Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C19885D3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19885D3
Overview
Introduction

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

Summary

Testing the association between copy number variation 79 arm-level events and 12 molecular subtypes across 427 patients, 142 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

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

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 11q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

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

  • 16p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 19p 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_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 11p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

  • 12q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 142 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 302 (71%) 125 3.64e-10
(3.25e-07) 		4.41e-11
(3.96e-08) 		2.29e-36
(2.13e-33) 		2.06e-12
(1.86e-09) 		9.42e-05
(0.0764) 		0.000189
(0.151) 		2.35e-23
(2.17e-20) 		1.64e-18
(1.51e-15) 		0.898
(1.00) 		8.23e-05
(0.0671) 		1.11e-12
(1e-09) 		0.262
(1.00)
14q loss 128 (30%) 299 7.33e-07
(0.000634) 		1.65e-06
(0.00142) 		1.93e-28
(1.79e-25) 		7.33e-07
(0.000634) 		0.0018
(1.00) 		0.0452
(1.00) 		1.77e-11
(1.6e-08) 		3.82e-10
(3.41e-07) 		0.253
(1.00) 		7e-05
(0.0574) 		2.24e-05
(0.0188) 		0.0847
(1.00)
17p loss 222 (52%) 205 2.1e-07
(0.000183) 		1.07e-06
(0.000922) 		4.86e-29
(4.51e-26) 		1.28e-09
(1.14e-06) 		0.0197
(1.00) 		0.000923
(0.701) 		2.79e-12
(2.52e-09) 		4.56e-13
(4.13e-10) 		0.791
(1.00) 		0.1
(1.00) 		9.39e-10
(8.34e-07) 		0.117
(1.00)
18p loss 237 (56%) 190 1.46e-12
(1.32e-09) 		7.63e-10
(6.78e-07) 		1.05e-44
(9.76e-42) 		8.23e-18
(7.53e-15) 		0.000751
(0.574) 		0.000607
(0.469) 		4.68e-24
(4.33e-21) 		6.15e-18
(5.64e-15) 		1
(1.00) 		0.00645
(1.00) 		7.56e-15
(6.88e-12) 		0.0094
(1.00)
18q loss 252 (59%) 175 6.4e-12
(5.77e-09) 		9.6e-10
(8.52e-07) 		1.12e-42
(1.04e-39) 		2.95e-15
(2.69e-12) 		0.00418
(1.00) 		0.000814
(0.621) 		1.23e-25
(1.14e-22) 		7.59e-18
(6.95e-15) 		0.701
(1.00) 		0.0101
(1.00) 		2.26e-13
(2.05e-10) 		0.0822
(1.00)
13q gain 245 (57%) 182 6.26e-05
(0.0514) 		2.74e-05
(0.0229) 		2.8e-31
(2.6e-28) 		0.00175
(1.00) 		0.0313
(1.00) 		0.0523
(1.00) 		1.63e-09
(1.44e-06) 		2.82e-09
(2.5e-06) 		0.426
(1.00) 		0.0944
(1.00) 		5.26e-06
(0.00448) 		0.555
(1.00)
7p gain 233 (55%) 194 0.0062
(1.00) 		0.00107
(0.809) 		4.56e-15
(4.16e-12) 		0.000635
(0.489) 		0.000279
(0.221) 		0.00982
(1.00) 		9.49e-09
(8.35e-06) 		1.01e-08
(8.91e-06) 		0.536
(1.00) 		0.00959
(1.00) 		9.14e-06
(0.00774) 		0.946
(1.00)
16p gain 102 (24%) 325 4.47e-05
(0.0368) 		3.7e-05
(0.0307) 		1.42e-20
(1.31e-17) 		0.0982
(1.00) 		0.16
(1.00) 		0.277
(1.00) 		7.78e-05
(0.0637) 		8.6e-06
(0.00731) 		0.558
(1.00) 		0.00152
(1.00) 		0.0116
(1.00) 		0.878
(1.00)
16q gain 99 (23%) 328 3.12e-05
(0.0261) 		6.06e-05
(0.0498) 		1.07e-19
(9.83e-17) 		0.194
(1.00) 		0.228
(1.00) 		0.287
(1.00) 		8.18e-05
(0.0669) 		2.43e-05
(0.0204) 		0.718
(1.00) 		0.000709
(0.545) 		0.00329
(1.00) 		0.616
(1.00)
4p loss 127 (30%) 300 8.45e-05
(0.0688) 		0.00747
(1.00) 		2.37e-14
(2.15e-11) 		0.000458
(0.359) 		0.105
(1.00) 		0.0966
(1.00) 		4.02e-06
(0.00343) 		1.61e-06
(0.00138) 		0.452
(1.00) 		0.0575
(1.00) 		2.73e-05
(0.0229) 		0.531
(1.00)
4q loss 115 (27%) 312 0.000163
(0.131) 		0.00647
(1.00) 		2.06e-14
(1.88e-11) 		9.46e-06
(0.00801) 		0.104
(1.00) 		0.194
(1.00) 		0.00034
(0.269) 		3.4e-06
(0.00291) 		0.219
(1.00) 		0.0229
(1.00) 		4.4e-05
(0.0363) 		0.246
(1.00)
8p loss 133 (31%) 294 0.0235
(1.00) 		0.0017
(1.00) 		3.21e-16
(2.93e-13) 		3.63e-05
(0.0302) 		0.0105
(1.00) 		0.00109
(0.821) 		3.5e-07
(0.000304) 		4.33e-06
(0.00369) 		0.56
(1.00) 		0.109
(1.00) 		2.85e-06
(0.00244) 		0.474
(1.00)
15q loss 145 (34%) 282 0.00172
(1.00) 		0.00205
(1.00) 		8.83e-21
(8.15e-18) 		0.0006
(0.465) 		0.0123
(1.00) 		0.0325
(1.00) 		2.85e-09
(2.52e-06) 		1.57e-08
(1.38e-05) 		0.852
(1.00) 		0.000138
(0.112) 		4.58e-05
(0.0377) 		0.429
(1.00)
22q loss 138 (32%) 289 0.000418
(0.327) 		0.00019
(0.152) 		1.66e-18
(1.53e-15) 		0.000321
(0.253) 		0.17
(1.00) 		0.64
(1.00) 		2.66e-07
(0.000231) 		0.000173
(0.139) 		0.136
(1.00) 		0.00104
(0.79) 		1.04e-05
(0.00878) 		0.291
(1.00)
7q gain 211 (49%) 216 0.00407
(1.00) 		0.00312
(1.00) 		6.88e-10
(6.12e-07) 		0.015
