Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C13N2221
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/C13N2221
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 70 arm-level events and 8 molecular subtypes across 197 patients, 105 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

  • 6q gain cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 11q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 5p loss cnv correlated to 'METHLYATION_CNMF'.

  • 5q loss cnv correlated to 'METHLYATION_CNMF'.

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

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

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

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 16q loss cnv correlated to 'METHLYATION_CNMF'.

  • 17p loss cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 21q loss cnv correlated to 'CN_CNMF'.

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

  • xq loss cnv correlated to 'CN_CNMF',  '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 70 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, 105 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 Chi-square test Chi-square 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 101 (51%) 96 2.13e-09
(1.14e-06) 		1.13e-08
(6.01e-06) 		8.32e-08
(4.36e-05) 		1.26e-09
(6.75e-07) 		0.0016
(0.699) 		0.0132
(1.00) 		9.58e-05
(0.0453) 		0.000225
(0.105)
xq gain 63 (32%) 134 7.77e-18
(4.33e-15) 		2.44e-07
(0.000127) 		1.5e-07
(7.84e-05) 		6.08e-10
(3.26e-07) 		0.00765
(1.00) 		0.0649
(1.00) 		0.000427
(0.196) 		0.00249
(1.00)
3p loss 14 (7%) 183 8.71e-05
(0.0415) 		1.2e-06
(0.00061) 		3.88e-05
(0.0187) 		0.000446
(0.203) 		0.267
(1.00) 		0.0053
(1.00) 		0.0404
(1.00) 		5.06e-06
(0.00253)
9q loss 24 (12%) 173 9.84e-05
(0.0464) 		2.2e-09
(1.17e-06) 		1.09e-08
(5.82e-06) 		3.49e-05
(0.0169) 		0.1
(1.00) 		0.000868
(0.39) 		0.0635
(1.00) 		8.37e-06
(0.00414)
3p gain 55 (28%) 142 9.27e-18
(5.15e-15) 		1.06e-05
(0.00523) 		9.1e-07
(0.000463) 		4.78e-06
(0.00239) 		0.0795
(1.00) 		0.284
(1.00) 		0.0915
(1.00) 		0.013
(1.00)
3q gain 65 (33%) 132 1.46e-16
(8.07e-14) 		7.11e-06
(0.00354) 		2.56e-07
(0.000133) 		0.000151
(0.0712) 		0.0489
(1.00) 		0.0937
(1.00) 		0.162
(1.00) 		0.00285
(1.00)
7p gain 117 (59%) 80 2.22e-16
(1.23e-13) 		2.1e-06
(0.00106) 		3.62e-14
(1.99e-11) 		2.76e-13
(1.5e-10) 		0.161
(1.00) 		0.492
(1.00) 		0.0993
(1.00) 		0.00128
(0.567)
7q gain 118 (60%) 79 6.05e-16
(3.34e-13) 		5.14e-06
(0.00256) 		1.45e-13
(7.96e-11) 		6.29e-13
(3.42e-10) 		0.221
(1.00) 		0.653
(1.00) 		0.143
(1.00) 		0.0047
(1.00)
16p gain 105 (53%) 92 3.45e-08
(1.82e-05) 		7.34e-09
(3.91e-06) 		1.28e-06
(0.000646) 		3.4e-10
(1.83e-07) 		0.0122
(1.00) 		0.0185
(1.00) 		0.000677
(0.307) 		0.000964
(0.431)
17p gain 118 (60%) 79 6.51e-16
(3.58e-13) 		2.04e-07
(0.000106) 		2.55e-13
(1.39e-10) 		9.34e-12
(5.06e-09) 		0.0937
(1.00) 		0.178
(1.00) 		0.0254
(1.00) 		0.00327
(1.00)
9p loss 22 (11%) 175 3.49e-06
(0.00175) 		3.39e-07
(0.000175) 		1.05e-07
(5.48e-05) 		8.61e-05
(0.0412) 		0.151
(1.00) 		0.0514
(1.00) 		0.169
(1.00) 		0.00167
(0.727)
10q loss 12 (6%) 185 0.000379
(0.175) 		7.12e-06
(0.00354) 		0.000342
(0.159) 		0.0187
(1.00) 		0.187
(1.00) 		0.00151
(0.663) 		0.0514
(1.00) 		0.000217
(0.102)
1q gain 14 (7%) 183 8.71e-05
(0.0415) 		2.57e-10
(1.39e-07) 		3.88e-05
(0.0187) 		0.00386
(1.00) 		0.413
(1.00) 		0.125
(1.00) 		0.61
(1.00) 		0.0105
(1.00)
17q gain 133 (68%) 64 5.4e-12
(2.93e-09) 		0.00147
(0.646) 		6.31e-08
(3.32e-05) 		5.79e-08
(3.05e-05) 		0.448
(1.00) 		0.316
(1.00) 		0.364
(1.00) 		0.0722
(1.00)
4p loss 18 (9%) 179 2.93e-05
(0.0143) 		1.61e-13
(8.83e-11) 		9.95e-07
(0.000505) 		0.00383
(1.00) 		0.332
(1.00) 		0.173
(1.00) 		0.706
(1.00) 		0.00586
(1.00)
4q loss 19 (10%) 178 2.25e-07
(0.000117) 		8.74e-11
(4.73e-08) 		3.41e-07
(0.000175) 		0.0062
(1.00) 		0.409
(1.00) 		0.374
(1.00) 		0.842
(1.00) 		0.0527
(1.00)
