Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C14748QZ
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/C14748QZ
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 450 patients, 118 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 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

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

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

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

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

  • 8q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

  • 18p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 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',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 1q loss cnv correlated to 'CN_CNMF'.

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

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

  • 5q loss cnv correlated to 'CN_CNMF'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

  • 17q loss cnv correlated to 'CN_CNMF'.

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

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

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 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, 118 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 321 (71%) 129 1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.00034
(0.27) 		0.00059
(0.459) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.795
(1.00) 		0.00125
(0.955) 		0.894
(1.00) 		0.0066
(1.00)
14q loss 139 (31%) 311 2e-05
(0.0167) 		5e-05
(0.0411) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.00192
(1.00) 		0.0241
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.296
(1.00) 		0.0214
(1.00) 		0.0825
(1.00) 		0.00533
(1.00)
17p loss 237 (53%) 213 1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.0195
(1.00) 		0.00395
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.796
(1.00) 		0.0376
(1.00) 		0.607
(1.00) 		0.0012
(0.92)
18p loss 254 (56%) 196 1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.0014
(1.00) 		0.00374
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.991
(1.00) 		0.019
(1.00) 		0.464
(1.00) 		0.00043
(0.338)
18q loss 271 (60%) 179 1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.00588
(1.00) 		0.00324
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.747
(1.00) 		0.0126
(1.00) 		0.258
(1.00) 		0.00048
(0.377)
11q gain 51 (11%) 399 0.0002
(0.161) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.00211
(1.00) 		0.028
(1.00) 		0.605
(1.00) 		3e-05
(0.0248) 		2e-05
(0.0167) 		0.628
(1.00) 		0.00617
(1.00) 		1
(1.00) 		0.0348
(1.00)
13q gain 256 (57%) 194 0.00012
(0.0973) 		3e-05
(0.0248) 		1e-05
(0.00914) 		0.00058
(0.452) 		0.0369
(1.00) 		0.119
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00914) 		0.44
(1.00) 		0.793
(1.00) 		0.138
(1.00) 		0.166
(1.00)
4p loss 138 (31%) 312 5e-05
(0.0411) 		0.00142
(1.00) 		1e-05
(0.00914) 		0.00015
(0.121) 		0.103
(1.00) 		0.362
(1.00) 		0.0001
(0.0817) 		1e-05
(0.00914) 		0.464
(1.00) 		0.379
(1.00) 		0.0601
(1.00) 		0.024
(1.00)
7p gain 246 (55%) 204 0.0056
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.0004
(0.316) 		0.00033
(0.263) 		0.00213
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00914) 		0.536
(1.00) 		0.477
(1.00) 		0.96
(1.00) 		0.0178
(1.00)
7q gain 224 (50%) 226 0.0038
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.00827
(1.00) 		0.0058
(1.00) 		0.0097
(1.00) 		0.0002