(1.00) 		0.00597
(1.00) 		0.00988
(1.00) 		4.34e-07
(0.000377) 		1.47e-07
(0.000128) 		0.478
(1.00) 		0.00531
(1.00) 		2.95e-05
(0.0246) 		0.868
(1.00)
11p gain 50 (12%) 377 0.000744
(0.569) 		0.000283
(0.224) 		1.08e-10
(9.69e-08) 		0.000125
(0.102) 		0.0762
(1.00) 		0.0918
(1.00) 		7.78e-05
(0.0637) 		0.00146
(1.00) 		0.89
(1.00) 		0.0263
(1.00) 		0.0128
(1.00) 		0.135
(1.00)
11q gain 48 (11%) 379 0.000204
(0.163) 		9.21e-05
(0.0748) 		1.39e-11
(1.25e-08) 		0.000924
(0.701) 		0.0306
(1.00) 		0.242
(1.00) 		2.42e-06
(0.00208) 		0.00038
(0.299) 		0.644
(1.00) 		0.00802
(1.00) 		0.00659
(1.00) 		0.159
(1.00)
20p gain 229 (54%) 198 0.00122
(0.915) 		1.01e-06
(0.000868) 		4.13e-13
(3.75e-10) 		0.00074
(0.567) 		0.0413
(1.00) 		0.153
(1.00) 		2.22e-08
(1.94e-05) 		2.35e-06
(0.00202) 		0.646
(1.00) 		0.0115
(1.00) 		0.000704
(0.541) 		0.816
(1.00)
9q loss 49 (11%) 378 0.118
(1.00) 		0.0606
(1.00) 		3.98e-05
(0.0329) 		0.000245
(0.195) 		0.967
(1.00) 		0.356
(1.00) 		0.000284
(0.225) 		0.000543
(0.424) 		0.438
(1.00) 		0.00869
(1.00) 		1.32e-05
(0.0111) 		0.352
(1.00)
10q loss 68 (16%) 359 0.0247
(1.00) 		0.0177
(1.00) 		2.5e-10
(2.24e-07) 		0.000575
(0.448) 		0.0121
(1.00) 		0.0638
(1.00) 		3.66e-06
(0.00312) 		3.26e-05
(0.0272) 		0.61
(1.00) 		0.0508
(1.00) 		0.000148
(0.12) 		0.842
(1.00)
1p loss 91 (21%) 336 0.0275
(1.00) 		0.0597
(1.00) 		6.89e-11
(6.18e-08) 		0.000922
(0.701) 		0.577
(1.00) 		0.547
(1.00) 		9.15e-05
(0.0744) 		8.94e-06
(0.00758) 		0.777
(1.00) 		0.00391
(1.00) 		0.00429
(1.00) 		0.00674
(1.00)
5q loss 74 (17%) 353 0.306
(1.00) 		0.18
(1.00) 		6.77e-07
(0.000586) 		0.00666
(1.00) 		0.00894
(1.00) 		0.00729
(1.00) 		3.71e-05
(0.0307) 		3.46e-06
(0.00296) 		0.979
(1.00) 		0.459
(1.00) 		0.0022
(1.00) 		1
(1.00)
10p loss 64 (15%) 363 0.021
(1.00) 		0.034
(1.00) 		2.94e-08
(2.58e-05) 		0.00388
(1.00) 		0.0136
(1.00) 		0.124
(1.00) 		9.78e-06
(0.00826) 		0.000196
(0.157) 		0.487
(1.00) 		0.00606
(1.00) 		0.00134
(1.00) 		0.55
(1.00)
3q gain 61 (14%) 366 0.0966
(1.00) 		0.00403
(1.00) 		7.9e-08
(6.9e-05) 		0.0767
(1.00) 		0.0963
(1.00) 		0.0521
(1.00) 		8.2e-05
(0.0669) 		0.0122
(1.00) 		0.658
(1.00) 		0.28
(1.00) 		0.154
(1.00) 		0.497
(1.00)
6p gain 79 (19%) 348 0.0721
(1.00) 		2.05e-05
(0.0173) 		4.39e-10
(3.91e-07) 		0.0687
(1.00) 		0.646
(1.00) 		0.596
(1.00) 		0.00256
(1.00) 		0.000575
(0.448) 		0.584
(1.00) 		0.296
(1.00) 		0.00195
(1.00) 		0.22
(1.00)
6q gain 72 (17%) 355 0.19
(1.00) 		0.00115
(0.862) 		7.78e-08
(6.81e-05) 		0.254
(1.00) 		0.95
(1.00) 		0.242
(1.00) 		0.0234
(1.00) 		0.0189
(1.00) 		0.516
(1.00) 		0.459
(1.00) 		0.000188
(0.151) 		0.167
(1.00)
17q gain 75 (18%) 352 0.122
(1.00) 		0.0945
(1.00) 		1.9e-07
(0.000165) 		0.00101
(0.769) 		0.345
(1.00) 		0.0575
(1.00) 		6.61e-07
(0.000573) 		0.000367
(0.289) 		0.0229
(1.00) 		0.473
(1.00) 		0.152
(1.00) 		0.324
(1.00)
11q loss 59 (14%) 368 0.0422
(1.00) 		0.00207
(1.00) 		0.000312
(0.247) 		0.00129
(0.966) 		0.601
(1.00) 		0.871
(1.00) 		0.124
(1.00) 		0.018
(1.00) 		0.851
(1.00) 		0.383
(1.00) 		0.000219
(0.175) 		0.583
(1.00)
12p loss 44 (10%) 383 0.0616
(1.00) 		0.0113
(1.00) 		1.66e-10
(1.48e-07) 		0.042
(1.00) 		0.401
(1.00) 		0.6
(1.00) 		0.000246
(0.196) 		0.00278
(1.00) 		0.867
(1.00) 		0.211
(1.00) 		0.00289
(1.00) 		0.664
(1.00)
12q loss 47 (11%) 380 0.11
(1.00) 		0.0105
(1.00) 		3.76e-09
(3.31e-06) 		0.0136
(1.00) 		0.513
(1.00) 		0.686
(1.00) 		2.94e-05
(0.0246) 		0.000692
(0.533) 		0.944
(1.00) 		0.105
(1.00) 		0.000596
(0.462) 		0.189
(1.00)
2q gain 70 (16%) 357 0.0743
(1.00) 		0.036
(1.00) 		0.000209
(0.167) 		0.0233
(1.00) 		0.289
(1.00) 		0.518
(1.00) 		0.0306
(1.00) 		0.0535
(1.00) 		0.493
(1.00) 		0.111
(1.00) 		0.471
(1.00) 		0.167
(1.00)
3p gain 42 (10%) 385 0.137
(1.00) 		0.137
(1.00) 		2.06e-05
(0.0173) 		0.37
(1.00) 		0.151
(1.00) 		0.0417
(1.00) 		0.0355
(1.00) 		0.226
(1.00) 		0.678
(1.00) 		0.333
(1.00) 		0.595
(1.00) 		0.218
(1.00)
8q gain 212 (50%) 215 0.872
(1.00) 		0.143
(1.00) 		4.71e-18
(4.32e-15) 		0.00979
(1.00) 		0.127
(1.00) 		0.0437
(1.00) 		0.00133
(0.997) 		0.00156
(1.00) 		0.724
(1.00) 		0.79
(1.00) 		0.0245
(1.00) 		0.0543
(1.00)
18p gain 22 (5%) 405 0.0918
(1.00) 		0.463
(1.00) 		8.6e-06
(0.00731) 		0.000501
(0.392) 		0.829
(1.00) 		0.636
(1.00) 		0.0202
(1.00) 		0.00505
(1.00) 		0.181
(1.00) 		0.0495
(1.00) 		0.268
(1.00) 		0.43
(1.00)
19p gain 67 (16%) 360 0.148
(1.00) 		0.0732
(1.00) 		3.99e-05
(0.0329) 		0.0681
(1.00) 		0.259
(1.00) 		0.211