10p loss 12 (6%) 185 1.61e-05
(0.00792) 		8.85e-05
(0.0421) 		0.000342
(0.159) 		0.0509
(1.00) 		0.566
(1.00) 		0.00444
(1.00) 		0.235
(1.00) 		0.00328
(1.00)
14q loss 35 (18%) 162 8.06e-17
(4.48e-14) 		7.82e-05
(0.0375) 		0.000506
(0.23) 		0.0021
(0.911) 		0.382
(1.00) 		0.489
(1.00) 		0.255
(1.00) 		0.216
(1.00)
18q loss 32 (16%) 165 0.000385
(0.177) 		6e-10
(3.23e-07) 		4.51e-08
(2.38e-05) 		0.0014
(0.619) 		0.0519
(1.00) 		0.327
(1.00) 		0.0778
(1.00) 		0.0166
(1.00)
22q loss 44 (22%) 153 1.52e-05
(0.00748) 		1.26e-08
(6.69e-06) 		1.5e-07
(7.84e-05) 		0.00572
(1.00) 		0.515
(1.00) 		0.0394
(1.00) 		0.106
(1.00) 		0.0107
(1.00)
xq loss 20 (10%) 177 2.45e-06
(0.00123) 		4.64e-07
(0.000238) 		0.000195
(0.0916) 		0.105
(1.00) 		0.0974
(1.00) 		0.102
(1.00) 		0.167
(1.00) 		0.0348
(1.00)
2p gain 36 (18%) 161 9.4e-29
(5.25e-26) 		9.46e-05
(0.0449) 		0.0283
(1.00) 		0.0488
(1.00) 		0.0838
(1.00) 		0.659
(1.00) 		0.0135
(1.00) 		0.566
(1.00)
2q gain 39 (20%) 158 1.19e-28
(6.64e-26) 		3.13e-05
(0.0152) 		0.0483
(1.00) 		0.043
(1.00) 		0.108
(1.00) 		0.896
(1.00) 		0.0242
(1.00) 		0.882
(1.00)
5p gain 26 (13%) 171 1.34e-06
(0.000678) 		0.101
(1.00) 		0.0389
(1.00) 		2.12e-05
(0.0104) 		0.111
(1.00) 		0.191
(1.00) 		0.0374
(1.00) 		0.355
(1.00)
5q gain 26 (13%) 171 1.76e-05
(0.00863) 		0.169
(1.00) 		0.0729
(1.00) 		2.12e-05
(0.0104) 		0.111
(1.00) 		0.429
(1.00) 		0.12
(1.00) 		0.707
(1.00)
13q loss 18 (9%) 179 0.0113
(1.00) 		1.31e-13
(7.21e-11) 		1.52e-05
(0.00748) 		0.0163
(1.00) 		0.0264
(1.00) 		0.00872
(1.00) 		0.0659
(1.00) 		0.000851
(0.383)
15q loss 19 (10%) 178 3.74e-05
(0.0181) 		4.07e-05
(0.0196) 		0.004
(1.00) 		0.00792
(1.00) 		0.187
(1.00) 		0.214
(1.00) 		0.124
(1.00) 		0.16
(1.00)
18p loss 30 (15%) 167 0.00349
(1.00) 		7.62e-08
(4e-05) 		4.04e-07
(0.000208) 		0.00308
(1.00) 		0.0432
(1.00) 		0.465
(1.00) 		0.0515
(1.00) 		0.0446
(1.00)
1p gain 5 (3%) 192 0.0331
(1.00) 		8.84e-07
(0.000451) 		0.0217
(1.00) 		0.194
(1.00) 		0.13
(1.00) 		0.289
(1.00) 		0.106
(1.00) 		0.0266
(1.00)
6q gain 6 (3%) 191 0.0326
(1.00) 		0.00037
(0.171) 		0.131
(1.00) 		0.673
(1.00) 		0.127
(1.00) 		0.745
(1.00) 		0.244
(1.00) 		0.166
(1.00)
11q gain 8 (4%) 189 0.000435
(0.199) 		0.00124
(0.553) 		0.146
(1.00) 		0.0317
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.593
(1.00)
1p loss 21 (11%) 176 1.3e-06
(0.000656) 		0.0114
(1.00) 		0.00746
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.879
(1.00)
1q loss 13 (7%) 184 0.000441
(0.201) 		0.236
(1.00) 		0.328
(1.00) 		0.51
(1.00) 		0.678
(1.00) 		0.142
(1.00) 		0.72
(1.00) 		0.298
(1.00)
5p loss 7 (4%) 190 0.333
(1.00) 		8.3e-07
(0.000425) 		0.0309
(1.00) 		0.00358
(1.00) 		0.00634
(1.00) 		0.0584
(1.00) 		0.0111
(1.00) 		0.0452
(1.00)
5q loss 7 (4%) 190 0.439
(1.00) 		8.3e-07
(0.000425) 		0.0309
(1.00) 		0.00358
(1.00) 		0.00634
(1.00) 		0.0584
(1.00) 		0.0111
(1.00) 		0.0452
(1.00)
11q loss 14 (7%) 183 0.000373
(0.172) 		0.00124
(0.551) 		0.00348
(1.00) 		0.234
(1.00) 		0.551
(1.00) 		0.378
(1.00) 		0.242
(1.00) 		0.165
(1.00)
16q loss 5 (3%) 192 0.0117
(1.00) 		0.000346
(0.161) 		0.0217
(1.00) 		0.194
(1.00) 		0.536
(1.00) 		0.374
(1.00) 		0.629
(1.00) 		0.0193
(1.00)
17p loss 8 (4%) 189 0.14
(1.00) 		8e-05
(0.0383) 		0.000925
(0.414) 		0.0272
(1.00) 		0.179
(1.00) 		0.109
(1.00) 		0.226
(1.00) 		0.0465
(1.00)
21q loss 32 (16%) 165 0.000151
(0.0712) 		0.153
(1.00) 		0.546
(1.00) 		1
(1.00) 		0.577
(1.00) 		0.704
(1.00) 		0.321
(1.00) 		0.848
(1.00)
4p gain 6 (3%) 191 0.333
(1.00) 		0.542
(1.00) 		0.393
(1.00) 		0.877
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.251
(1.00)
4q gain 5 (3%) 192 0.687
(1.00) 		0.542
(1.00) 		0.628
(1.00) 		1
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.742
(1.00) 		0.675
(1.00)
6p gain 8 (4%) 189 0.217
(1.00) 		0.00556
(1.00) 		0.021
(1.00) 		0.226
(1.00) 		0.0753
(1.00) 		0.373
(1.00) 		0.356
(1.00) 		0.0465
(1.00)
8p gain 14 (7%) 183 0.406
(1.00) 		0.139
(1.00) 		0.0248
