Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1MC8XRH
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/C1MC8XRH
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 71 arm-level events and 8 molecular subtypes across 224 patients, 111 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 8q gain cnv correlated to 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 5p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 10q loss cnv correlated to 'MRNASEQ_CNMF'.

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

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • 17p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

  • xq loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 111 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
16q gain 114 (51%) 110 1e-05
(0.00565) 		0.0579
(1.00) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00011
(0.0522) 		1e-05
(0.00565) 		0.00032
(0.147) 		2e-05
(0.01)
3p gain 63 (28%) 161 1e-05
(0.00565) 		0.00033
(0.151) 		1e-05
(0.00565) 		9e-05
(0.0429) 		0.0789
(1.00) 		0.0031
(1.00) 		0.235
(1.00) 		1e-05
(0.00565)
7p gain 133 (59%) 91 1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.124
(1.00) 		0.00594
(1.00) 		0.0235
(1.00) 		1e-05
(0.00565)
7q gain 134 (60%) 90 1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.165
(1.00) 		0.00775
(1.00) 		0.0365
(1.00) 		2e-05
(0.01)
16p gain 118 (53%) 106 1e-05
(0.00565) 		0.0969
(1.00) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00102
(0.451) 		1e-05
(0.00565) 		0.00071
(0.319) 		8e-05
(0.0384)
17p gain 133 (59%) 91 1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.0218
(1.00) 		0.00545
(1.00) 		0.0199
(1.00) 		1e-05
(0.00565)
xq gain 70 (31%) 154 1e-05
(0.00565) 		0.00022
(0.103) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00092
(0.408) 		0.0172
(1.00) 		0.00089
(0.397) 		2e-05
(0.01)
9p loss 27 (12%) 197 1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		4e-05
(0.0197) 		0.0512
(1.00) 		0.0935
(1.00) 		0.33
(1.00) 		5e-05
(0.0243)
9q loss 29 (13%) 195 1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		2e-05
(0.01) 		0.0198
(1.00) 		0.016
(1.00) 		0.149
(1.00) 		2e-05
(0.01)
17q gain 149 (67%) 75 1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.156
(1.00) 		0.0166
(1.00) 		0.188
(1.00) 		0.00063
(0.285)
4p loss 21 (9%) 203 6e-05
(0.029) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00108
(0.476) 		0.193
(1.00) 		0.0122
(1.00) 		0.843
(1.00) 		1e-05
(0.00565)
4q loss 22 (10%) 202 6e-05
(0.029) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00311
(1.00) 		0.304
(1.00) 		0.0569
(1.00) 		0.886
(1.00) 		2e-05
(0.01)
13q loss 21 (9%) 203 5e-05
(0.0243) 		5e-05
(0.0243) 		1e-05
(0.00565) 		0.00117
(0.511) 		0.0104
(1.00) 		0.00147
(0.635) 		0.0249
(1.00) 		1e-05
(0.00565)
18q loss 35 (16%) 189 0.00019