(0.161) 		1e-05
(0.00914) 		0.414
(1.00) 		0.64
(1.00) 		0.818
(1.00) 		0.00961
(1.00)
11p gain 54 (12%) 396 0.00078
(0.604) 		0.0001
(0.0817) 		1e-05
(0.00914) 		0.00031
(0.247) 		0.0938
(1.00) 		0.433
(1.00) 		0.00333
(1.00) 		0.00014
(0.113) 		0.819
(1.00) 		0.00425
(1.00) 		0.925
(1.00) 		0.0906
(1.00)
16p gain 107 (24%) 343 1e-05
(0.00914) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.166
(1.00) 		0.16
(1.00) 		0.104
(1.00) 		0.00258
(1.00) 		1e-05
(0.00914) 		0.573
(1.00) 		0.187
(1.00) 		0.904
(1.00) 		0.139
(1.00)
16q gain 105 (23%) 345 4e-05
(0.0329) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.255
(1.00) 		0.183
(1.00) 		0.155
(1.00) 		0.00268
(1.00) 		1e-05
(0.00914) 		0.802
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.177
(1.00)
20p gain 243 (54%) 207 0.00309
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00914) 		0.0005
(0.391) 		0.0441
(1.00) 		0.236
(1.00) 		3e-05
(0.0248) 		1e-05
(0.00914) 		0.702
(1.00) 		0.0698
(1.00) 		0.15
(1.00) 		0.244
(1.00)
4q loss 126 (28%) 324 0.00026
(0.208) 		0.00917
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.105
(1.00) 		0.253
(1.00) 		0.0027
(1.00) 		1e-05
(0.00914) 		0.259
(1.00) 		0.247
(1.00) 		0.251
(1.00) 		0.205
(1.00)
8p loss 142 (32%) 308 0.0149
(1.00) 		0.00077
(0.597) 		1e-05
(0.00914) 		0.00042
(0.331) 		0.0148
(1.00) 		0.0116
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.624
(1.00) 		0.133
(1.00) 		0.811
(1.00) 		0.0209
(1.00)
12q loss 49 (11%) 401 0.109
(1.00) 		0.00776
(1.00) 		1e-05
(0.00914) 		0.00692
(1.00) 		0.519
(1.00) 		0.686
(1.00) 		0.00021
(0.168) 		0.00022
(0.176) 		0.954
(1.00) 		0.683
(1.00) 		0.916
(1.00) 		0.021
(1.00)
15q loss 157 (35%) 293 0.00177
(1.00) 		0.00154
(1.00) 		1e-05
(0.00914) 		0.00038
(0.301) 		0.0137
(1.00) 		0.0501
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.901
(1.00) 		0.841
(1.00) 		0.142
(1.00) 		0.0667
(1.00)
22q loss 146 (32%) 304 0.00051
(0.398) 		0.00033
(0.263) 		1e-05
(0.00914) 		0.00133
(1.00) 		0.175
(1.00) 		0.307
(1.00) 		0.00031
(0.247) 		1e-05
(0.00914) 		0.185
(1.00) 		0.402
(1.00) 		0.614
(1.00) 		0.449
(1.00)
3q gain 66 (15%) 384 0.0957
(1.00) 		0.00014
(0.113) 		1e-05
(0.00914) 		0.0503
(1.00) 		0.0949
(1.00) 		0.283
(1.00) 		0.0007
(0.543) 		0.00618
(1.00) 		0.67
(1.00) 		0.637
(1.00) 		0.789
(1.00) 		0.0578
(1.00)
6p gain 84 (19%) 366 0.213
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00914) 		0.228
(1.00) 		0.563
(1.00) 		0.989
(1.00) 		0.0196
(1.00) 		0.00599
(1.00) 		0.589
(1.00) 		0.975
(1.00) 		0.266
(1.00) 		0.163
(1.00)
6q gain 76 (17%) 374 0.184
(1.00) 		1e-05
(0.00914) 		1e-05
(0.00914) 		0.329
(1.00) 		0.956
(1.00) 		0.519
(1.00) 		0.133
(1.00) 		0.163
(1.00) 		0.527
(1.00) 		0.954
(1.00) 		0.611
(1.00) 		0.166
(1.00)
17q gain 82 (18%) 368 0.166
(1.00) 		0.0409
(1.00) 		1e-05
(0.00914) 		0.00034
(0.27) 		0.463
(1.00) 		0.0302
(1.00) 		1e-05
(0.00914) 		0.00048
(0.377) 		0.00753
(1.00) 		0.0967
(1.00) 		0.521
(1.00) 		0.7
(1.00)
18p gain 22 (5%) 428 0.092
(1.00) 		0.674
(1.00) 		3e-05
(0.0248) 		0.00096
(0.739) 		0.828
(1.00) 		0.893
(1.00) 		0.016
(1.00) 		1e-05
(0.00914) 		0.27
(1.00) 		0.174
(1.00) 		0.911
(1.00) 		0.481
(1.00)
1p loss 98 (22%) 352 0.0262
(1.00) 		0.177
(1.00) 		1e-05
(0.00914) 		0.00157
(1.00) 		0.579
(1.00) 		0.775
(1.00) 		0.00122
(0.933) 		2e-05
(0.0167) 		0.779
(1.00) 		0.022
(1.00) 		0.949
(1.00) 		0.537
(1.00)
9q loss 54 (12%) 396 0.119
(1.00) 		0.0612
(1.00) 		0.00011
(0.0894) 		0.00013
(0.105) 		0.976