(1.00) 		0.266
(1.00) 		0.227
(1.00) 		0.172
(1.00) 		0.61
(1.00) 		0.112
(1.00)
8q gain 17 (9%) 180 0.173
(1.00) 		0.00142
(0.626) 		0.00266
(1.00) 		0.115
(1.00) 		0.0464
(1.00) 		0.082
(1.00) 		0.144
(1.00) 		0.0377
(1.00)
9p gain 3 (2%) 194 0.543
(1.00) 		0.194
(1.00) 		0.284
(1.00) 		1
(1.00) 		0.187
(1.00) 		0.508
(1.00) 		0.0874
(1.00)
10p gain 5 (3%) 192 0.106
(1.00) 		0.619
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.459
(1.00) 		0.231
(1.00) 		0.423
(1.00)
10q gain 5 (3%) 192 0.106
(1.00) 		0.619
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.459
(1.00) 		0.231
(1.00) 		0.423
(1.00)
11p gain 10 (5%) 187 0.0269
(1.00) 		0.00384
(1.00) 		0.144
(1.00) 		0.0326
(1.00) 		0.435
(1.00) 		0.824
(1.00) 		0.361
(1.00) 		0.529
(1.00)
12p gain 80 (41%) 117 0.000805
(0.364) 		0.156
(1.00) 		0.0452
(1.00) 		0.0014
(0.618) 		0.194
(1.00) 		0.0249
(1.00) 		0.109
(1.00) 		0.06
(1.00)
12q gain 80 (41%) 117 0.000805
(0.364) 		0.156
(1.00) 		0.0452
(1.00) 		0.0014
(0.618) 		0.194
(1.00) 		0.0249
(1.00) 		0.109
(1.00) 		0.06
(1.00)
13q gain 22 (11%) 175 0.219
(1.00) 		0.526
(1.00) 		0.242
(1.00) 		0.832
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.753
(1.00)
14q gain 3 (2%) 194 0.722
(1.00) 		0.0666
(1.00) 		0.194
(1.00) 		0.284
(1.00) 		1
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.0874
(1.00)
15q gain 5 (3%) 192 0.0331
(1.00) 		0.174
(1.00) 		0.202
(1.00) 		0.165
(1.00) 		0.536
(1.00) 		0.572
(1.00) 		0.443
(1.00) 		0.675
(1.00)
18p gain 9 (5%) 188 0.412
(1.00) 		0.226
(1.00) 		0.661
(1.00) 		0.693
(1.00) 		0.25
(1.00) 		0.00458
(1.00) 		0.195
(1.00) 		0.0675
(1.00)
18q gain 5 (3%) 192 0.232
(1.00) 		0.452
(1.00) 		0.589
(1.00) 		0.23
(1.00) 		1
(1.00) 		0.0633
(1.00) 		0.629
(1.00) 		0.675
(1.00)
19p gain 3 (2%) 194 0.162
(1.00) 		0.561
(1.00) 		0.194
(1.00) 		0.503
(1.00) 		0.323
(1.00) 		0.536
(1.00) 		0.289
(1.00) 		0.491
(1.00)
19q gain 3 (2%) 194 0.162
(1.00) 		0.561
(1.00) 		0.194
(1.00) 		0.503
(1.00) 		0.323
(1.00) 		0.536
(1.00) 		0.289
(1.00) 		0.491
(1.00)
20p gain 66 (34%) 131 0.000554
(0.252) 		0.0105
(1.00) 		0.0255
(1.00) 		0.0627
(1.00) 		0.0453
(1.00) 		0.69
(1.00) 		0.161
(1.00) 		0.344
(1.00)
20q gain 68 (35%) 129 0.00197
(0.857) 		0.00717
(1.00) 		0.0624
(1.00) 		0.0848
(1.00) 		0.0313
(1.00) 		0.823
(1.00) 		0.183
(1.00) 		0.52
(1.00)
21q gain 12 (6%) 185 0.248
(1.00) 		0.53
(1.00) 		0.0353
(1.00) 		0.231
(1.00) 		0.931
(1.00) 		0.438
(1.00) 		0.531
(1.00) 		0.762
(1.00)
22q gain 3 (2%) 194 0.365
(1.00) 		0.791
(1.00) 		0.512
(1.00) 		0.778
(1.00) 		0.0696
(1.00) 		0.28
(1.00) 		0.198
(1.00) 		0.23
(1.00)
3q loss 4 (2%) 193 0.0739
(1.00) 		0.00545
(1.00) 		0.0652
(1.00) 		0.101
(1.00) 		0.128
(1.00) 		0.503
(1.00) 		0.207
(1.00) 		0.0824
(1.00)
6p loss 13 (7%) 184 0.0926
(1.00) 		0.0194
(1.00) 		0.0997
(1.00) 		0.333
(1.00) 		0.445
(1.00) 		0.283
(1.00) 		0.469
(1.00) 		0.563
(1.00)
6q loss 16 (8%) 181 0.0152
(1.00) 		0.0247
(1.00) 		0.0231
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.692
(1.00) 		0.109
(1.00)
8p loss 7 (4%) 190 0.516
(1.00) 		0.992
(1.00) 		0.278
(1.00) 		0.501
(1.00) 		0.312
(1.00) 		0.108
(1.00) 		0.396
(1.00) 		0.067
(1.00)
8q loss 4 (2%) 193 0.426
(1.00) 		0.663
(1.00) 		0.328
(1.00) 		0.682
(1.00) 		0.847
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.586
(1.00)
11p loss 10 (5%) 187 0.0231
(1.00) 		0.00202
(0.876) 		0.029
(1.00) 		0.331
(1.00) 		0.777
(1.00) 		0.182
(1.00) 		0.303
(1.00) 		0.0708
(1.00)
16p loss 4 (2%) 193 0.0649
(1.00) 		0.00545
(1.00) 		0.0652
(1.00) 		0.101
(1.00) 		0.847
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.0824
(1.00)
19p loss 12 (6%) 185 0.00407
(1.00) 		0.0562
(1.00) 		0.0464
(1.00) 		0.0856
(1.00) 		0.295
(1.00) 		0.185
(1.00) 		0.0739
(1.00) 		0.31
(1.00)
19q loss 11 (6%) 186 0.0126
(1.00) 		0.0146
(1.00) 		0.0708
(1.00) 		0.575
(1.00) 		0.468
(1.00) 		0.28
(1.00) 		0.135
(1.00) 		0.106
(1.00)
'1p gain' versus 'METHLYATION_CNMF'

