Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1FQ9V1J
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/C1FQ9V1J
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 69 arm-level events and 8 molecular subtypes across 172 patients, 99 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 16q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

  • 1p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 5p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_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',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • 17p loss cnv correlated to 'METHLYATION_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 'MRNASEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

  • 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 69 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, 99 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
9q loss 24 (14%) 148 3.03e-06
(0.00153) 		1.53e-07
(7.98e-05) 		1.15e-07
(6.05e-05) 		5.41e-07
(0.000278) 		0.00551
(1.00) 		6.03e-05
(0.029) 		0.0347
(1.00) 		9.58e-05
(0.0453)
7p gain 100 (58%) 72 5.47e-19
(3.02e-16) 		7.55e-08
(4e-05) 		3.55e-13
(1.93e-10) 		1.38e-07
(7.23e-05) 		0.099
(1.00) 		0.000239
(0.11) 		0.167
(1.00) 		0.0104
(1.00)
17p gain 102 (59%) 70 1.41e-17
(7.72e-15) 		1.13e-07
(5.98e-05) 		1.35e-10
(7.3e-08) 		3.84e-09
(2.06e-06) 		0.0228
(1.00) 		0.000259
(0.119) 		0.144
(1.00) 		0.00791
(1.00)
1q gain 14 (8%) 158 3.59e-06
(0.00181) 		1.14e-06
(0.000578) 		6.28e-05
(0.0301) 		0.00132
(0.575) 		0.235
(1.00) 		5.12e-05
(0.0247) 		0.383
(1.00) 		0.0262
(1.00)
7q gain 101 (59%) 71 1.87e-18
(1.03e-15) 		2.12e-07
(0.00011) 		4.88e-13
(2.65e-10) 		2.01e-07
(0.000105) 		0.141
(1.00) 		0.00126
(0.554) 		0.222
(1.00) 		0.0408
(1.00)
3p loss 14 (8%) 158 1.61e-05
(0.00798) 		4.47e-07
(0.00023) 		0.000314
(0.143) 		0.00108
(0.475) 		0.0114
(1.00) 		0.00334
(1.00) 		0.415
(1.00) 		0.000104
(0.049)
4p loss 18 (10%) 154 2.69e-07
(0.00014) 		1.02e-07
(5.42e-05) 		3.57e-07
(0.000184) 		7.8e-06
(0.0039) 		0.436
(1.00) 		0.0653
(1.00) 		0.665
(1.00) 		0.0255
(1.00)
4q loss 19 (11%) 153 7.23e-08
(3.86e-05) 		2.57e-08
(1.38e-05) 		1.27e-07
(6.64e-05) 		2.76e-05
(0.0135) 		0.599
(1.00) 		0.124
(1.00) 		0.582
(1.00) 		0.0426
(1.00)
9p loss 22 (13%) 150 1.69e-06
(0.000858) 		3.99e-07
(0.000206) 		9.89e-07
(0.000504) 		0.000187
(0.0863) 		0.0222
(1.00) 		0.00945
(1.00) 		0.0641
(1.00) 		0.0121
(1.00)
10q loss 12 (7%) 160 3.05e-06
(0.00153) 		1.91e-05
(0.00943) 		0.000746
(0.333) 		0.0275
(1.00) 		0.0607
(1.00) 		1.42e-05
(0.00707) 		0.0869
(1.00) 		0.000139
(0.0648)
13q loss 17 (10%) 155 1.21e-05
(0.00602) 		1.42e-08
(7.64e-06) 		7.84e-06
(0.00391) 		7.82e-05
(0.0372) 		0.0107
(1.00) 		0.0021
(0.896) 		0.06
(1.00) 		0.00627
(1.00)
18q loss 30 (17%) 142 3.3e-05
(0.0161) 		2.97e-07
(0.000154) 		2.6e-07
(0.000135) 		0.000177
(0.0819) 		0.0654