(0.0889) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00541
(1.00) 		0.0477
(1.00) 		0.00281
(1.00) 		0.0746
(1.00) 		0.00041
(0.187)
22q loss 50 (22%) 174 8e-05
(0.0384) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.0396
(1.00) 		0.9
(1.00) 		0.912
(1.00) 		0.392
(1.00) 		2e-05
(0.01)
1q gain 16 (7%) 208 0.0136
(1.00) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00612
(1.00) 		0.491
(1.00) 		0.0193
(1.00) 		0.552
(1.00) 		4e-05
(0.0197)
3q gain 74 (33%) 150 1e-05
(0.00565) 		0.00606
(1.00) 		2e-05
(0.01) 		0.00062
(0.281) 		0.0568
(1.00) 		0.00427
(1.00) 		0.539
(1.00) 		1e-05
(0.00565)
3p loss 17 (8%) 207 0.00072
(0.323) 		4e-05
(0.0197) 		1e-05
(0.00565) 		0.00335
(1.00) 		0.158
(1.00) 		0.194
(1.00) 		0.107
(1.00) 		4e-05
(0.0197)
18p loss 34 (15%) 190 0.00024
(0.112) 		1e-05
(0.00565) 		1e-05
(0.00565) 		0.00618
(1.00) 		0.193
(1.00) 		0.00536
(1.00) 		0.269
(1.00) 		0.00176
(0.755)
5q gain 30 (13%) 194 0.00024
(0.112) 		0.00387
(1.00) 		0.0443
(1.00) 		0.00054
(0.246) 		0.264
(1.00) 		0.0538
(1.00) 		0.134
(1.00) 		0.0214
(1.00)
10p loss 13 (6%) 211 0.00443
(1.00) 		0.00029
(0.134) 		8e-05
(0.0384) 		0.158
(1.00) 		0.146
(1.00) 		0.933
(1.00) 		0.459
(1.00) 		0.0402
(1.00)
11q loss 16 (7%) 208 0.00028
(0.129) 		0.0005
(0.228) 		0.00153
(0.659) 		0.259
(1.00) 		0.518
(1.00) 		0.53
(1.00) 		0.615
(1.00) 		0.126
(1.00)
14q loss 39 (17%) 185 1e-05
(0.00565) 		0.00605
(1.00) 		5e-05
(0.0243) 		0.00146
(0.632) 		0.211
(1.00) 		0.491
(1.00) 		0.362
(1.00) 		0.0781
(1.00)
15q loss 25 (11%) 199 0.00024
(0.112) 		0.00093
(0.412) 		0.00011
(0.0522) 		0.0175
(1.00) 		0.149
(1.00) 		0.112
(1.00) 		0.252
(1.00) 		0.0277
(1.00)
17p loss 10 (4%) 214 0.0199
(1.00) 		1e-05
(0.00565) 		0.00011
(0.0522) 		0.0166
(1.00) 		0.0853
(1.00) 		0.0267
(1.00) 		0.096
(1.00) 		0.00089
(0.397)
xq loss 21 (9%) 203 0.00112
(0.491) 		0.00029
(0.134) 		0.0001
(0.0476) 		0.212
(1.00) 		0.0271
(1.00) 		0.499
(1.00) 		0.0888
(1.00) 		0.0756
(1.00)
1p gain 7 (3%) 217 0.06
(1.00) 		0.00128
(0.556) 		0.00964
(1.00) 		0.0413
(1.00) 		0.312
(1.00) 		0.235
(1.00) 		0.307
(1.00) 		0.00012
(0.0565)
2p gain 39 (17%) 185 1e-05
(0.00565) 		0.0139
(1.00) 		0.0485
(1.00) 		0.0952
(1.00) 		0.0169
(1.00) 		0.613
(1.00) 		0.0504
(1.00) 		0.368
(1.00)
2q gain 42 (19%) 182 1e-05
(0.00565) 		0.0231
(1.00) 		0.0982
(1.00) 		0.0981
(1.00) 		0.0652
(1.00) 		0.417
(1.00) 		0.223
(1.00) 		0.707
(1.00)
5p gain 30 (13%) 194 0.00019
(0.0889) 		0.00334
(1.00) 		0.0256
(1.00) 		0.00064
(0.289) 		0.458
(1.00) 		0.069
(1.00) 		0.135
(1.00) 		0.0163
(1.00)
8q gain 19 (8%) 205 0.0979
(1.00) 		4e-05
(0.0197) 		0.00433
(1.00) 		0.355
(1.00) 		0.152
(1.00) 		0.0141
(1.00) 		0.149
(1.00) 		0.00344
(1.00)
12p gain 91 (41%) 133 1e-05
(0.00565) 		0.128
(1.00) 		0.137
(1.00) 		0.00295