P value = 8.84e-07 (Chi-square test), Q value = 0.00045

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
1P GAIN MUTATED 0 5 0 0 0
1P GAIN WILD-TYPE 38 19 33 48 38

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
1Q GAIN MUTATED 2 0 9 0 3
1Q GAIN WILD-TYPE 69 40 28 21 25

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 2.57e-10 (Chi-square test), Q value = 1.4e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
1Q GAIN MUTATED 1 10 2 0 0
1Q GAIN WILD-TYPE 37 14 31 48 38

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.019

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
1Q GAIN MUTATED 1 13 0 0
1Q GAIN WILD-TYPE 38 54 59 32

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 9.4e-29 (Chi-square test), Q value = 5.3e-26

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
2P GAIN MUTATED 1 2 6 0 27
2P GAIN WILD-TYPE 70 38 31 21 1

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 9.46e-05 (Chi-square test), Q value = 0.045

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
2P GAIN MUTATED 3 7 4 18 1
2P GAIN WILD-TYPE 35 17 29 30 37

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1.19e-28 (Chi-square test), Q value = 6.6e-26

Table S7.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
2Q GAIN MUTATED 1 2 7 1 28
2Q GAIN WILD-TYPE 70 38 30 20 0

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 3.13e-05 (Chi-square test), Q value = 0.015

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
2Q GAIN MUTATED 4 7 4 20 1
2Q GAIN WILD-TYPE 34 17 29 28 37

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 9.27e-18 (Chi-square test), Q value = 5.2e-15

Table S9.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
3P GAIN MUTATED 8 6 3 20 18
3P GAIN WILD-TYPE 63 34 34 1 10

Figure S9.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 1.06e-05 (Chi-square test), Q value = 0.0052

Table S10.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
3P GAIN MUTATED 11 3 3 26 6
3P GAIN WILD-TYPE 27 21 30 22 32

Figure S10.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 9.1e-07 (Fisher's exact test), Q value = 0.00046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
3P GAIN MUTATED 19 4 22 10
3P GAIN WILD-TYPE 20 63 37 22