(1.00) 		0.133
(1.00) 		0.33
(1.00) 		0.24
(1.00)
22q loss 41 (24%) 131 6.88e-07
(0.000352) 		4.73e-07
(0.000243) 		7.37e-08
(3.92e-05) 		0.00135
(0.586) 		0.136
(1.00) 		0.00011
(0.0516) 		0.0464
(1.00) 		0.0764
(1.00)
17q gain 117 (68%) 55 5.2e-12
(2.83e-09) 		0.00117
(0.515) 		9.37e-07
(0.000478) 		1.09e-05
(0.00542) 		0.293
(1.00) 		0.0743
(1.00) 		0.49
(1.00) 		0.122
(1.00)
xq gain 54 (31%) 118 1.51e-14
(8.25e-12) 		0.0064
(1.00) 		6.96e-06
(0.00349) 		7.75e-05
(0.037) 		0.00805
(1.00) 		0.00767
(1.00) 		0.0132
(1.00) 		0.136
(1.00)
10p loss 12 (7%) 160 7.31e-08
(3.9e-05) 		7.49e-05
(0.0358) 		0.000746
(0.333) 		0.164
(1.00) 		0.289
(1.00) 		0.000114
(0.0535) 		0.337
(1.00) 		0.000558
(0.252)
14q loss 34 (20%) 138 1.12e-11
(6.09e-09) 		0.00438
(1.00) 		0.000267
(0.122) 		8.21e-07
(0.000419) 		0.0755
(1.00) 		0.00436
(1.00) 		0.268
(1.00) 		0.15
(1.00)
18p loss 28 (16%) 144 0.000337
(0.153) 		3.92e-06
(0.00197) 		2.03e-06
(0.00103) 		0.000598
(0.27) 		0.0472
(1.00) 		0.113
(1.00) 		0.324
(1.00) 		0.348
(1.00)
xq loss 20 (12%) 152 2.26e-05
(0.0111) 		4.35e-05
(0.0211) 		3.08e-05
(0.015) 		0.0337
(1.00) 		0.198
(1.00) 		0.0546
(1.00) 		0.265
(1.00) 		0.0121
(1.00)
3p gain 46 (27%) 126 5.8e-19
(3.19e-16) 		0.0244
(1.00) 		6.68e-05
(0.032) 		0.082
(1.00) 		0.16
(1.00) 		0.0034
(1.00) 		0.318
(1.00) 		0.0152
(1.00)
3q gain 55 (32%) 117 1.64e-17
(8.99e-15) 		0.0342
(1.00) 		2.29e-05
(0.0113) 		0.0876
(1.00) 		0.132
(1.00) 		0.022
(1.00) 		0.435
(1.00) 		0.0208
(1.00)
16p gain 89 (52%) 83 3.34e-10
(1.8e-07) 		0.242
(1.00) 		0.000528
(0.239) 		0.0006
(0.27) 		0.0384
(1.00) 		0.0232
(1.00) 		0.00305
(1.00) 		0.017
(1.00)
16q gain 85 (49%) 87 2.88e-11
(1.56e-08) 		0.0896
(1.00) 		5.28e-05
(0.0254) 		0.00257
(1.00) 		0.00897
(1.00) 		0.0015
(0.648) 		0.00176
(0.753) 		0.00313
(1.00)
11q loss 14 (8%) 158 1.61e-05
(0.00798) 		0.000148
(0.069) 		0.0224
(1.00) 		0.0183
(1.00) 		0.0706
(1.00) 		0.071
(1.00) 		0.415
(1.00) 		0.0262
(1.00)
15q loss 19 (11%) 153 9.33e-05
(0.0442) 		0.00407
(1.00) 		0.0119
(1.00) 		1.11e-07
(5.84e-05) 		0.14
(1.00) 		0.423
(1.00) 		0.144
(1.00) 		0.16
(1.00)
1p gain 5 (3%) 167 0.000436
(0.198) 		0.00267
(1.00) 		0.0294
(1.00) 		0.0467
(1.00) 		0.236
(1.00) 		0.0412
(1.00) 		0.233
(1.00) 		0.264
(1.00)
2p gain 32 (19%) 140 7.44e-08
(3.95e-05) 		0.0123
(1.00) 		0.181
(1.00) 		0.755
(1.00) 		0.114
(1.00) 		0.706
(1.00) 		0.0451
(1.00) 		0.801
(1.00)
2q gain 35 (20%) 137 2.67e-09
(1.44e-06) 		0.0262
(1.00) 		0.529
(1.00) 		0.653
(1.00) 		0.145
(1.00) 		1
(1.00) 		0.0398
(1.00) 		0.941
(1.00)
8q gain 15 (9%) 157 0.04
(1.00) 		2.45e-05
(0.012) 		0.00472
(1.00) 		0.214
(1.00) 		0.00743
(1.00) 		0.0135
(1.00) 		0.0683
(1.00) 		0.00495
(1.00)
12p gain 68 (40%) 104 0.000236
(0.109) 		0.461
(1.00) 		0.0156
(1.00) 		0.131
(1.00) 		0.288
(1.00) 		0.069
(1.00) 		0.0597
(1.00) 		0.209
(1.00)
12q gain 68 (40%) 104 0.000236
