Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1B56H0C
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1B56H0C
Overview
Introduction

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

Summary

Testing the association between copy number variation 60 arm-level results and 12 molecular subtypes across 269 patients, 98 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 6p gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

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

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

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 60 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 98 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test
1p loss 0 (0%) 192 0.00361
(1.00) 		8.75e-06
(0.00501) 		1.82e-25
(1.14e-22) 		4.62e-58
(2.92e-55) 		7.62e-05
(0.0424) 		0.0316
(1.00) 		1.99e-14
(1.23e-11) 		1.24e-35
(7.84e-33) 		3.34e-11
(2.03e-08) 		8.75e-08
(5.2e-05) 		1.89e-13
(1.16e-10) 		3.1e-10
(1.88e-07)
19q loss 0 (0%) 184 0.3
(1.00) 		0.0404
(1.00) 		2.7e-23
(1.68e-20) 		1.12e-43
(7.04e-41) 		0.000312
(0.168) 		0.0815
(1.00) 		1.1e-12
(6.72e-10) 		1.37e-29
(8.6e-27) 		1.54e-07
(9.11e-05) 		6.36e-07
(0.000374) 		6.28e-10
(3.79e-07) 		3.46e-08
(2.08e-05)
7p gain 0 (0%) 219 0.175
(1.00) 		0.653
(1.00) 		4.04e-26
(2.53e-23) 		8.93e-13
(5.48e-10) 		5.46e-05
(0.0306) 		0.00775
(1.00) 		1.04e-06
(0.000606) 		6.21e-05
(0.0348) 		0.00427
(1.00) 		1.02e-06
(0.000597) 		1.5e-05
(0.00851) 		3.71e-11
(2.25e-08)
10p loss 0 (0%) 233 0.271
(1.00) 		0.561
(1.00) 		1.42e-15
(8.78e-13) 		4.74e-27
(2.98e-24) 		3.9e-07
(0.00023) 		0.000609
(0.321) 		2.38e-11
(1.45e-08) 		4.53e-05
(0.0255) 		0.00888
(1.00) 		5.81e-07
(0.000342) 		2.19e-13
(1.34e-10) 		1.44e-13
(8.87e-11)
10q loss 0 (0%) 231 0.271
(1.00) 		0.561
(1.00) 		1.2e-14
(7.44e-12) 		7.62e-25
(4.76e-22) 		1.76e-06
(0.00102) 		0.00094
(0.489) 		2.44e-11
(1.49e-08) 		7.54e-05
(0.042) 		0.00631
(1.00) 		2.13e-07
(0.000126) 		2.11e-12
(1.29e-09) 		7.12e-14
(4.39e-11)
20q gain 0 (0%) 249 6.77e-07
(0.000397) 		6.38e-08
(3.8e-05) 		0.000123
(0.0678) 		0.237
(1.00) 		6.66e-06
(0.00383) 		0.00133
(0.687) 		0.00426
(1.00) 		0.000174
(0.095) 		6.25e-07
(0.000368) 		1.86e-09
(1.12e-06)
7q gain 0 (0%) 201 0.282
(1.00) 		0.382
(1.00) 		2.57e-23
(1.6e-20) 		2.54e-11
(1.54e-08) 		0.0023
(1.00) 		0.0534
(1.00) 		1.65e-05
(0.00939) 		0.000223
(0.121) 		0.01
(1.00) 		0.000939
(0.489) 		0.000266
(0.145) 		1.79e-08
(1.08e-05)
19p gain 0 (0%) 252 1.33e-07
(7.89e-05) 		1.82e-08
(1.09e-05) 		0.0248
(1.00) 		0.0472
(1.00) 		0.000122
(0.0673) 		8.41e-05
(0.0466) 		0.00944
(1.00) 		0.00157
(0.803) 		5.01e-05
(0.0281) 		3.92e-08
(2.35e-05)
19q gain 0 (0%) 257 1.32e-05
(0.00755) 		2.38e-06
(0.00138) 		0.0226
(1.00) 		0.383
(1.00) 		0.00144
(0.743) 		0.00296
(1.00) 		0.0169
(1.00) 		0.00567
(1.00) 		1.68e-05
(0.00954) 		2.44e-06
(0.00141)
20p gain 0 (0%) 249 6.77e-07
(0.000397) 		5.31e-08
(3.17e-05) 		0.00427
(1.00) 		0.384
(1.00) 		0.000553
(0.295) 		0.0418
(1.00) 		0.0873
(1.00) 		0.00144
(0.744) 		7.42e-06
(0.00426) 		1.21e-07
