 50 77 7 69

Figure S51.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00011

Table S52.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
14Q LOSS MUTATED 34 4 7 7
14Q LOSS WILD-TYPE 33 54 32 13

Figure S52.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0012

Table S53.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
14Q LOSS MUTATED 6 2 44
14Q LOSS WILD-TYPE 58 16 58

Figure S53.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 9.29e-22 (Fisher's exact test), Q value = 6.6e-19

Table S54.  Gene #64: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
15Q LOSS MUTATED 70 9 19 1
15Q LOSS WILD-TYPE 100 178 13 23

Figure S54.  Get High-res Image Gene #64: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.003

Table S55.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
17P LOSS MUTATED 40 7 5 13
17P LOSS WILD-TYPE 23 25 25 10

Figure S55.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.039

Table S56.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
17P LOSS MUTATED 7 28 6 24
17P LOSS WILD-TYPE 37 20 7 19

Figure S56.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 4.44e-23 (Fisher's exact test), Q value = 3.2e-20

Table S57.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
17P LOSS MUTATED 109 26 16 13
17P LOSS WILD-TYPE 61 161 16 11

Figure S57.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-07 (Fisher's exact test), Q value = 0.00016

Table S58.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
17P LOSS MUTATED 61 19 17
17P LOSS WILD-TYPE 44 67 46

Figure S58.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.09e-05 (Fisher's exact test), Q value = 0.034

Table S59.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
17P LOSS MUTATED 15 7 59
17P LOSS WILD-TYPE 49 11 43

Figure S59.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.04e-14 (Fisher's exact test), Q value = 1.4e-11

Table S60.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
18P LOSS MUTATED 53 5 5 16
18P LOSS WILD-TYPE 10 27 25 7

Figure S60.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.47e-10 (Fisher's exact test), Q value = 4.5e-07

Table S61.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
18P LOSS MUTATED 6 31 8 34
18P LOSS WILD-TYPE 38 17 5 9

Figure S61.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 2.44e-46 (Fisher's exact test), Q value = 1.8e-43

Table S62.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
18P LOSS MUTATED 143 26 27 13
18P LOSS WILD-TYPE 27 161 5 11

Figure S62.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.15e-13 (Fisher's exact test), Q value = 3.6e-10

Table S63.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
18P LOSS MUTATED 81 24 21
18P LOSS WILD-TYPE 24 62 42

Figure S63.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 8.24e-05 (Fisher's exact test), Q value = 0.054

Table S64.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 23 48 51
18P LOSS MUTATED 85 7 12 26
18P LOSS WILD-TYPE 57 16 36 25

Figure S64.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.92e-13 (Fisher's exact test), Q value = 4.1e-10

Table S65.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
18P LOSS MUTATED 57 13 16 15
18P LOSS WILD-TYPE 10 45 23 5

Figure S65.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.6e-14 (Fisher's exact test), Q value = 3.2e-11

Table S66.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
18P LOSS MUTATED 12 9 80
18P LOSS WILD-TYPE 52 9 22

Figure S66.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.4e-13 (Fisher's exact test), Q value = 9.8e-11

Table S67.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 32 30 23
18Q LOSS MUTATED 54 6 6 16
18Q LOSS WILD-TYPE 9 26 24 7

Figure S67.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-09 (Fisher's exact test), Q value = 1.1e-06

Table S68.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 48 13 43
18Q LOSS MUTATED 7 32 9 34
18Q LOSS WILD-TYPE 37 16 4 9

Figure S68.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 8.88e-46 (Fisher's exact test), Q value = 6.4e-43

Table S69.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
18Q LOSS MUTATED 149 33 27 16
18Q LOSS WILD-TYPE 21 154 5 8

Figure S69.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.62e-15 (Fisher's exact test), Q value = 2.5e-12

Table S70.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
18Q LOSS MUTATED 88 28 22
18Q LOSS WILD-TYPE 17 58 41

Figure S70.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 7e-09

Table S71.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 58 39 20
18Q LOSS MUTATED 57 15 18 16
18Q LOSS WILD-TYPE 10 43 21 4

Figure S71.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-15 (Fisher's exact test), Q value = 1.2e-12

Table S72.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 18 102
18Q LOSS MUTATED 12 11 83
18Q LOSS WILD-TYPE 52 7 19

Figure S72.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 8.88e-08 (Fisher's exact test), Q value = 6.1e-05

Table S73.  Gene #73: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
20P LOSS MUTATED 27 2 0 4
20P LOSS WILD-TYPE 143 185 32 20

Figure S73.  Get High-res Image Gene #73: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.0018

Table S74.  Gene #74: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
21Q LOSS MUTATED 40 15 13 3
21Q LOSS WILD-TYPE 130 172 19 21

Figure S74.  Get High-res Image Gene #74: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 7.4e-09

Table S75.  Gene #75: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
22Q LOSS MUTATED 56 11 12 2
22Q LOSS WILD-TYPE 114 176 20 22

Figure S75.  Get High-res Image Gene #75: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 413

  • Number of significantly arm-level cnvs = 76

  • 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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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