(0.109) 		0.461
(1.00) 		0.0156
(1.00) 		0.131
(1.00) 		0.288
(1.00) 		0.069
(1.00) 		0.0597
(1.00) 		0.209
(1.00)
1p loss 21 (12%) 151 0.000121
(0.0569) 		0.0547
(1.00) 		0.00227
(0.964) 		0.00356
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.953
(1.00) 		0.897
(1.00)
5p loss 7 (4%) 165 0.322
(1.00) 		0.00151
(0.654) 		0.0149
(1.00) 		3.34e-05
(0.0163) 		0.0185
(1.00) 		0.0885
(1.00) 		0.0309
(1.00) 		0.065
(1.00)
5q loss 7 (4%) 165 0.322
(1.00) 		0.00151
(0.654) 		0.0149
(1.00) 		3.34e-05
(0.0163) 		0.0185
(1.00) 		0.0885
(1.00) 		0.0309
(1.00) 		0.065
(1.00)
6q loss 15 (9%) 157 9.92e-05
(0.0468) 		0.000871
(0.386) 		0.0107
(1.00) 		0.0326
(1.00) 		0.567
(1.00) 		0.548
(1.00) 		0.703
(1.00) 		0.26
(1.00)
17p loss 8 (5%) 164 0.0153
(1.00) 		0.000166
(0.077) 		0.00178
(0.761) 		0.00336
(1.00) 		0.284
(1.00) 		0.073
(1.00) 		0.312
(1.00) 		0.0396
(1.00)
19q loss 11 (6%) 161 8.49e-05
(0.0403) 		0.0419
(1.00) 		0.092
(1.00) 		0.147
(1.00) 		0.0391
(1.00) 		0.117
(1.00) 		0.286
(1.00) 		0.051
(1.00)
21q loss 30 (17%) 142 0.000173
(0.0802) 		0.188
(1.00) 		0.668
(1.00) 		0.072
(1.00) 		0.686
(1.00) 		0.191
(1.00) 		0.284
(1.00) 		0.758
(1.00)
4p gain 6 (3%) 166 0.885
(1.00) 		0.162
(1.00) 		0.937
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.593
(1.00) 		0.04
(1.00)
4q gain 5 (3%) 167 1
(1.00) 		0.162
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.739
(1.00) 		0.639
(1.00) 		0.45
(1.00) 		0.192
(1.00)
5p gain 26 (15%) 146 0.00089
(0.392) 		0.00144
(0.624) 		0.106
(1.00) 		0.000617
(0.277) 		0.0685
(1.00) 		0.0972
(1.00) 		0.235
(1.00) 		0.305
(1.00)
5q gain 26 (15%) 146 0.00226
(0.963) 		0.00811
(1.00) 		0.107
(1.00) 		0.000617
(0.277) 		0.0685
(1.00) 		0.297
(1.00) 		0.235
(1.00) 		0.368
(1.00)
6p gain 8 (5%) 164 0.167
(1.00) 		0.0459
(1.00) 		0.0364
(1.00) 		0.244
(1.00) 		0.0298
(1.00) 		0.104
(1.00) 		0.00941
(1.00) 		0.291
(1.00)
6q gain 6 (3%) 166 0.0442
(1.00) 		0.0413
(1.00) 		0.172
(1.00) 		0.373
(1.00) 		0.165
(1.00) 		0.247
(1.00) 		0.065
(1.00) 		0.426
(1.00)
8p gain 12 (7%) 160 0.141
(1.00) 		0.00289
(1.00) 		0.134
(1.00) 		0.859
(1.00) 		0.108
(1.00) 		0.0544
(1.00) 		0.312
(1.00) 		0.0321
(1.00)
9p gain 3 (2%) 169 0.697
(1.00) 		0.261
(1.00) 		0.0951
(1.00) 		0.775
(1.00) 		0.0876
(1.00) 		0.777
(1.00) 		0.0594
(1.00)
10p gain 5 (3%) 167 0.0494
(1.00) 		0.0398
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.41
(1.00) 		0.13
(1.00) 		0.353
(1.00)
10q gain 5 (3%) 167 0.0494
(1.00) 		0.0398
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.41
(1.00) 		0.13
(1.00) 		0.353
(1.00)
11p gain 8 (5%) 164 0.0153
(1.00) 		0.00151
(0.654) 		0.657
(1.00) 		0.0124
(1.00) 		0.0775
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.249
(1.00)
11q gain 7 (4%) 165 0.00996
(1.00) 		0.000671
(0.3) 		0.513
(1.00) 		0.0347
(1.00) 		0.177
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.588
(1.00)