(7.19e-05)
4p loss 0 (0%) 251 0.415
(1.00) 		0.0907
(1.00) 		0.000564
(0.3) 		1.03e-06
(0.000602) 		0.725
(1.00) 		0.628
(1.00) 		0.000408
(0.219) 		2.96e-06
(0.00171) 		0.000452
(0.242) 		0.85
(1.00) 		0.00912
(1.00) 		0.15
(1.00)
4q loss 0 (0%) 241 0.839
(1.00) 		0.404
(1.00) 		0.000572
(0.304) 		9.78e-06
(0.00558) 		0.612
(1.00) 		0.634
(1.00) 		0.000283
(0.154) 		6.26e-05
(0.035) 		0.000734
(0.386) 		0.887
(1.00) 		0.000559
(0.298) 		0.0563
(1.00)
11p loss 0 (0%) 244 0.815
(1.00) 		0.106
(1.00) 		2.14e-08
(1.28e-05) 		0.000216
(0.118) 		0.0298
(1.00) 		0.612
(1.00) 		0.00718
(1.00) 		0.00904
(1.00) 		0.00341
(1.00) 		0.647
(1.00) 		0.000168
(0.0924) 		0.123
(1.00)
22q loss 0 (0%) 249 1
(1.00) 		0.0879
(1.00) 		1.97e-05
(0.0111) 		2.38e-05
(0.0134) 		7.62e-05
(0.0424) 		0.0711
(1.00) 		0.000595
(0.314) 		0.00146
(0.75) 		0.00996
(1.00) 		0.254
(1.00) 		0.000762
(0.4) 		0.00776
(1.00)
10p gain 0 (0%) 245 7.42e-05
(0.0414) 		2.02e-06
(0.00117) 		0.136
(1.00) 		0.414
(1.00) 		0.964
(1.00) 		0.0523
(1.00) 		0.731
(1.00) 		0.554
(1.00) 		0.0939
(1.00) 		0.229
(1.00)
1q loss 0 (0%) 259 0.0889
(1.00) 		0.0202
(1.00) 		0.0502
(1.00) 		0.000172
(0.0943) 		0.0176
(1.00) 		1
(1.00) 		0.0353
(1.00) 		0.000107
(0.0592) 		0.000584
(0.309) 		0.854
(1.00) 		0.00249
(1.00) 		0.0869
(1.00)
1p gain 0 (0%) 261 0.0133
(1.00) 		0.00765
(1.00) 		0.0748
(1.00) 		0.74
(1.00) 		0.00022
(0.12) 		0.0317
(1.00) 		0.278
(1.00) 		0.017
(1.00) 		0.0064
(1.00) 		0.00323
(1.00)
1q gain 0 (0%) 259 0.000349
(0.187) 		0.0123
(1.00) 		0.464
(1.00) 		1
(1.00) 		0.0999
(1.00) 		0.279
(1.00) 		0.39
(1.00) 		0.252
(1.00) 		0.0331
(1.00) 		0.125
(1.00)
3q gain 0 (0%) 266 0.171
(1.00) 		0.211
(1.00) 		0.0655
(1.00) 		0.387
(1.00) 		0.239
(1.00) 		0.372
(1.00) 		0.000322
(0.173) 		0.0321
(1.00)
6p gain 0 (0%) 266 0.0146
(1.00) 		0.626
(1.00) 		0.0655
(1.00) 		0.387
(1.00) 		0.203
(1.00) 		0.0795
(1.00) 		1.81e-16
(1.13e-13) 		0.196
(1.00)
8p gain 0 (0%) 252 0.000308
(0.166) 		0.0761
(1.00) 		0.117
(1.00) 		0.783
(1.00) 		0.201
(1.00) 		0.405
(1.00) 		0.281
(1.00) 		0.843
(1.00) 		0.315
(1.00) 		0.155
(1.00)
8q gain 0 (0%) 247 3.05e-05
(0.0172) 		0.0158
(1.00) 		0.0251
(1.00) 		0.414
(1.00) 		0.11
(1.00) 		0.0624
(1.00) 		0.0975
(1.00) 		0.702
(1.00) 		0.29
(1.00) 		0.00865
(1.00)
3p loss 0 (0%) 259 0.00226
(1.00) 		0.178
(1.00) 		0.00225
(1.00) 		0.0705
(1.00) 		0.000305
(0.165) 		0.00866
(1.00) 		0.0613
(1.00) 		0.305
(1.00) 		0.0233
(1.00) 		0.0371
(1.00)
3q loss 0 (0%) 256 0.175
(1.00) 		0.561
(1.00) 		5.87e-06
(0.00338) 		0.0504
(1.00) 		0.0798
(1.00) 		0.0472
(1.00) 		0.0405
(1.00) 		0.074
(1.00) 		0.214
(1.00) 		0.472
(1.00) 		0.42
(1.00) 		0.0494
(1.00)
6q loss 0 (0%) 237 0.000158
(0.087) 		0.02
(1.00) 		0.223
(1.00) 		0.879
(1.00) 		0.497
(1.00) 		0.199
(1.00) 		0.0015
(0.771) 		0.561
(1.00) 		0.703
(1.00) 		0.105
(1.00)
9p loss 0 (0%) 220 0.0519
(1.00) 		0.653
(1.00) 		9.12e-06
(0.00522) 		0.0243
(1.00) 		0.0489
(1.00) 		0.0519
(1.00) 		0.866
(1.00) 		0.422
(1.00) 		0.827
(1.00) 		0.236
(1.00) 		0.604
(1.00) 		0.448
(1.00)
13q loss 0 (0%) 238 1