(1.00) 		0.663
(1.00) 		0.00183
(1.00) 		0.00421
(1.00) 		0.445
(1.00) 		0.163
(1.00) 		0.225
(1.00) 		0.37
(1.00)
10p loss 69 (15%) 381 0.0205
(1.00) 		0.0243
(1.00) 		1e-05
(0.00914) 		0.00126
(0.961) 		0.0131
(1.00) 		0.351
(1.00) 		0.0014
(1.00) 		0.00011
(0.0894) 		0.499
(1.00) 		0.233
(1.00) 		0.502
(1.00) 		0.0935
(1.00)
10q loss 73 (16%) 377 0.0248
(1.00) 		0.0424
(1.00) 		1e-05
(0.00914) 		0.00038
(0.301) 		0.0117
(1.00) 		0.174
(1.00) 		0.00151
(1.00) 		1e-05
(0.00914) 		0.61
(1.00) 		0.394
(1.00) 		0.0721
(1.00) 		0.451
(1.00)
12p loss 47 (10%) 403 0.0607
(1.00) 		0.00794
(1.00) 		1e-05
(0.00914) 		0.00625
(1.00) 		0.41
(1.00) 		0.8
(1.00) 		0.00094
(0.725) 		5e-05
(0.0411) 		0.88
(1.00) 		0.412
(1.00) 		0.442
(1.00) 		0.0212
(1.00)
2q gain 78 (17%) 372 0.0704
(1.00) 		0.0222
(1.00) 		0.0001
(0.0817) 		0.00406
(1.00) 		0.288
(1.00) 		0.147
(1.00) 		0.0366
(1.00) 		0.00083
(0.641) 		0.492
(1.00) 		0.0747
(1.00) 		1
(1.00) 		0.561
(1.00)
3p gain 46 (10%) 404 0.137
(1.00) 		0.00662
(1.00) 		3e-05
(0.0248) 		0.253
(1.00) 		0.147
(1.00) 		0.123
(1.00) 		0.0543
(1.00) 		0.126
(1.00) 		0.69
(1.00) 		0.849
(1.00) 		0.723
(1.00) 		0.391
(1.00)
8q gain 227 (50%) 223 0.881
(1.00) 		0.0196
(1.00) 		1e-05
(0.00914) 		0.0431
(1.00) 		0.0741
(1.00) 		0.0356
(1.00) 		0.00463
(1.00) 		0.00066
(0.513) 		0.655
(1.00) 		0.0144
(1.00) 		0.407
(1.00) 		0.0741
(1.00)
18q gain 13 (3%) 437 0.145
(1.00) 		1
(1.00) 		0.00223
(1.00) 		0.00771
(1.00) 		0.676
(1.00) 		0.478
(1.00) 		0.00559
(1.00) 		1e-05
(0.00914) 		0.56
(1.00) 		0.184
(1.00) 		0.447
(1.00) 		0.195
(1.00)
19p gain 73 (16%) 377 0.145
(1.00) 		0.0767
(1.00) 		6e-05
(0.0491) 		0.0641
(1.00) 		0.258
(1.00) 		0.226
(1.00) 		0.1
(1.00) 		0.001
(0.769) 		0.0666
(1.00) 		0.323
(1.00) 		0.179
(1.00) 		0.0188
(1.00)
19q gain 82 (18%) 368 0.111
(1.00) 		0.0555
(1.00) 		0.00699
(1.00) 		0.22
(1.00) 		0.0434
(1.00) 		0.0406
(1.00) 		0.143
(1.00) 		0.0001
(0.0817) 		0.145
(1.00) 		0.645
(1.00) 		0.04
(1.00) 		0.00057
(0.445)
1q loss 57 (13%) 393 0.274
(1.00) 		0.56
(1.00) 		0.00016
(0.129) 		0.0817
(1.00) 		0.441
(1.00) 		0.562
(1.00) 		0.0228
(1.00) 		0.00297
(1.00) 		0.662
(1.00) 		0.00356
(1.00) 		0.188
(1.00) 		0.847
(1.00)
5q loss 77 (17%) 373 0.165
(1.00) 		0.305
(1.00) 		1e-05
(0.00914) 		0.0126
(1.00) 		0.0233
(1.00) 		0.143
(1.00) 		0.0057
(1.00) 		0.00144
(1.00) 		0.903
(1.00) 		0.701
(1.00) 		0.757
(1.00) 		0.351
(1.00)
9p loss 54 (12%) 396 0.573
(1.00) 		0.0651
(1.00) 		8e-05
(0.0654) 		0.0012
(0.92) 		0.907
(1.00) 		0.36
(1.00) 		0.0119
(1.00) 		0.00194
(1.00) 		0.373
(1.00) 		0.276
(1.00) 		0.412
(1.00) 		0.319
(1.00)
17q loss 66 (15%) 384 0.0768
(1.00) 		0.378
(1.00) 		2e-05
(0.0167) 		0.00813
(1.00) 		0.458
(1.00) 		0.509
(1.00) 		0.0572
(1.00) 		0.0293
(1.00) 		0.361
(1.00) 		0.304
(1.00) 		0.702
(1.00) 		0.164
(1.00)
20p loss 44 (10%) 406 0.0889
(1.00) 		0.0025
(1.00) 		0.00022
(0.176) 		0.0927
(1.00) 		0.908
(1.00) 		0.26
(1.00) 		0.00254
(1.00) 		0.0197
(1.00) 		0.828
(1.00) 		0.046
(1.00) 		0.484
(1.00) 		0.626
(1.00)
21q loss 124 (28%) 326 0.0101
(1.00) 		0.0836
(1.00) 		1e-05
(0.00914) 		0.0528
(1.00) 		0.226
(1.00) 		0.6
(1.00) 		0.00886
(1.00) 		0.00997
(1.00) 		0.459
(1.00) 		0.0512
(1.00) 		0.814
(1.00) 		0.379
(1.00)
xq loss 54 (12%) 396 0.0162
(1.00) 		0.251
(1.00) 		0.00017
(0.137) 		0.162
(1.00) 		0.246
(1.00) 		0.374
(1.00) 		0.137
(1.00) 		0.24
(1.00) 		0.07
(1.00) 		0.661
(1.00) 		0.484
(1.00) 		0.0682
(1.00)
1p gain 33 (7%) 417 0.812
(1.00) 		0.634
(1.00) 		0.0276
(1.00) 		0.764
(1.00) 		0.0116
(1.00) 		0.0755
(1.00) 		0.141
(1.00) 		0.161
(1.00) 		0.676
(1.00) 		0.102
(1.00) 		0.309
(1.00) 		0.162
(1.00)
1q gain 79 (18%) 371 0.543
(1.00) 		0.828
(1.00) 		0.0143
(1.00) 		0.154
(1.00) 		0.242
(1.00) 		0.00745
(1.00) 		0.191
(1.00) 		0.507
(1.00) 		0.939
(1.00) 		0.113
(1.00) 		0.0731
(1.00) 		0.485
(1.00)
2p gain 82 (18%) 368 0.0704
(1.00) 		0.0227
(1.00) 		0.00048
(0.377) 		0.0068
(1.00) 		0.11
(1.00) 		0.132
(1.00) 		0.00558
(1.00) 		0.00315
(1.00) 		0.407
(1.00) 		0.0159
(1.00) 		0.901
(1.00) 		0.81
(1.00)
4p gain 12 (3%) 438 0.0559
(1.00) 		0.128
(1.00) 		0.315
(1.00) 		0.922
(1.00) 		0.125
(1.00) 		0.241
(1.00) 		0.611
(1.00) 		0.578
(1.00)
4q gain 17 (4%) 433 0.127
(1.00) 		0.12
(1.00) 		0.096
(1.00) 		0.79
(1.00) 		0.00672
(1.00) 		0.119
(1.00) 		0.247
(1.00) 		0.451
(1.00) 		0.149
(1.00) 		0.136
(1.00)
5p gain 70 (16%) 380 0.417
(1.00) 		0.181
(1.00) 		0.0653
(1.00) 		0.413
(1.00) 		0.466
(1.00) 		0.997
(1.00) 		0.876
(1.00) 		0.0351
(1.00) 		0.821
(1.00) 		0.357
(1.00) 		0.725
(1.00) 		0.558
(1.00)
5q gain 44 (10%) 406 0.875
(1.00) 		0.776
(1.00) 		0.0147
(1.00) 		0.493
(1.00) 		0.478
(1.00) 		0.645
(1.00) 		0.214
(1.00) 		0.0647
(1.00) 		0.505
(1.00) 		0.0941
(1.00) 		1
(1.00) 		0.854
(1.00)
8p gain 132 (29%) 318 0.974
(1.00) 		0.965
(1.00) 		0.00693
(1.00) 		1
(1.00) 		0.303
(1.00) 		0.388
(1.00) 		0.00947
(1.00) 		0.0688
(1.00) 		0.572
(1.00) 		0.183
(1.00) 		0.88
(1.00) 		0.918
(1.00)
9p gain 81 (18%) 369 0.193
(1.00) 		0.135
(1.00) 		0.00081
(0.626) 		0.822
(1.00) 		0.00179
(1.00) 		0.382
(1.00) 		0.558
(1.00) 		0.316
(1.00) 		0.874
(1.00) 		0.924
(1.00) 		0.0716
(1.00) 		0.144
(1.00)
9q gain 70 (16%) 380 0.166
(1.00) 		0.204
(1.00) 		0.024
(1.00) 		0.497
(1.00) 		0.00046
(0.362) 		0.569
(1.00) 		0.874
(1.00) 		0.784
(1.00) 		0.423
(1.00) 		0.264
(1.00) 		0.309
(1.00) 		0.536
(1.00)
10p gain 37 (8%) 413 0.596
(1.00) 		1
(1.00) 		0.0063
(1.00) 		0.865
(1.00) 		0.0216
(1.00) 		0.0716
(1.00) 		0.503
(1.00) 		0.49
(1.00) 		0.422
(1.00) 		0.722
(1.00) 		0.932
(1.00) 		0.354
(1.00)
10q gain 23 (5%) 427 0.17
(1.00) 		0.441
(1.00) 		0.0519
(1.00) 		0.106
(1.00) 		0.366
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.753
(1.00) 		0.862
(1.00) 		0.889
(1.00) 		0.247
(1.00)
12p gain 92 (20%) 358 0.177
(1.00) 		1
(1.00) 		0.00587
(1.00) 		0.00677
(1.00) 		0.724
(1.00) 		0.767
(1.00) 		0.205
(1.00) 		0.291
(1.00) 		0.28
(1.00) 		0.415
(1.00) 		0.533
(1.00) 		0.935
(1.00)
12q gain 86 (19%) 364 0.197
(1.00) 		0.896
(1.00) 		0.00528
(1.00) 		0.00514
(1.00) 		0.546
(1.00) 		0.793
(1.00) 		0.0592
(1.00) 		0.365
(1.00) 		0.112
(1.00) 		0.105
(1.00) 		0.531
(1.00) 		0.658
(1.00)
14q gain 35 (8%) 415 0.343
(1.00) 		0.638
(1.00) 		0.291
(1.00) 		0.924
(1.00) 		0.404
(1.00) 		0.756
(1.00) 		0.238
(1.00) 		0.371
(1.00) 		0.67
(1.00) 		0.183
(1.00) 		0.238
(1.00) 		0.34
(1.00)
15q gain 12 (3%) 438 1
(1.00) 		0.812
(1.00) 		0.348
(1.00) 		0.814
(1.00) 		0.0814
(1.00) 		0.0791
(1.00) 		0.877
(1.00) 		0.963
(1.00) 		0.924
(1.00) 		0.769
(1.00)
17p gain 28 (6%) 422 0.841
(1.00) 		0.563
(1.00) 		0.805
(1.00) 		0.448
(1.00) 		0.211
(1.00) 		0.431
(1.00) 		0.0753
(1.00) 		0.0596
(1.00) 		0.518
(1.00) 		0.826
(1.00) 		0.548
(1.00) 		0.461
(1.00)
21q gain 24 (5%) 426 0.0351
(1.00) 		0.298
(1.00) 		0.00791
(1.00) 		0.812
(1.00) 		0.731
(1.00) 		0.972
(1.00) 		0.391
(1.00) 		0.243
(1.00) 		0.22
(1.00) 		0.267
(1.00)
22q gain 12 (3%) 438 1
(1.00) 		0.788
(1.00) 		0.0505
(1.00) 		0.128
(1.00) 		0.604
(1.00) 		0.322
(1.00) 		0.283
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.829
(1.00) 		0.483
(1.00)
xq gain 74 (16%) 376 0.0141
(1.00) 		0.264
(1.00) 		0.00205
(1.00) 		0.166
(1.00) 		0.13
(1.00) 		0.508
(1.00) 		0.208
(1.00) 		0.832
(1.00) 		0.477
(1.00) 		0.95
(1.00) 		0.325
(1.00) 		0.27
(1.00)
2p loss 6 (1%) 444 0.898
(1.00) 		0.812
(1.00) 		0.311
(1.00) 		0.704
(1.00) 		0.787
(1.00) 		0.0869
(1.00) 		0.131
(1.00) 		0.638
(1.00) 		0.478
(1.00)
2q loss 7 (2%) 443 1
(1.00) 		0.508
(1.00) 		0.59
(1.00) 		0.311
(1.00) 		0.437
(1.00) 		0.0359
(1.00) 		0.0665
(1.00) 		0.39
(1.00) 		0.244
(1.00)
3p loss 55 (12%) 395 0.782
(1.00) 		0.487
(1.00) 		0.0379
(1.00) 		0.349
(1.00) 		0.6
(1.00) 		0.626
(1.00) 		0.258
(1.00) 		0.206
(1.00) 		0.614
(1.00) 		0.605
(1.00) 		0.303
(1.00) 		0.654
(1.00)
3q loss 34 (8%) 416 0.825
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.758
(1.00) 		0.409
(1.00) 		0.873
(1.00) 		0.949
(1.00) 		0.146
(1.00) 		0.263
(1.00) 		0.933
(1.00) 		0.897
(1.00) 		0.126
(1.00)
5p loss 56 (12%) 394 0.823
(1.00) 		0.945
(1.00) 		0.00038
(0.301) 		0.00488
(1.00) 		0.365
(1.00) 		0.74
(1.00) 		0.128
(1.00) 		0.0182
(1.00) 		0.834
(1.00) 		0.735
(1.00) 		0.304
(1.00) 		0.396
(1.00)
6p loss 34 (8%) 416 1
(1.00) 		0.455
(1.00) 		0.557
(1.00) 		0.368
(1.00) 		0.174
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.983
(1.00) 		0.617
(1.00) 		0.786
(1.00) 		0.0261
(1.00) 		0.0833
(1.00)
6q loss 46 (10%) 404 0.822
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.423
(1.00) 		0.201
(1.00) 		0.0979
(1.00) 		0.665
(1.00) 		0.62
(1.00) 		0.607
(1.00) 		0.963
(1.00) 		0.0594
(1.00) 		0.0659
(1.00)
7q loss 3 (1%) 447 0.122
(1.00)
8q loss 25 (6%) 425 0.81
(1.00) 		0.401
(1.00) 		0.005
(1.00) 		0.2
(1.00) 		0.428
(1.00) 		0.662
(1.00) 		0.744
(1.00) 		0.0731
(1.00) 		0.388
(1.00) 		0.745
(1.00) 		0.405
(1.00) 		0.00224
(1.00)
11p loss 51 (11%) 399 0.223
(1.00) 		0.193
(1.00) 		0.0033
(1.00) 		0.00718
(1.00) 		0.807
(1.00) 		0.869
(1.00) 		0.215
(1.00) 		0.0216
(1.00) 		0.911
(1.00) 		0.242
(1.00) 		0.638
(1.00) 		0.769
(1.00)
11q loss 63 (14%) 387 0.0412
(1.00) 		0.0156
(1.00) 		0.00305
(1.00) 		0.00119
(0.914) 		0.602
(1.00) 		0.93
(1.00) 		0.292
(1.00) 		0.00577
(1.00) 		0.841
(1.00) 		0.681
(1.00) 		0.777
(1.00) 		0.836
(1.00)
13q loss 12 (3%) 438 0.874
(1.00) 		0.438
(1.00) 		0.345
(1.00) 		0.0408
(1.00) 		0.00155
(1.00) 		0.0917
(1.00) 		0.665
(1.00) 		0.598
(1.00) 		0.595
(1.00) 		0.106
(1.00) 		0.0355
(1.00) 		0.804
(1.00)
16p loss 31 (7%) 419 0.409
(1.00) 		0.69
(1.00) 		0.584
(1.00) 		0.386
(1.00) 		0.386
(1.00) 		0.0126
(1.00) 		0.0225
(1.00) 		0.139
(1.00) 		0.505
(1.00) 		0.479
(1.00) 		0.624
(1.00) 		1
(1.00)
16q loss 29 (6%) 421 0.406
(1.00) 		0.686
(1.00) 		0.113
(1.00) 		0.576
(1.00) 		0.218
(1.00) 		0.0331
(1.00) 		0.177
(1.00) 		0.293
(1.00) 		0.524
(1.00) 		0.754
(1.00) 		0.624
(1.00) 		1
(1.00)
19p loss 40 (9%) 410 1
(1.00) 		0.343
(1.00) 		0.00753
(1.00) 		0.323
(1.00) 		0.571
(1.00) 		0.354
(1.00) 		0.0459
(1.00) 		0.0131
(1.00) 		0.0422
(1.00) 		0.00509
(1.00) 		0.651
(1.00) 		0.63
(1.00)
19q loss 36 (8%) 414 0.734
(1.00) 		0.704
(1.00) 		0.00982
(1.00) 		0.369
(1.00) 		0.231
(1.00) 		0.132
(1.00) 		0.109
(1.00) 		0.00647
(1.00) 		0.287
(1.00) 		0.0657
(1.00) 		0.321
(1.00) 		0.466
(1.00)
20q loss 4 (1%) 446 0.65
(1.00) 		0.55
(1.00) 		0.525
(1.00) 		0.389
(1.00) 		0.304
(1.00)
'2q gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.082