13q gain 19 (11%) 153 0.0467
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.722
(1.00) 		1
(1.00) 		1
(1.00) 		0.923
(1.00) 		1
(1.00)
14q gain 3 (2%) 169 0.258
(1.00) 		0.0398
(1.00) 		0.557
(1.00) 		0.0951
(1.00) 		1
(1.00) 		0.0876
(1.00) 		1
(1.00) 		0.0594
(1.00)
15q gain 5 (3%) 167 0.0173
(1.00) 		0.0413
(1.00) 		0.299
(1.00) 		0.0731
(1.00) 		0.527
(1.00) 		0.639
(1.00) 		0.736
(1.00) 		0.353
(1.00)
18p gain 9 (5%) 163 0.17
(1.00) 		0.423
(1.00) 		0.714
(1.00) 		0.911
(1.00) 		0.138
(1.00) 		0.0432
(1.00) 		0.358
(1.00) 		0.21
(1.00)
18q gain 5 (3%) 167 0.151
(1.00) 		0.253
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.239
(1.00) 		0.627
(1.00) 		1
(1.00)
19p gain 3 (2%) 169 0.258
(1.00) 		0.457
(1.00) 		0.557
(1.00) 		0.412
(1.00) 		0.525
(1.00) 		0.0146
(1.00) 		0.51
(1.00) 		0.295
(1.00)
19q gain 3 (2%) 169 0.258
(1.00) 		0.457
(1.00) 		0.557
(1.00) 		0.412
(1.00) 		0.525
(1.00) 		0.0146
(1.00) 		0.51
(1.00) 		0.295
(1.00)
20p gain 58 (34%) 114 0.00127
(0.555) 		0.108
(1.00) 		0.0777
(1.00) 		0.323
(1.00) 		0.301
(1.00) 		0.646
(1.00) 		0.879
(1.00) 		0.758
(1.00)
20q gain 60 (35%) 112 0.00551
(1.00) 		0.109
(1.00) 		0.142
(1.00) 		0.452
(1.00) 		0.276
(1.00) 		0.729
(1.00) 		0.8
(1.00) 		0.747
(1.00)
21q gain 12 (7%) 160 1
(1.00) 		0.413
(1.00) 		0.0523
(1.00) 		0.102
(1.00) 		0.393
(1.00) 		0.516
(1.00) 		0.227
(1.00) 		0.337
(1.00)
1q loss 13 (8%) 159 0.0467
(1.00) 		0.471
(1.00) 		0.632
(1.00) 		0.00455
(1.00) 		0.877
(1.00) 		0.21
(1.00) 		0.516
(1.00) 		0.366
(1.00)
3q loss 4 (2%) 168 0.00248
(1.00) 		0.0104
(1.00) 		0.117
(1.00) 		0.0228
(1.00) 		0.328
(1.00) 		0.585
(1.00) 		0.388
(1.00) 		0.0564
(1.00)
6p loss 12 (7%) 160 0.0066
(1.00) 		0.0419
(1.00) 		0.0453
(1.00) 		0.0142
(1.00) 		0.49
(1.00) 		0.399
(1.00) 		0.869
(1.00) 		0.337
(1.00)
8p loss 6 (3%) 166 0.0442
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.419
(1.00) 		0.374
(1.00) 		0.196
(1.00) 		0.38
(1.00) 		0.118
(1.00)
8q loss 4 (2%) 168 0.0931
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.0951
(1.00) 		1
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.381
(1.00)
11p loss 10 (6%) 162 0.000836
(0.371) 		0.00389
(1.00) 		0.0146
(1.00) 		0.0278
(1.00) 		0.0846
(1.00) 		0.172
(1.00) 		0.428
(1.00) 		0.0135
(1.00)
16p loss 4 (2%) 168 0.0931
(1.00) 		0.0104
(1.00) 		0.117
(1.00) 		0.0228
(1.00) 		1
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.0564
(1.00)
16q loss 5 (3%) 167 0.0173
(1.00) 		0.00267
(1.00) 		0.0294
(1.00) 		0.0467
(1.00) 		0.623
(1.00) 		0.318
(1.00) 		0.627
(1.00) 		0.00835
(1.00)
19p loss 12 (7%) 160 0.000874
(0.386) 		0.0107
(1.00) 		0.111
(1.00) 		0.0329
(1.00) 		0.0284
(1.00) 		0.0521
(1.00) 		0.566
(1.00) 		0.0182
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 0.000436 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
1P GAIN MUTATED 0 0 0 5
1P GAIN WILD-TYPE 33 68 37 29