(1.00) 		0.0138
(1.00) 		6.34e-19
(3.94e-16) 		0.0642
(1.00) 		0.0968
(1.00) 		0.939
(1.00) 		0.395
(1.00) 		0.159
(1.00) 		0.632
(1.00) 		0.613
(1.00) 		0.665
(1.00) 		0.187
(1.00)
3p gain 0 (0%) 266 1
(1.00) 		0.839
(1.00) 		0.397
(1.00) 		0.245
(1.00) 		0.239
(1.00) 		0.372
(1.00) 		0.00083
(0.434) 		0.551
(1.00)
4p gain 0 (0%) 265 0.0221
(1.00) 		0.309
(1.00) 		0.531
(1.00) 		1
(1.00) 		0.269
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.145
(1.00) 		0.0183
(1.00) 		0.515
(1.00)
9p gain 0 (0%) 263 0.0471
(1.00) 		0.298
(1.00) 		0.322
(1.00) 		0.531
(1.00) 		0.333
(1.00) 		0.861
(1.00) 		0.614
(1.00) 		0.34
(1.00) 		0.0728
(1.00) 		0.322
(1.00)
9q gain 0 (0%) 260 0.00848
(1.00) 		0.0902
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.0393
(1.00) 		0.355
(1.00) 		0.215
(1.00) 		0.576
(1.00) 		0.0344
(1.00) 		0.341
(1.00)
11p gain 0 (0%) 258 0.859
(1.00) 		0.29
(1.00) 		0.11
(1.00) 		0.68
(1.00) 		0.207
(1.00) 		0.0113
(1.00) 		0.336
(1.00) 		0.87
(1.00) 		0.0687
(1.00) 		0.192
(1.00)
11q gain 0 (0%) 254 0.303
(1.00) 		0.241
(1.00) 		0.0267
(1.00) 		0.196
(1.00) 		0.318
(1.00) 		0.0498
(1.00) 		0.519
(1.00) 		0.666
(1.00) 		0.155
(1.00) 		0.0491
(1.00)
12p gain 0 (0%) 256 0.000763
(0.4) 		0.3
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.0341
(1.00) 		0.0486
(1.00) 		0.247
(1.00) 		0.0839
(1.00) 		0.00257
(1.00) 		0.0441
(1.00)
12q gain 0 (0%) 264 0.0979
(1.00) 		1
(1.00) 		0.286
(1.00) 		0.721
(1.00) 		0.166
(1.00) 		0.22
(1.00) 		0.405
(1.00) 		0.146
(1.00) 		0.0181
(1.00) 		0.0519
(1.00)
18p gain 0 (0%) 262 0.234
(1.00) 		0.669
(1.00) 		0.0925
(1.00) 		0.771
(1.00) 		0.159
(1.00) 		0.248
(1.00) 		0.516
(1.00) 		0.796
(1.00) 		0.919
(1.00) 		0.681
(1.00)
18q gain 0 (0%) 265 0.15
(1.00) 		0.23
(1.00) 		0.053
(1.00) 		1
(1.00) 		0.021
(1.00) 		0.196
(1.00) 		0.667
(1.00) 		0.305
(1.00) 		0.767
(1.00) 		0.515
(1.00)
21q gain 0 (0%) 263 0.0808
(1.00) 		0.0789
(1.00) 		0.114
(1.00) 		0.465
(1.00) 		0.119
(1.00) 		0.0954
(1.00) 		0.298
(1.00) 		0.452
(1.00) 		0.188
(1.00) 		0.0761
(1.00)
2p loss 0 (0%) 263 0.00518
(1.00) 		1
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.0208
(1.00) 		0.178
(1.00) 		0.62
(1.00) 		0.452
(1.00) 		0.563
(1.00) 		0.864
(1.00)
2q loss 0 (0%) 265 0.0522
(1.00) 		0.798
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.331
(1.00) 		0.273
(1.00) 		0.503
(1.00) 		0.708
(1.00) 		0.849
(1.00) 		0.383
(1.00)
5p loss 0 (0%) 256 1
(1.00) 		0.042
(1.00) 		0.00429
(1.00) 		0.203
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.881
(1.00) 		0.445
(1.00) 		0.35
(1.00) 		0.702
(1.00) 		0.0521
(1.00) 		0.806
(1.00)
5q loss 0 (0%) 258 0.415
(1.00) 		0.00228
(1.00) 		0.00181
(0.923) 		0.165
(1.00) 		0.0203
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.179
(1.00) 		0.28
(1.00) 		0.405
(1.00) 		0.00128
(0.661) 		0.35
(1.00)
6p loss 0 (0%) 259 0.122
(1.00) 		0.00747
(1.00) 		0.096
(1.00) 		0.806
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.0877
(1.00) 		0.662
(1.00) 		0.00806
(1.00)
8p loss 0 (0%) 263 0.0176
(1.00) 		0.0588
(1.00) 		0.232
(1.00) 		0.465
(1.00) 		0.333
(1.00) 		0.419
(1.00) 		0.614
(1.00) 		0.193
(1.00) 		0.307
(1.00) 		0.0455
(1.00)
8q loss 0 (0%) 265 0.15
(1.00) 		0.00404
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.269
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.088
(1.00) 		0.72
(1.00) 		0.0352
(1.00)
9q loss 0 (0%) 262 0.0997
(1.00) 		0.032
(1.00) 		0.954
(1.00) 		0.299
(1.00) 		0.508
(1.00) 		0.00883
(1.00) 		0.0343
(1.00) 		0.796
(1.00) 		0.00901
(1.00) 		0.387
(1.00)
11q loss 0 (0%) 262 0.0182
(1.00) 		0.328
(1.00) 		0.026
(1.00) 		1
(1.00) 		0.0157
(1.00) 		0.248
(1.00) 		0.344
(1.00) 		0.796
(1.00) 		0.0122
(1.00) 		0.681
(1.00)
12p loss 0 (0%) 265 0.338
(1.00) 		0.714
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.803
(1.00) 		0.973
(1.00) 		0.221
(1.00) 		0.0144
(1.00) 		0.811
(1.00)
12q loss 0 (0%) 258 0.0096
(1.00) 		0.121
(1.00) 		0.364
(1.00) 		0.323
(1.00) 		0.127
(1.00) 		0.354
(1.00) 		0.368
(1.00) 		0.151
(1.00) 		0.233
(1.00) 		0.54
(1.00)
14q loss 0 (0%) 241 0.0195
(1.00) 		0.000572
(0.304) 		0.0719
(1.00) 		0.282
(1.00) 		0.0134
(1.00) 		0.11
(1.00) 		0.0035
(1.00) 		0.00522
(1.00) 		0.0492
(1.00) 		0.161
(1.00)
15q loss 0 (0%) 253 0.317
(1.00) 		0.000974
(0.505) 		0.513
(1.00) 		0.0371
(1.00) 		0.765
(1.00) 		0.00483
(1.00) 		0.494
(1.00) 		0.916
(1.00) 		0.24
(1.00) 		0.693
(1.00)
16p loss 0 (0%) 266 0.0693
(1.00) 		0.626
(1.00) 		0.286
(1.00) 		0.317
(1.00) 		1
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.146
(1.00) 		0.911
(1.00) 		0.124
(1.00)
16q loss 0 (0%) 262 0.0406
(1.00) 		0.0277
(1.00) 		0.0694
(1.00) 		0.353
(1.00) 		0.159
(1.00) 		0.248
(1.00) 		0.764
(1.00) 		0.142
(1.00) 		0.28
(1.00) 		0.198
(1.00)
17p loss 0 (0%) 265 0.171
(1.00) 		0.125
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.021
(1.00) 		0.196
(1.00) 		0.496
(1.00) 		0.305
(1.00) 		0.209
(1.00) 		0.218
(1.00)
18p loss 0 (0%) 248 0.344
(1.00) 		0.212
(1.00) 		0.024
(1.00) 		0.0101
(1.00) 		0.664
(1.00) 		0.131
(1.00) 		0.747
(1.00) 		0.367
(1.00) 		0.0744
(1.00) 		0.208
(1.00) 		0.32
(1.00) 		0.116
(1.00)
18q loss 0 (0%) 249 0.0889
(1.00) 		0.0468
(1.00) 		0.0188
(1.00) 		0.000854
(0.446) 		0.282
(1.00) 		0.234
(1.00) 		0.518
(1.00) 		0.0879
(1.00) 		0.0778
(1.00) 		0.529
(1.00) 		0.255
(1.00) 		0.179
(1.00)
19p loss 0 (0%) 262 0.615
(1.00) 		0.117
(1.00) 		0.525
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.0683
(1.00) 		0.299
(1.00) 		0.097
(1.00) 		0.101
(1.00) 		0.403
(1.00) 		0.184
(1.00) 		0.681
(1.00)
20p loss 0 (0%) 266 0.312
(1.00) 		0.626
(1.00) 		0.792
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.308
(1.00) 		0.641
(1.00) 		0.76
(1.00) 		0.76
(1.00)
21q loss 0 (0%) 258 0.0989
(1.00) 		0.674
(1.00) 		0.399
(1.00) 		0.68
(1.00) 		0.437
(1.00) 		0.179
(1.00) 		0.105
(1.00) 		0.00783
(1.00) 		0.347
(1.00) 		0.454
(1.00)
Xq loss 0 (0%) 263 0.0471
(1.00) 		0.298
(1.00) 		0.637
(1.00) 		0.353
(1.00) 		0.333
(1.00) 		0.419
(1.00) 		0.182
(1.00) 		0.00209
(1.00) 		0.589
(1.00) 		0.0761
(1.00)
'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
1P GAIN CNV 8 0 0
1P GAIN WILD-TYPE 86 78 97

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.000349 (Fisher's exact test), Q value = 0.19

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
1Q GAIN CNV 0 4 6 0
1Q GAIN WILD-TYPE 52 53 48 106

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000322 (Chi-square test), Q value = 0.17

Table S3.  Gene #4: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
3Q GAIN CNV 0 2 0 0 0 0 1 0
3Q GAIN WILD-TYPE 44 46 35 71 27 31 3 8

Figure S3.  Get High-res Image Gene #4: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.81e-16 (Chi-square test), Q value = 1.1e-13

Table S4.  Gene #6: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
6P GAIN CNV 0 1 0 0 0 0 2 0
6P GAIN WILD-TYPE 44 47 35 71 27 31 2 8

Figure S4.  Get High-res Image Gene #6: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 4.04e-26 (Fisher's exact test), Q value = 2.5e-23

Table S5.  Gene #7: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
7P GAIN CNV 2 41 4 3
7P GAIN WILD-TYPE 50 16 50 103

Figure S5.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 8.93e-13 (Fisher's exact test), Q value = 5.5e-10

Table S6.  Gene #7: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
7P GAIN CNV 16 27 4 2
7P GAIN WILD-TYPE 106 15 62 32

Figure S6.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 5.46e-05 (Fisher's exact test), Q value = 0.031

Table S7.  Gene #7: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
7P GAIN CNV 9 23 8 5
7P GAIN WILD-TYPE 43 39 60 69

Figure S7.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00061

Table S8.  Gene #7: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
7P GAIN CNV 33 11 6
7P GAIN WILD-TYPE 61 67 91

Figure S8.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.21e-05 (Fisher's exact test), Q value = 0.035

Table S9.  Gene #7: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
7P GAIN CNV 3 40 7
7P GAIN WILD-TYPE 33 101 85

Figure S9.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.02e-06 (Fisher's exact test), Q value = 6e-04

Table S10.  Gene #7: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
7P GAIN CNV 9 33 8
7P GAIN WILD-TYPE 5 112 101

Figure S10.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.0085

Table S11.  Gene #7: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
7P GAIN CNV 6 21 8 5 1 8 1 0
7P GAIN WILD-TYPE 38 27 27 66 26 23 3 8

Figure S11.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.71e-11 (Fisher's exact test), Q value = 2.2e-08

Table S12.  Gene #7: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
7P GAIN CNV 25 16 9
7P GAIN WILD-TYPE 17 89 112

Figure S12.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2.57e-23 (Fisher's exact test), Q value = 1.6e-20

Table S13.  Gene #8: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
7Q GAIN CNV 5 46 6 11
7Q GAIN WILD-TYPE 47 11 48 95

Figure S13.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.54e-11 (Fisher's exact test), Q value = 1.5e-08

Table S14.  Gene #8: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
7Q GAIN CNV 25 30 9 3
7Q GAIN WILD-TYPE 97 12 57 31

Figure S14.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.0094

Table S15.  Gene #8: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
7Q GAIN CNV 39 17 12
7Q GAIN WILD-TYPE 55 61 85

Figure S15.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
7Q GAIN CNV 6 50 12
7Q GAIN WILD-TYPE 30 91 80

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

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000266 (Chi-square test), Q value = 0.14

Table S17.  Gene #8: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
7Q GAIN CNV 7 23 12 9 5 11 1 0
7Q GAIN WILD-TYPE 37 25 23 62 22 20 3 8

Figure S17.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.79e-08 (Fisher's exact test), Q value = 1.1e-05

Table S18.  Gene #8: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
7Q GAIN CNV 27 21 20
7Q GAIN WILD-TYPE 15 84 101

Figure S18.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.000308 (Fisher's exact test), Q value = 0.17

Table S19.  Gene #9: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
8P GAIN CNV 6 4 7 0
8P GAIN WILD-TYPE 46 53 47 106

Figure S19.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.017

Table S20.  Gene #10: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
8Q GAIN CNV 8 6 8 0
8Q GAIN WILD-TYPE 44 51 46 106

Figure S20.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.041

Table S21.  Gene #13: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
10P GAIN CNV 12 3 7 2
10P GAIN WILD-TYPE 40 54 47 104

Figure S21.  Get High-res Image Gene #13: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0012

Table S22.  Gene #13: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
10P GAIN CNV 23 0 0 1
10P GAIN WILD-TYPE 99 42 66 33

Figure S22.  Get High-res Image Gene #13: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 7.9e-05

Table S23.  Gene #20: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
19P GAIN CNV 1 14 1 1
19P GAIN WILD-TYPE 51 43 53 105

Figure S23.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1.82e-08 (Fisher's exact test), Q value = 1.1e-05

Table S24.  Gene #20: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
19P GAIN CNV 4 13 0 0
19P GAIN WILD-TYPE 118 29 66 34

Figure S24.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.067

Table S25.  Gene #20: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
19P GAIN CNV 14 2 1
19P GAIN WILD-TYPE 80 76 96

Figure S25.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.41e-05 (Fisher's exact test), Q value = 0.047

Table S26.  Gene #20: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
19P GAIN CNV 0 17 0
19P GAIN WILD-TYPE 36 124 92

Figure S26.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.01e-05 (Chi-square test), Q value = 0.028

Table S27.  Gene #20: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
19P GAIN CNV 2 11 0 2 0 1 1 0
19P GAIN WILD-TYPE 42 37 35 69 27 30 3 8

Figure S27.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.92e-08 (Fisher's exact test), Q value = 2.3e-05

Table S28.  Gene #20: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
19P GAIN CNV 12 4 1
19P GAIN WILD-TYPE 30 101 120

Figure S28.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0075

Table S29.  Gene #21: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
19Q GAIN CNV 0 10 1 1
19Q GAIN WILD-TYPE 52 47 53 105

Figure S29.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.0014

Table S30.  Gene #21: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
19Q GAIN CNV 2 9 0 0
19Q GAIN WILD-TYPE 120 33 66 34

Figure S30.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.68e-05 (Chi-square test), Q value = 0.0095

Table S31.  Gene #21: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
19Q GAIN CNV 0 9 0 2 0 0 1 0
19Q GAIN WILD-TYPE 44 39 35 69 27 31 3 8

Figure S31.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.44e-06 (Fisher's exact test), Q value = 0.0014

Table S32.  Gene #21: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
19Q GAIN CNV 9 2 1
19Q GAIN WILD-TYPE 33 103 120

Figure S32.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 6.77e-07 (Fisher's exact test), Q value = 4e-04

Table S33.  Gene #22: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
20P GAIN CNV 2 13 5 0
20P GAIN WILD-TYPE 50 44 49 106

Figure S33.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 5.31e-08 (Fisher's exact test), Q value = 3.2e-05

Table S34.  Gene #22: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
20P GAIN CNV 3 14 1 2
20P GAIN WILD-TYPE 119 28 65 32

Figure S34.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.42e-06 (Chi-square test), Q value = 0.0043

Table S35.  Gene #22: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
20P GAIN CNV 0 11 0 3 1 3 2 0
20P GAIN WILD-TYPE 44 37 35 68 26 28 2 8

Figure S35.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-07 (Fisher's exact test), Q value = 7.2e-05

Table S36.  Gene #22: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
20P GAIN CNV 13 5 2
20P GAIN WILD-TYPE 29 100 119

Figure S36.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 6.77e-07 (Fisher's exact test), Q value = 4e-04

Table S37.  Gene #23: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
20Q GAIN CNV 2 13 5 0
20Q GAIN WILD-TYPE 50 44 49 106

Figure S37.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 6.38e-08 (Fisher's exact test), Q value = 3.8e-05

Table S38.  Gene #23: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
20Q GAIN CNV 5 14 1 0
20Q GAIN WILD-TYPE 117 28 65 34

Figure S38.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.068

Table S39.  Gene #23: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
20Q GAIN CNV 4 11 2 0
20Q GAIN WILD-TYPE 48 51 66 74

Figure S39.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0038

Table S40.  Gene #23: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
20Q GAIN CNV 17 1 2
20Q GAIN WILD-TYPE 77 77 95

Figure S40.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.095

Table S41.  Gene #23: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
20Q GAIN CNV 5 13 2
20Q GAIN WILD-TYPE 9 132 107

Figure S41.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.25e-07 (Chi-square test), Q value = 0.00037

Table S42.  Gene #23: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
20Q GAIN CNV 1 12 0 1 1 3 2 0
20Q GAIN WILD-TYPE 43 36 35 70 26 28 2 8

Figure S42.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.86e-09 (Fisher's exact test), Q value = 1.1e-06

Table S43.  Gene #23: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
20Q GAIN CNV 13 7 0
20Q GAIN WILD-TYPE 29 98 121

Figure S43.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.75e-06 (Fisher's exact test), Q value = 0.005

Table S44.  Gene #25: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
1P LOSS CNV 7 2 0 0
1P LOSS WILD-TYPE 0 4 10 4

Figure S44.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.82e-25 (Fisher's exact test), Q value = 1.1e-22

Table S45.  Gene #25: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
1P LOSS CNV 0 0 12 65
1P LOSS WILD-TYPE 52 57 42 41

Figure S45.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.62e-58 (Fisher's exact test), Q value = 2.9e-55

Table S46.  Gene #25: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
1P LOSS CNV 1 0 66 7
1P LOSS WILD-TYPE 121 42 0 27

Figure S46.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 7.62e-05 (Fisher's exact test), Q value = 0.042

Table S47.  Gene #25: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
1P LOSS CNV 8 10 25 34
1P LOSS WILD-TYPE 44 52 43 40

Figure S47.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.99e-14 (Fisher's exact test), Q value = 1.2e-11

Table S48.  Gene #25: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
1P LOSS CNV 2 31 44
1P LOSS WILD-TYPE 92 47 53

Figure S48.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-35 (Fisher's exact test), Q value = 7.8e-33

Table S49.  Gene #25: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
1P LOSS CNV 36 4 37
1P LOSS WILD-TYPE 0 137 55

Figure S49.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 3.34e-11 (Chi-square test), Q value = 2e-08

Table S50.  Gene #25: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
1P LOSS CNV 6 1 38 12 20
1P LOSS WILD-TYPE 56 47 51 4 33

Figure S50.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.75e-08 (Fisher's exact test), Q value = 5.2e-05

Table S51.  Gene #25: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
1P LOSS CNV 0 26 51
1P LOSS WILD-TYPE 14 119 58

Figure S51.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.89e-13 (Chi-square test), Q value = 1.2e-10

Table S52.  Gene #25: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
1P LOSS CNV 0 3 7 31 21 11 0 4
1P LOSS WILD-TYPE 44 45 28 40 6 20 4 4

Figure S52.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.1e-10 (Fisher's exact test), Q value = 1.9e-07

Table S53.  Gene #25: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
1P LOSS CNV 1 19 57
1P LOSS WILD-TYPE 41 86 64

Figure S53.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.094

Table S54.  Gene #26: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
1Q LOSS CNV 1 0 9 0
1Q LOSS WILD-TYPE 121 42 57 34

Figure S54.  Get High-res Image Gene #26: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S55.  Gene #26: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
1Q LOSS CNV 5 0 5
1Q LOSS WILD-TYPE 31 141 87

Figure S55.  Get High-res Image Gene #26: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.16

Table S56.  Gene #29: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
3P LOSS CNV 9 1 0
3P LOSS WILD-TYPE 85 77 97

Figure S56.  Get High-res Image Gene #29: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 5.87e-06 (Fisher's exact test), Q value = 0.0034

Table S57.  Gene #30: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
3Q LOSS CNV 8 0 5 0
3Q LOSS WILD-TYPE 44 57 49 106

Figure S57.  Get High-res Image Gene #30: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 6e-04

Table S58.  Gene #31: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
4P LOSS CNV 3 0 15 0
4P LOSS WILD-TYPE 119 42 51 34

Figure S58.  Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000408 (Fisher's exact test), Q value = 0.22

Table S59.  Gene #31: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
4P LOSS CNV 0 10 8
4P LOSS WILD-TYPE 94 68 89

Figure S59.  Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.96e-06 (Fisher's exact test), Q value = 0.0017

Table S60.  Gene #31: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
4P LOSS CNV 10 2 6
4P LOSS WILD-TYPE 26 139 86

Figure S60.  Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.000452 (Chi-square test), Q value = 0.24

Table S61.  Gene #31: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
4P LOSS CNV 1 1 6 5 5
4P LOSS WILD-TYPE 61 47 83 11 48

Figure S61.  Get High-res Image Gene #31: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 9.78e-06 (Fisher's exact test), Q value = 0.0056

Table S62.  Gene #32: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
4Q LOSS CNV 9 0 18 1
4Q LOSS WILD-TYPE 113 42 48 33

Figure S62.  Get High-res Image Gene #32: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.000283 (Fisher's exact test), Q value = 0.15

Table S63.  Gene #32: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
4Q LOSS CNV 2 16 10
4Q LOSS WILD-TYPE 92 62 87

Figure S63.  Get High-res Image Gene #32: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-05 (Fisher's exact test), Q value = 0.035

Table S64.  Gene #32: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
4Q LOSS CNV 12 8 8
4Q LOSS WILD-TYPE 24 133 84

Figure S64.  Get High-res Image Gene #32: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.087

Table S65.  Gene #36: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
6Q LOSS CNV 3 9 15 5
6Q LOSS WILD-TYPE 49 48 39 101

Figure S65.  Get High-res Image Gene #36: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.0052

Table S66.  Gene #39: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
9P LOSS CNV 5 18 18 8
9P LOSS WILD-TYPE 47 39 36 98

Figure S66.  Get High-res Image Gene #39: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 8.8e-13

Table S67.  Gene #41: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
10P LOSS CNV 1 28 5 2
10P LOSS WILD-TYPE 51 29 49 104

Figure S67.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 4.74e-27 (Fisher's exact test), Q value = 3e-24

Table S68.  Gene #41: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
10P LOSS CNV 1 31 3 0
10P LOSS WILD-TYPE 121 11 63 34

Figure S68.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 3.9e-07 (Fisher's exact test), Q value = 0.00023

Table S69.  Gene #41: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10P LOSS CNV 4 21 3 3
10P LOSS WILD-TYPE 48 41 65 71

Figure S69.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 2.38e-11 (Fisher's exact test), Q value = 1.5e-08

Table S70.  Gene #41: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
10P LOSS CNV 31 1 4
10P LOSS WILD-TYPE 63 77 93

Figure S70.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.53e-05 (Fisher's exact test), Q value = 0.026

Table S71.  Gene #41: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
10P LOSS CNV 1 31 4
10P LOSS WILD-TYPE 35 110 88

Figure S71.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034

Table S72.  Gene #41: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
10P LOSS CNV 8 24 4
10P LOSS WILD-TYPE 6 121 105

Figure S72.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.19e-13 (Chi-square test), Q value = 1.3e-10

Table S73.  Gene #41: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
10P LOSS CNV 0 24 1 4 1 6 0 0
10P LOSS WILD-TYPE 44 24 34 67 26 25 4 8

Figure S73.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.44e-13 (Fisher's exact test), Q value = 8.9e-11

Table S74.  Gene #41: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
10P LOSS CNV 23 9 4
10P LOSS WILD-TYPE 19 96 117

Figure S74.  Get High-res Image Gene #41: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1.2e-14 (Fisher's exact test), Q value = 7.4e-12

Table S75.  Gene #42: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
10Q LOSS CNV 2 28 6 2
10Q LOSS WILD-TYPE 50 29 48 104

Figure S75.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 7.62e-25 (Fisher's exact test), Q value = 4.8e-22

Table S76.  Gene #42: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
10Q LOSS CNV 3 31 3 0
10Q LOSS WILD-TYPE 119 11 63 34

Figure S76.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.001

Table S77.  Gene #42: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10Q LOSS CNV 5 21 4 3
10Q LOSS WILD-TYPE 47 41 64 71

Figure S77.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.44e-11 (Fisher's exact test), Q value = 1.5e-08

Table S78.  Gene #42: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
10Q LOSS CNV 32 1 5
10Q LOSS WILD-TYPE 62 77 92

Figure S78.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.54e-05 (Fisher's exact test), Q value = 0.042

Table S79.  Gene #42: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
10Q LOSS CNV 1 32 5
10Q LOSS WILD-TYPE 35 109 87

Figure S79.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.13e-07 (Fisher's exact test), Q value = 0.00013

Table S80.  Gene #42: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
10Q LOSS CNV 9 24 5
10Q LOSS WILD-TYPE 5 121 104

Figure S80.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.11e-12 (Chi-square test), Q value = 1.3e-09

Table S81.  Gene #42: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
10Q LOSS CNV 0 24 1 4 2 6 1 0
10Q LOSS WILD-TYPE 44 24 34 67 25 25 3 8

Figure S81.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.12e-14 (Fisher's exact test), Q value = 4.4e-11

Table S82.  Gene #42: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
10Q LOSS CNV 24 9 5
10Q LOSS WILD-TYPE 18 96 116

Figure S82.  Get High-res Image Gene #42: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2.14e-08 (Fisher's exact test), Q value = 1.3e-05

Table S83.  Gene #43: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
11P LOSS CNV 12 2 11 0
11P LOSS WILD-TYPE 40 55 43 106

Figure S83.  Get High-res Image Gene #43: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.12

Table S84.  Gene #43: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
11P LOSS CNV 21 2 0 2
11P LOSS WILD-TYPE 101 40 66 32

Figure S84.  Get High-res Image Gene #43: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000168 (Chi-square test), Q value = 0.092

Table S85.  Gene #43: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
11P LOSS CNV 3 8 4 5 0 1 3 1
11P LOSS WILD-TYPE 41 40 31 66 27 30 1 7

Figure S85.  Get High-res Image Gene #43: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 6.34e-19 (Fisher's exact test), Q value = 3.9e-16

Table S86.  Gene #47: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
13Q LOSS CNV 3 1 27 0
13Q LOSS WILD-TYPE 49 56 27 106

Figure S86.  Get High-res Image Gene #47: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 2.7e-23 (Fisher's exact test), Q value = 1.7e-20

Table S87.  Gene #56: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
19Q LOSS CNV 1 0 20 64
19Q LOSS WILD-TYPE 51 57 34 42

Figure S87.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.12e-43 (Fisher's exact test), Q value = 7e-41

Table S88.  Gene #56: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
19Q LOSS CNV 7 2 64 9
19Q LOSS WILD-TYPE 115 40 2 25

Figure S88.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.000312 (Fisher's exact test), Q value = 0.17

Table S89.  Gene #56: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
19Q LOSS CNV 8 16 24 37
19Q LOSS WILD-TYPE 44 46 44 37

Figure S89.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1.1e-12 (Fisher's exact test), Q value = 6.7e-10

Table S90.  Gene #56: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 78 97
19Q LOSS CNV 5 33 47
19Q LOSS WILD-TYPE 89 45 50

Figure S90.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-29 (Fisher's exact test), Q value = 8.6e-27

Table S91.  Gene #56: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 141 92
19Q LOSS CNV 35 9 41
19Q LOSS WILD-TYPE 1 132 51

Figure S91.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1.54e-07 (Chi-square test), Q value = 9.1e-05

Table S92.  Gene #56: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 48 89 16 53
19Q LOSS CNV 8 6 41 11 19
19Q LOSS WILD-TYPE 54 42 48 5 34

Figure S92.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.36e-07 (Fisher's exact test), Q value = 0.00037

Table S93.  Gene #56: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 145 109
19Q LOSS CNV 1 30 54
19Q LOSS WILD-TYPE 13 115 55

Figure S93.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.28e-10 (Chi-square test), Q value = 3.8e-07

Table S94.  Gene #56: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 44 48 35 71 27 31 4 8
19Q LOSS CNV 2 6 9 34 20 11 0 3
19Q LOSS WILD-TYPE 42 42 26 37 7 20 4 5

Figure S94.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.46e-08 (Fisher's exact test), Q value = 2.1e-05

Table S95.  Gene #56: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 105 121
19Q LOSS CNV 3 23 59
19Q LOSS WILD-TYPE 39 82 62

Figure S95.  Get High-res Image Gene #56: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.011

Table S96.  Gene #59: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 57 54 106
22Q LOSS CNV 3 8 9 0
22Q LOSS WILD-TYPE 49 49 45 106

Figure S96.  Get High-res Image Gene #59: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.38e-05 (Fisher's exact test), Q value = 0.013

Table S97.  Gene #59: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 42 66 34
22Q LOSS CNV 7 11 0 2
22Q LOSS WILD-TYPE 115 31 66 32

Figure S97.  Get High-res Image Gene #59: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 7.62e-05 (Fisher's exact test), Q value = 0.042

Table S98.  Gene #59: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
22Q LOSS CNV 2 14 2 2
22Q LOSS WILD-TYPE 50 48 66 72

Figure S98.  Get High-res Image Gene #59: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 269

  • Number of significantly arm-level cnvs = 60

  • Number of molecular subtypes = 12

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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)
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