(1.00) 		0.00774
(1.00) 		0.017
(1.00) 		0.0779
(1.00) 		0.00764
(1.00) 		0.0051
(1.00) 		0.324
(1.00)
1q loss 52 (12%) 375 0.273
(1.00) 		0.544
(1.00) 		3.6e-05
(0.03) 		0.0609
(1.00) 		0.439
(1.00) 		0.227
(1.00) 		0.00463
(1.00) 		0.00244
(1.00) 		0.652
(1.00) 		0.0109
(1.00) 		0.00654
(1.00) 		0.106
(1.00)
5p loss 54 (13%) 373 0.636
(1.00) 		0.865
(1.00) 		0.000155
(0.125) 		0.00839
(1.00) 		0.329
(1.00) 		0.558
(1.00) 		0.0303
(1.00) 		0.0115
(1.00) 		0.729
(1.00) 		0.537
(1.00) 		0.0947
(1.00) 		0.934
(1.00)
9p loss 49 (11%) 378 0.571
(1.00) 		0.0136
(1.00) 		3.98e-05
(0.0329) 		0.00247
(1.00) 		0.886
(1.00) 		0.34
(1.00) 		0.00074
(0.567) 		0.000543
(0.424) 		0.369
(1.00) 		0.126
(1.00) 		0.00083
(0.632) 		0.247
(1.00)
11p loss 49 (11%) 378 0.226
(1.00) 		0.041
(1.00) 		0.00232
(1.00) 		0.0216
(1.00) 		0.723
(1.00) 		0.693
(1.00) 		0.211
(1.00) 		0.0227
(1.00) 		0.824
(1.00) 		0.703
(1.00) 		0.000239
(0.19) 		0.808
(1.00)
21q loss 117 (27%) 310 0.00992
(1.00) 		0.00758
(1.00) 		5.1e-09
(4.49e-06) 		0.0606
(1.00) 		0.229
(1.00) 		0.186
(1.00) 		0.00448
(1.00) 		0.000621
(0.479) 		0.465
(1.00) 		0.298
(1.00) 		0.0018
(1.00) 		0.462
(1.00)
1p gain 30 (7%) 397 0.81
(1.00) 		0.658
(1.00) 		0.0266
(1.00) 		1
(1.00) 		0.0126
(1.00) 		0.0858
(1.00) 		0.701
(1.00) 		0.0426
(1.00) 		0.669
(1.00) 		0.611
(1.00) 		0.779
(1.00) 		1
(1.00)
1q gain 75 (18%) 352 0.528
(1.00) 		0.686
(1.00) 		0.00194
(1.00) 		0.206
(1.00) 		0.243
(1.00) 		0.0298
(1.00) 		0.439
(1.00) 		0.0336
(1.00) 		0.925
(1.00) 		0.957
(1.00) 		0.0342
(1.00) 		0.765
(1.00)
2p gain 74 (17%) 353 0.0743
(1.00) 		0.036
(1.00) 		0.000373
(0.294) 		0.0195
(1.00) 		0.112
(1.00) 		0.404
(1.00) 		0.00758
(1.00) 		0.0155
(1.00) 		0.396
(1.00) 		0.0623
(1.00) 		0.282
(1.00) 		0.00347
(1.00)
4p gain 9 (2%) 418 0.0164
(1.00) 		0.38
(1.00) 		0.316
(1.00) 		0.708
(1.00) 		0.375
(1.00) 		0.177
(1.00) 		0.61
(1.00) 		0.887
(1.00) 		0.505
(1.00) 		1
(1.00)
4q gain 15 (4%) 412 0.127
(1.00) 		0.32
(1.00) 		0.00739
(1.00) 		1
(1.00) 		0.0068
(1.00) 		0.745
(1.00) 		0.236
(1.00) 		0.237
(1.00) 		0.143
(1.00) 		0.0966
(1.00) 		0.394
(1.00) 		1
(1.00)
5p gain 63 (15%) 364 0.357
(1.00) 		0.153
(1.00) 		0.0349
(1.00) 		0.446
(1.00) 		0.518
(1.00) 		0.964
(1.00) 		0.667
(1.00) 		0.00622
(1.00) 		0.85
(1.00) 		0.319
(1.00) 		0.21
(1.00) 		0.558
(1.00)
5q gain 39 (9%) 388 0.784
(1.00) 		0.683
(1.00) 		0.0191
(1.00) 		0.492
(1.00) 		0.392
(1.00) 		0.453
(1.00) 		0.53
(1.00) 		0.0655
(1.00) 		0.546
(1.00) 		0.444
(1.00) 		0.8
(1.00) 		1
(1.00)
8p gain 123 (29%) 304 0.963
(1.00) 		0.482
(1.00) 		0.00249
(1.00) 		0.845
(1.00) 		0.514
(1.00) 		0.161
(1.00) 		0.0242
(1.00) 		0.101
(1.00) 		0.597
(1.00) 		0.319
(1.00) 		0.926
(1.00) 		0.385
(1.00)
9p gain 74 (17%) 353 0.198
(1.00) 		0.0611
(1.00) 		0.00361
(1.00) 		0.705
(1.00) 		0.00185
(1.00) 		0.584
(1.00) 		0.37
(1.00) 		0.381
(1.00) 		0.859
(1.00) 		0.979
(1.00) 		0.0762
(1.00) 		0.808
(1.00)
9q gain 65 (15%) 362 0.171
(1.00) 		0.0221
(1.00) 		0.0367
(1.00) 		0.642
(1.00) 		0.000403
(0.316) 		0.598
(1.00) 		0.518
(1.00) 		0.858
(1.00) 		0.411
(1.00) 		0.461
(1.00) 		0.309
(1.00) 		0.822
(1.00)
10p gain 32 (7%) 395 0.597
(1.00) 		0.888
(1.00) 		0.0351
(1.00) 		0.501
(1.00) 		0.0241
(1.00) 		0.0499
(1.00) 		0.264
(1.00) 		0.0653
(1.00) 		0.402
(1.00) 		0.182
(1.00) 		0.00933
(1.00) 		0.511
(1.00)
10q gain 18 (4%) 409 0.17
(1.00) 		0.829
(1.00) 		0.279
(1.00) 		0.105
(1.00) 		0.363
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.747
(1.00) 		0.38
(1.00) 		0.0371
(1.00) 		0.324
(1.00)
12p gain 87 (20%) 340 0.179
(1.00) 		0.339
(1.00) 		0.0416
(1.00) 		0.0256
(1.00) 		0.717
(1.00) 		0.921
(1.00) 		0.531
(1.00) 		0.885
(1.00) 		0.274
(1.00) 		0.356
(1.00) 		0.456
(1.00) 		0.673
(1.00)
12q gain 80 (19%) 347 0.198
(1.00) 		0.422
(1.00) 		0.0131
(1.00) 		0.0083
(1.00) 		0.545
(1.00) 		0.76
(1.00) 		0.21
(1.00) 		0.42
(1.00) 		0.112
(1.00) 		0.241
(1.00) 		0.253
(1.00) 		0.444
(1.00)
14q gain 34 (8%) 393 0.34
(1.00) 		0.299
(1.00) 		0.254
(1.00) 		0.63
(1.00) 		0.417
(1.00) 		0.39
(1.00) 		0.286
(1.00) 		0.348
(1.00) 		0.662
(1.00) 		0.854
(1.00) 		0.295
(1.00) 		0.745
(1.00)
15q gain 11 (3%) 416 1
(1.00) 		0.315
(1.00) 		0.367
(1.00) 		0.203
(1.00) 		0.0808
(1.00) 		0.167
(1.00) 		0.864
(1.00) 		0.86
(1.00) 		0.923
(1.00) 		0.619
(1.00) 		0.675
(1.00) 		0.555
(1.00)
17p gain 25 (6%) 402 0.841
(1.00) 		0.189
(1.00) 		0.256
(1.00) 		0.509
(1.00) 		0.213
(1.00) 		0.616
(1.00) 		0.134