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.78e-06 (Fisher's exact test), Q value = 0.0024

Table S12.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
3P GAIN MUTATED 34 15 6
3P GAIN WILD-TYPE 36 56 50

Figure S12.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1.46e-16 (Chi-square test), Q value = 8.1e-14

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
3Q GAIN MUTATED 12 7 5 21 20
3Q GAIN WILD-TYPE 59 33 32 0 8

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 7.11e-06 (Chi-square test), Q value = 0.0035

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
3Q GAIN MUTATED 12 4 5 30 8
3Q GAIN WILD-TYPE 26 20 28 18 30

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2.56e-07 (Fisher's exact test), Q value = 0.00013

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
3Q GAIN MUTATED 22 6 22 15
3Q GAIN WILD-TYPE 17 61 37 17

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.071

Table S16.  Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
3Q GAIN MUTATED 36 19 10
3Q GAIN WILD-TYPE 34 52 46

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1.34e-06 (Chi-square test), Q value = 0.00068

Table S17.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
5P GAIN MUTATED 5 0 15 3 3
5P GAIN WILD-TYPE 66 40 22 18 25

Figure S17.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.01

Table S18.  Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
5P GAIN MUTATED 2 20 4
5P GAIN WILD-TYPE 68 51 52

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1.76e-05 (Chi-square test), Q value = 0.0086

Table S19.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
5Q GAIN MUTATED 6 0 14 3 3
5Q GAIN WILD-TYPE 65 40 23 18 25

Figure S19.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.01

Table S20.  Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
5Q GAIN MUTATED 2 20 4
5Q GAIN WILD-TYPE 68 51 52

Figure S20.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.17

Table S21.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
6Q GAIN MUTATED 0 4 0 0 1
6Q GAIN WILD-TYPE 38 20 33 48 37

Figure S21.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 2.22e-16 (Chi-square test), Q value = 1.2e-13

Table S22.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
7P GAIN MUTATED 23 40 11 20 23
7P GAIN WILD-TYPE 48 0 26 1 5

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2.1e-06 (Chi-square test), Q value = 0.0011

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
7P GAIN MUTATED 18 9 11 39 30
7P GAIN WILD-TYPE 20 15 22 9 8

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.62e-14 (Fisher's exact test), Q value = 2e-11

Table S24.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
7P GAIN MUTATED 21 17 53 26
7P GAIN WILD-TYPE 18 50 6 6

Figure S24.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-13 (Fisher's exact test), Q value = 1.5e-10

Table S25.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
7P GAIN MUTATED 65 27 25
7P GAIN WILD-TYPE 5 44 31

Figure S25.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.05e-16 (Chi-square test), Q value = 3.3e-13

Table S26.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
7Q GAIN MUTATED 23 40 12 20 23
7Q GAIN WILD-TYPE 48 0 25 1 5

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 5.14e-06 (Chi-square test), Q value = 0.0026

Table S27.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
7Q GAIN MUTATED 18 9 12 39 30
7Q GAIN WILD-TYPE 20 15 21 9 8

Figure S27.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.45e-13 (Fisher's exact test), Q value = 8e-11

Table S28.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
7Q GAIN MUTATED 21 18 53 26
7Q GAIN WILD-TYPE 18 49 6 6

Figure S28.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.29e-13 (Fisher's exact test), Q value = 3.4e-10

Table S29.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
7Q GAIN MUTATED 65 28 25
7Q GAIN WILD-TYPE 5 43 31

Figure S29.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000435 (Chi-square test), Q value = 0.2

Table S30.  Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
11Q GAIN MUTATED 0 0 6 0 2
11Q GAIN WILD-TYPE 71 40 31 21 26

Figure S30.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 3.45e-08 (Chi-square test), Q value = 1.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
16P GAIN MUTATED 30 17 13 21 24
16P GAIN WILD-TYPE 41 23 24 0 4

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

'16p gain' versus 'METHLYATION_CNMF'

P value = 7.34e-09 (Chi-square test), Q value = 3.9e-06

Table S32.  Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
16P GAIN MUTATED 20 8 16 44 10
16P GAIN WILD-TYPE 18 16 17 4 28

Figure S32.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00065

Table S33.  Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
16P GAIN MUTATED 32 20 36 17
16P GAIN WILD-TYPE 7 47 23 15

Figure S33.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.4e-10 (Fisher's exact test), Q value = 1.8e-07

Table S34.  Gene #27: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
16P GAIN MUTATED 54 40 11
16P GAIN WILD-TYPE 16 31 45

Figure S34.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 2.13e-09 (Chi-square test), Q value = 1.1e-06

Table S35.  Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
16Q GAIN MUTATED 30 16 10 21 24
16Q GAIN WILD-TYPE 41 24 27 0 4

Figure S35.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1.13e-08 (Chi-square test), Q value = 6e-06

Table S36.  Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
16Q GAIN MUTATED 20 7 15 43 10
16Q GAIN WILD-TYPE 18 17 18 5 28

Figure S36.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 8.32e-08 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
16Q GAIN MUTATED 32 17 35 17
16Q GAIN WILD-TYPE 7 50 24 15

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

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-09 (Fisher's exact test), Q value = 6.8e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
16Q GAIN MUTATED 53 37 11
16Q GAIN WILD-TYPE 17 34 45

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

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.58e-05 (Fisher's exact test), Q value = 0.045

Table S39.  Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 71 69
16Q GAIN MUTATED 35 22 44
16Q GAIN WILD-TYPE 22 49 25

Figure S39.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 99 23
16Q GAIN MUTATED 27 65 9
16Q GAIN WILD-TYPE 48 34 14

Figure S40.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 6.51e-16 (Chi-square test), Q value = 3.6e-13

Table S41.  Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
17P GAIN MUTATED 26 39 9 19 25
17P GAIN WILD-TYPE 45 1 28 2 3

Figure S41.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 2.04e-07 (Chi-square test), Q value = 0.00011

Table S42.  Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
17P GAIN MUTATED 17 9 11 39 32
17P GAIN WILD-TYPE 21 15 22 9 6

Figure S42.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 2.55e-13 (Fisher's exact test), Q value = 1.4e-10

Table S43.  Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
17P GAIN MUTATED 27 16 52 23
17P GAIN WILD-TYPE 12 51 7 9

Figure S43.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.34e-12 (Fisher's exact test), Q value = 5.1e-09

Table S44.  Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
17P GAIN MUTATED 64 32 22
17P GAIN WILD-TYPE 6 39 34

Figure S44.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.4e-12 (Chi-square test), Q value = 2.9e-09

Table S45.  Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
17Q GAIN MUTATED 33 39 15 19 27
17Q GAIN WILD-TYPE 38 1 22 2 1

Figure S45.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6.31e-08 (Fisher's exact test), Q value = 3.3e-05

Table S46.  Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
17Q GAIN MUTATED 30 27 52 24
17Q GAIN WILD-TYPE 9 40 7 8

Figure S46.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.79e-08 (Fisher's exact test), Q value = 3.1e-05

Table S47.  Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
17Q GAIN MUTATED 64 42 27
17Q GAIN WILD-TYPE 6 29 29

Figure S47.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 7.77e-18 (Chi-square test), Q value = 4.3e-15

Table S48.  Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
XQ GAIN MUTATED 5 15 3 18 22
XQ GAIN WILD-TYPE 66 25 34 3 6

Figure S48.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 2.44e-07 (Chi-square test), Q value = 0.00013

Table S49.  Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
XQ GAIN MUTATED 8 2 6 31 9
XQ GAIN WILD-TYPE 30 22 27 17 29

Figure S49.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 7.8e-05

Table S50.  Gene #39: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
XQ GAIN MUTATED 18 6 31 8
XQ GAIN WILD-TYPE 21 61 28 24

Figure S50.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.08e-10 (Fisher's exact test), Q value = 3.3e-07

Table S51.  Gene #39: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
XQ GAIN MUTATED 42 16 5
XQ GAIN WILD-TYPE 28 55 51

Figure S51.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000427 (Fisher's exact test), Q value = 0.2

Table S52.  Gene #39: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 71 69
XQ GAIN MUTATED 18 12 33
XQ GAIN WILD-TYPE 39 59 36

Figure S52.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.3e-06 (Chi-square test), Q value = 0.00066

Table S53.  Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
1P LOSS MUTATED 4 0 13 0 4
1P LOSS WILD-TYPE 67 40 24 21 24

Figure S53.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.000441 (Chi-square test), Q value = 0.2

Table S54.  Gene #41: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
1Q LOSS MUTATED 2 0 8 0 3
1Q LOSS WILD-TYPE 69 40 29 21 25

Figure S54.  Get High-res Image Gene #41: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.042

Table S55.  Gene #42: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
3P LOSS MUTATED 2 0 9 0 3
3P LOSS WILD-TYPE 69 40 28 21 25

Figure S55.  Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.2e-06 (Chi-square test), Q value = 0.00061

Table S56.  Gene #42: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
3P LOSS MUTATED 0 7 6 0 0
3P LOSS WILD-TYPE 38 17 27 48 38

Figure S56.  Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.019

Table S57.  Gene #42: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
3P LOSS MUTATED 1 13 0 0
3P LOSS WILD-TYPE 38 54 59 32

Figure S57.  Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000446 (Fisher's exact test), Q value = 0.2

Table S58.  Gene #42: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
3P LOSS MUTATED 0 11 3
3P LOSS WILD-TYPE 70 60 53

Figure S58.  Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.06e-06 (Fisher's exact test), Q value = 0.0025

Table S59.  Gene #42: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 99 23
3P LOSS MUTATED 5 1 8
3P LOSS WILD-TYPE 70 98 15

Figure S59.  Get High-res Image Gene #42: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.014

Table S60.  Gene #44: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
4P LOSS MUTATED 4 0 11 0 3
4P LOSS WILD-TYPE 67 40 26 21 25

Figure S60.  Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.61e-13 (Chi-square test), Q value = 8.8e-11

Table S61.  Gene #44: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
4P LOSS MUTATED 1 13 2 1 0
4P LOSS WILD-TYPE 37 11 31 47 38

Figure S61.  Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 9.95e-07 (Fisher's exact test), Q value = 0.00051

Table S62.  Gene #44: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
4P LOSS MUTATED 1 17 0 0
4P LOSS WILD-TYPE 38 50 59 32