(1.00) 		0.0165
(1.00) 		0.115
(1.00) 		0.0943
(1.00) 		0.00202
(0.865)
12q gain 91 (41%) 133 1e-05
(0.00565) 		0.13
(1.00) 		0.133
(1.00) 		0.00311
(1.00) 		0.0168
(1.00) 		0.116
(1.00) 		0.094
(1.00) 		0.00235
(1.00)
20p gain 77 (34%) 147 2e-05
(0.01) 		0.0562
(1.00) 		0.0505
(1.00) 		0.0144
(1.00) 		0.0217
(1.00) 		0.0135
(1.00) 		0.00864
(1.00) 		0.042
(1.00)
20q gain 79 (35%) 145 2e-05
(0.01) 		0.0673
(1.00) 		0.0975
(1.00) 		0.0198
(1.00) 		0.0316
(1.00) 		0.026
(1.00) 		0.014
(1.00) 		0.0409
(1.00)
1p loss 23 (10%) 201 6e-05
(0.029) 		0.0776
(1.00) 		0.00292
(1.00) 		0.496
(1.00) 		0.889
(1.00) 		0.29
(1.00) 		0.789
(1.00) 		0.459
(1.00)
5p loss 7 (3%) 217 0.0716
(1.00) 		0.00117
(0.511) 		0.0301
(1.00) 		0.015
(1.00) 		0.0184
(1.00) 		0.015
(1.00) 		0.0182
(1.00) 		0.00015
(0.0703)
5q loss 7 (3%) 217 0.0711
(1.00) 		0.0011
(0.483) 		0.0291
(1.00) 		0.0151
(1.00) 		0.0188
(1.00) 		0.0153
(1.00) 		0.0194
(1.00) 		1e-05
(0.00565)
10q loss 13 (6%) 211 0.00459
(1.00) 		0.00127
(0.552) 		0.00011
(0.0522) 		0.12
(1.00) 		0.0379
(1.00) 		0.872
(1.00) 		0.183
(1.00) 		0.0155
(1.00)
21q loss 35 (16%) 189 0.00012
(0.0565) 		0.306
(1.00) 		0.155
(1.00) 		0.971
(1.00) 		0.271
(1.00) 		0.434
(1.00) 		0.337
(1.00) 		0.101
(1.00)
4p gain 7 (3%) 217 0.377
(1.00) 		0.169
(1.00) 		0.188
(1.00) 		0.896
(1.00) 		0.799
(1.00) 		0.785
(1.00) 		0.798
(1.00) 		0.869
(1.00)
4q gain 6 (3%) 218 0.526
(1.00) 		0.168
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.45
(1.00) 		0.58
(1.00) 		0.445
(1.00) 		0.945
(1.00)
6p gain 9 (4%) 215 0.00497
(1.00) 		0.0173
(1.00) 		0.0168
(1.00) 		0.493
(1.00) 		0.142
(1.00) 		0.154
(1.00) 		0.521
(1.00) 		0.0749
(1.00)
6q gain 7 (3%) 217 0.0243
(1.00) 		0.0116
(1.00) 		0.105
(1.00) 		0.329
(1.00) 		0.457
(1.00) 		0.479
(1.00) 		0.507
(1.00) 		0.102
(1.00)
8p gain 15 (7%) 209 0.329
(1.00) 		0.00393
(1.00) 		0.0747
(1.00) 		0.478
(1.00) 		0.477
(1.00) 		0.156
(1.00) 		0.716
(1.00) 		0.0244
(1.00)
9p gain 3 (1%) 221 0.379
(1.00) 		0.154
(1.00) 		0.653
(1.00) 		0.776
(1.00) 		0.456
(1.00) 		0.776
(1.00) 		0.0169
(1.00)
10p gain 8 (4%) 216 0.628
(1.00) 		0.11
(1.00) 		0.161
(1.00) 		0.821
(1.00) 		0.0422
(1.00) 		0.576
(1.00) 		0.155
(1.00) 		0.17
(1.00)
10q gain 8 (4%) 216 0.631
(1.00) 		0.109
(1.00) 		0.158
(1.00) 		0.822
(1.00) 		0.0428
(1.00) 		0.576
(1.00) 		0.155
(1.00) 		0.171
(1.00)
11p gain 12 (5%) 212 0.065
(1.00) 		0.00619
(1.00) 		0.0292
(1.00) 		0.0231
(1.00) 		0.707
(1.00) 		0.862
(1.00) 		0.708
(1.00) 		0.147
(1.00)
11q gain 10 (4%) 214 0.0201
(1.00) 		0.00452
(1.00) 		0.0231
(1.00) 		0.0589
(1.00) 		0.921
(1.00) 		1
(1.00) 		0.922
(1.00) 		0.101
(1.00)
13q gain 25 (11%) 199 0.00628
(1.00) 		0.815
(1.00) 		0.199
(1.00) 		0.632
(1.00) 		0.773
(1.00) 		0.084
(1.00) 		0.622
(1.00) 		0.789
(1.00)
14q gain 3 (1%) 221 0.272