(1.00) 		0.119
(1.00) 		0.498
(1.00) 		0.35
(1.00) 		0.939
(1.00) 		0.779
(1.00)
18q gain 14 (3%) 413 0.144
(1.00) 		0.635
(1.00) 		0.0016
(1.00) 		0.00291
(1.00) 		0.597
(1.00) 		0.194
(1.00) 		0.0039
(1.00) 		0.0591
(1.00) 		0.415
(1.00) 		0.121
(1.00) 		0.145
(1.00) 		0.485
(1.00)
19q gain 76 (18%) 351 0.087
(1.00) 		0.0129
(1.00) 		0.00517
(1.00) 		0.358
(1.00) 		0.0415
(1.00) 		0.0864
(1.00) 		0.0352
(1.00) 		0.0169
(1.00) 		0.181
(1.00) 		0.0079
(1.00) 		0.0223
(1.00) 		0.15
(1.00)
21q gain 21 (5%) 406 0.0357
(1.00) 		0.275
(1.00) 		0.0263
(1.00) 		0.894
(1.00) 		0.731
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.34
(1.00) 		0.222
(1.00) 		0.229
(1.00) 		0.37
(1.00) 		1
(1.00)
22q gain 10 (2%) 417 1
(1.00) 		1
(1.00) 		0.129
(1.00) 		0.38
(1.00) 		0.637
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.159
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.858
(1.00) 		0.125
(1.00)
xq gain 68 (16%) 359 0.0351
(1.00) 		0.297
(1.00) 		0.00287
(1.00) 		0.169
(1.00) 		0.256
(1.00) 		0.163
(1.00) 		0.441
(1.00) 		0.153
(1.00) 		0.278
(1.00) 		0.762
(1.00) 		0.22
(1.00) 		0.419
(1.00)
2p loss 6 (1%) 421 0.898
(1.00) 		0.315
(1.00) 		0.0339
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.341
(1.00) 		0.639
(1.00) 		0.43
(1.00)
2q loss 7 (2%) 420 1
(1.00) 		0.156
(1.00) 		0.185
(1.00) 		0.31
(1.00) 		0.465
(1.00) 		0.0644
(1.00) 		0.201
(1.00) 		0.389
(1.00) 		0.328
(1.00)
3p loss 50 (12%) 377 0.78
(1.00) 		0.364
(1.00) 		0.00399
(1.00) 		0.136
(1.00) 		0.605
(1.00) 		0.566
(1.00) 		0.0443
(1.00) 		0.048
(1.00) 		0.609
(1.00) 		0.503
(1.00) 		0.000604
(0.467) 		0.475
(1.00)
3q loss 31 (7%) 396 0.825
(1.00) 		1
(1.00) 		0.029
(1.00) 		0.558
(1.00) 		0.396
(1.00) 		0.492
(1.00) 		0.722
(1.00) 		0.387
(1.00) 		0.247
(1.00) 		0.908
(1.00) 		0.0124
(1.00) 		0.352
(1.00)
6p loss 33 (8%) 394 1
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.515
(1.00) 		0.186
(1.00) 		0.576
(1.00) 		0.961
(1.00) 		0.685
(1.00) 		0.613
(1.00) 		0.114
(1.00) 		0.0331
(1.00) 		0.214
(1.00)
6q loss 44 (10%) 383 0.822
(1.00) 		0.811
(1.00) 		0.961
(1.00) 		0.367
(1.00) 		0.202
(1.00) 		0.202
(1.00) 		0.772
(1.00) 		0.733
(1.00) 		0.581
(1.00) 		0.168
(1.00) 		0.286
(1.00) 		0.444
(1.00)
7q loss 3 (1%) 424 0.118
(1.00) 		0.615
(1.00) 		0.422
(1.00) 		0.619
(1.00) 		0.561
(1.00) 		0.6
(1.00)
8q loss 23 (5%) 404 0.81
(1.00) 		0.658
(1.00) 		0.00383
(1.00) 		0.34
(1.00) 		0.274
(1.00) 		0.108
(1.00) 		0.903
(1.00) 		0.141
(1.00) 		0.509
(1.00) 		0.0768
(1.00) 		0.149
(1.00) 		0.49
(1.00)
13q loss 12 (3%) 415 0.874
(1.00) 		0.194
(1.00) 		0.157
(1.00) 		0.0406
(1.00) 		0.0016
(1.00) 		0.00818
(1.00) 		0.764
(1.00) 		0.216
(1.00) 		0.598
(1.00) 		0.0716
(1.00) 		0.0792
(1.00) 		0.15
(1.00)
16p loss 27 (6%) 400 0.406
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.392
(1.00) 		0.335
(1.00) 		0.0673
(1.00) 		0.136
(1.00) 		0.509
(1.00) 		0.252
(1.00) 		0.248
(1.00) 		0.392
(1.00)
16q loss 25 (6%) 402 0.406
(1.00) 		0.711
(1.00) 		0.595
(1.00) 		0.591
(1.00) 		0.137
(1.00) 		0.251
(1.00) 		0.28
(1.00) 		0.434
(1.00) 		0.404
(1.00) 		0.626
(1.00) 		0.196
(1.00) 		0.781
(1.00)
17q loss 61 (14%) 366 0.113
(1.00) 		0.686
(1.00) 		0.000588
(0.457) 		0.0138
(1.00) 		0.574
(1.00) 		0.476
(1.00) 		0.0589
(1.00) 		0.0179
(1.00) 		0.569
(1.00) 		0.251
(1.00) 		0.00325
(1.00) 		0.0301
(1.00)
19p loss 38 (9%) 389 1
(1.00) 		0.167
(1.00) 		0.028
(1.00) 		0.377
(1.00) 		0.606
(1.00) 		0.26
(1.00) 		0.0902
(1.00) 		0.00532
(1.00) 		0.0413
(1.00) 		0.499
(1.00) 		0.468
(1.00) 		0.0461
(1.00)
19q loss 32 (7%) 395 0.838
(1.00) 		0.297
(1.00) 		0.0601
(1.00) 		0.531
(1.00) 		0.18
(1.00) 		0.119
(1.00) 		0.261
(1.00) 		0.0235
(1.00) 		0.338
(1.00) 		0.723
(1.00) 		0.369
(1.00) 		0.129
(1.00)
20p loss 43 (10%) 384 0.194
(1.00) 		0.137
(1.00) 		0.00105
(0.794) 		0.205
(1.00) 		0.863
(1.00) 		0.471
(1.00) 		0.0696
(1.00) 		0.13
(1.00) 		0.879
(1.00) 		0.147
(1.00) 		0.124
(1.00) 		0.0863
(1.00)
20q loss 6 (1%) 421 1
(1.00) 		0.822
(1.00) 		0.0321
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.769
(1.00) 		1
(1.00) 		1
(1.00) 		0.198
(1.00) 		0.319
(1.00)
xq loss 46 (11%) 381 0.0298
(1.00) 		0.2
(1.00) 		0.0105
(1.00) 		0.247
(1.00) 		0.0857
(1.00) 		0.205
(1.00) 		0.168
(1.00) 		0.325
(1.00) 		0.0785
(1.00) 		0.521
(1.00) 		0.0498
(1.00) 		0.2
(1.00)
'2q gain' versus 'CN_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
2Q GAIN MUTATED 43 18 9
2Q GAIN WILD-TYPE 128 177 52