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

'1q gain' versus 'CN_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
1Q GAIN MUTATED 0 2 1 11
1Q GAIN WILD-TYPE 33 66 36 23

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00058

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
1Q GAIN MUTATED 0 12 1
1Q GAIN WILD-TYPE 43 31 69

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 6.28e-05 (Fisher's exact test), Q value = 0.03

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
1Q GAIN MUTATED 13 0 1 0
1Q GAIN WILD-TYPE 45 49 30 23

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.12e-05 (Fisher's exact test), Q value = 0.025

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
1Q GAIN MUTATED 5 0 9
1Q GAIN WILD-TYPE 13 80 65

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 7.44e-08 (Fisher's exact test), Q value = 3.9e-05

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
2P GAIN MUTATED 12 2 3 15
2P GAIN WILD-TYPE 21 66 34 19

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 2.67e-09 (Fisher's exact test), Q value = 1.4e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
2Q GAIN MUTATED 13 2 3 17
2Q GAIN WILD-TYPE 20 66 34 17

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

'3p gain' versus 'CN_CNMF'

P value = 5.8e-19 (Fisher's exact test), Q value = 3.2e-16

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
3P GAIN MUTATED 31 6 5 4
3P GAIN WILD-TYPE 2 62 32 30

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 6.68e-05 (Fisher's exact test), Q value = 0.032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
3P GAIN MUTATED 4 19 12 9
3P GAIN WILD-TYPE 54 30 19 14

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

'3q gain' versus 'CN_CNMF'

P value = 1.64e-17 (Fisher's exact test), Q value = 9e-15

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
3Q GAIN MUTATED 32 9 6 8
3Q GAIN WILD-TYPE 1 59 31 26

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
3Q GAIN MUTATED 6 19 14 13
3Q GAIN WILD-TYPE 52 30 17 10

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 5.47e-19 (Fisher's exact test), Q value = 3e-16

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
7P GAIN MUTATED 31 19 37 13
7P GAIN WILD-TYPE 2 49 0 21

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 7.55e-08 (Fisher's exact test), Q value = 4e-05

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
7P GAIN MUTATED 20 13 57
7P GAIN WILD-TYPE 23 30 13

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.55e-13 (Fisher's exact test), Q value = 1.9e-10

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
7P GAIN MUTATED 14 44 15 20
7P GAIN WILD-TYPE 44 5 16 3

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-07 (Fisher's exact test), Q value = 7.2e-05

Table S15.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
7P GAIN MUTATED 9 31 53
7P GAIN WILD-TYPE 22 35 11

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000239 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
7P GAIN MUTATED 3 55 42
7P GAIN WILD-TYPE 15 25 32

Figure S16.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.87e-18 (Fisher's exact test), Q value = 1e-15

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
7Q GAIN MUTATED 31 20 37 13
7Q GAIN WILD-TYPE 2 48 0 21

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00011

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
7Q GAIN MUTATED 20 14 57
7Q GAIN WILD-TYPE 23 29 13

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4.88e-13 (Fisher's exact test), Q value = 2.7e-10

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
7Q GAIN MUTATED 14 44 16 20
7Q GAIN WILD-TYPE 44 5 15 3

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-07 (Fisher's exact test), Q value = 0.00011

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
7Q GAIN MUTATED 9 32 53
7Q GAIN WILD-TYPE 22 34 11

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.012

Table S21.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
8Q GAIN MUTATED 1 11 1
8Q GAIN WILD-TYPE 42 32 69

Figure S21.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.11

Table S22.  Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
12P GAIN MUTATED 21 16 20 11
12P GAIN WILD-TYPE 12 52 17 23

Figure S22.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.11

Table S23.  Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
12Q GAIN MUTATED 21 16 20 11
12Q GAIN WILD-TYPE 12 52 17 23

Figure S23.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 3.34e-10 (Fisher's exact test), Q value = 1.8e-07

Table S24.  Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
16P GAIN MUTATED 33 28 15 13
16P GAIN WILD-TYPE 0 40 22 21

Figure S24.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000528 (Fisher's exact test), Q value = 0.24

Table S25.  Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
16P GAIN MUTATED 19 28 24 13
16P GAIN WILD-TYPE 39 21 7 10

Figure S25.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 2.88e-11 (Fisher's exact test), Q value = 1.6e-08

Table S26.  Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
16Q GAIN MUTATED 33 28 14 10
16Q GAIN WILD-TYPE 0 40 23 24

Figure S26.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 5.28e-05 (Fisher's exact test), Q value = 0.025

Table S27.  Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
16Q GAIN MUTATED 16 27 24 13
16Q GAIN WILD-TYPE 42 22 7 10

Figure S27.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1.41e-17 (Fisher's exact test), Q value = 7.7e-15

Table S28.  Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
17P GAIN MUTATED 32 21 36 13
17P GAIN WILD-TYPE 1 47 1 21

Figure S28.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 6e-05

Table S29.  Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
17P GAIN MUTATED 19 15 58
17P GAIN WILD-TYPE 24 28 12

Figure S29.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1.35e-10 (Fisher's exact test), Q value = 7.3e-08

Table S30.  Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
17P GAIN MUTATED 15 44 19 15
17P GAIN WILD-TYPE 43 5 12 8

Figure S30.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.84e-09 (Fisher's exact test), Q value = 2.1e-06

Table S31.  Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
17P GAIN MUTATED 7 32 54
17P GAIN WILD-TYPE 24 34 10

Figure S31.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000259 (Fisher's exact test), Q value = 0.12