Figure S62.  Get High-res Image Gene #44: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.25e-07 (Chi-square test), Q value = 0.00012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
4Q LOSS MUTATED 3 0 13 0 3
4Q LOSS WILD-TYPE 68 40 24 21 25

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

'4q loss' versus 'METHLYATION_CNMF'

P value = 8.74e-11 (Chi-square test), Q value = 4.7e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
4Q LOSS MUTATED 1 12 4 1 0
4Q LOSS WILD-TYPE 37 12 29 47 38

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

'4q loss' versus 'MRNASEQ_CNMF'

P value = 3.41e-07 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
4Q LOSS MUTATED 1 18 0 0
4Q LOSS WILD-TYPE 38 49 59 32

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

'5p loss' versus 'METHLYATION_CNMF'

P value = 8.3e-07 (Chi-square test), Q value = 0.00042

Table S66.  Gene #46: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
5P LOSS MUTATED 1 6 0 0 0
5P LOSS WILD-TYPE 37 18 33 48 38

Figure S66.  Get High-res Image Gene #46: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 8.3e-07 (Chi-square test), Q value = 0.00042

Table S67.  Gene #47: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
5Q LOSS MUTATED 1 6 0 0 0
5Q LOSS WILD-TYPE 37 18 33 48 38

Figure S67.  Get High-res Image Gene #47: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 3.49e-06 (Chi-square test), Q value = 0.0017

Table S68.  Gene #52: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
9P LOSS MUTATED 8 0 13 0 1
9P LOSS WILD-TYPE 63 40 24 21 27

Figure S68.  Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.39e-07 (Chi-square test), Q value = 0.00018

Table S69.  Gene #52: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
9P LOSS MUTATED 4 10 5 0 0
9P LOSS WILD-TYPE 34 14 28 48 38

Figure S69.  Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.05e-07 (Fisher's exact test), Q value = 5.5e-05

Table S70.  Gene #52: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
9P LOSS MUTATED 2 20 0 0
9P LOSS WILD-TYPE 37 47 59 32

Figure S70.  Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.61e-05 (Fisher's exact test), Q value = 0.041

Table S71.  Gene #52: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
9P LOSS MUTATED 0 13 9
9P LOSS WILD-TYPE 70 58 47

Figure S71.  Get High-res Image Gene #52: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 9.84e-05 (Chi-square test), Q value = 0.046

Table S72.  Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
9Q LOSS MUTATED 10 0 12 0 2
9Q LOSS WILD-TYPE 61 40 25 21 26

Figure S72.  Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 2.2e-09 (Chi-square test), Q value = 1.2e-06

Table S73.  Gene #53: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
9Q LOSS MUTATED 4 12 5 0 0
9Q LOSS WILD-TYPE 34 12 28 48 38

Figure S73.  Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.09e-08 (Fisher's exact test), Q value = 5.8e-06

Table S74.  Gene #53: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
9Q LOSS MUTATED 2 22 0 0
9Q LOSS WILD-TYPE 37 45 59 32

Figure S74.  Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.49e-05 (Fisher's exact test), Q value = 0.017

Table S75.  Gene #53: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
9Q LOSS MUTATED 0 13 11
9Q LOSS WILD-TYPE 70 58 45

Figure S75.  Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.37e-06 (Fisher's exact test), Q value = 0.0041

Table S76.  Gene #53: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 99 23
9Q LOSS MUTATED 15 2 7
9Q LOSS WILD-TYPE 60 97 16

Figure S76.  Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1.61e-05 (Chi-square test), Q value = 0.0079

Table S77.  Gene #54: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
10P LOSS MUTATED 0 0 8 0 4
10P LOSS WILD-TYPE 71 40 29 21 24

Figure S77.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 8.85e-05 (Chi-square test), Q value = 0.042

Table S78.  Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
10P LOSS MUTATED 0 6 3 1 0
10P LOSS WILD-TYPE 38 18 30 47 38

Figure S78.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.16

Table S79.  Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
10P LOSS MUTATED 0 11 1 0
10P LOSS WILD-TYPE 39 56 58 32

Figure S79.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.000379 (Chi-square test), Q value = 0.17

Table S80.  Gene #55: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
10Q LOSS MUTATED 1 0 7 0 4
10Q LOSS WILD-TYPE 70 40 30 21 24

Figure S80.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 7.12e-06 (Chi-square test), Q value = 0.0035

Table S81.  Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
10Q LOSS MUTATED 0 7 3 1 0
10Q LOSS WILD-TYPE 38 17 30 47 38

Figure S81.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.16

Table S82.  Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
10Q LOSS MUTATED 0 11 1 0
10Q LOSS WILD-TYPE 39 56 58 32

Figure S82.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000217 (Fisher's exact test), Q value = 0.1

Table S83.  Gene #55: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 99 23
10Q LOSS MUTATED 5 1 6
10Q LOSS WILD-TYPE 70 98 17

Figure S83.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.000373 (Chi-square test), Q value = 0.17

Table S84.  Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
11Q LOSS MUTATED 2 0 8 0 4
11Q LOSS WILD-TYPE 69 40 29 21 24

Figure S84.  Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.31e-13 (Chi-square test), Q value = 7.2e-11