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

'3p gain' versus 'CN_CNMF'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
3P GAIN MUTATED 31 9 2
3P GAIN WILD-TYPE 140 186 59

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

'3q gain' versus 'CN_CNMF'

P value = 7.9e-08 (Fisher's exact test), Q value = 6.9e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
3Q GAIN MUTATED 44 10 7
3Q GAIN WILD-TYPE 127 185 54

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 8.2e-05 (Fisher's exact test), Q value = 0.067

Table S4.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
3Q GAIN MUTATED 33 9 17
3Q GAIN WILD-TYPE 98 125 127

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.017

Table S5.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
6P GAIN MUTATED 3 5 19
6P GAIN WILD-TYPE 53 38 28

Figure S5.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 4.39e-10 (Fisher's exact test), Q value = 3.9e-07

Table S6.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
6P GAIN MUTATED 57 14 8
6P GAIN WILD-TYPE 114 181 53

Figure S6.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 7.78e-08 (Fisher's exact test), Q value = 6.8e-05

Table S7.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
6Q GAIN MUTATED 49 13 10
6Q GAIN WILD-TYPE 122 182 51

Figure S7.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000188 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
6Q GAIN MUTATED 25 6 7
6Q GAIN WILD-TYPE 54 72 56

Figure S8.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 4.56e-15 (Fisher's exact test), Q value = 4.2e-12

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
7P GAIN MUTATED 128 66 39
7P GAIN WILD-TYPE 43 129 22

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.000279 (Fisher's exact test), Q value = 0.22

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
7P GAIN MUTATED 53 63 19 37
7P GAIN WILD-TYPE 25 64 7 57

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

'7p gain' versus 'MRNASEQ_CNMF'

P value = 9.49e-09 (Fisher's exact test), Q value = 8.4e-06

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
7P GAIN MUTATED 98 52 73
7P GAIN WILD-TYPE 33 82 71

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.01e-08 (Fisher's exact test), Q value = 8.9e-06

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
7P GAIN MUTATED 84 104 35
7P GAIN WILD-TYPE 81 39 66

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.14e-06 (Fisher's exact test), Q value = 0.0077

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
7P GAIN MUTATED 57 28 41
7P GAIN WILD-TYPE 22 50 22

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 6.88e-10 (Fisher's exact test), Q value = 6.1e-07

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
7Q GAIN MUTATED 113 64 34
7Q GAIN WILD-TYPE 58 131 27

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4.34e-07 (Fisher's exact test), Q value = 0.00038

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
7Q GAIN MUTATED 89 48 65
7Q GAIN WILD-TYPE 42 86 79

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-07 (Fisher's exact test), Q value = 0.00013

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
7Q GAIN MUTATED 73 96 33
7Q GAIN WILD-TYPE 92 47 68

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.025

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
7Q GAIN MUTATED 50 25 41
7Q GAIN WILD-TYPE 29 53 22

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4.71e-18 (Fisher's exact test), Q value = 4.3e-15

Table S18.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
8Q GAIN MUTATED 92 63 57
8Q GAIN WILD-TYPE 79 132 4

Figure S18.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000283 (Fisher's exact test), Q value = 0.22

Table S19.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
11P GAIN MUTATED 3 1 13
11P GAIN WILD-TYPE 53 42 34

Figure S19.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1.08e-10 (Fisher's exact test), Q value = 9.7e-08

Table S20.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
11P GAIN MUTATED 41 4 5
11P GAIN WILD-TYPE 130 191 56

Figure S20.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.1

Table S21.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11P GAIN MUTATED 24 2 7
11P GAIN WILD-TYPE 90 86 61

Figure S21.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 7.78e-05 (Fisher's exact test), Q value = 0.064

Table S22.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
11P GAIN MUTATED 24 4 21
11P GAIN WILD-TYPE 107 130 123

Figure S22.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNA_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.16

Table S23.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
11Q GAIN MUTATED 1 9 0 8
11Q GAIN WILD-TYPE 34 52 29 13

Figure S23.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.21e-05 (Fisher's exact test), Q value = 0.075

Table S24.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
11Q GAIN MUTATED 3 1 14
11Q GAIN WILD-TYPE 53 42 33

Figure S24.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1.39e-11 (Fisher's exact test), Q value = 1.2e-08

Table S25.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
11Q GAIN MUTATED 39 2 7
11Q GAIN WILD-TYPE 132 193 54

Figure S25.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 2.42e-06 (Fisher's exact test), Q value = 0.0021

Table S26.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
11Q GAIN MUTATED 25 2 19
11Q GAIN WILD-TYPE 106 132 125

Figure S26.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 6.26e-05 (Fisher's exact test), Q value = 0.051

Table S27.  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 MUTATED 14 47 10 15
13Q GAIN WILD-TYPE 21 14 19 6

Figure S27.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.023

Table S28.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
13Q GAIN MUTATED 38 13 35
13Q GAIN WILD-TYPE 18 30 12

Figure S28.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 2.8e-31 (Fisher's exact test), Q value = 2.6e-28

Table S29.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
13Q GAIN MUTATED 152 59 34
13Q GAIN WILD-TYPE 19 136 27

Figure S29.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.4e-06

Table S30.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
13Q GAIN MUTATED 100 51 83
13Q GAIN WILD-TYPE 31 83 61