Table S32.  Gene #29: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
17P GAIN MUTATED 3 55 44
17P GAIN WILD-TYPE 15 25 30

Figure S32.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.2e-12 (Fisher's exact test), Q value = 2.8e-09

Table S33.  Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
17Q GAIN MUTATED 32 29 36 20
17Q GAIN WILD-TYPE 1 39 1 14

Figure S33.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00048

Table S34.  Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
17Q GAIN MUTATED 25 45 22 16
17Q GAIN WILD-TYPE 33 4 9 7

Figure S34.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0054

Table S35.  Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
17Q GAIN MUTATED 12 41 55
17Q GAIN WILD-TYPE 19 25 9

Figure S35.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1.51e-14 (Fisher's exact test), Q value = 8.2e-12

Table S36.  Gene #38: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
XQ GAIN MUTATED 28 5 15 6
XQ GAIN WILD-TYPE 5 63 22 28

Figure S36.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 6.96e-06 (Fisher's exact test), Q value = 0.0035

Table S37.  Gene #38: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
XQ GAIN MUTATED 6 27 12 7
XQ GAIN WILD-TYPE 52 22 19 16

Figure S37.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.75e-05 (Fisher's exact test), Q value = 0.037

Table S38.  Gene #38: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
XQ GAIN MUTATED 2 19 31
XQ GAIN WILD-TYPE 29 47 33

Figure S38.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.057

Table S39.  Gene #39: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
1P LOSS MUTATED 1 9 0 11
1P LOSS WILD-TYPE 32 59 37 23

Figure S39.  Get High-res Image Gene #39: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.008

Table S40.  Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
3P LOSS MUTATED 0 4 0 10
3P LOSS WILD-TYPE 33 64 37 24

Figure S40.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4.47e-07 (Fisher's exact test), Q value = 0.00023

Table S41.  Gene #41: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
3P LOSS MUTATED 1 12 0
3P LOSS WILD-TYPE 42 31 70

Figure S41.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.14

Table S42.  Gene #41: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
3P LOSS MUTATED 12 0 2 0
3P LOSS WILD-TYPE 46 49 29 23

Figure S42.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.049

Table S43.  Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 87 71
3P LOSS MUTATED 5 1 8
3P LOSS WILD-TYPE 9 86 63

Figure S43.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 2.69e-07 (Fisher's exact test), Q value = 0.00014

Table S44.  Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
4P LOSS MUTATED 0 5 0 13
4P LOSS WILD-TYPE 33 63 37 21

Figure S44.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.02e-07 (Fisher's exact test), Q value = 5.4e-05

Table S45.  Gene #43: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
4P LOSS MUTATED 1 15 1
4P LOSS WILD-TYPE 42 28 69

Figure S45.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 3.57e-07 (Fisher's exact test), Q value = 0.00018

Table S46.  Gene #43: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
4P LOSS MUTATED 17 0 0 0
4P LOSS WILD-TYPE 41 49 31 23

Figure S46.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.8e-06 (Fisher's exact test), Q value = 0.0039

Table S47.  Gene #43: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
4P LOSS MUTATED 10 7 0
4P LOSS WILD-TYPE 21 59 64

Figure S47.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.23e-08 (Fisher's exact test), Q value = 3.9e-05

Table S48.  Gene #44: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
4Q LOSS MUTATED 0 5 0 14
4Q LOSS WILD-TYPE 33 63 37 20

Figure S48.  Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 2.57e-08 (Fisher's exact test), Q value = 1.4e-05

Table S49.  Gene #44: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
4Q LOSS MUTATED 1 16 1
4Q LOSS WILD-TYPE 42 27 69

Figure S49.  Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1.27e-07 (Fisher's exact test), Q value = 6.6e-05

Table S50.  Gene #44: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
4Q LOSS MUTATED 18 0 0 0
4Q LOSS WILD-TYPE 40 49 31 23

Figure S50.  Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-05 (Fisher's exact test), Q value = 0.014

Table S51.  Gene #44: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
4Q LOSS MUTATED 9 9 0
4Q LOSS WILD-TYPE 22 57 64

Figure S51.  Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.016

Table S52.  Gene #45: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
5P LOSS MUTATED 6 0 0
5P LOSS WILD-TYPE 25 66 64

Figure S52.  Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.016

Table S53.  Gene #46: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
5Q LOSS MUTATED 6 0 0
5Q LOSS WILD-TYPE 25 66 64

Figure S53.  Get High-res Image Gene #46: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 9.92e-05 (Fisher's exact test), Q value = 0.047

Table S54.  Gene #48: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
6Q LOSS MUTATED 1 4 0 10
6Q LOSS WILD-TYPE 32 64 37 24

Figure S54.  Get High-res Image Gene #48: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.00086

Table S55.  Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
9P LOSS MUTATED 1 7 0 14
9P LOSS WILD-TYPE 32 61 37 20

Figure S55.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.99e-07 (Fisher's exact test), Q value = 0.00021

Table S56.  Gene #51: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
9P LOSS MUTATED 5 14 0
9P LOSS WILD-TYPE 38 29 70

Figure S56.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 9.89e-07 (Fisher's exact test), Q value = 5e-04

Table S57.  Gene #51: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
9P LOSS MUTATED 19 0 1 1
9P LOSS WILD-TYPE 39 49 30 22

Figure S57.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000187 (Fisher's exact test), Q value = 0.086

Table S58.  Gene #51: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
9P LOSS MUTATED 9 11 1
9P LOSS WILD-TYPE 22 55 63

Figure S58.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 3.03e-06 (Fisher's exact test), Q value = 0.0015

Table S59.  Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
9Q LOSS MUTATED 1 9 0 14
9Q LOSS WILD-TYPE 32 59 37 20

Figure S59.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 8e-05

Table S60.  Gene #52: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
9Q LOSS MUTATED 6 15 0
9Q LOSS WILD-TYPE 37 28 70

Figure S60.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 6.1e-05

Table S61.  Gene #52: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
9Q LOSS MUTATED 21 0 1 1
9Q LOSS WILD-TYPE 37 49 30 22

Figure S61.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.41e-07 (Fisher's exact test), Q value = 0.00028

Table S62.  Gene #52: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
9Q LOSS MUTATED 12 11 0
9Q LOSS WILD-TYPE 19 55 64

Figure S62.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.03e-05 (Fisher's exact test), Q value = 0.029

Table S63.  Gene #52: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
9Q LOSS MUTATED 5 2 17
9Q LOSS WILD-TYPE 13 78 57

Figure S63.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S64.  Gene #52: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 87 71
9Q LOSS MUTATED 4 3 17
9Q LOSS WILD-TYPE 10 84 54

Figure S64.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 7.31e-08 (Fisher's exact test), Q value = 3.9e-05

Table S65.  Gene #53: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
10P LOSS MUTATED 0 1 0 11
10P LOSS WILD-TYPE 33 67 37 23

Figure S65.  Get High-res Image Gene #53: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 7.49e-05 (Fisher's exact test), Q value = 0.036

Table S66.  Gene #53: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
10P LOSS MUTATED 0 9 1
10P LOSS WILD-TYPE 43 34 69

Figure S66.  Get High-res Image Gene #53: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.053

Table S67.  Gene #53: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
10P LOSS MUTATED 6 1 5
10P LOSS WILD-TYPE 12 79 69

Figure S67.  Get High-res Image Gene #53: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 3.05e-06 (Fisher's exact test), Q value = 0.0015

Table S68.  Gene #54: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
10Q LOSS MUTATED 0 2 0 10
10Q LOSS WILD-TYPE 33 66 37 24

Figure S68.  Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.0094

Table S69.  Gene #54: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
10Q LOSS MUTATED 0 10 1
10Q LOSS WILD-TYPE 43 33 69

Figure S69.  Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.0071

Table S70.  Gene #54: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
10Q LOSS MUTATED 6 0 6
10Q LOSS WILD-TYPE 12 80 68

Figure S70.  Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.065

Table S71.  Gene #54: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 87 71
10Q LOSS MUTATED 5 1 6
10Q LOSS WILD-TYPE 9 86 65

Figure S71.  Get High-res Image Gene #54: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.008

Table S72.  Gene #56: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
11Q LOSS MUTATED 0 4 0 10
11Q LOSS WILD-TYPE 33 64 37 24

Figure S72.  Get High-res Image Gene #56: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.069

Table S73.  Gene #56: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
11Q LOSS MUTATED 1 11 2
11Q LOSS WILD-TYPE 42 32 68

Figure S73.  Get High-res Image Gene #56: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.006

Table S74.  Gene #57: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
13Q LOSS MUTATED 0 6 0 11
13Q LOSS WILD-TYPE 33 62 37 23

Figure S74.  Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.42e-08 (Fisher's exact test), Q value = 7.6e-06

Table S75.  Gene #57: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
13Q LOSS MUTATED 0 15 1
13Q LOSS WILD-TYPE 43 28 69

Figure S75.  Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 7.84e-06 (Fisher's exact test), Q value = 0.0039

Table S76.  Gene #57: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
13Q LOSS MUTATED 16 1 0 0
13Q LOSS WILD-TYPE 42 48 31 23

Figure S76.  Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.82e-05 (Fisher's exact test), Q value = 0.037

Table S77.  Gene #57: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
13Q LOSS MUTATED 10 6 1
13Q LOSS WILD-TYPE 21 60 63

Figure S77.  Get High-res Image Gene #57: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.12e-11 (Fisher's exact test), Q value = 6.1e-09