(1.00) 		0.0384
(1.00) 		0.596
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.018
(1.00)
15q gain 5 (2%) 219 0.141
(1.00) 		0.0383
(1.00) 		0.257
(1.00) 		0.624
(1.00) 		0.534
(1.00) 		0.511
(1.00) 		0.526
(1.00) 		0.109
(1.00)
18p gain 11 (5%) 213 0.577
(1.00) 		0.0636
(1.00) 		0.451
(1.00) 		0.431
(1.00) 		0.193
(1.00) 		0.14
(1.00) 		0.195
(1.00) 		0.852
(1.00)
18q gain 8 (4%) 216 0.327
(1.00) 		0.0403
(1.00) 		0.55
(1.00) 		0.323
(1.00) 		0.406
(1.00) 		0.0156
(1.00) 		0.397
(1.00) 		0.302
(1.00)
19p gain 5 (2%) 219 0.14
(1.00) 		0.853
(1.00) 		0.0231
(1.00) 		0.329
(1.00) 		0.744
(1.00) 		0.61
(1.00) 		0.737
(1.00) 		0.166
(1.00)
19q gain 5 (2%) 219 0.142
(1.00) 		0.856
(1.00) 		0.0245
(1.00) 		0.326
(1.00) 		0.743
(1.00) 		0.608
(1.00) 		0.74
(1.00) 		0.164
(1.00)
21q gain 14 (6%) 210 1
(1.00) 		0.232
(1.00) 		0.111
(1.00) 		0.65
(1.00) 		0.139
(1.00) 		0.243
(1.00) 		0.126
(1.00) 		0.881
(1.00)
22q gain 4 (2%) 220 0.49
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.218
(1.00) 		0.17
(1.00) 		0.431
(1.00) 		0.836
(1.00) 		0.779
(1.00)
1q loss 16 (7%) 208 0.00057
(0.259) 		0.58
(1.00) 		0.306
(1.00) 		0.392
(1.00) 		0.55
(1.00) 		0.0968
(1.00) 		0.648
(1.00) 		0.462
(1.00)
2p loss 3 (1%) 221 0.274
(1.00) 		0.0372
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.0577
(1.00)
3q loss 5 (2%) 219 0.141
(1.00) 		0.0379
(1.00) 		0.0235
(1.00) 		0.107
(1.00) 		0.625
(1.00) 		0.3
(1.00) 		0.627
(1.00) 		0.474
(1.00)
6p loss 16 (7%) 208 0.00232
(0.991) 		0.241
(1.00) 		0.0132
(1.00) 		0.158
(1.00) 		0.136
(1.00) 		0.118
(1.00) 		0.0565
(1.00) 		0.024
(1.00)
6q loss 19 (8%) 205 0.00081
(0.362) 		0.0404
(1.00) 		0.00163
(0.701) 		0.262
(1.00) 		0.63
(1.00) 		0.447
(1.00) 		0.756
(1.00) 		0.0119
(1.00)
8p loss 11 (5%) 213 0.0631
(1.00) 		0.569
(1.00) 		0.00935
(1.00) 		0.0376
(1.00) 		0.548
(1.00) 		0.78
(1.00) 		0.427
(1.00) 		0.195
(1.00)
8q loss 6 (3%) 218 0.0299
(1.00) 		0.857
(1.00) 		0.0739
(1.00) 		0.328
(1.00) 		0.61
(1.00) 		0.268
(1.00) 		0.601
(1.00) 		0.348
(1.00)
11p loss 14 (6%) 210 0.00109
(0.48) 		0.00303
(1.00) 		0.00338
(1.00) 		0.0671
(1.00) 		0.241
(1.00) 		0.155
(1.00) 		0.308
(1.00) 		0.0125
(1.00)
16p loss 4 (2%) 220 0.267
(1.00) 		0.00932
(1.00) 		0.0446
(1.00) 		0.274
(1.00) 		1
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.0761
(1.00)
16q loss 6 (3%) 218 0.126
(1.00) 		0.00066
(0.297) 		0.00922
(1.00) 		0.146
(1.00) 		0.377
(1.00) 		0.192
(1.00) 		0.38
(1.00) 		0.00796
(1.00)
19p loss 13 (6%) 211 0.00722
(1.00) 		0.00383
(1.00) 		0.0378
(1.00) 		0.398
(1.00) 		0.137
(1.00) 		0.494
(1.00) 		0.15
(1.00) 		0.15
(1.00)
19q loss 12 (5%) 212 0.00702
(1.00) 		0.01
(1.00) 		0.0501
(1.00) 		0.932
(1.00) 		0.177
(1.00) 		0.551
(1.00) 		0.214
(1.00) 		0.112
(1.00)
'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.057