Figure S30.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.82e-09 (Fisher's exact test), Q value = 2.5e-06

Table S31.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
13Q GAIN MUTATED 97 104 33
13Q GAIN WILD-TYPE 68 39 68

Figure S31.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.26e-06 (Fisher's exact test), Q value = 0.0045

Table S32.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
13Q GAIN MUTATED 59 29 41
13Q GAIN WILD-TYPE 20 49 22

Figure S32.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 4.47e-05 (Fisher's exact test), Q value = 0.037

Table S33.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
16P GAIN MUTATED 5 21 2 13
16P GAIN WILD-TYPE 30 40 27 8

Figure S33.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.7e-05 (Fisher's exact test), Q value = 0.031

Table S34.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
16P GAIN MUTATED 13 4 24
16P GAIN WILD-TYPE 43 39 23

Figure S34.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1.42e-20 (Fisher's exact test), Q value = 1.3e-17

Table S35.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
16P GAIN MUTATED 81 12 9
16P GAIN WILD-TYPE 90 183 52

Figure S35.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 7.78e-05 (Fisher's exact test), Q value = 0.064

Table S36.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
16P GAIN MUTATED 41 16 44
16P GAIN WILD-TYPE 90 118 100

Figure S36.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.6e-06 (Fisher's exact test), Q value = 0.0073

Table S37.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
16P GAIN MUTATED 50 43 8
16P GAIN WILD-TYPE 115 100 93

Figure S37.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.026

Table S38.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
16Q GAIN MUTATED 4 19 2 13
16Q GAIN WILD-TYPE 31 42 27 8

Figure S38.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.05

Table S39.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
16Q GAIN MUTATED 13 3 22
16Q GAIN WILD-TYPE 43 40 25

Figure S39.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1.07e-19 (Fisher's exact test), Q value = 9.8e-17

Table S40.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
16Q GAIN MUTATED 78 11 10
16Q GAIN WILD-TYPE 93 184 51

Figure S40.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 8.18e-05 (Fisher's exact test), Q value = 0.067

Table S41.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
16Q GAIN MUTATED 40 15 42
16Q GAIN WILD-TYPE 91 119 102

Figure S41.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.02

Table S42.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
16Q GAIN MUTATED 47 42 8
16Q GAIN WILD-TYPE 118 101 93

Figure S42.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1.9e-07 (Fisher's exact test), Q value = 0.00017

Table S43.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
17Q GAIN MUTATED 49 14 12
17Q GAIN WILD-TYPE 122 181 49

Figure S43.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6.61e-07 (Fisher's exact test), Q value = 0.00057

Table S44.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
17Q GAIN MUTATED 43 11 20
17Q GAIN WILD-TYPE 88 123 124

Figure S44.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 8.6e-06 (Fisher's exact test), Q value = 0.0073

Table S45.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
18P GAIN MUTATED 0 14 8
18P GAIN WILD-TYPE 171 181 53

Figure S45.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 3.99e-05 (Fisher's exact test), Q value = 0.033

Table S46.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
19P GAIN MUTATED 42 15 10
19P GAIN WILD-TYPE 129 180 51

Figure S46.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00087

Table S47.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20P GAIN MUTATED 41 10 31
20P GAIN WILD-TYPE 15 33 16

Figure S47.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 4.13e-13 (Fisher's exact test), Q value = 3.7e-10

Table S48.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
20P GAIN MUTATED 127 69 33
20P GAIN WILD-TYPE 44 126 28

Figure S48.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2.22e-08 (Fisher's exact test), Q value = 1.9e-05

Table S49.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
20P GAIN MUTATED 90 45 84
20P GAIN WILD-TYPE 41 89 60

Figure S49.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.002

Table S50.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
20P GAIN MUTATED 93 93 33
20P GAIN WILD-TYPE 72 50 68

Figure S50.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 3.64e-10 (Fisher's exact test), Q value = 3.2e-07

Table S51.  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 MUTATED 13 58 15 18
20Q GAIN WILD-TYPE 22 3 14 3

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.41e-11 (Fisher's exact test), Q value = 4e-08

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20Q GAIN MUTATED 49 13 42
20Q GAIN WILD-TYPE 7 30 5

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 2.29e-36 (Fisher's exact test), Q value = 2.1e-33

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
20Q GAIN MUTATED 167 82 53
20Q GAIN WILD-TYPE 4 113 8

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2.06e-12 (Fisher's exact test), Q value = 1.9e-09

Table S54.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
20Q GAIN MUTATED 106 44 42
20Q GAIN WILD-TYPE 8 44 26

Figure S54.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 9.42e-05 (Fisher's exact test), Q value = 0.076

Table S55.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
20Q GAIN MUTATED 63 93 21 48
20Q GAIN WILD-TYPE 15 34 5 46

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000189 (Fisher's exact test), Q value = 0.15

Table S56.  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 MUTATED 13 29 53 130
20Q GAIN WILD-TYPE 13 27 10 50

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2.35e-23 (Fisher's exact test), Q value = 2.2e-20

Table S57.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
20Q GAIN MUTATED 127 58 103
20Q GAIN WILD-TYPE 4 76 41

Figure S57.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.64e-18 (Fisher's exact test), Q value = 1.5e-15

Table S58.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
20Q GAIN MUTATED 118 131 39
20Q GAIN WILD-TYPE 47 12 62

Figure S58.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.23e-05 (Fisher's exact test), Q value = 0.067

Table S59.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
20Q GAIN MUTATED 42 124 115
20Q GAIN WILD-TYPE 38 50 28

Figure S59.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-12 (Fisher's exact test), Q value = 1e-09

Table S60.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
20Q GAIN MUTATED 74 33 50
20Q GAIN WILD-TYPE 5 45 13

Figure S60.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 6.89e-11 (Fisher's exact test), Q value = 6.2e-08

Table S61.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
1P LOSS MUTATED 65 20 6
1P LOSS WILD-TYPE 106 175 55

Figure S61.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 9.15e-05 (Fisher's exact test), Q value = 0.074

Table S62.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
1P LOSS MUTATED 43 15 30
1P LOSS WILD-TYPE 88 119 114

Figure S62.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.94e-06 (Fisher's exact test), Q value = 0.0076

Table S63.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
1P LOSS MUTATED 36 45 7
1P LOSS WILD-TYPE 129 98 94

Figure S63.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.03

Table S64.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
1Q LOSS MUTATED 36 12 4
1Q LOSS WILD-TYPE 135 183 57

Figure S64.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 8.45e-05 (Fisher's exact test), Q value = 0.069

Table S65.  Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
4P LOSS MUTATED 8 28 1 9
4P LOSS WILD-TYPE 27 33 28 12

Figure S65.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 2.37e-14 (Fisher's exact test), Q value = 2.1e-11

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
4P LOSS MUTATED 87 27 13
4P LOSS WILD-TYPE 84 168 48

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0034

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
4P LOSS MUTATED 58 22 44
4P LOSS WILD-TYPE 73 112 100

Figure S67.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.0014

Table S68.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
4P LOSS MUTATED 53 59 12
4P LOSS WILD-TYPE 112 84 89