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
2Q GAIN MUTATED 20 48 10
2Q GAIN WILD-TYPE 183 134 55

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

'3p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
3P GAIN MUTATED 9 34 3
3P GAIN WILD-TYPE 194 148 62

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

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
3Q GAIN MUTATED 2 6 12
3Q GAIN WILD-TYPE 40 66 20

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
3Q GAIN MUTATED 10 49 7
3Q GAIN WILD-TYPE 193 133 58

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

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-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 42 72 32
6P GAIN MUTATED 5 7 16
6P GAIN WILD-TYPE 37 65 16

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

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
6P GAIN MUTATED 15 59 10
6P GAIN WILD-TYPE 188 123 55

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

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S7.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
6Q GAIN MUTATED 5 4 14
6Q GAIN WILD-TYPE 37 68 18

Figure S7.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S8.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
6Q GAIN MUTATED 14 50 12
6Q GAIN WILD-TYPE 189 132 53

Figure S8.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
7P GAIN MUTATED 10 33 26
7P GAIN WILD-TYPE 32 39 6

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

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
7P GAIN MUTATED 70 131 45
7P GAIN WILD-TYPE 133 51 20

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
7P GAIN MUTATED 99 66 72
7P GAIN WILD-TYPE 41 85 71

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
7P GAIN MUTATED 70 55 29 75 8
7P GAIN WILD-TYPE 36 19 61 53 28

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

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S13.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
7Q GAIN MUTATED 8 27 24
7Q GAIN WILD-TYPE 34 45 8

Figure S13.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
7Q GAIN MUTATED 69 115 40
7Q GAIN WILD-TYPE 134 67 25

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

'7q gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
7Q GAIN MUTATED 89 62 64
7Q GAIN WILD-TYPE 51 89 79

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
7Q GAIN MUTATED 64 51 28 67 5
7Q GAIN WILD-TYPE 42 23 62 61 31

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

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S17.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
8Q GAIN MUTATED 69 99 59
8Q GAIN WILD-TYPE 134 83 6

Figure S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.082

Table S18.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
11P GAIN MUTATED 1 5 11
11P GAIN WILD-TYPE 41 67 21

Figure S18.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S19.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
11P GAIN MUTATED 7 40 7
11P GAIN WILD-TYPE 196 142 58

Figure S19.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.25

Table S20.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
11P GAIN MUTATED 25 3 7
11P GAIN WILD-TYPE 93 89 64

Figure S20.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
11P GAIN MUTATED 15 13 2 22 0
11P GAIN WILD-TYPE 91 61 88 106 36

Figure S21.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

Table S22.  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 S22.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S23.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
11Q GAIN MUTATED 1 4 13
11Q GAIN WILD-TYPE 41 68 19

Figure S23.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S24.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
11Q GAIN MUTATED 3 39 9
11Q GAIN WILD-TYPE 200 143 56

Figure S24.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S25.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
11Q GAIN MUTATED 26 4 19
11Q GAIN WILD-TYPE 114 147 124

Figure S25.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S26.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
11Q GAIN MUTATED 16 13 0 20 0
11Q GAIN WILD-TYPE 90 61 90 108 36

Figure S26.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.097

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 46 10 15
13Q GAIN WILD-TYPE 21 15 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 = 3e-05 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
13Q GAIN MUTATED 12 46 27
13Q GAIN WILD-TYPE 30 26 5

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

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
13Q GAIN MUTATED 64 153 39
13Q GAIN WILD-TYPE 139 29 26

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

'13q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
13Q GAIN MUTATED 102 65 80
13Q GAIN WILD-TYPE 38 86 63

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

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
13Q GAIN MUTATED 71 56 25 86 9
13Q GAIN WILD-TYPE 35 18 65 42 27

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

'16p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S32.  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 S32.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S33.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
16P GAIN MUTATED 4 16 21
16P GAIN WILD-TYPE 38 56 11

Figure S33.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S34.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
16P GAIN MUTATED 15 80 12
16P GAIN WILD-TYPE 188 102 53

Figure S34.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S35.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
16P GAIN MUTATED 19 26 8 50 0
16P GAIN WILD-TYPE 87 48 82 78 36

Figure S35.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S36.  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 S36.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S37.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
16Q GAIN MUTATED 3 16 19
16Q GAIN WILD-TYPE 39 56 13

Figure S37.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S38.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
16Q GAIN MUTATED 14 80 11
16Q GAIN WILD-TYPE 189 102 54

Figure S38.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S39.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
16Q GAIN MUTATED 20 26 8 47 0
16Q GAIN WILD-TYPE 86 48 82 81 36

Figure S39.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S40.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
17Q GAIN MUTATED 17 50 15
17Q GAIN WILD-TYPE 186 132 50

Figure S40.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S41.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
17Q GAIN MUTATED 44 15 20
17Q GAIN WILD-TYPE 96 136 123

Figure S41.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S42.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
18P GAIN MUTATED 14 0 8
18P GAIN WILD-TYPE 189 182 57

Figure S42.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S43.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
18P GAIN MUTATED 3 1 13 1 4
18P GAIN WILD-TYPE 103 73 77 127 32

Figure S43.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S44.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
18Q GAIN MUTATED 0 1 8 0 4
18Q GAIN WILD-TYPE 106 73 82 128 32

Figure S44.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S45.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
19P GAIN MUTATED 17 46 10
19P GAIN WILD-TYPE 186 136 55

Figure S45.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.082

Table S46.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
19Q GAIN MUTATED 17 25 12 23 0
19Q GAIN WILD-TYPE 89 49 78 105 36

Figure S46.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
20P GAIN MUTATED 10 52 21
20P GAIN WILD-TYPE 32 20 11

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

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
20P GAIN MUTATED 74 135 34
20P GAIN WILD-TYPE 129 47 31

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

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
20P GAIN MUTATED 89 59 85
20P GAIN WILD-TYPE 51 92 58

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

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
20P GAIN MUTATED 69 42 29 89 4
20P GAIN WILD-TYPE 37 32 61 39 32

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

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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 = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
20Q GAIN MUTATED 12 61 31
20Q GAIN WILD-TYPE 30 11 1

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

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
20Q GAIN MUTATED 88 179 54
20Q GAIN WILD-TYPE 115 3 11

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

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
20Q GAIN MUTATED 112 46 44
20Q GAIN WILD-TYPE 6 46 27

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

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S55.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
20Q GAIN MUTATED 135 72 102
20Q GAIN WILD-TYPE 5 79 41

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S56.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
20Q GAIN MUTATED 91 68 33 112 5
20Q GAIN WILD-TYPE 15 6 57 16 31

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S57.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
1P LOSS MUTATED 23 68 7
1P LOSS WILD-TYPE 180 114 58

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S58.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
1P LOSS MUTATED 24 28 7 33 3
1P LOSS WILD-TYPE 82 46 83 95 33

Figure S58.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S59.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
1Q LOSS MUTATED 13 38 6
1Q LOSS WILD-TYPE 190 144 59

Figure S59.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S60.  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 S60.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S61.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
4P LOSS MUTATED 29 92 17
4P LOSS WILD-TYPE 174 90 48

Figure S61.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S62.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
4P LOSS MUTATED 49 14 20
4P LOSS WILD-TYPE 69 78 51

Figure S62.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.082

Table S63.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
4P LOSS MUTATED 60 29 42
4P LOSS WILD-TYPE 80 122 101

Figure S63.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S64.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
4P LOSS MUTATED 37 33 8 49 4
4P LOSS WILD-TYPE 69 41 82 79 32

Figure S64.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.21

Table S65.  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 25 1 9
4Q LOSS WILD-TYPE 28 36 28 12

Figure S65.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S66.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
4Q LOSS MUTATED 24 89 13
4Q LOSS WILD-TYPE 179 93 52

Figure S66.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S67.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
4Q LOSS MUTATED 47 10 18
4Q LOSS WILD-TYPE 71 82 53

Figure S67.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S68.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
4Q LOSS MUTATED 35 30 6 44 4
4Q LOSS WILD-TYPE 71 44 84 84 32

Figure S68.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S69.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
5Q LOSS MUTATED 15 46 16
5Q LOSS WILD-TYPE 188 136 49

Figure S69.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S70.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
8P LOSS MUTATED 23 86 33
8P LOSS WILD-TYPE 180 96 32

Figure S70.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S71.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
8P LOSS MUTATED 62 25 50
8P LOSS WILD-TYPE 78 126 93

Figure S71.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S72.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
8P LOSS MUTATED 34 35 11 54 3
8P LOSS WILD-TYPE 72 39 79 74 33

Figure S72.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.065

Table S73.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
9P LOSS MUTATED 11 35 8
9P LOSS WILD-TYPE 192 147 57

Figure S73.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.089

Table S74.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
9Q LOSS MUTATED 11 35 8
9Q LOSS WILD-TYPE 192 147 57

Figure S74.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S75.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
9Q LOSS MUTATED 24 2 10
9Q LOSS WILD-TYPE 94 90 61

Figure S75.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S76.  Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
10P LOSS MUTATED 11 44 14
10P LOSS WILD-TYPE 192 138 51

Figure S76.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.089

Table S77.  Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
10P LOSS MUTATED 17 21 6 21 0
10P LOSS WILD-TYPE 89 53 84 107 36

Figure S77.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S78.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
10Q LOSS MUTATED 10 48 15
10Q LOSS WILD-TYPE 193 134 50

Figure S78.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S79.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
10Q LOSS MUTATED 19 22 4 24 0
10Q LOSS WILD-TYPE 87 52 86 104 36

Figure S79.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S80.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
12P LOSS MUTATED 2 38 7
12P LOSS WILD-TYPE 201 144 58

Figure S80.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S81.  Gene #62: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
12P LOSS MUTATED 13 14 1 18 0
12P LOSS WILD-TYPE 93 60 89 110 36

Figure S81.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S82.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
12Q LOSS MUTATED 5 37 7
12Q LOSS WILD-TYPE 198 145 58

Figure S82.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #63: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
12Q LOSS MUTATED 28 7 14
12Q LOSS WILD-TYPE 112 144 129

Figure S83.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S84.  Gene #63: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
12Q LOSS MUTATED 15 14 2 18 0
12Q LOSS WILD-TYPE 91 60 88 110 36

Figure S84.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S85.  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 10
14Q LOSS WILD-TYPE 30 28 27 11

Figure S85.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S86.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
14Q LOSS MUTATED 4 29 17
14Q LOSS WILD-TYPE 38 43 15

Figure S86.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S87.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
14Q LOSS MUTATED 19 110 10
14Q LOSS WILD-TYPE 184 72 55

Figure S87.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S88.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
14Q LOSS MUTATED 54 12 15
14Q LOSS WILD-TYPE 64 80 56

Figure S88.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S89.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
14Q LOSS MUTATED 63 20 50
14Q LOSS WILD-TYPE 77 131 93

Figure S89.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S90.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
14Q LOSS MUTATED 41 31 4 56 1
14Q LOSS WILD-TYPE 65 43 86 72 35

Figure S90.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S91.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
15Q LOSS MUTATED 27 115 15
15Q LOSS WILD-TYPE 176 67 50

Figure S91.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S92.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
15Q LOSS MUTATED 75 27 48
15Q LOSS WILD-TYPE 65 124 95

Figure S92.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S93.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
15Q LOSS MUTATED 43 38 8 59 2
15Q LOSS WILD-TYPE 63 36 82 69 34

Figure S93.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S94.  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 S94.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S95.  Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
17P LOSS MUTATED 8 46 24
17P LOSS WILD-TYPE 34 26 8

Figure S95.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S96.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
17P LOSS MUTATED 45 147 45
17P LOSS WILD-TYPE 158 35 20

Figure S96.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S97.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
17P LOSS MUTATED 87 28 32
17P LOSS WILD-TYPE 31 64 39

Figure S97.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S98.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
17P LOSS MUTATED 101 48 79
17P LOSS WILD-TYPE 39 103 64

Figure S98.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S99.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
17P LOSS MUTATED 70 50 18 86 4
17P LOSS WILD-TYPE 36 24 72 42 32

Figure S99.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S100.  Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
17Q LOSS MUTATED 14 43 9
17Q LOSS WILD-TYPE 189 139 56

Figure S100.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S101.  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 S101.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S102.  Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
18P LOSS MUTATED 6 46 28
18P LOSS WILD-TYPE 36 26 4

Figure S102.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S103.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
18P LOSS MUTATED 46 167 41
18P LOSS WILD-TYPE 157 15 24

Figure S103.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S104.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
18P LOSS MUTATED 103 26 33
18P LOSS WILD-TYPE 15 66 38

Figure S104.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S105.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
18P LOSS MUTATED 124 42 78
18P LOSS WILD-TYPE 16 109 65

Figure S105.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S106.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
18P LOSS MUTATED 79 58 14 92 1
18P LOSS WILD-TYPE 27 16 76 36 35

Figure S106.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S107.  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 S107.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S108.  Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
18Q LOSS MUTATED 7 48 28
18Q LOSS WILD-TYPE 35 24 4

Figure S108.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S109.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
18Q LOSS MUTATED 54 168 49
18Q LOSS WILD-TYPE 149 14 16

Figure S109.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S110.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 92 71
18Q LOSS MUTATED 104 34 37
18Q LOSS WILD-TYPE 14 58 34

Figure S110.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S111.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
18Q LOSS MUTATED 126 53 82
18Q LOSS WILD-TYPE 14 98 61

Figure S111.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S112.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
18Q LOSS MUTATED 83 62 20 95 1
18Q LOSS WILD-TYPE 23 12 70 33 35

Figure S112.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S113.  Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
20P LOSS MUTATED 8 24 12
20P LOSS WILD-TYPE 195 158 53

Figure S113.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S114.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
21Q LOSS MUTATED 35 79 10
21Q LOSS WILD-TYPE 168 103 55

Figure S114.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S115.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
22Q LOSS MUTATED 34 101 11
22Q LOSS WILD-TYPE 169 81 54

Figure S115.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.25

Table S116.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 151 143
22Q LOSS MUTATED 60 32 48
22Q LOSS WILD-TYPE 80 119 95

Figure S116.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S117.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 106 74 90 128 36
22Q LOSS MUTATED 38 33 10 56 3
22Q LOSS WILD-TYPE 68 41 80 72 33

Figure S117.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S118.  Gene #79: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 182 65
XQ LOSS MUTATED 13 36 5
XQ LOSS WILD-TYPE 190 146 60

Figure S118.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 450

  • 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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