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
1P GAIN MUTATED 0 3 0 0 0 0 4
1P GAIN WILD-TYPE 27 31 36 32 35 40 16

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
1Q GAIN MUTATED 1 13 1
1Q GAIN WILD-TYPE 55 43 95

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
1Q GAIN MUTATED 1 14 0 0
1Q GAIN WILD-TYPE 46 56 62 32

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
1Q GAIN MUTATED 1 6 0 0 3 0 6
1Q GAIN WILD-TYPE 26 28 36 32 32 40 14

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
2P GAIN MUTATED 1 15 23
2P GAIN WILD-TYPE 83 92 10

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
2Q GAIN MUTATED 1 16 25
2Q GAIN WILD-TYPE 83 91 8

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
3P GAIN MUTATED 31 6 26
3P GAIN WILD-TYPE 53 101 7

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
3P GAIN MUTATED 16 5 36
3P GAIN WILD-TYPE 40 51 60

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S9.  Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
3P GAIN MUTATED 23 5 25 8
3P GAIN WILD-TYPE 24 65 37 24

Figure S9.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.043

Table S10.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
3P GAIN MUTATED 21 9 31
3P GAIN WILD-TYPE 52 63 35

Figure S10.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S11.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
3P GAIN MUTATED 13 1 11 8 5 22 3
3P GAIN WILD-TYPE 14 33 25 24 30 18 17

Figure S11.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
3Q GAIN MUTATED 33 13 28
3Q GAIN WILD-TYPE 51 94 5

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
3Q GAIN MUTATED 26 8 25 13
3Q GAIN WILD-TYPE 21 62 37 19

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
3Q GAIN MUTATED 16 2 12 9 6 25 4
3Q GAIN WILD-TYPE 11 32 24 23 29 15 16

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.089

Table S15.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
5P GAIN MUTATED 2 21 7
5P GAIN WILD-TYPE 82 86 26

Figure S15.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
5Q GAIN MUTATED 2 21 7
5Q GAIN WILD-TYPE 82 86 26

Figure S16.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.25

Table S17.  Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
5Q GAIN MUTATED 18 9 2
5Q GAIN WILD-TYPE 55 63 64

Figure S17.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
7P GAIN MUTATED 79 27 27
7P GAIN WILD-TYPE 5 80 6

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S19.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
7P GAIN MUTATED 28 17 78
7P GAIN WILD-TYPE 28 39 18

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
7P GAIN MUTATED 27 20 55 25
7P GAIN WILD-TYPE 20 50 7 7

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
7P GAIN MUTATED 31 36 60
7P GAIN WILD-TYPE 42 36 6

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S22.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
7P GAIN MUTATED 15 9 27 24 20 32 6
7P GAIN WILD-TYPE 12 25 9 8 15 8 14

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S23.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
7Q GAIN MUTATED 79 28 27
7Q GAIN WILD-TYPE 5 79 6

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
7Q GAIN MUTATED 28 18 78
7Q GAIN WILD-TYPE 28 38 18

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S25.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
7Q GAIN MUTATED 27 21 55 25
7Q GAIN WILD-TYPE 20 49 7 7

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S26.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
7Q GAIN MUTATED 32 36 60
7Q GAIN WILD-TYPE 41 36 6

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S27.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
7Q GAIN MUTATED 15 10 27 24 20 32 6
7Q GAIN WILD-TYPE 12 24 9 8 15 8 14

Figure S27.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S28.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
8Q GAIN MUTATED 2 13 2
8Q GAIN WILD-TYPE 54 43 94

Figure S28.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S29.  Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
12P GAIN MUTATED 39 28 24
12P GAIN WILD-TYPE 45 79 9

Figure S29.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S30.  Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
12Q GAIN MUTATED 39 28 24
12Q GAIN WILD-TYPE 45 79 9

Figure S30.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S31.  Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
16P GAIN MUTATED 55 34 29
16P GAIN WILD-TYPE 29 73 4

Figure S31.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S32.  Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
16P GAIN MUTATED 39 22 37 15
16P GAIN WILD-TYPE 8 48 25 17

Figure S32.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S33.  Gene #27: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
16P GAIN MUTATED 44 18 51
16P GAIN WILD-TYPE 29 54 15

Figure S33.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S34.  Gene #27: '16p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 48 71
16P GAIN MUTATED 60 37 21
16P GAIN WILD-TYPE 45 11 50

Figure S34.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.038

Table S35.  Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
16P GAIN MUTATED 18 15 22 12 14 32 5
16P GAIN WILD-TYPE 9 19 14 20 21 8 15

Figure S35.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S36.  Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
16Q GAIN MUTATED 54 31 29
16Q GAIN WILD-TYPE 30 76 4

Figure S36.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S37.  Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
16Q GAIN MUTATED 39 19 36 15
16Q GAIN WILD-TYPE 8 51 26 17

Figure S37.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S38.  Gene #28: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
16Q GAIN MUTATED 42 17 50
16Q GAIN WILD-TYPE 31 55 16

Figure S38.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S39.  Gene #28: '16q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 72 78
16Q GAIN MUTATED 42 47 25
16Q GAIN WILD-TYPE 32 25 53

Figure S39.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S40.  Gene #28: '16q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 48 71
16Q GAIN MUTATED 57 37 20
16Q GAIN WILD-TYPE 48 11 51

Figure S40.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.15

Table S41.  Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 69 81
16Q GAIN MUTATED 45 42 27
16Q GAIN WILD-TYPE 29 27 54

Figure S41.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S42.  Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
16Q GAIN MUTATED 18 12 22 11 14 32 5
16Q GAIN WILD-TYPE 9 22 14 21 21 8 15

Figure S42.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S43.  Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
17P GAIN MUTATED 80 25 28
17P GAIN WILD-TYPE 4 82 5

Figure S43.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S44.  Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
17P GAIN MUTATED 27 16 80
17P GAIN WILD-TYPE 29 40 16

Figure S44.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S45.  Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
17P GAIN MUTATED 32 19 54 22
17P GAIN WILD-TYPE 15 51 8 10

Figure S45.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S46.  Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
17P GAIN MUTATED 35 33 59
17P GAIN WILD-TYPE 38 39 7

Figure S46.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S47.  Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
17P GAIN MUTATED 14 9 27 25 18 33 7
17P GAIN WILD-TYPE 13 25 9 7 17 7 13

Figure S47.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S48.  Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
17Q GAIN MUTATED 81 38 30
17Q GAIN WILD-TYPE 3 69 3

Figure S48.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S49.  Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
17Q GAIN MUTATED 31 27 80
17Q GAIN WILD-TYPE 25 29 16

Figure S49.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S50.  Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
17Q GAIN MUTATED 35 31 54 23
17Q GAIN WILD-TYPE 12 39 8 9

Figure S50.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S51.  Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
17Q GAIN MUTATED 44 40 59
17Q GAIN WILD-TYPE 29 32 7

Figure S51.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S52.  Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
20P GAIN MUTATED 34 22 21
20P GAIN WILD-TYPE 50 85 12

Figure S52.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S53.  Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
20Q GAIN MUTATED 34 24 21
20Q GAIN WILD-TYPE 50 83 12

Figure S53.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S54.  Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
XQ GAIN MUTATED 37 10 23
XQ GAIN WILD-TYPE 47 97 10

Figure S54.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.1

Table S55.  Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
XQ GAIN MUTATED 11 9 42
XQ GAIN WILD-TYPE 45 47 54

Figure S55.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S56.  Gene #39: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
XQ GAIN MUTATED 22 9 32 6
XQ GAIN WILD-TYPE 25 61 30 26

Figure S56.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S57.  Gene #39: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
XQ GAIN MUTATED 22 10 37
XQ GAIN WILD-TYPE 51 62 29

Figure S57.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S58.  Gene #39: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
XQ GAIN MUTATED 9 3 17 12 4 21 4
XQ GAIN WILD-TYPE 18 31 19 20 31 19 16

Figure S58.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S59.  Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
1P LOSS MUTATED 0 17 6
1P LOSS WILD-TYPE 84 90 27

Figure S59.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S60.  Gene #43: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
3P LOSS MUTATED 3 12 1
3P LOSS WILD-TYPE 53 44 95

Figure S60.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S61.  Gene #43: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
3P LOSS MUTATED 1 14 0 0
3P LOSS WILD-TYPE 46 56 62 32

Figure S61.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S62.  Gene #43: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
3P LOSS MUTATED 0 9 1 0 5 0 2
3P LOSS WILD-TYPE 27 25 35 32 30 40 18

Figure S62.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S63.  Gene #45: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
4P LOSS MUTATED 0 16 5
4P LOSS WILD-TYPE 84 91 28

Figure S63.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S64.  Gene #45: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
4P LOSS MUTATED 3 16 1
4P LOSS WILD-TYPE 53 40 95

Figure S64.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S65.  Gene #45: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
4P LOSS MUTATED 1 19 0 0
4P LOSS WILD-TYPE 46 51 62 32

Figure S65.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S66.  Gene #45: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
4P LOSS MUTATED 1 5 3 0 2 0 10
4P LOSS WILD-TYPE 26 29 33 32 33 40 10

Figure S66.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S67.  Gene #46: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
4Q LOSS MUTATED 0 17 5
4Q LOSS WILD-TYPE 84 90 28

Figure S67.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S68.  Gene #46: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
4Q LOSS MUTATED 3 17 1
4Q LOSS WILD-TYPE 53 39 95

Figure S68.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S69.  Gene #46: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
4Q LOSS MUTATED 1 20 0 0
4Q LOSS WILD-TYPE 46 50 62 32

Figure S69.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S70.  Gene #46: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
4Q LOSS MUTATED 1 6 3 0 2 1 9
4Q LOSS WILD-TYPE 26 28 33 32 33 39 11

Figure S70.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.07

Table S71.  Gene #47: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
5P LOSS MUTATED 0 0 0 0 1 1 5
5P LOSS WILD-TYPE 27 34 36 32 34 39 15

Figure S71.  Get High-res Image Gene #47: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S72.  Gene #48: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
5Q LOSS MUTATED 0 0 0 0 0 1 6
5Q LOSS WILD-TYPE 27 34 36 32 35 39 14

Figure S72.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S73.  Gene #53: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
9P LOSS MUTATED 0 21 6
9P LOSS WILD-TYPE 84 86 27

Figure S73.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S74.  Gene #53: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
9P LOSS MUTATED 8 15 1
9P LOSS WILD-TYPE 48 41 95

Figure S74.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S75.  Gene #53: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
9P LOSS MUTATED 2 24 0 0
9P LOSS WILD-TYPE 45 46 62 32

Figure S75.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S76.  Gene #53: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
9P LOSS MUTATED 10 16 0
9P LOSS WILD-TYPE 63 56 66

Figure S76.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S77.  Gene #53: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
9P LOSS MUTATED 0 7 5 0 9 1 5
9P LOSS WILD-TYPE 27 27 31 32 26 39 15

Figure S77.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S78.  Gene #54: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
9Q LOSS MUTATED 0 22 7
9Q LOSS WILD-TYPE 84 85 26

Figure S78.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S79.  Gene #54: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
9Q LOSS MUTATED 9 16 1
9Q LOSS WILD-TYPE 47 40 95

Figure S79.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S80.  Gene #54: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
9Q LOSS MUTATED 2 26 0 0
9Q LOSS WILD-TYPE 45 44 62 32

Figure S80.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S81.  Gene #54: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
9Q LOSS MUTATED 10 18 0
9Q LOSS WILD-TYPE 63 54 66

Figure S81.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S82.  Gene #54: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
9Q LOSS MUTATED 0 7 4 0 9 2 7
9Q LOSS WILD-TYPE 27 27 32 32 26 38 13

Figure S82.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S83.  Gene #55: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
10P LOSS MUTATED 0 9 2
10P LOSS WILD-TYPE 56 47 94

Figure S83.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.038

Table S84.  Gene #55: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
10P LOSS MUTATED 0 12 1 0
10P LOSS WILD-TYPE 47 58 61 32

Figure S84.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S85.  Gene #56: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
10Q LOSS MUTATED 0 12 1 0
10Q LOSS WILD-TYPE 47 58 61 32

Figure S85.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.13

Table S86.  Gene #58: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
11Q LOSS MUTATED 0 10 6
11Q LOSS WILD-TYPE 84 97 27

Figure S86.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.23

Table S87.  Gene #58: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
11Q LOSS MUTATED 3 11 2
11Q LOSS WILD-TYPE 53 45 94

Figure S87.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S88.  Gene #59: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
13Q LOSS MUTATED 0 15 6
13Q LOSS WILD-TYPE 84 92 27

Figure S88.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S89.  Gene #59: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
13Q LOSS MUTATED 2 15 3
13Q LOSS WILD-TYPE 54 41 93

Figure S89.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S90.  Gene #59: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
13Q LOSS MUTATED 0 19 2 0
13Q LOSS WILD-TYPE 47 51 60 32

Figure S90.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S91.  Gene #59: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
13Q LOSS MUTATED 0 3 4 0 5 0 9
13Q LOSS WILD-TYPE 27 31 32 32 30 40 11

Figure S91.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S92.  Gene #60: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
14Q LOSS MUTATED 0 32 7
14Q LOSS WILD-TYPE 84 75 26

Figure S92.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S93.  Gene #60: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
14Q LOSS MUTATED 7 25 4 2
14Q LOSS WILD-TYPE 40 45 58 30

Figure S93.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.11

Table S94.  Gene #61: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
15Q LOSS MUTATED 1 18 6
15Q LOSS WILD-TYPE 83 89 27

Figure S94.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S95.  Gene #61: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
15Q LOSS MUTATED 4 17 2 0
15Q LOSS WILD-TYPE 43 53 60 32

Figure S95.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S96.  Gene #64: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
17P LOSS MUTATED 0 9 0
17P LOSS WILD-TYPE 56 47 96

Figure S96.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S97.  Gene #64: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
17P LOSS MUTATED 0 10 0 0
17P LOSS WILD-TYPE 47 60 62 32

Figure S97.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.11

Table S98.  Gene #65: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
18P LOSS MUTATED 3 24 7
18P LOSS WILD-TYPE 81 83 26

Figure S98.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S99.  Gene #65: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
18P LOSS MUTATED 7 21 4
18P LOSS WILD-TYPE 49 35 92

Figure S99.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S100.  Gene #65: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
18P LOSS MUTATED 4 24 1 3
18P LOSS WILD-TYPE 43 46 61 29

Figure S100.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.089

Table S101.  Gene #66: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
18Q LOSS MUTATED 3 25 7
18Q LOSS WILD-TYPE 81 82 26

Figure S101.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S102.  Gene #66: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
18Q LOSS MUTATED 7 22 4
18Q LOSS WILD-TYPE 49 34 92

Figure S102.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S103.  Gene #66: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
18Q LOSS MUTATED 4 25 1 3
18Q LOSS WILD-TYPE 43 45 61 29

Figure S103.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.19

Table S104.  Gene #66: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
18Q LOSS MUTATED 2 7 5 1 9 2 9
18Q LOSS WILD-TYPE 25 27 31 31 26 38 11

Figure S104.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.057

Table S105.  Gene #69: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
21Q LOSS MUTATED 8 13 14
21Q LOSS WILD-TYPE 76 94 19

Figure S105.  Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.038

Table S106.  Gene #70: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
22Q LOSS MUTATED 6 36 8
22Q LOSS WILD-TYPE 78 71 25

Figure S106.  Get High-res Image Gene #70: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S107.  Gene #70: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
22Q LOSS MUTATED 8 29 10
22Q LOSS WILD-TYPE 48 27 86

Figure S107.  Get High-res Image Gene #70: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S108.  Gene #70: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
22Q LOSS MUTATED 7 35 4 2
22Q LOSS WILD-TYPE 40 35 58 30

Figure S108.  Get High-res Image Gene #70: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S109.  Gene #70: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
22Q LOSS MUTATED 2 19 8 1 8 5 7
22Q LOSS WILD-TYPE 25 15 28 31 27 35 13

Figure S109.  Get High-res Image Gene #70: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S110.  Gene #71: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
XQ LOSS MUTATED 3 13 3
XQ LOSS WILD-TYPE 53 43 93

Figure S110.  Get High-res Image Gene #71: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.048

Table S111.  Gene #71: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
XQ LOSS MUTATED 2 16 2 0
XQ LOSS WILD-TYPE 45 54 60 32

Figure S111.  Get High-res Image Gene #71: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 224

  • Number of significantly arm-level cnvs = 71

  • Number of molecular subtypes = 8

  • 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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