Figure S68.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.023

Table S69.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
4P LOSS MUTATED 32 8 21
4P LOSS WILD-TYPE 47 70 42

Figure S69.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MRNA_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.13

Table S70.  Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
4Q LOSS MUTATED 7 26 1 9
4Q LOSS WILD-TYPE 28 35 28 12

Figure S70.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.06e-14 (Fisher's exact test), Q value = 1.9e-11

Table S71.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
4Q LOSS MUTATED 81 22 12
4Q LOSS WILD-TYPE 90 173 49

Figure S71.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 9.46e-06 (Fisher's exact test), Q value = 0.008

Table S72.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
4Q LOSS MUTATED 43 8 18
4Q LOSS WILD-TYPE 71 80 50

Figure S72.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.4e-06 (Fisher's exact test), Q value = 0.0029

Table S73.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
4Q LOSS MUTATED 49 53 10
4Q LOSS WILD-TYPE 116 90 91

Figure S73.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.036

Table S74.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
4Q LOSS MUTATED 27 6 20
4Q LOSS WILD-TYPE 52 72 43

Figure S74.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.000155 (Fisher's exact test), Q value = 0.13

Table S75.  Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
5P LOSS MUTATED 33 11 10
5P LOSS WILD-TYPE 138 184 51

Figure S75.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 6.77e-07 (Fisher's exact test), Q value = 0.00059

Table S76.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
5Q LOSS MUTATED 46 14 14
5Q LOSS WILD-TYPE 125 181 47

Figure S76.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 3.71e-05 (Fisher's exact test), Q value = 0.031

Table S77.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
5Q LOSS MUTATED 39 12 21
5Q LOSS WILD-TYPE 92 122 123

Figure S77.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.46e-06 (Fisher's exact test), Q value = 0.003

Table S78.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
5Q LOSS MUTATED 29 39 4
5Q LOSS WILD-TYPE 136 104 97

Figure S78.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 3.21e-16 (Fisher's exact test), Q value = 2.9e-13

Table S79.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
8P LOSS MUTATED 81 22 30
8P LOSS WILD-TYPE 90 173 31

Figure S79.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 3.63e-05 (Fisher's exact test), Q value = 0.03

Table S80.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
8P LOSS MUTATED 52 15 17
8P LOSS WILD-TYPE 62 73 51

Figure S80.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 3.5e-07 (Fisher's exact test), Q value = 3e-04

Table S81.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
8P LOSS MUTATED 60 21 50
8P LOSS WILD-TYPE 71 113 94

Figure S81.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0037

Table S82.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
8P LOSS MUTATED 56 61 14
8P LOSS WILD-TYPE 109 82 87

Figure S82.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.0024

Table S83.  Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
8P LOSS MUTATED 36 9 25
8P LOSS WILD-TYPE 43 69 38

Figure S83.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 3.98e-05 (Fisher's exact test), Q value = 0.033

Table S84.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
9P LOSS MUTATED 33 9 7
9P LOSS WILD-TYPE 138 186 54

Figure S84.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 3.98e-05 (Fisher's exact test), Q value = 0.033

Table S85.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
9Q LOSS MUTATED 33 9 7
9Q LOSS WILD-TYPE 138 186 54

Figure S85.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.000245 (Fisher's exact test), Q value = 0.2

Table S86.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
9Q LOSS MUTATED 23 2 9
9Q LOSS WILD-TYPE 91 86 59

Figure S86.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.23

Table S87.  Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
9Q LOSS MUTATED 28 8 12
9Q LOSS WILD-TYPE 103 126 132

Figure S87.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.011

Table S88.  Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
9Q LOSS MUTATED 20 1 9
9Q LOSS WILD-TYPE 59 77 54

Figure S88.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.94e-08 (Fisher's exact test), Q value = 2.6e-05

Table S89.  Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
10P LOSS MUTATED 43 9 12
10P LOSS WILD-TYPE 128 186 49

Figure S89.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 9.78e-06 (Fisher's exact test), Q value = 0.0083

Table S90.  Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
10P LOSS MUTATED 36 9 17
10P LOSS WILD-TYPE 95 125 127

Figure S90.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.16

Table S91.  Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
10P LOSS MUTATED 21 35 6
10P LOSS WILD-TYPE 144 108 95

Figure S91.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 2.5e-10 (Fisher's exact test), Q value = 2.2e-07

Table S92.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
10Q LOSS MUTATED 48 8 12
10Q LOSS WILD-TYPE 123 187 49

Figure S92.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3.66e-06 (Fisher's exact test), Q value = 0.0031

Table S93.  Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
10Q LOSS MUTATED 38 9 19
10Q LOSS WILD-TYPE 93 125 125

Figure S93.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.027

Table S94.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
10Q LOSS MUTATED 24 37 5
10Q LOSS WILD-TYPE 141 106 96

Figure S94.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.12

Table S95.  Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
10Q LOSS MUTATED 21 3 13
10Q LOSS WILD-TYPE 58 75 50

Figure S95.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.19

Table S96.  Gene #60: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
11P LOSS MUTATED 16 1 8
11P LOSS WILD-TYPE 63 77 55

Figure S96.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.000312 (Fisher's exact test), Q value = 0.25

Table S97.  Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
11Q LOSS MUTATED 38 16 5
11Q LOSS WILD-TYPE 133 179 56

Figure S97.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.17

Table S98.  Gene #61: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
11Q LOSS MUTATED 17 2 13
11Q LOSS WILD-TYPE 62 76 50

Figure S98.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1.66e-10 (Fisher's exact test), Q value = 1.5e-07

Table S99.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
12P LOSS MUTATED 36 2 6
12P LOSS WILD-TYPE 135 193 55

Figure S99.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.2

Table S100.  Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
12P LOSS MUTATED 25 5 14
12P LOSS WILD-TYPE 106 129 130

Figure S100.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 3.76e-09 (Fisher's exact test), Q value = 3.3e-06

Table S101.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
12Q LOSS MUTATED 37 4 6
12Q LOSS WILD-TYPE 134 191 55

Figure S101.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.025

Table S102.  Gene #63: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
12Q LOSS MUTATED 28 5 14
12Q LOSS WILD-TYPE 103 129 130

Figure S102.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00063

Table S103.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
14Q LOSS MUTATED 5 33 2 11
14Q LOSS WILD-TYPE 30 28 27 10

Figure S103.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.65e-06 (Fisher's exact test), Q value = 0.0014

Table S104.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
14Q LOSS MUTATED 22 3 26
14Q LOSS WILD-TYPE 34 40 21

Figure S104.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.93e-28 (Fisher's exact test), Q value = 1.8e-25

Table S105.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
14Q LOSS MUTATED 103 18 7
14Q LOSS WILD-TYPE 68 177 54

Figure S105.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00063

Table S106.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
14Q LOSS MUTATED 50 10 15
14Q LOSS WILD-TYPE 64 78 53

Figure S106.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.77e-11 (Fisher's exact test), Q value = 1.6e-08

Table S107.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
14Q LOSS MUTATED 61 13 51
14Q LOSS WILD-TYPE 70 121 93

Figure S107.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.82e-10 (Fisher's exact test), Q value = 3.4e-07

Table S108.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
14Q LOSS MUTATED 58 60 7
14Q LOSS WILD-TYPE 107 83 94

Figure S108.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.057

Table S109.  Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
14Q LOSS MUTATED 9 61 50
14Q LOSS WILD-TYPE 71 113 93

Figure S109.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.019

Table S110.  Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
14Q LOSS MUTATED 33 8 19
14Q LOSS WILD-TYPE 46 70 44

Figure S110.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 8.83e-21 (Fisher's exact test), Q value = 8.1e-18

Table S111.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
15Q LOSS MUTATED 103 27 15
15Q LOSS WILD-TYPE 68 168 46

Figure S111.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 2.85e-09 (Fisher's exact test), Q value = 2.5e-06

Table S112.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
15Q LOSS MUTATED 70 23 50
15Q LOSS WILD-TYPE 61 111 94

Figure S112.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-08 (Fisher's exact test), Q value = 1.4e-05

Table S113.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
15Q LOSS MUTATED 61 69 13
15Q LOSS WILD-TYPE 104 74 88

Figure S113.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.11

Table S114.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
15Q LOSS MUTATED 13 61 62
15Q LOSS WILD-TYPE 67 113 81

Figure S114.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.58e-05 (Fisher's exact test), Q value = 0.038

Table S115.  Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
15Q LOSS MUTATED 35 12 28
15Q LOSS WILD-TYPE 44 66 35

Figure S115.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 2.1e-07 (Fisher's exact test), Q value = 0.00018

Table S116.  Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
17P LOSS MUTATED 9 46 8 15
17P LOSS WILD-TYPE 26 15 21 6

Figure S116.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00092

Table S117.  Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
17P LOSS MUTATED 35 9 34
17P LOSS WILD-TYPE 21 34 13

Figure S117.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 4.86e-29 (Fisher's exact test), Q value = 4.5e-26

Table S118.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
17P LOSS MUTATED 136 45 41
17P LOSS WILD-TYPE 35 150 20

Figure S118.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.28e-09 (Fisher's exact test), Q value = 1.1e-06

Table S119.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
17P LOSS MUTATED 84 27 29
17P LOSS WILD-TYPE 30 61 39

Figure S119.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 2.79e-12 (Fisher's exact test), Q value = 2.5e-09

Table S120.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
17P LOSS MUTATED 94 38 82
17P LOSS WILD-TYPE 37 96 62

Figure S120.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.56e-13 (Fisher's exact test), Q value = 4.1e-10

Table S121.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
17P LOSS MUTATED 90 101 23
17P LOSS WILD-TYPE 75 42 78

Figure S121.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.39e-10 (Fisher's exact test), Q value = 8.3e-07

Table S122.  Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
17P LOSS MUTATED 60 20 35
17P LOSS WILD-TYPE 19 58 28

Figure S122.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 1.46e-12 (Fisher's exact test), Q value = 1.3e-09

Table S123.  Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18P LOSS MUTATED 7 51 6 16
18P LOSS WILD-TYPE 28 10 23 5

Figure S123.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 7.63e-10 (Fisher's exact test), Q value = 6.8e-07

Table S124.  Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18P LOSS MUTATED 35 7 38
18P LOSS WILD-TYPE 21 36 9

Figure S124.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1.05e-44 (Fisher's exact test), Q value = 9.8e-42

Table S125.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
18P LOSS MUTATED 157 43 37
18P LOSS WILD-TYPE 14 152 24

Figure S125.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 8.23e-18 (Fisher's exact test), Q value = 7.5e-15

Table S126.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
18P LOSS MUTATED 98 24 32
18P LOSS WILD-TYPE 16 64 36

Figure S126.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 4.68e-24 (Fisher's exact test), Q value = 4.3e-21

Table S127.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
18P LOSS MUTATED 114 35 80
18P LOSS WILD-TYPE 17 99 64

Figure S127.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.15e-18 (Fisher's exact test), Q value = 5.6e-15

Table S128.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
18P LOSS MUTATED 93 113 23
18P LOSS WILD-TYPE 72 30 78

Figure S128.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.56e-15 (Fisher's exact test), Q value = 6.9e-12

Table S129.  Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
18P LOSS MUTATED 66 17 38
18P LOSS WILD-TYPE 13 61 25

Figure S129.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 6.4e-12 (Fisher's exact test), Q value = 5.8e-09

Table S130.  Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18Q LOSS MUTATED 8 52 7 16
18Q LOSS WILD-TYPE 27 9 22 5

Figure S130.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.6e-10 (Fisher's exact test), Q value = 8.5e-07

Table S131.  Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18Q LOSS MUTATED 36 8 39
18Q LOSS WILD-TYPE 20 35 8

Figure S131.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1.12e-42 (Fisher's exact test), Q value = 1e-39

Table S132.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
18Q LOSS MUTATED 157 49 46
18Q LOSS WILD-TYPE 14 146 15

Figure S132.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 2.95e-15 (Fisher's exact test), Q value = 2.7e-12

Table S133.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
18Q LOSS MUTATED 100 31 34
18Q LOSS WILD-TYPE 14 57 34

Figure S133.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1.23e-25 (Fisher's exact test), Q value = 1.1e-22

Table S134.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
18Q LOSS MUTATED 119 39 85
18Q LOSS WILD-TYPE 12 95 59

Figure S134.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.59e-18 (Fisher's exact test), Q value = 7e-15

Table S135.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
18Q LOSS MUTATED 96 119 28
18Q LOSS WILD-TYPE 69 24 73

Figure S135.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.26e-13 (Fisher's exact test), Q value = 2.1e-10

Table S136.  Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
18Q LOSS MUTATED 68 22 41
18Q LOSS WILD-TYPE 11 56 22

Figure S136.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 5.1e-09 (Fisher's exact test), Q value = 4.5e-06

Table S137.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
21Q LOSS MUTATED 75 33 9
21Q LOSS WILD-TYPE 96 162 52

Figure S137.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S138.  Gene #78: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
22Q LOSS MUTATED 24 5 23
22Q LOSS WILD-TYPE 32 38 24

Figure S138.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.66e-18 (Fisher's exact test), Q value = 1.5e-15

Table S139.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
22Q LOSS MUTATED 98 31 9
22Q LOSS WILD-TYPE 73 164 52

Figure S139.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.66e-07 (Fisher's exact test), Q value = 0.00023

Table S140.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
22Q LOSS MUTATED 62 22 50
22Q LOSS WILD-TYPE 69 112 94

Figure S140.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S141.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
22Q LOSS MUTATED 59 58 17
22Q LOSS WILD-TYPE 106 85 84

Figure S141.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0088

Table S142.  Gene #78: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
22Q LOSS MUTATED 31 8 25
22Q LOSS WILD-TYPE 48 70 38

Figure S142.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 427

  • Number of significantly arm-level cnvs = 79

  • 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

Q value calculation

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

Download Results

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

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