Table S78.  Gene #58: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
14Q LOSS MUTATED 1 11 0 22
14Q LOSS WILD-TYPE 32 57 37 12

Figure S78.  Get High-res Image Gene #58: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.12

Table S79.  Gene #58: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
14Q LOSS MUTATED 21 2 5 3
14Q LOSS WILD-TYPE 37 47 26 20

Figure S79.  Get High-res Image Gene #58: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.21e-07 (Fisher's exact test), Q value = 0.00042

Table S80.  Gene #58: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
14Q LOSS MUTATED 16 12 3
14Q LOSS WILD-TYPE 15 54 61

Figure S80.  Get High-res Image Gene #58: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 9.33e-05 (Fisher's exact test), Q value = 0.044

Table S81.  Gene #59: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
15Q LOSS MUTATED 1 7 0 11
15Q LOSS WILD-TYPE 32 61 37 23

Figure S81.  Get High-res Image Gene #59: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 5.8e-05

Table S82.  Gene #59: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
15Q LOSS MUTATED 13 3 1
15Q LOSS WILD-TYPE 18 63 63

Figure S82.  Get High-res Image Gene #59: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.077

Table S83.  Gene #62: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
17P LOSS MUTATED 0 7 0
17P LOSS WILD-TYPE 43 36 70

Figure S83.  Get High-res Image Gene #62: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.000337 (Fisher's exact test), Q value = 0.15

Table S84.  Gene #63: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
18P LOSS MUTATED 1 12 2 13
18P LOSS WILD-TYPE 32 56 35 21

Figure S84.  Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 3.92e-06 (Fisher's exact test), Q value = 0.002

Table S85.  Gene #63: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
18P LOSS MUTATED 4 18 4
18P LOSS WILD-TYPE 39 25 66

Figure S85.  Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 2.03e-06 (Fisher's exact test), Q value = 0.001

Table S86.  Gene #63: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
18P LOSS MUTATED 20 0 2 2
18P LOSS WILD-TYPE 38 49 29 21

Figure S86.  Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.016

Table S87.  Gene #64: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
18Q LOSS MUTATED 1 12 2 15
18Q LOSS WILD-TYPE 32 56 35 19

Figure S87.  Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00015

Table S88.  Gene #64: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
18Q LOSS MUTATED 4 20 4
18Q LOSS WILD-TYPE 39 23 66

Figure S88.  Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2.6e-07 (Fisher's exact test), Q value = 0.00014

Table S89.  Gene #64: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
18Q LOSS MUTATED 22 0 2 2
18Q LOSS WILD-TYPE 36 49 29 21

Figure S89.  Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.082

Table S90.  Gene #64: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
18Q LOSS MUTATED 10 14 2
18Q LOSS WILD-TYPE 21 52 62

Figure S90.  Get High-res Image Gene #64: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.04

Table S91.  Gene #66: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
19Q LOSS MUTATED 1 0 2 8
19Q LOSS WILD-TYPE 32 68 35 26

Figure S91.  Get High-res Image Gene #66: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.08

Table S92.  Gene #67: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
21Q LOSS MUTATED 8 5 3 14
21Q LOSS WILD-TYPE 25 63 34 20

Figure S92.  Get High-res Image Gene #67: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.88e-07 (Fisher's exact test), Q value = 0.00035

Table S93.  Gene #68: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
22Q LOSS MUTATED 1 15 5 20
22Q LOSS WILD-TYPE 32 53 32 14

Figure S93.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.73e-07 (Fisher's exact test), Q value = 0.00024

Table S94.  Gene #68: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
22Q LOSS MUTATED 5 24 9
22Q LOSS WILD-TYPE 38 19 61

Figure S94.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 7.37e-08 (Fisher's exact test), Q value = 3.9e-05

Table S95.  Gene #68: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
22Q LOSS MUTATED 29 5 4 0
22Q LOSS WILD-TYPE 29 44 27 23

Figure S95.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S96.  Gene #68: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
22Q LOSS MUTATED 12 13 16
22Q LOSS WILD-TYPE 6 67 58

Figure S96.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 2.26e-05 (Fisher's exact test), Q value = 0.011

Table S97.  Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
XQ LOSS MUTATED 2 4 1 13
XQ LOSS WILD-TYPE 31 64 36 21

Figure S97.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 4.35e-05 (Fisher's exact test), Q value = 0.021

Table S98.  Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
XQ LOSS MUTATED 1 13 3
XQ LOSS WILD-TYPE 42 30 67

Figure S98.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.015

Table S99.  Gene #69: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
XQ LOSS MUTATED 16 2 0 0
XQ LOSS WILD-TYPE 42 47 31 23

Figure S99.  Get High-res Image Gene #69: '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 = 172

  • Number of significantly arm-level cnvs = 69

  • 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle