Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1SB43R8
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/C1SB43R8
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 12 molecular subtypes across 413 patients, 91 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',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 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',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CNMF' and '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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 91 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 		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 Chi-square test
20q gain 0 (0%) 146 6.32e-12
(5.36e-09) 		4.18e-14
(3.57e-11) 		9.42e-47
(8.18e-44) 		3.13e-10
(2.62e-07) 		0.000362
(0.281) 		1.58e-06
(0.0013) 		2.61e-13
(2.21e-10) 		3.58e-11
(3.02e-08) 		0.103
(1.00) 		0.429
(1.00) 		1.31e-09
(1.1e-06) 		3.82e-17
(3.29e-14)
13q gain 0 (0%) 202 1.06e-05
(0.00852) 		1.66e-05
(0.0133) 		2.95e-33
(2.56e-30) 		0.000101
(0.0798) 		0.0188
(1.00) 		0.0051
(1.00) 		1.71e-06
(0.0014) 		7.16e-05
(0.0569) 		0.045
(1.00) 		0.466
(1.00) 		8.88e-06
(0.00717) 		1.3e-06
(0.00107)
14q loss 0 (0%) 319 3.18e-08
(2.65e-05) 		2.14e-06
(0.00175) 		1.58e-22
(1.36e-19) 		2.12e-06
(0.00174) 		0.00838
(1.00) 		0.0266
(1.00) 		1.5e-06
(0.00123) 		8.78e-05
(0.0694) 		0.532
(1.00) 		0.194
(1.00) 		8.42e-05
(0.0666) 		0.00011
(0.0868)
17p loss 0 (0%) 249 1.45e-05
(0.0117) 		8.74e-06
(0.00707) 		4.44e-23
(3.84e-20) 		1.35e-07
(0.000112) 		0.0615
(1.00) 		0.0393
(1.00) 		2.65e-06
(0.00217) 		8.2e-06
(0.00664) 		0.147
(1.00) 		0.0464
(1.00) 		5.42e-06
(0.0044) 		0.000154
(0.121)
18p loss 0 (0%) 204 6.64e-14
(5.65e-11) 		1.17e-09
(9.83e-07) 		2.44e-46
(2.12e-43) 		4.33e-14
(3.69e-11) 		0.00169
(1.00) 		0.000495
(0.383) 		6.98e-15
(5.98e-12) 		5.87e-09
(4.89e-06) 		0.251
(1.00) 		0.497
(1.00) 		1.32e-11
(1.11e-08) 		9.72e-11
(8.17e-08)
18q loss 0 (0%) 188 3.42e-13
(2.9e-10) 		8.79e-11
(7.4e-08) 		8.88e-46
(7.7e-43) 		4.45e-15
(3.81e-12) 		0.0162
(1.00) 		0.00138
(1.00) 		4.47e-14
(3.8e-11) 		1.36e-08
(1.13e-05) 		0.0612
(1.00) 		0.499
(1.00) 		4.5e-09
(3.76e-06) 		1.23e-09
(1.03e-06)
7p gain 0 (0%) 213 0.00304
(1.00) 		0.00223
(1.00) 		1.92e-15
(1.64e-12) 		0.000215
(0.168) 		0.374
(1.00) 		0.0397
(1.00) 		1.09e-07
(9.01e-05) 		2.85e-05
(0.0228) 		0.425
(1.00) 		0.958
(1.00) 		0.00348
(1.00) 		2.69e-06
(0.00219)
20p gain 0 (0%) 225 0.00113
(0.855) 		4.97e-07
(0.00041) 		4.29e-20
(3.7e-17) 		0.0123
(1.00) 		0.0344
(1.00) 		0.0371
(1.00) 		3.35e-05
(0.0267) 		0.000197
(0.154) 		0.174
(1.00) 		0.0758
(1.00) 		0.00164
(1.00) 		5.77e-07
(0.000476)
7q gain 0 (0%) 238 0.0145
(1.00) 		0.013
(1.00) 		7.05e-11
(5.93e-08) 		0.00532
(1.00) 		0.65
(1.00) 		0.072
(1.00) 		3.01e-06
(0.00245) 		0.000186
(0.146) 		0.474
(1.00) 		0.752
(1.00) 		0.0327
(1.00) 		9.25e-05
(0.073)
15q loss 0 (0%) 314 0.0108
(1.00) 		0.00275
(1.00) 		9.29e-22
(8.02e-19) 		0.00691
(1.00) 		0.0803
(1.00) 		0.393
(1.00) 		4.07e-05
(0.0325) 		7.35e-05
(0.0583) 		0.488
(1.00) 		0.0435
(1.00) 		0.0128
(1.00) 		0.0014
(1.00)
8p loss 0 (0%) 320 7.79e-05
(0.0618) 		0.00122
(0.922) 		7.76e-17
(6.67e-14) 		0.000519
(0.401) 		0.282
(1.00) 		0.0412
(1.00) 		0.141
(1.00) 		0.0665
(1.00) 		0.2
(1.00) 		0.356
(1.00) 		0.000365
(0.283) 		0.0167
(1.00)
11q loss 0 (0%) 386 0.288
(1.00) 		0.0386
(1.00) 		7.92e-06
(0.00642) 		9.3e-06
(0.00749) 		0.384
(1.00) 		0.6
(1.00) 		0.207
(1.00) 		0.129
(1.00) 		0.358
(1.00) 		0.202
(1.00) 		0.021
(1.00) 		0.0516
(1.00)
22q loss 0 (0%) 332 0.00032
(0.25) 		0.000581
(0.447) 		1.06e-11
(8.97e-09) 		0.0939
(1.00) 		0.341
(1.00) 		0.138
(1.00) 		0.00972
(1.00) 		0.0011
(0.837) 		0.624
(1.00) 		0.123
(1.00) 		0.00323
(1.00) 		0.0541
(1.00)
2q gain 0 (0%) 374 0.0737
(1.00) 		0.051
(1.00) 		0.000173
(0.135) 		0.00292
(1.00) 		0.0311
(1.00) 		0.393
(1.00) 		0.00109
(0.83) 		0.0384
(1.00) 		0.529
(1.00) 		0.405
(1.00) 		0.144
(1.00) 		0.0198
(1.00)
8p gain 0 (0%) 333 0.738
(1.00) 		0.423
(1.00) 		9.22e-06
(0.00744) 		0.0385
(1.00) 		0.117
(1.00) 		0.383
(1.00) 		0.175
(1.00) 		0.0327
(1.00) 		0.615
(1.00) 		0.571
(1.00) 		0.217
(1.00) 		0.572
(1.00)
8q gain 0 (0%) 251 0.73
(1.00) 		0.432
(1.00) 		9.39e-12
(7.95e-09) 		0.000577
(0.445) 		0.751
(1.00) 		0.021
(1.00) 		0.0072
(1.00) 		0.127
(1.00) 		0.0986
(1.00) 		0.154
(1.00) 		0.101
(1.00) 		0.33
(1.00)
11p gain 0 (0%) 395 0.138
(1.00) 		0.00139
(1.00) 		0.000314
(0.245) 		0.00116
(0.879) 		0.575
(1.00) 		0.804
(1.00) 		0.871
(1.00) 		0.889
(1.00) 		0.634
(1.00) 		0.882
(1.00) 		0.322
(1.00) 		0.417
(1.00)
11q gain 0 (0%) 391 0.0214
(1.00) 		0.00277
(1.00) 		3.72e-06
(0.00303) 		0.0018
(1.00) 		0.265
(1.00) 		0.808
(1.00) 		0.151
(1.00) 		0.22
(1.00) 		0.386
(1.00) 		0.693
(1.00) 		0.0353
(1.00) 		0.168
(1.00)
16p gain 0 (0%) 346 0.00749
(1.00) 		0.000804
(0.616) 		1.08e-14
(9.26e-12) 		0.15
(1.00) 		0.64
(1.00) 		0.0329
(1.00) 		0.051
(1.00) 		0.18
(1.00) 		0.126
(1.00) 		0.0474
(1.00) 		0.252
(1.00) 		0.0124
(1.00)
16q gain 0 (0%) 347 0.00602
(1.00) 		0.00116
(0.879) 		1.44e-16
(1.24e-13) 		0.169
(1.00) 		0.65
(1.00) 		0.0199
(1.00) 		0.051
(1.00) 		0.18
(1.00) 		0.314
(1.00) 		0.232
(1.00) 		0.056
(1.00) 		0.00292
(1.00)
17q gain 0 (0%) 365 0.0531
(1.00) 		0.0544
(1.00) 		0.000913
(0.698) 		0.00472
(1.00) 		0.866
(1.00) 		0.197
(1.00) 		1.16e-05
(0.00933) 		0.015
(1.00) 		0.0581
(1.00) 		0.753
(1.00) 		0.187
(1.00) 		0.00341
(1.00)
1p loss 0 (0%) 362 0.00283
(1.00) 		0.000972
(0.741) 		7.09e-08
(5.88e-05) 		0.00287
(1.00) 		0.576
(1.00) 		0.698
(1.00) 		0.0984
(1.00) 		0.286
(1.00) 		0.18
(1.00) 		0.274
(1.00) 		0.797
(1.00) 		0.021
(1.00)
4p loss 0 (0%) 329 0.00271
(1.00) 		0.0199
(1.00) 		1.05e-11
(8.9e-09) 		0.00392
(1.00) 		0.241
(1.00) 		0.708
(1.00) 		0.000754
(0.579) 		0.000599
(0.461) 		0.083
(1.00) 		0.29
(1.00) 		0.0683
(1.00) 		0.0134
(1.00)
4q loss 0 (0%) 345 0.00361
(1.00) 		0.0107
(1.00) 		2.26e-10
(1.89e-07) 		0.00224
(1.00) 		0.175
(1.00) 		0.427
(1.00) 		0.00348
(1.00) 		0.0158
(1.00) 		0.00266
(1.00) 		0.0359
(1.00) 		0.127
(1.00) 		0.00627
(1.00)
5q loss 0 (0%) 375 0.0922
(1.00) 		0.0192
(1.00) 		1.11e-05
(0.00896) 		0.369
(1.00) 		0.191
(1.00) 		0.234
(1.00) 		0.00763
(1.00) 		0.105
(1.00) 		0.551
(1.00) 		0.48
(1.00) 		0.517
(1.00) 		0.101
(1.00)
9p loss 0 (0%) 386 0.81
(1.00) 		0.123
(1.00) 		4.4e-05
(0.035) 		0.0892
(1.00) 		0.133
(1.00) 		0.33
(1.00) 		0.0424
(1.00) 		0.105
(1.00) 		0.53
(1.00) 		0.744
(1.00) 		0.187
(1.00) 		0.0348
(1.00)
9q loss 0 (0%) 387 0.308
(1.00) 		0.139
(1.00) 		2.55e-06
(0.00209) 		0.00101
(0.767) 		0.133
(1.00) 		0.33
(1.00) 		0.000898
(0.687) 		0.036
(1.00) 		0.114
(1.00) 		0.675
(1.00) 		0.0261
(1.00) 		0.00474
(1.00)
11p loss 0 (0%) 391 0.445
(1.00) 		0.068
(1.00) 		8.34e-05
(0.066) 		0.000405
(0.314) 		0.439
(1.00) 		0.248
(1.00) 		0.0489
(1.00) 		0.0184
(1.00) 		0.0401
(1.00) 		0.162
(1.00) 		0.0484
(1.00) 		0.0466
(1.00)
12p loss 0 (0%) 392 0.0792
(1.00) 		0.123
(1.00) 		7.1e-05
(0.0565) 		0.222
(1.00) 		0.463
(1.00) 		0.922
(1.00) 		0.0802
(1.00) 		0.0817
(1.00) 		0.72
(1.00) 		0.208
(1.00) 		0.0689
(1.00) 		0.254
(1.00)
12q loss 0 (0%) 393 0.208
(1.00) 		0.139
(1.00) 		0.000101
(0.0798) 		0.152
(1.00) 		0.805
(1.00) 		0.88
(1.00) 		0.0161
(1.00) 		0.04
(1.00) 		0.411
(1.00) 		0.362
(1.00) 		0.0689
(1.00) 		0.254
(1.00)
20p loss 0 (0%) 380 0.0091
(1.00) 		0.00948
(1.00) 		8.88e-08
(7.36e-05) 		0.0671
(1.00) 		0.614
(1.00) 		0.472
(1.00) 		0.353
(1.00) 		0.308
(1.00) 		0.906
(1.00) 		0.53
(1.00) 		0.252
(1.00) 		0.422
(1.00)
21q loss 0 (0%) 342 0.0141
(1.00) 		0.00227
(1.00) 		2.6e-06
(0.00212) 		0.358
(1.00) 		0.524
(1.00) 		0.572
(1.00) 		0.122
(1.00) 		0.342
(1.00) 		0.0731
(1.00) 		0.608
(1.00) 		0.458
(1.00) 		0.3
(1.00)
1p gain 0 (0%) 402 0.576
(1.00) 		0.837
(1.00) 		0.275
(1.00) 		0.384
(1.00) 		0.425
(1.00) 		0.683
(1.00) 		0.46
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.0847
(1.00)
1q gain 0 (0%) 366 0.0405
(1.00) 		0.536
(1.00) 		0.0788
(1.00) 		0.347
(1.00) 		0.38
(1.00) 		0.0481
(1.00) 		0.12
(1.00) 		0.299
(1.00) 		0.437
(1.00) 		0.837
(1.00) 		0.52
(1.00) 		0.473
(1.00)
2p gain 0 (0%) 373 0.124
(1.00) 		0.0746
(1.00) 		0.00409
(1.00) 		0.0278
(1.00) 		0.0492
(1.00) 		0.393
(1.00) 		0.000386
(0.299) 		0.0199
(1.00) 		0.508
(1.00) 		0.355
(1.00) 		0.236
(1.00) 		0.0137
(1.00)
3p gain 0 (0%) 393 0.298
(1.00) 		0.43
(1.00) 		0.071
(1.00) 		0.387
(1.00) 		0.623
(1.00) 		0.721
(1.00) 		0.974
(1.00) 		0.676
(1.00) 		0.626
(1.00) 		0.184
(1.00) 		0.87
(1.00) 		0.0877
(1.00)
3q gain 0 (0%) 383 0.375
(1.00) 		0.164
(1.00) 		0.000969
(0.739) 		0.211
(1.00) 		0.833
(1.00) 		0.752
(1.00) 		0.415
(1.00) 		0.635
(1.00) 		0.357
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.15
(1.00)
4p gain 0 (0%) 410 0.746
(1.00) 		0.48
(1.00) 		0.248
(1.00) 		0.0788
(1.00) 		0.208
(1.00) 		0.0334
(1.00) 		0.513
(1.00) 		0.231
(1.00)
4q gain 0 (0%) 408 0.842
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.493
(1.00) 		0.579
(1.00) 		0.335
(1.00)
5p gain 0 (0%) 374 0.174
(1.00) 		0.0554
(1.00) 		0.00223
(1.00) 		0.0493
(1.00) 		0.631
(1.00) 		0.881
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.53
(1.00) 		0.41
(1.00) 		0.978
(1.00)
5q gain 0 (0%) 392 0.545
(1.00) 		0.631
(1.00) 		0.0391
(1.00) 		0.188
(1.00) 		0.429
(1.00) 		0.293
(1.00) 		0.749
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.948
(1.00) 		0.261
(1.00) 		0.689
(1.00)
6p gain 0 (0%) 363 0.589
(1.00) 		0.0136
(1.00) 		0.0267
(1.00) 		0.675
(1.00) 		0.711
(1.00) 		0.443
(1.00) 		0.0367
(1.00) 		0.268
(1.00) 		0.513
(1.00) 		0.246
(1.00) 		0.758
(1.00) 		0.399
(1.00)
6q gain 0 (0%) 368 0.348
(1.00) 		0.0274
(1.00) 		0.0317
(1.00) 		0.312
(1.00) 		0.554
(1.00) 		0.433
(1.00) 		0.156
(1.00) 		0.621
(1.00) 		0.441
(1.00) 		0.309
(1.00) 		0.152
(1.00) 		0.737
(1.00)
9p gain 0 (0%) 367 0.00645
(1.00) 		0.192
(1.00) 		0.28
(1.00) 		0.391
(1.00) 		0.0664
(1.00) 		0.179
(1.00) 		0.879
(1.00) 		0.76
(1.00) 		0.767
(1.00) 		0.763
(1.00) 		1
(1.00) 		0.728
(1.00)
9q gain 0 (0%) 374 0.011
(1.00) 		0.073
(1.00) 		0.0641
(1.00) 		0.0953
(1.00) 		0.0174
(1.00) 		0.034
(1.00) 		0.362
(1.00) 		0.659
(1.00) 		0.0589
(1.00) 		0.635
(1.00) 		0.518
(1.00) 		0.289
(1.00)
10p gain 0 (0%) 395 0.691
(1.00) 		0.52
(1.00) 		0.104
(1.00) 		0.0429
(1.00) 		0.428
(1.00) 		0.917
(1.00) 		0.904
(1.00) 		0.466
(1.00) 		0.761
(1.00) 		0.941
(1.00) 		0.0496
(1.00) 		0.493
(1.00)
10q gain 0 (0%) 406 0.114
(1.00) 		0.0308
(1.00) 		0.837
(1.00) 		0.861
(1.00) 		0.933
(1.00) 		0.219
(1.00) 		0.202
(1.00) 		0.151
(1.00) 		0.876
(1.00) 		0.871
(1.00)
12p gain 0 (0%) 347 0.267
(1.00) 		0.382
(1.00) 		0.00442
(1.00) 		0.00967
(1.00) 		0.888
(1.00) 		0.813
(1.00) 		0.361
(1.00) 		0.682
(1.00) 		0.069
(1.00) 		0.21
(1.00) 		0.0216
(1.00) 		0.151
(1.00)
12q gain 0 (0%) 353 0.341
(1.00) 		0.542
(1.00) 		0.00181
(1.00) 		0.00165
(1.00) 		0.791
(1.00) 		0.669
(1.00) 		0.27
(1.00) 		0.691
(1.00) 		0.0121
(1.00) 		0.268
(1.00) 		0.0394
(1.00) 		0.242
(1.00)
14q gain 0 (0%) 398 0.482
(1.00) 		0.443
(1.00) 		0.0566
(1.00) 		0.198
(1.00) 		0.221
(1.00) 		0.309
(1.00) 		0.145
(1.00) 		0.127
(1.00) 		1
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.527
(1.00)
15q gain 0 (0%) 408 0.0732
(1.00) 		0.685
(1.00) 		0.07
(1.00) 		0.0333
(1.00) 		0.783
(1.00) 		0.481
(1.00) 		0.473
(1.00) 		0.427
(1.00) 		0.685
(1.00) 		0.779
(1.00)
17p gain 0 (0%) 404 0.618
(1.00) 		0.891
(1.00) 		0.454
(1.00) 		0.23
(1.00) 		0.0316
(1.00) 		0.225
(1.00) 		0.737
(1.00) 		0.891
(1.00) 		0.876
(1.00) 		0.333
(1.00)
18p gain 0 (0%) 398 0.144
(1.00) 		0.635
(1.00) 		0.00548
(1.00) 		0.0118
(1.00) 		0.75
(1.00) 		0.968
(1.00) 		0.171
(1.00) 		0.0581
(1.00) 		0.144
(1.00) 		0.388
(1.00) 		0.468
(1.00) 		0.312
(1.00)
18q gain 0 (0%) 404 0.0232
(1.00) 		0.0238
(1.00) 		0.52
(1.00) 		0.158
(1.00) 		0.142
(1.00) 		0.267
(1.00) 		0.274
(1.00) 		0.327
(1.00) 		0.452
(1.00) 		0.0725
(1.00)
19p gain 0 (0%) 379 0.0563
(1.00) 		0.208
(1.00) 		0.00554
(1.00) 		0.0422
(1.00) 		0.294
(1.00) 		0.0782
(1.00) 		0.321
(1.00) 		0.481
(1.00) 		0.588
(1.00) 		0.573
(1.00) 		0.0805
(1.00) 		0.0926
(1.00)
19q gain 0 (0%) 372 0.0476
(1.00) 		0.0537
(1.00) 		0.437
(1.00) 		0.051
(1.00) 		0.124
(1.00) 		0.0183
(1.00) 		0.145
(1.00) 		0.297
(1.00) 		0.924
(1.00) 		0.942
(1.00) 		0.744
(1.00) 		0.147
(1.00)
21q gain 0 (0%) 402 0.17
(1.00) 		0.195
(1.00) 		0.0858
(1.00) 		0.334
(1.00) 		0.358
(1.00) 		0.275
(1.00) 		0.282
(1.00) 		0.73
(1.00) 		0.704
(1.00) 		0.684
(1.00) 		0.398
(1.00) 		0.436
(1.00)
Xq gain 0 (0%) 401 0.0659
(1.00) 		0.777
(1.00) 		0.0331
(1.00) 		0.568
(1.00) 		0.171
(1.00) 		0.344
(1.00) 		0.446
(1.00) 		0.765
(1.00) 		0.352
(1.00) 		0.41
(1.00) 		0.227
(1.00) 		0.618
(1.00)
1q loss 0 (0%) 395 0.356
(1.00) 		0.135
(1.00) 		0.0103
(1.00) 		0.294
(1.00) 		0.66
(1.00) 		0.791
(1.00) 		0.151
(1.00) 		0.196
(1.00) 		0.941
(1.00) 		0.44
(1.00) 		0.227
(1.00) 		0.373
(1.00)
2p loss 0 (0%) 409 0.559
(1.00) 		0.111
(1.00) 		0.433
(1.00) 		0.662
(1.00) 		0.132
(1.00)
2q loss 0 (0%) 407 1
(1.00) 		0.156
(1.00) 		0.601
(1.00) 		0.298
(1.00) 		0.245
(1.00) 		0.175
(1.00) 		0.0588
(1.00)
3p loss 0 (0%) 386 0.413
(1.00) 		0.187
(1.00) 		0.00251
(1.00) 		0.284
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.458
(1.00) 		0.556
(1.00) 		0.212
(1.00) 		0.143
(1.00) 		0.37
(1.00) 		0.0399
(1.00)
3q loss 0 (0%) 401 0.745
(1.00) 		0.631
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.0158
(1.00) 		0.261
(1.00) 		0.267
(1.00) 		0.683
(1.00) 		0.423
(1.00) 		0.822
(1.00) 		1
(1.00) 		0.957
(1.00)
5p loss 0 (0%) 388 0.81
(1.00) 		0.189
(1.00) 		0.00176
(1.00) 		0.126
(1.00) 		0.478
(1.00) 		0.704
(1.00) 		0.126
(1.00) 		0.416
(1.00) 		0.841
(1.00) 		0.907
(1.00) 		0.297
(1.00) 		0.0881
(1.00)
6p loss 0 (0%) 401 0.456
(1.00) 		0.247
(1.00) 		0.00285
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.942
(1.00) 		0.666
(1.00) 		0.45
(1.00) 		0.642
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.779
(1.00)
6q loss 0 (0%) 392 0.915
(1.00) 		0.789
(1.00) 		0.0743
(1.00) 		0.697
(1.00) 		0.332
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.864
(1.00) 		1
(1.00) 		1
(1.00) 		0.914
(1.00)
8q loss 0 (0%) 405 0.339
(1.00) 		0.777
(1.00) 		0.00966
(1.00) 		0.854
(1.00) 		0.141
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.833
(1.00)
10p loss 0 (0%) 391 0.7
(1.00) 		0.673
(1.00) 		0.000828
(0.634) 		0.471
(1.00) 		0.201
(1.00) 		0.962
(1.00) 		0.518
(1.00) 		0.352
(1.00) 		0.24
(1.00) 		0.681
(1.00) 		1
(1.00) 		0.583
(1.00)
10q loss 0 (0%) 389 0.597
(1.00) 		0.711
(1.00) 		0.000526
(0.406) 		0.152
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.295
(1.00) 		0.04
(1.00) 		0.697
(1.00) 		0.393
(1.00) 		0.37
(1.00) 		0.243
(1.00)
13q loss 0 (0%) 407 0.0209
(1.00) 		0.293
(1.00) 		0.0238
(1.00) 		0.0931
(1.00) 		0.425
(1.00) 		0.464
(1.00) 		0.869
(1.00) 		0.723
(1.00) 		0.107
(1.00) 		0.0778
(1.00)
16p loss 0 (0%) 404 0.274
(1.00) 		0.554
(1.00) 		0.305
(1.00) 		0.0311
(1.00) 		0.61
(1.00) 		0.904
(1.00) 		1
(1.00) 		1
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.575
(1.00)
16q loss 0 (0%) 406 0.519
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.199
(1.00) 		0.493
(1.00) 		0.175
(1.00) 		0.17
(1.00)
17q loss 0 (0%) 381 0.0918
(1.00) 		0.227
(1.00) 		0.00216
(1.00) 		0.302
(1.00) 		0.412
(1.00) 		0.16
(1.00) 		0.0813
(1.00) 		0.109
(1.00) 		0.322
(1.00) 		0.291
(1.00) 		0.451
(1.00) 		0.237
(1.00)
19p loss 0 (0%) 399 1
(1.00) 		0.32
(1.00) 		0.00275
(1.00) 		0.13
(1.00) 		0.783
(1.00) 		0.361
(1.00) 		0.00708
(1.00) 		0.0789
(1.00) 		0.693
(1.00) 		0.0876
(1.00) 		0.629
(1.00) 		0.107
(1.00)
19q loss 0 (0%) 400 0.924
(1.00) 		0.381
(1.00) 		0.0115
(1.00) 		0.13
(1.00) 		0.906
(1.00) 		0.363
(1.00) 		0.00708
(1.00) 		0.0789
(1.00) 		0.57
(1.00) 		0.0611
(1.00) 		0.629
(1.00) 		0.107
(1.00)
Xq loss 0 (0%) 408 0.842
(1.00) 		1
(1.00) 		0.152
(1.00) 		0.821
(1.00) 		0.851
(1.00) 		0.14
(1.00) 		0.644
(1.00) 		0.26
(1.00)
'2q gain' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.14

Table S1.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S1.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.92e-15 (Fisher's exact test), Q value = 1.6e-12

Table S2.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.17

Table S3.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
7P GAIN CNV 71 38 23
7P GAIN WILD-TYPE 36 45 41

Figure S3.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.09e-07 (Fisher's exact test), Q value = 9e-05

Table S4.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
7P GAIN CNV 19 43 20 11
7P GAIN WILD-TYPE 12 16 27 43

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.85e-05 (Fisher's exact test), Q value = 0.023

Table S5.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
7P GAIN CNV 13 43 37
7P GAIN WILD-TYPE 36 19 43

Figure S5.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.69e-06 (Chi-square test), Q value = 0.0022

Table S6.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
7P GAIN CNV 10 28 13 29 29
7P GAIN WILD-TYPE 12 21 49 17 13

Figure S6.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 7.05e-11 (Fisher's exact test), Q value = 5.9e-08

Table S7.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S7.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.0025

Table S8.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
7Q GAIN CNV 16 39 18 10
7Q GAIN WILD-TYPE 15 20 29 44

Figure S8.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000186 (Fisher's exact test), Q value = 0.15

Table S9.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
7Q GAIN CNV 12 39 32
7Q GAIN WILD-TYPE 37 23 48

Figure S9.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.25e-05 (Chi-square test), Q value = 0.073

Table S10.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
7Q GAIN CNV 10 26 11 27 21
7Q GAIN WILD-TYPE 12 23 51 19 21

Figure S10.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0074

Table S11.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S11.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 9.39e-12 (Fisher's exact test), Q value = 8e-09

Table S12.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S12.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.25

Table S13.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S13.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.003

Table S14.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S14.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0085

Table S15.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
13Q GAIN CNV 10 45 9 13
13Q GAIN WILD-TYPE 25 16 20 8

Figure S15.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.013

Table S16.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
13Q GAIN CNV 35 10 32
13Q GAIN WILD-TYPE 21 33 15

Figure S16.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 2.95e-33 (Fisher's exact test), Q value = 2.6e-30

Table S17.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S17.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.08

Table S18.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
13Q GAIN CNV 72 33 26
13Q GAIN WILD-TYPE 35 50 38

Figure S18.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0014

Table S19.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
13Q GAIN CNV 19 40 20 11
13Q GAIN WILD-TYPE 12 19 27 43

Figure S19.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-05 (Fisher's exact test), Q value = 0.057

Table S20.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
13Q GAIN CNV 11 39 40
13Q GAIN WILD-TYPE 38 23 40

Figure S20.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.88e-06 (Fisher's exact test), Q value = 0.0072

Table S21.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 79 65
13Q GAIN CNV 25 56 34
13Q GAIN WILD-TYPE 52 23 31

Figure S21.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.3e-06 (Chi-square test), Q value = 0.0011

Table S22.  Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
13Q GAIN CNV 11 32 14 28 30
13Q GAIN WILD-TYPE 11 17 48 18 12

Figure S22.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1.08e-14 (Fisher's exact test), Q value = 9.3e-12

Table S23.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S23.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1.44e-16 (Fisher's exact test), Q value = 1.2e-13

Table S24.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S24.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0093

Table S25.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
17Q GAIN CNV 4 16 0 2
17Q GAIN WILD-TYPE 27 43 47 52

Figure S25.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00041

Table S26.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20P GAIN CNV 36 7 30
20P GAIN WILD-TYPE 20 36 17

Figure S26.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 4.29e-20 (Fisher's exact test), Q value = 3.7e-17

Table S27.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S27.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.35e-05 (Fisher's exact test), Q value = 0.027

Table S28.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
20P GAIN CNV 15 31 20 7
20P GAIN WILD-TYPE 16 28 27 47

Figure S28.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.15

Table S29.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
20P GAIN CNV 7 29 37
20P GAIN WILD-TYPE 42 33 43

Figure S29.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.77e-07 (Chi-square test), Q value = 0.00048

Table S30.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
20P GAIN CNV 9 28 7 26 22
20P GAIN WILD-TYPE 13 21 55 20 20

Figure S30.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 6.32e-12 (Fisher's exact test), Q value = 5.4e-09

Table S31.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
20Q GAIN CNV 10 57 14 18
20Q GAIN WILD-TYPE 25 4 15 3

Figure S31.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.18e-14 (Fisher's exact test), Q value = 3.6e-11

Table S32.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20Q GAIN CNV 48 9 42
20Q GAIN WILD-TYPE 8 34 5

Figure S32.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 9.42e-47 (Fisher's exact test), Q value = 8.2e-44

Table S33.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S33.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 3.13e-10 (Fisher's exact test), Q value = 2.6e-07

Table S34.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
20Q GAIN CNV 91 35 33
20Q GAIN WILD-TYPE 16 48 31

Figure S34.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0013

Table S35.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
20Q GAIN CNV 11 21 50 123
20Q GAIN WILD-TYPE 15 35 13 57

Figure S35.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2.61e-13 (Fisher's exact test), Q value = 2.2e-10

Table S36.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
20Q GAIN CNV 19 53 30 11
20Q GAIN WILD-TYPE 12 6 17 43

Figure S36.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.58e-11 (Fisher's exact test), Q value = 3e-08

Table S37.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
20Q GAIN CNV 9 49 55
20Q GAIN WILD-TYPE 40 13 25

Figure S37.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.31e-09 (Fisher's exact test), Q value = 1.1e-06

Table S38.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 79 65
20Q GAIN CNV 27 66 44
20Q GAIN WILD-TYPE 50 13 21

Figure S38.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.82e-17 (Chi-square test), Q value = 3.3e-14

Table S39.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
20Q GAIN CNV 19 40 9 37 32
20Q GAIN WILD-TYPE 3 9 53 9 10

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 7.09e-08 (Fisher's exact test), Q value = 5.9e-05

Table S40.  Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S40.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.05e-11 (Fisher's exact test), Q value = 8.9e-09

Table S41.  Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S41.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.26e-10 (Fisher's exact test), Q value = 1.9e-07

Table S42.  Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S42.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.009

Table S43.  Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S43.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNA_CNMF'

P value = 7.79e-05 (Fisher's exact test), Q value = 0.062

Table S44.  Gene #52: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
8P LOSS CNV 2 25 3 8
8P LOSS WILD-TYPE 33 36 26 13

Figure S44.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 7.76e-17 (Fisher's exact test), Q value = 6.7e-14

Table S45.  Gene #52: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S45.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.035

Table S46.  Gene #54: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S46.  Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 2.55e-06 (Fisher's exact test), Q value = 0.0021

Table S47.  Gene #55: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S47.  Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.066

Table S48.  Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S48.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 7.92e-06 (Fisher's exact test), Q value = 0.0064

Table S49.  Gene #59: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S49.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 9.3e-06 (Fisher's exact test), Q value = 0.0075

Table S50.  Gene #59: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
11Q LOSS CNV 14 0 0
11Q LOSS WILD-TYPE 93 83 64

Figure S50.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.057

Table S51.  Gene #60: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S51.  Get High-res Image Gene #60: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.08

Table S52.  Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S52.  Get High-res Image Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 3.18e-08 (Fisher's exact test), Q value = 2.6e-05

Table S53.  Gene #63: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
14Q LOSS CNV 2 31 1 8
14Q LOSS WILD-TYPE 33 30 28 13

Figure S53.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0018

Table S54.  Gene #63: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
14Q LOSS CNV 21 1 20
14Q LOSS WILD-TYPE 35 42 27

Figure S54.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.58e-22 (Fisher's exact test), Q value = 1.4e-19

Table S55.  Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S55.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0017

Table S56.  Gene #63: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
14Q LOSS CNV 36 6 6
14Q LOSS WILD-TYPE 71 77 58

Figure S56.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.0012

Table S57.  Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
14Q LOSS CNV 8 23 6 1
14Q LOSS WILD-TYPE 23 36 41 53

Figure S57.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.78e-05 (Fisher's exact test), Q value = 0.069

Table S58.  Gene #63: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
14Q LOSS CNV 1 20 17
14Q LOSS WILD-TYPE 48 42 63

Figure S58.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.42e-05 (Fisher's exact test), Q value = 0.067

Table S59.  Gene #63: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 79 65
14Q LOSS CNV 6 27 9
14Q LOSS WILD-TYPE 71 52 56

Figure S59.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Chi-square test), Q value = 0.087

Table S60.  Gene #63: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
14Q LOSS CNV 8 11 0 14 9
14Q LOSS WILD-TYPE 14 38 62 32 33

Figure S60.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 9.29e-22 (Fisher's exact test), Q value = 8e-19

Table S61.  Gene #64: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S61.  Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 4.07e-05 (Fisher's exact test), Q value = 0.032

Table S62.  Gene #64: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
15Q LOSS CNV 8 20 10 1
15Q LOSS WILD-TYPE 23 39 37 53

Figure S62.  Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.35e-05 (Fisher's exact test), Q value = 0.058

Table S63.  Gene #64: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
15Q LOSS CNV 1 20 18
15Q LOSS WILD-TYPE 48 42 62

Figure S63.  Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.012

Table S64.  Gene #67: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
17P LOSS CNV 7 38 6 12
17P LOSS WILD-TYPE 28 23 23 9

Figure S64.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.74e-06 (Fisher's exact test), Q value = 0.0071

Table S65.  Gene #67: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
17P LOSS CNV 29 6 28
17P LOSS WILD-TYPE 27 37 19

Figure S65.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 4.44e-23 (Fisher's exact test), Q value = 3.8e-20

Table S66.  Gene #67: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S66.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.35e-07 (Fisher's exact test), Q value = 0.00011

Table S67.  Gene #67: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
17P LOSS CNV 62 17 18
17P LOSS WILD-TYPE 45 66 46

Figure S67.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 2.65e-06 (Fisher's exact test), Q value = 0.0022

Table S68.  Gene #67: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
17P LOSS CNV 14 36 14 8
17P LOSS WILD-TYPE 17 23 33 46

Figure S68.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.2e-06 (Fisher's exact test), Q value = 0.0066

Table S69.  Gene #67: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
17P LOSS CNV 7 36 29
17P LOSS WILD-TYPE 42 26 51

Figure S69.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.42e-06 (Fisher's exact test), Q value = 0.0044

Table S70.  Gene #67: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 79 65
17P LOSS CNV 15 45 22
17P LOSS WILD-TYPE 62 34 43

Figure S70.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000154 (Chi-square test), Q value = 0.12

Table S71.  Gene #67: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
17P LOSS CNV 12 21 8 22 19
17P LOSS WILD-TYPE 10 28 54 24 23

Figure S71.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 6.64e-14 (Fisher's exact test), Q value = 5.7e-11

Table S72.  Gene #69: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18P LOSS CNV 5 51 6 15
18P LOSS WILD-TYPE 30 10 23 6

Figure S72.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.17e-09 (Fisher's exact test), Q value = 9.8e-07

Table S73.  Gene #69: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18P LOSS CNV 35 6 36
18P LOSS WILD-TYPE 21 37 11

Figure S73.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 2.44e-46 (Fisher's exact test), Q value = 2.1e-43

Table S74.  Gene #69: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S74.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 4.33e-14 (Fisher's exact test), Q value = 3.7e-11

Table S75.  Gene #69: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
18P LOSS CNV 83 21 22
18P LOSS WILD-TYPE 24 62 42

Figure S75.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 6.98e-15 (Fisher's exact test), Q value = 6e-12

Table S76.  Gene #69: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
18P LOSS CNV 14 49 21 5
18P LOSS WILD-TYPE 17 10 26 49

Figure S76.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.87e-09 (Fisher's exact test), Q value = 4.9e-06

Table S77.  Gene #69: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
18P LOSS CNV 6 42 41
18P LOSS WILD-TYPE 43 20 39

Figure S77.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.32e-11 (Fisher's exact test), Q value = 1.1e-08

Table S78.  Gene #69: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 79 65
18P LOSS CNV 16 60 30
18P LOSS WILD-TYPE 61 19 35

Figure S78.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.72e-11 (Chi-square test), Q value = 8.2e-08

Table S79.  Gene #69: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
18P LOSS CNV 19 29 7 28 23
18P LOSS WILD-TYPE 3 20 55 18 19

Figure S79.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 3.42e-13 (Fisher's exact test), Q value = 2.9e-10

Table S80.  Gene #70: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18Q LOSS CNV 6 52 7 15
18Q LOSS WILD-TYPE 29 9 22 6

Figure S80.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.79e-11 (Fisher's exact test), Q value = 7.4e-08

Table S81.  Gene #70: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18Q LOSS CNV 36 6 38
18Q LOSS WILD-TYPE 20 37 9

Figure S81.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 8.88e-46 (Fisher's exact test), Q value = 7.7e-43

Table S82.  Gene #70: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S82.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 4.45e-15 (Fisher's exact test), Q value = 3.8e-12

Table S83.  Gene #70: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 83 64
18Q LOSS CNV 89 26 23
18Q LOSS WILD-TYPE 18 57 41

Figure S83.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 4.47e-14 (Fisher's exact test), Q value = 3.8e-11

Table S84.  Gene #70: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
18Q LOSS CNV 18 51 21 8
18Q LOSS WILD-TYPE 13 8 26 46

Figure S84.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-08 (Fisher's exact test), Q value = 1.1e-05

Table S85.  Gene #70: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
18Q LOSS CNV 9 46 43
18Q LOSS WILD-TYPE 40 16 37

Figure S85.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-09 (Fisher's exact test), Q value = 3.8e-06

Table S86.  Gene #70: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 79 65
18Q LOSS CNV 22 61 33
18Q LOSS WILD-TYPE 55 18 32

Figure S86.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.23e-09 (Chi-square test), Q value = 1e-06

Table S87.  Gene #70: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 49 62 46 42
18Q LOSS CNV 17 31 10 32 26
18Q LOSS WILD-TYPE 5 18 52 14 16

Figure S87.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 8.88e-08 (Fisher's exact test), Q value = 7.4e-05

Table S88.  Gene #73: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S88.  Get High-res Image Gene #73: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.0021

Table S89.  Gene #74: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S89.  Get High-res Image Gene #74: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.25

Table S90.  Gene #75: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
22Q LOSS CNV 2 24 3 6
22Q LOSS WILD-TYPE 33 37 26 15

Figure S90.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 9e-09

Table S91.  Gene #75: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S91.  Get High-res Image Gene #75: '22q loss' versus Molecular Subtype #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 = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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