Table S85.  Gene #58: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
13Q LOSS MUTATED 0 13 2 2 0
13Q LOSS WILD-TYPE 38 11 31 46 38

Figure S85.  Get High-res Image Gene #58: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0075

Table S86.  Gene #58: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
13Q LOSS MUTATED 0 16 2 0
13Q LOSS WILD-TYPE 39 51 57 32

Figure S86.  Get High-res Image Gene #58: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 8.06e-17 (Chi-square test), Q value = 4.5e-14

Table S87.  Gene #59: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
14Q LOSS MUTATED 5 0 25 0 5
14Q LOSS WILD-TYPE 66 40 12 21 23

Figure S87.  Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 7.82e-05 (Chi-square test), Q value = 0.038

Table S88.  Gene #59: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
14Q LOSS MUTATED 10 11 3 6 1
14Q LOSS WILD-TYPE 28 13 30 42 37

Figure S88.  Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.000506 (Fisher's exact test), Q value = 0.23

Table S89.  Gene #59: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
14Q LOSS MUTATED 7 22 4 2
14Q LOSS WILD-TYPE 32 45 55 30

Figure S89.  Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 3.74e-05 (Chi-square test), Q value = 0.018

Table S90.  Gene #60: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
15Q LOSS MUTATED 4 0 11 0 4
15Q LOSS WILD-TYPE 67 40 26 21 24

Figure S90.  Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 4.07e-05 (Chi-square test), Q value = 0.02

Table S91.  Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
15Q LOSS MUTATED 7 8 1 2 0
15Q LOSS WILD-TYPE 31 16 32 46 38

Figure S91.  Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.000346 (Chi-square test), Q value = 0.16

Table S92.  Gene #62: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
16Q LOSS MUTATED 0 4 1 0 0
16Q LOSS WILD-TYPE 38 20 32 48 38

Figure S92.  Get High-res Image Gene #62: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Chi-square test), Q value = 0.038

Table S93.  Gene #63: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
17P LOSS MUTATED 0 5 2 0 0
17P LOSS WILD-TYPE 38 19 31 48 38

Figure S93.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 7.62e-08 (Chi-square test), Q value = 4e-05

Table S94.  Gene #64: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
18P LOSS MUTATED 2 13 8 2 3
18P LOSS WILD-TYPE 36 11 25 46 35

Figure S94.  Get High-res Image Gene #64: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 4.04e-07 (Fisher's exact test), Q value = 0.00021

Table S95.  Gene #64: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
18P LOSS MUTATED 3 24 1 2
18P LOSS WILD-TYPE 36 43 58 30

Figure S95.  Get High-res Image Gene #64: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000385 (Chi-square test), Q value = 0.18

Table S96.  Gene #65: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
18Q LOSS MUTATED 12 2 14 0 4
18Q LOSS WILD-TYPE 59 38 23 21 24

Figure S96.  Get High-res Image Gene #65: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 6e-10 (Chi-square test), Q value = 3.2e-07

Table S97.  Gene #65: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
18Q LOSS MUTATED 2 15 8 2 3
18Q LOSS WILD-TYPE 36 9 25 46 35

Figure S97.  Get High-res Image Gene #65: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 4.51e-08 (Fisher's exact test), Q value = 2.4e-05

Table S98.  Gene #65: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
18Q LOSS MUTATED 3 26 1 2
18Q LOSS WILD-TYPE 36 41 58 30

Figure S98.  Get High-res Image Gene #65: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.071

Table S99.  Gene #68: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
21Q LOSS MUTATED 5 4 9 2 12
21Q LOSS WILD-TYPE 66 36 28 19 16

Figure S99.  Get High-res Image Gene #68: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1.52e-05 (Chi-square test), Q value = 0.0075

Table S100.  Gene #69: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
22Q LOSS MUTATED 15 4 19 0 6
22Q LOSS WILD-TYPE 56 36 18 21 22

Figure S100.  Get High-res Image Gene #69: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.26e-08 (Chi-square test), Q value = 6.7e-06

Table S101.  Gene #69: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
22Q LOSS MUTATED 5 15 14 6 1
22Q LOSS WILD-TYPE 33 9 19 42 37

Figure S101.  Get High-res Image Gene #69: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 7.8e-05

Table S102.  Gene #69: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
22Q LOSS MUTATED 7 31 4 2
22Q LOSS WILD-TYPE 32 36 55 30

Figure S102.  Get High-res Image Gene #69: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 2.45e-06 (Chi-square test), Q value = 0.0012

Table S103.  Gene #70: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
XQ LOSS MUTATED 4 1 13 1 1
XQ LOSS WILD-TYPE 67 39 24 20 27

Figure S103.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 4.64e-07 (Chi-square test), Q value = 0.00024

Table S104.  Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
XQ LOSS MUTATED 1 10 3 2 1
XQ LOSS WILD-TYPE 37 14 30 46 37

Figure S104.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.092

Table S105.  Gene #70: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
XQ LOSS MUTATED 2 16 2 0
XQ LOSS WILD-TYPE 37 51 57 32

Figure S105.  Get High-res Image Gene #70: '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 = 197

  • Number of significantly arm-level cnvs = 70

  • Number of molecular subtypes = 8

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

Chi-square test

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle